TissueInfo API 20130530171129
A B C D E F G H I J K L M N O P Q R S T U V W X Z

A

abdominal_ganglion - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
abducens_nerve - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
abductor_muscle - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
AC_COLNUM - Static variable in class edu.mssm.crover.tools.tissue.TissueInfoNullsJDBCImpl
The column index for the accession code.
accept(Table, String) - Method in class edu.mssm.crover.tables.AcceptAllColumnsFilter
 
accept(Table, Table.RowIterator) - Method in class edu.mssm.crover.tables.AcceptAllRowFilter
 
accept(Table, String) - Method in class edu.mssm.crover.tables.ColumnFilter
Determine if a column should be kept by the filtering process.
accept(Table, Table.RowIterator) - Method in class edu.mssm.crover.tables.IdentifierSetRowFilter
 
accept(Table, String) - Method in class edu.mssm.crover.tables.KeepSubSetColumnFilter
 
accept(Table, Table.RowIterator) - Method in class edu.mssm.crover.tables.RowFilter
Determine if a row should be kept by the filtering process.
AcceptAllColumnsFilter - Class in edu.mssm.crover.tables
 
AcceptAllColumnsFilter() - Constructor for class edu.mssm.crover.tables.AcceptAllColumnsFilter
 
AcceptAllRowFilter - Class in edu.mssm.crover.tables
 
AcceptAllRowFilter() - Constructor for class edu.mssm.crover.tables.AcceptAllRowFilter
 
accessory_nerve - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
accumulateScoresPerQuery - Variable in class edu.cornell.med.icb.tissueinfo.similarity.TiSimOptions
 
AccuracyCalculator - Class in edu.cornell.med.icb.stat
Calculates the accuracy of predictions.
AccuracyCalculator() - Constructor for class edu.cornell.med.icb.stat.AccuracyCalculator
 
add(String) - Method in class edu.cornell.med.icb.tissueinfo.similarity.clustering.Cluster
 
add(Table.RowIterator) - Method in class edu.mssm.crover.tables.treatments.Aggregation.Aggregate
Add the iterator ri to this aggregate.
addAnnotation(BiologicalAnnotation) - Method in class edu.mssm.crover.representation.Annotations
Adds an annotation to this list.
addAnnotation(BiologicalAnnotation) - Method in interface edu.mssm.crover.representation.BiologicalAnnotations
Adds an annotation to the list.
addColumn(String, Class) - Method in class edu.mssm.crover.tables.ArrayTable
Adds a new column to this table.
addColumn(String, Class) - Method in interface edu.mssm.crover.tables.Table
Adds a new column to this table.
addColumns(String, String[], HashSet) - Method in class edu.mssm.crover.tables.AddToTable
Checks whether the columns to be added to already exist in the table.
addColumns(Table, Reader) - Static method in class edu.mssm.crover.tables.readers.DSSPTableReader
Build the schema for a DSSP file.
addColumns(Table) - Static method in class edu.mssm.crover.tables.readers.LocusLinkTableReader
Parse the Mineset schema file to extract the column names and types.
addColumns(Table, Reader) - Static method in class edu.mssm.crover.tables.readers.MinesetTableReader
Parse the Mineset schema file to extract the column names and types.
addColumns(Table, Reader) - Static method in class edu.mssm.crover.tables.readers.TIWebMinesetReader
Parse the Mineset schema file to extract the column names and types.
addColumns(ArrayTable) - Method in interface edu.mssm.crover.tools.tissue.plugins.OptionHandler
Adds columns to the table.
addData(String, String, String[], String) - Method in class edu.mssm.crover.tables.AddToTable
Reads the input file (which should contain the same number of tab-delimited fields per line as columns you want to add to), and adds the information from each field in each line to the corresponding column.
addData(Table, Reader, int[]) - Static method in class edu.mssm.crover.tables.readers.DSSPTableReader
 
addData(Table, Reader, Filter) - Static method in class edu.mssm.crover.tables.readers.LocusLinkTableReader
 
addData(Table, Reader, String) - Static method in class edu.mssm.crover.tables.readers.MinesetTableReader
 
addData(Table, Reader) - Static method in class edu.mssm.crover.tables.readers.MinesetTableReader
 
addData(Table, Reader) - Static method in class edu.mssm.crover.tables.readers.TIWebMinesetReader
 
addDataPoint(double, double) - Method in class edu.cornell.med.icb.stat.LinearRegression
Add a point to the linear regression calculation.
addDataPoints(double[], double[]) - Method in class edu.cornell.med.icb.stat.LinearRegression
Add a points to the linear regression calculation.
addGene(Gene) - Method in class edu.cornell.med.icb.allen.xml.Genes
 
addGene(int, Gene) - Method in class edu.cornell.med.icb.allen.xml.Genes
 
addGeneExpression(GeneExpression) - Method in class edu.cornell.med.icb.allen.xml.GeneExpressions
 
addGeneExpression(int, GeneExpression) - Method in class edu.cornell.med.icb.allen.xml.GeneExpressions
 
addHit(Hit) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Iteration_hitsType
 
addHit(int, Hit) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Iteration_hitsType
 
addHit(Hit) - Method in class edu.mssm.crover.tools.tissue.xml.QuerySequence
 
addHit(int, Hit) - Method in class edu.mssm.crover.tools.tissue.xml.QuerySequence
 
addHsp(Hsp) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Hit_hspsType
 
addHsp(int, Hsp) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Hit_hspsType
 
addImageSeries(ImageSeries) - Method in class edu.cornell.med.icb.allen.xml.ImageSeries
 
addImageSeries(int, ImageSeries) - Method in class edu.cornell.med.icb.allen.xml.ImageSeries
 
addInfo(String, String, String, String) - Method in interface edu.mssm.crover.tools.tissue.TissueInfo
Add a new tissue information to TissueInfo.
addInfo(String, String, String, String) - Method in class edu.mssm.crover.tools.tissue.TissueInfoCacheImpl
Add a new tissue information to TissueInfo.
addInfo(String, String, String) - Method in class edu.mssm.crover.tools.tissue.TissueInfoJDBCImpl
Add a new tissue information to TissueInfo.
addInfo(String, String, String, String) - Method in class edu.mssm.crover.tools.tissue.TissueInfoJDBCImpl
Add a new tissue information to TissueInfo.
addInfo(String, String, String, String) - Method in class edu.mssm.crover.tools.tissue.TissueInfoMemoryImpl
Add a new tissue information to TissueInfo.
addInfo(String, String, String, String) - Method in class edu.mssm.crover.tools.tissue.TissueInfoMemoryImpl2
Add a new tissue information to TissueInfo.
addInfo(String, String, String, String) - Method in class edu.mssm.crover.tools.tissue.TissueInfoNullsJDBCImpl
Add a new tissue information to TissueInfo.
addPair(int, int) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TiSimOptions
 
addProjectionRule(MutableString, MutableString...) - Method in class edu.cornell.med.icb.tissueinfo.annotations.Projection
 
addQuerySequence(QuerySequence) - Method in class edu.mssm.crover.tools.tissue.xml.BlastHits
 
addQuerySequence(int, QuerySequence) - Method in class edu.mssm.crover.tools.tissue.xml.BlastHits
 
addReader(SequenceReader) - Method in class edu.mssm.crover.imports.SequenceReaderFactoryImpl
This SequenceReaderFactory supports the addition of new SequenceReaders at runtime.
addRelationship(MutableString, int) - Method in class edu.cornell.med.icb.tissueinfo.similarity.GeneTranscriptRelationships
 
addRelationship(int, int) - Method in class edu.cornell.med.icb.tissueinfo.similarity.GeneTranscriptRelationships
 
addToEsts(TissueDetails) - Method in class edu.mssm.crover.tools.tissue.QueryTissueSummary
Add the TissueDetails to the set of TissueDetails stored about each of the ESTs that match a query sequence.
addTokey(Tokey) - Method in class edu.mssm.crover.tools.tissue.xml.TissueInfo
 
addTokey(int, Tokey) - Method in class edu.mssm.crover.tools.tissue.xml.TissueInfo
 
AddToTable - Class in edu.mssm.crover.tables
Adds to columns (and creates them if necessary) from an input file.
AddToTable(String, String, String[], String) - Constructor for class edu.mssm.crover.tables.AddToTable
Adds the data to the specified table.
adductor_muscle - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
adipose - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
adrenal_cortex - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
adrenal_gland - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
adrenal_medulla - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
AffymetrixTxtFormatReader - Class in edu.mssm.crover.tables.readers
User: campagne Date: Sep 16, 2005 Time: 2:17:19 PM
AffymetrixTxtFormatReader() - Constructor for class edu.mssm.crover.tables.readers.AffymetrixTxtFormatReader
 
Age - Class in edu.cornell.med.icb.allen.xml
Class Age.
Age() - Constructor for class edu.cornell.med.icb.allen.xml.Age
 
AgeDescriptor - Class in edu.cornell.med.icb.allen.xml.descriptors
Class AgeDescriptor.
AgeDescriptor() - Constructor for class edu.cornell.med.icb.allen.xml.descriptors.AgeDescriptor
 
AgeTypeType - Class in edu.cornell.med.icb.allen.xml.types
Class AgeTypeType.
AgeTypeTypeDescriptor - Class in edu.cornell.med.icb.allen.xml.types.descriptors
Class AgeTypeTypeDescriptor.
AgeTypeTypeDescriptor() - Constructor for class edu.cornell.med.icb.allen.xml.types.descriptors.AgeTypeTypeDescriptor
 
aggregate(Table, Table, ObjectList<Cluster>, String) - Method in class edu.mssm.crover.tables.treatments.AggregateClusters
 
aggregate(String) - Method in class edu.mssm.crover.tables.treatments.Aggregation
 
aggregate(Table) - Method in class edu.mssm.crover.tables.treatments.Aggregation
Performs the aggregation operation on source, returns the new table.
AggregateClusters - Class in edu.mssm.crover.tables.treatments
 
AggregateClusters() - Constructor for class edu.mssm.crover.tables.treatments.AggregateClusters
 
Aggregation - Class in edu.mssm.crover.tables.treatments
Aggregation operation on tables, similar to Mineset aggregation.
Aggregation(Object) - Constructor for class edu.mssm.crover.tables.treatments.Aggregation
Variant useful for customization.
Aggregation() - Constructor for class edu.mssm.crover.tables.treatments.Aggregation
 
Aggregation.Aggregate - Class in edu.mssm.crover.tables.treatments
 
Aggregation.Aggregate() - Constructor for class edu.mssm.crover.tables.treatments.Aggregation.Aggregate
 
Aggregation.Aggregate(Table.RowIterator) - Constructor for class edu.mssm.crover.tables.treatments.Aggregation.Aggregate
 
agranulocyte - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
all - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
AllenGeneAtlas2Counts - Class in edu.cornell.med.icb.tissueinfo.similarity
Converts expression data from the Allen Gene Atlas to TEPSS counts.
AllenGeneAtlas2Counts() - Constructor for class edu.cornell.med.icb.tissueinfo.similarity.AllenGeneAtlas2Counts
 
alveolar_macrophage - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
alveoli - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
amnion - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
amygdala - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
AnnotateClustersMode - Class in edu.cornell.med.icb.tissueinfo.similarity
Calculates tissue weights for a set of clusters generated by ClusterMode.
AnnotateClustersMode() - Constructor for class edu.cornell.med.icb.tissueinfo.similarity.AnnotateClustersMode
 
AnnotatedBioSequence - Interface in edu.mssm.crover.representation
 
Annotation - Class in edu.mssm.crover.representation
Default implementation of BiologicalAnnotation.
Annotation() - Constructor for class edu.mssm.crover.representation.Annotation
 
Annotation(BiologicalOrigin) - Constructor for class edu.mssm.crover.representation.Annotation
 
AnnotationParser - Class in edu.cornell.med.icb.tissueinfo.annotations
 
AnnotationParser() - Constructor for class edu.cornell.med.icb.tissueinfo.annotations.AnnotationParser
 
Annotations - Class in edu.mssm.crover.representation
Default implementation of BiologicalAnnotations.
Annotations() - Constructor for class edu.mssm.crover.representation.Annotations
 
AnnotationSet - Class in edu.cornell.med.icb.tissueinfo.annotations
Associate sampleIds to annotations.
AnnotationSet() - Constructor for class edu.cornell.med.icb.tissueinfo.annotations.AnnotationSet
 
AnnotationSupport - Interface in edu.mssm.crover.representation
 
AnnotationType - Class in edu.cornell.med.icb.tissueinfo.annotations
 
AnnotationType(MutableString) - Constructor for class edu.cornell.med.icb.tissueinfo.annotations.AnnotationType
 
anterior_pituitary - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
aorta - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
append(String) - Method in class edu.mssm.crover.tables.ArrayTable.ColumnDescription
 
append(String, Object, int) - Method in class edu.mssm.crover.tables.ArrayTable.ColumnDescription.booleanStringAppender
 
append(String, Object, int) - Method in class edu.mssm.crover.tables.ArrayTable.ColumnDescription.charStringAppender
 
append(String, Object, int) - Method in class edu.mssm.crover.tables.ArrayTable.ColumnDescription.doubleStringAppender
 
append(String, Object, int) - Method in class edu.mssm.crover.tables.ArrayTable.ColumnDescription.floatStringAppender
 
append(String, Object, int) - Method in class edu.mssm.crover.tables.ArrayTable.ColumnDescription.intStringAppender
 
append(String, Object, int) - Method in class edu.mssm.crover.tables.ArrayTable.ColumnDescription.StringStringAppender
 
append(String, Object, int) - Method in interface edu.mssm.crover.tables.StringAppender
Parse the string, make sure the result is compatible with the type of the column this appender was attached to (this type is implementation specific), then append the type to the array (at the specified position).
appendBooleanValue(int, boolean) - Method in class edu.mssm.crover.tables.ArrayTable
Appends a boolean value to the specified column.
appendBooleanValue(int, int, boolean) - Method in class edu.mssm.crover.tables.ArrayTable
Appends a boolean value to the specified column, on the specified row.
appendBooleanValue(int, boolean) - Method in interface edu.mssm.crover.tables.Table
Appends a char value to the specified column.
appendCharValue(int, char) - Method in class edu.mssm.crover.tables.ArrayTable
Appends a char value to the specified column.
appendCharValue(int, int, char) - Method in class edu.mssm.crover.tables.ArrayTable
Appends a char value to the specified column on the specified row.
appendCharValue(int, char) - Method in interface edu.mssm.crover.tables.Table
Appends a char value to the specified column.
appendData(ArrayTable, TissueSummary) - Method in interface edu.mssm.crover.tools.tissue.plugins.OptionHandler
Appends data to the table.
appendDoubleValue(int, double) - Method in class edu.mssm.crover.tables.ArrayTable
Appends a double value to the specified column.
appendDoubleValue(int, int, double) - Method in class edu.mssm.crover.tables.ArrayTable
Appends a double value to the specified column on the specified row.
appendDoubleValue(int, double) - Method in interface edu.mssm.crover.tables.Table
Appends a double value to the specified column.
appendFloatValue(int, float) - Method in class edu.mssm.crover.tables.ArrayTable
Appends a float value to the specified column.
appendFloatValue(int, int, float) - Method in class edu.mssm.crover.tables.ArrayTable
Appends a float value to the specified column on the specified row.
appendFloatValue(int, float) - Method in interface edu.mssm.crover.tables.Table
Appends a float value to the specified column.
appendIntValue(int, int) - Method in class edu.mssm.crover.tables.ArrayTable
Appends an int value to the specified column.
appendIntValue(int, int, int) - Method in class edu.mssm.crover.tables.ArrayTable
Appends an int value to the specified column, on the specified row.
appendIntValue(int, int) - Method in interface edu.mssm.crover.tables.Table
Table are write once data storage.
appendix - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
appendObject(int, Object) - Method in class edu.mssm.crover.tables.ArrayTable
Appends a Object value to the specified column.
appendObject(int, int, Object) - Method in class edu.mssm.crover.tables.ArrayTable
Appends a Object value to the specified column on the specified row.
appendObject(int, Object) - Method in interface edu.mssm.crover.tables.Table
Appends a value of type Object to this column.
arachnoidea_mater - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
AreaUnderTheRocCurveCalculator - Class in edu.cornell.med.icb.stat
 
AreaUnderTheRocCurveCalculator() - Constructor for class edu.cornell.med.icb.stat.AreaUnderTheRocCurveCalculator
 
areDivided() - Method in class edu.mssm.crover.tools.tissue.LibraryDivision
Returns whether the libraries could be divided up or not.
array - Variable in class edu.mssm.crover.tables.ArrayTable.ColumnDescription
 
ArraysIterator - Class in edu.cornell.med.icb.tissueinfo.annotations
 
ArraysIterator(int[][]) - Constructor for class edu.cornell.med.icb.tissueinfo.annotations.ArraysIterator
 
ArraysIterator.ArrayIndices - Class in edu.cornell.med.icb.tissueinfo.annotations
 
ArraysIterator.ArrayIndices(int) - Constructor for class edu.cornell.med.icb.tissueinfo.annotations.ArraysIterator.ArrayIndices
 
ArraySizer - Class in edu.mssm.crover.tables
 
ArraySizer() - Constructor for class edu.mssm.crover.tables.ArraySizer
 
ArrayTable - Class in edu.mssm.crover.tables
Array-based implementation of the Table interface.
ArrayTable() - Constructor for class edu.mssm.crover.tables.ArrayTable
 
ArrayTable.ColumnDescription - Class in edu.mssm.crover.tables
Holds and describes a column of this table.
ArrayTable.ColumnDescription(String, Class) - Constructor for class edu.mssm.crover.tables.ArrayTable.ColumnDescription
Create a column of name idf, to contain elements of the given type.
ArrayTable.ColumnDescription(String, Class, StringAppender) - Constructor for class edu.mssm.crover.tables.ArrayTable.ColumnDescription
Allow you to provide a custom StringAppender.
ArrayTable.ColumnDescription.booleanComparator - Class in edu.mssm.crover.tables
 
ArrayTable.ColumnDescription.booleanComparator() - Constructor for class edu.mssm.crover.tables.ArrayTable.ColumnDescription.booleanComparator
 
ArrayTable.ColumnDescription.booleanCopier - Class in edu.mssm.crover.tables
Copy boolean types or objects contained in an array in a generic way.
ArrayTable.ColumnDescription.booleanCopier() - Constructor for class edu.mssm.crover.tables.ArrayTable.ColumnDescription.booleanCopier
 
ArrayTable.ColumnDescription.booleanStringAppender - Class in edu.mssm.crover.tables
Parse and appends a boolean.
ArrayTable.ColumnDescription.booleanStringAppender() - Constructor for class edu.mssm.crover.tables.ArrayTable.ColumnDescription.booleanStringAppender
 
ArrayTable.ColumnDescription.booleanStringConverter - Class in edu.mssm.crover.tables
Converts a boolean to a String.
ArrayTable.ColumnDescription.booleanStringConverter() - Constructor for class edu.mssm.crover.tables.ArrayTable.ColumnDescription.booleanStringConverter
 
ArrayTable.ColumnDescription.charComparator - Class in edu.mssm.crover.tables
 
ArrayTable.ColumnDescription.charComparator() - Constructor for class edu.mssm.crover.tables.ArrayTable.ColumnDescription.charComparator
 
ArrayTable.ColumnDescription.charCopier - Class in edu.mssm.crover.tables
Copy char types or objects contained in an array in a generic way.
ArrayTable.ColumnDescription.charCopier() - Constructor for class edu.mssm.crover.tables.ArrayTable.ColumnDescription.charCopier
 
ArrayTable.ColumnDescription.charStringAppender - Class in edu.mssm.crover.tables
Parse and appends a char.
ArrayTable.ColumnDescription.charStringAppender() - Constructor for class edu.mssm.crover.tables.ArrayTable.ColumnDescription.charStringAppender
 
ArrayTable.ColumnDescription.charStringConverter - Class in edu.mssm.crover.tables
Converts a char to a String.
ArrayTable.ColumnDescription.charStringConverter() - Constructor for class edu.mssm.crover.tables.ArrayTable.ColumnDescription.charStringConverter
 
ArrayTable.ColumnDescription.doubleComparator - Class in edu.mssm.crover.tables
 
ArrayTable.ColumnDescription.doubleComparator() - Constructor for class edu.mssm.crover.tables.ArrayTable.ColumnDescription.doubleComparator
 
ArrayTable.ColumnDescription.doubleCopier - Class in edu.mssm.crover.tables
Copy double types or objects contained in an array in a generic way.
ArrayTable.ColumnDescription.doubleCopier() - Constructor for class edu.mssm.crover.tables.ArrayTable.ColumnDescription.doubleCopier
 
ArrayTable.ColumnDescription.doubleStringAppender - Class in edu.mssm.crover.tables
Parse and appends a double.
ArrayTable.ColumnDescription.doubleStringAppender() - Constructor for class edu.mssm.crover.tables.ArrayTable.ColumnDescription.doubleStringAppender
 
ArrayTable.ColumnDescription.doubleStringConverter - Class in edu.mssm.crover.tables
Converts a float to a String.
ArrayTable.ColumnDescription.doubleStringConverter() - Constructor for class edu.mssm.crover.tables.ArrayTable.ColumnDescription.doubleStringConverter
 
ArrayTable.ColumnDescription.floatComparator - Class in edu.mssm.crover.tables
 
ArrayTable.ColumnDescription.floatComparator() - Constructor for class edu.mssm.crover.tables.ArrayTable.ColumnDescription.floatComparator
 
ArrayTable.ColumnDescription.floatCopier - Class in edu.mssm.crover.tables
Copy float types or objects contained in an array in a generic way.
ArrayTable.ColumnDescription.floatCopier() - Constructor for class edu.mssm.crover.tables.ArrayTable.ColumnDescription.floatCopier
 
ArrayTable.ColumnDescription.floatStringAppender - Class in edu.mssm.crover.tables
Parse and appends a float.
ArrayTable.ColumnDescription.floatStringAppender() - Constructor for class edu.mssm.crover.tables.ArrayTable.ColumnDescription.floatStringAppender
 
ArrayTable.ColumnDescription.floatStringConverter - Class in edu.mssm.crover.tables
Converts a float to a String.
ArrayTable.ColumnDescription.floatStringConverter() - Constructor for class edu.mssm.crover.tables.ArrayTable.ColumnDescription.floatStringConverter
 
ArrayTable.ColumnDescription.intComparator - Class in edu.mssm.crover.tables
 
ArrayTable.ColumnDescription.intComparator() - Constructor for class edu.mssm.crover.tables.ArrayTable.ColumnDescription.intComparator
 
ArrayTable.ColumnDescription.intCopier - Class in edu.mssm.crover.tables
Copy int types or objects contained in an array in a generic way.
ArrayTable.ColumnDescription.intCopier() - Constructor for class edu.mssm.crover.tables.ArrayTable.ColumnDescription.intCopier
 
ArrayTable.ColumnDescription.intStringAppender - Class in edu.mssm.crover.tables
Parse and appends an int.
ArrayTable.ColumnDescription.intStringAppender() - Constructor for class edu.mssm.crover.tables.ArrayTable.ColumnDescription.intStringAppender
 
ArrayTable.ColumnDescription.intStringConverter - Class in edu.mssm.crover.tables
Converts an int to a String.
ArrayTable.ColumnDescription.intStringConverter() - Constructor for class edu.mssm.crover.tables.ArrayTable.ColumnDescription.intStringConverter
 
ArrayTable.ColumnDescription.objectComparator - Class in edu.mssm.crover.tables
Returns true when equals returns true on the two values.
ArrayTable.ColumnDescription.objectComparator() - Constructor for class edu.mssm.crover.tables.ArrayTable.ColumnDescription.objectComparator
 
ArrayTable.ColumnDescription.objectCopier - Class in edu.mssm.crover.tables
Copy objects contained in an array in a generic way.
ArrayTable.ColumnDescription.objectCopier() - Constructor for class edu.mssm.crover.tables.ArrayTable.ColumnDescription.objectCopier
 
ArrayTable.ColumnDescription.ObjectStringConverter - Class in edu.mssm.crover.tables
 
ArrayTable.ColumnDescription.ObjectStringConverter() - Constructor for class edu.mssm.crover.tables.ArrayTable.ColumnDescription.ObjectStringConverter
 
ArrayTable.ColumnDescription.StringStringAppender - Class in edu.mssm.crover.tables
Parse and appends Strings.
ArrayTable.ColumnDescription.StringStringAppender() - Constructor for class edu.mssm.crover.tables.ArrayTable.ColumnDescription.StringStringAppender
 
ArrayTable.RowIterator - Class in edu.mssm.crover.tables
 
ArrayTable.RowIterator(int, int) - Constructor for class edu.mssm.crover.tables.ArrayTable.RowIterator
 
artery - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
ascending_colon - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
assignCategories(List<String>) - Method in class edu.mssm.crover.tools.tissue.LibraryDivision
Assigns each library one of two categories randomly.
assignCategories(List<String>, long) - Method in class edu.mssm.crover.tools.tissue.LibraryDivision
Assigns each library one of two categories randomly using a user-defined seed.
assignCategories(List<String>, Random) - Method in class edu.mssm.crover.tools.tissue.LibraryDivision
Assigns each library one of two categories randomly using a user-defined seed.
associate(String, String, String) - Method in class edu.cornell.med.icb.tissueinfo.annotations.AnnotationSet
Associate a sampleId with an annotation (type, value)
associate(MutableString, MutableString, MutableString) - Method in class edu.cornell.med.icb.tissueinfo.annotations.AnnotationSet
Associate a sampleId with an annotation (type, value).
associate(int, MutableString) - Method in class edu.cornell.med.icb.tissueinfo.annotations.AnnotationType
 
associate(int, int) - Method in class edu.cornell.med.icb.tissueinfo.annotations.AnnotationType
 
astrocyte - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
atrium - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
auditory_nerve - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
autonomic_NS - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
Avgdensity - Class in edu.cornell.med.icb.allen.xml
Class Avgdensity.
Avgdensity() - Constructor for class edu.cornell.med.icb.allen.xml.Avgdensity
 
AvgdensityDescriptor - Class in edu.cornell.med.icb.allen.xml.descriptors
Class AvgdensityDescriptor.
AvgdensityDescriptor() - Constructor for class edu.cornell.med.icb.allen.xml.descriptors.AvgdensityDescriptor
 
AvgdensityTypeType - Class in edu.cornell.med.icb.allen.xml.types
Class AvgdensityTypeType.
AvgdensityTypeTypeDescriptor - Class in edu.cornell.med.icb.allen.xml.types.descriptors
Class AvgdensityTypeTypeDescriptor.
AvgdensityTypeTypeDescriptor() - Constructor for class edu.cornell.med.icb.allen.xml.types.descriptors.AvgdensityTypeTypeDescriptor
 
Avglevel - Class in edu.cornell.med.icb.allen.xml
Class Avglevel.
Avglevel() - Constructor for class edu.cornell.med.icb.allen.xml.Avglevel
 
AvglevelDescriptor - Class in edu.cornell.med.icb.allen.xml.descriptors
Class AvglevelDescriptor.
AvglevelDescriptor() - Constructor for class edu.cornell.med.icb.allen.xml.descriptors.AvglevelDescriptor
 
AvglevelTypeType - Class in edu.cornell.med.icb.allen.xml.types
Class AvglevelTypeType.
AvglevelTypeTypeDescriptor - Class in edu.cornell.med.icb.allen.xml.types.descriptors
Class AvglevelTypeTypeDescriptor.
AvglevelTypeTypeDescriptor() - Constructor for class edu.cornell.med.icb.allen.xml.types.descriptors.AvglevelTypeTypeDescriptor
 
axon - Interface in edu.mssm.crover.tools.tissue.hierarchy
 

B

b_cell - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
BackwardMode - Class in edu.cornell.med.icb.tissueinfo.similarity
Backward tiSimilarity screen.
BackwardMode() - Constructor for class edu.cornell.med.icb.tissueinfo.similarity.BackwardMode
 
BaselineNormalizedConfidenceScorer - Class in edu.cornell.med.icb.tissueinfo.similarity.scorers
Confidence scorer normalized with BaselineNormalizedScorer.
BaselineNormalizedConfidenceScorer() - Constructor for class edu.cornell.med.icb.tissueinfo.similarity.scorers.BaselineNormalizedConfidenceScorer
 
BaselineNormalizerScorer - Class in edu.cornell.med.icb.tissueinfo.similarity.scorers
A scorer that normalizes the score produced by another scorer given the sums of EST counts in the query and target.
BaselineNormalizerScorer(ExpressionProfileSimilarityScorer) - Constructor for class edu.cornell.med.icb.tissueinfo.similarity.scorers.BaselineNormalizerScorer
 
basename - Variable in class edu.cornell.med.icb.tissueinfo.similarity.TiSimOptions
 
basename - Variable in class edu.cornell.med.icb.tissueinfo.similarity.TissueESTCountsHelper
 
basophil - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
begin() - Method in class edu.mssm.crover.tables.AddToTable
Notifies this class that a batch of interaction now begin.
begin() - Method in class edu.mssm.crover.tables.JDBCTable
Notifies this class that a batch of interaction now begin.
begin() - Method in class edu.mssm.crover.tables.QueryTable
Notifies this class that a batch of interaction now begin.
begin() - Method in class edu.mssm.crover.tables.TableActivityWatcher
Notifies this class that a batch of interaction now begin.
begin(Table, Table) - Method in class edu.mssm.crover.tables.treatments.Aggregation
Override to add the aggregation columns to the destination table.
begin(Table) - Method in class edu.mssm.crover.tables.treatments.CompositionTableTreatment
 
begin(Object) - Method in class edu.mssm.crover.tables.treatments.TableTreatment
 
begin(Table) - Method in class edu.mssm.crover.tables.treatments.TableTreatment
 
begin() - Method in class edu.mssm.crover.tools.tissue.DumpNullsTissueInfo
Notifies this class that a batch of interaction now begins.
begin() - Method in class edu.mssm.crover.tools.tissue.DumpTissueInfo
Notifies this class that a batch of interaction now begins.
begin() - Method in interface edu.mssm.crover.tools.tissue.TissueInfo
Notifies this class that a batch of interaction now begin.
begin() - Method in class edu.mssm.crover.tools.tissue.TissueInfoCacheImpl
Notifies this class that a batch of interaction now begin.
begin() - Method in class edu.mssm.crover.tools.tissue.TissueInfoJDBCImpl
Notifies this class that a batch of interaction now begin.
begin() - Method in class edu.mssm.crover.tools.tissue.TissueInfoMemoryImpl
Notifies this class that a batch of interaction now begin.
begin() - Method in class edu.mssm.crover.tools.tissue.TissueInfoMemoryImpl2
Notifies this class that a batch of interaction now begin.
begin() - Method in class edu.mssm.crover.tools.tissue.TissueInfoNullsJDBCImpl
Notifies this class that a batch of interaction now begin.
begin() - Method in interface edu.mssm.crover.tools.tissue.TIWeb
Notifies this class that a batch of interaction now begin.
begin() - Method in class edu.mssm.crover.tools.tissue.TIWebJDBCImpl
Notifies this class that a batch of interaction now begin.
bile_duct - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
BinaryConfidenceScorer - Class in edu.cornell.med.icb.tissueinfo.similarity.scorers
 
BinaryConfidenceScorer() - Constructor for class edu.cornell.med.icb.tissueinfo.similarity.scorers.BinaryConfidenceScorer
 
BinaryScorer - Class in edu.cornell.med.icb.tissueinfo.similarity.scorers
 
BinaryScorer() - Constructor for class edu.cornell.med.icb.tissueinfo.similarity.scorers.BinaryScorer
 
BiologicalAnnotation - Interface in edu.mssm.crover.representation
Represents a single annotation.
BiologicalAnnotations - Interface in edu.mssm.crover.representation
Extendable annotation support for AnnotatedBioSequence objects.
BiologicalDescription - Interface in edu.mssm.crover.representation
This interface is not specified.
BiologicalOrigin - Interface in edu.mssm.crover.representation
Represents the origin of an information.
BiologicalSequence - Interface in edu.mssm.crover.representation
Interface to a represent a biological protein sequence.
bladder - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
blast(int, BiologicalSequence, String) - Method in class edu.mssm.crover.tools.blast.BlastCommand
Runs BLAST.
blast(String, BiologicalSequence, String) - Method in class edu.mssm.crover.tools.blast.BlastCommand
 
BlastCommand - Class in edu.mssm.crover.tools.blast
This implementation wraps around Blast.
BlastCommand() - Constructor for class edu.mssm.crover.tools.blast.BlastCommand
 
BlastCommand(BlastContext) - Constructor for class edu.mssm.crover.tools.blast.BlastCommand
 
BlastContext - Class in edu.mssm.crover.tools.blast
 
BlastContext() - Constructor for class edu.mssm.crover.tools.blast.BlastContext
Constructs a default context for invocation of Blast.
BlastHits - Class in edu.mssm.crover.tools.tissue.xml
Class BlastHits.
BlastHits() - Constructor for class edu.mssm.crover.tools.tissue.xml.BlastHits
 
BlastHitsDescriptor - Class in edu.mssm.crover.tools.tissue.xml.descriptors
Class BlastHitsDescriptor.
BlastHitsDescriptor() - Constructor for class edu.mssm.crover.tools.tissue.xml.descriptors.BlastHitsDescriptor
 
BlastOutput - Class in edu.mssm.crover.tools.blast.parsers.xml.v3
Class BlastOutput.
BlastOutput() - Constructor for class edu.mssm.crover.tools.blast.parsers.xml.v3.BlastOutput
 
BlastOutput_iterations - Class in edu.mssm.crover.tools.blast.parsers.xml.v3
Class BlastOutput_iterations.
BlastOutput_iterations() - Constructor for class edu.mssm.crover.tools.blast.parsers.xml.v3.BlastOutput_iterations
 
BlastOutput_iterationsDescriptor - Class in edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors
Class BlastOutput_iterationsDescriptor.
BlastOutput_iterationsDescriptor() - Constructor for class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutput_iterationsDescriptor
 
BlastOutput_iterationsType - Class in edu.mssm.crover.tools.blast.parsers.xml.v3
Class BlastOutput_iterationsType.
BlastOutput_iterationsType() - Constructor for class edu.mssm.crover.tools.blast.parsers.xml.v3.BlastOutput_iterationsType
 
BlastOutput_iterationsTypeDescriptor - Class in edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors
Class BlastOutput_iterationsTypeDescriptor.
BlastOutput_iterationsTypeDescriptor() - Constructor for class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutput_iterationsTypeDescriptor
 
BlastOutput_param - Class in edu.mssm.crover.tools.blast.parsers.xml.v3
Class BlastOutput_param.
BlastOutput_param() - Constructor for class edu.mssm.crover.tools.blast.parsers.xml.v3.BlastOutput_param
 
BlastOutput_paramDescriptor - Class in edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors
Class BlastOutput_paramDescriptor.
BlastOutput_paramDescriptor() - Constructor for class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutput_paramDescriptor
 
BlastOutput_paramType - Class in edu.mssm.crover.tools.blast.parsers.xml.v3
Class BlastOutput_paramType.
BlastOutput_paramType() - Constructor for class edu.mssm.crover.tools.blast.parsers.xml.v3.BlastOutput_paramType
 
BlastOutput_paramTypeDescriptor - Class in edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors
Class BlastOutput_paramTypeDescriptor.
BlastOutput_paramTypeDescriptor() - Constructor for class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutput_paramTypeDescriptor
 
BlastOutputDescriptor - Class in edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors
Class BlastOutputDescriptor.
BlastOutputDescriptor() - Constructor for class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutputDescriptor
 
BlastResult - Class in edu.mssm.crover.tools.blast
Encapsulates different versions of BlastOutput.
BlastResult() - Constructor for class edu.mssm.crover.tools.blast.BlastResult
 
blockSizeOption - Variable in class edu.cornell.med.icb.tissueinfo.similarity.TiSimOptions
 
blood - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
blood_vessel - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
bone - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
bone_marrow - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
bowel - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
brain - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
brain_stem - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
breast - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
bronchii - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
brookid - Variable in class edu.mssm.crover.tables.treatments.CompositionTableTreatmentParameter
 
brown_adipose - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
buildColumnIndices(Table, String) - Static method in class edu.mssm.crover.tables.RowProcessor
 

C

cacheTranscriptCounts() - Method in class edu.cornell.med.icb.tissueinfo.similarity.TiSimilaritySearchEngine
 
cacheTranscriptCounts(int[][]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TiSimilaritySearchEngine
 
caecum - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
calculateFisherFromMatrix(int, int, int, int) - Method in class gominer.Fisher
 
calculateNonZeroTissueCount(int[]) - Static method in class edu.cornell.med.icb.tissueinfo.similarity.TiSimilarity
 
calculateStats() - Method in class edu.cornell.med.icb.stat.ZScoreCalculator
Calculate mean and std deviation of scores.
calculateWeights(List<float[]>, int) - Static method in class edu.cornell.med.icb.tissueinfo.similarity.TiWeights
 
cardiac_muscle - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
cartilage - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
caudate_nucleus - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
central_NS - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
cerebellar_cortex - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
cerebellum - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
cerebral_cortex - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
cerebrum - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
cervix - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
chainid_filter - Variable in class edu.mssm.crover.tables.treatments.CompositionTableTreatmentParameter
 
checkActive() - Method in class edu.mssm.crover.db.relational.ConnectionPool
 
checkKey(String) - Method in class edu.mssm.crover.tables.TableActivityWatcher
Checks if the key exists in the table.
CheckLibrary - Class in edu.mssm.crover.tools.tissue
Finds CuratedTissues for raw tissues, if they exist.
checkSequenceDB(String, String) - Method in class edu.mssm.crover.tools.blast.BlastCommand
Checks if the command is installed on this machine.
checkSize(int) - Method in class edu.mssm.crover.tables.ArrayTable
Check wether the internal storage needs to be expanded, performs the required reallocation when it does.
choroid - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
chunk - Variable in class edu.mssm.crover.tables.ArrayTable
 
circulatory - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
circumvallate_papillae - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
clean() - Method in class edu.mssm.crover.tables.ArrayTable
Cleans this column.
clean() - Method in class edu.mssm.crover.tables.ArrayTable.ColumnDescription
Cleans this table.
cleanCuratedTissues(TreeSet<String>) - Method in class edu.mssm.crover.tools.tissue.NullParser
Cleans the curated tissues.
clone() - Method in class edu.mssm.crover.tables.ArrayTable.RowIterator
 
clone() - Method in interface edu.mssm.crover.tables.Table.RowIterator
 
close() - Method in class edu.cornell.med.icb.tissueinfo.similarity.TissueESTCountsReader
Closes this stream and releases any system resources associated with it.
close() - Method in class edu.cornell.med.icb.tissueinfo.similarity.TissueESTCountsWriter
 
Cluster - Class in edu.cornell.med.icb.tissueinfo.similarity.clustering
Describes transcripts in a TEPSS cluster.
Cluster() - Constructor for class edu.cornell.med.icb.tissueinfo.similarity.clustering.Cluster
 
ClusterFileParser - Class in edu.cornell.med.icb.tissueinfo.similarity.clustering
 
ClusterFileParser() - Constructor for class edu.cornell.med.icb.tissueinfo.similarity.clustering.ClusterFileParser
 
ClusterMode - Class in edu.cornell.med.icb.tissueinfo.similarity
 
ClusterMode() - Constructor for class edu.cornell.med.icb.tissueinfo.similarity.ClusterMode
 
cochlea - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
coeliac_ganglion - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
collectItem(int, double, double, int, int) - Method in class edu.cornell.med.icb.tissueinfo.similarity.ForwardMode
 
collectTranscriptSet - Variable in class edu.cornell.med.icb.tissueinfo.similarity.ForwardMode
 
CologneReader - Class in edu.mssm.crover.tables.readers
original file:
CologneReader() - Constructor for class edu.mssm.crover.tables.readers.CologneReader
 
colon - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
ColumbiaTmmReader - Class in edu.mssm.crover.tables.readers
 
ColumbiaTmmReader() - Constructor for class edu.mssm.crover.tables.readers.ColumbiaTmmReader
 
COLUMN_HIT_NON_TUMOR - Static variable in class edu.mssm.crover.tools.tissue.TIQuery
The heading for the number of hits found in non-tumour tissue column.
COLUMN_HIT_NON_TUMOR - Static variable in class edu.mssm.crover.tools.tissue.TIQuerySql
The heading for the number of hits found in non-tumour tissue column.
COLUMN_HIT_TUMOR - Static variable in class edu.mssm.crover.tools.tissue.TIQuery
The heading for the number of hits found in tumour tissue column.
COLUMN_HIT_TUMOR - Static variable in class edu.mssm.crover.tools.tissue.TIQuerySql
The heading for the number of hits found in tumour tissue column.
COLUMN_MOST_EXPRESSED_IN - Static variable in class edu.mssm.crover.tools.tissue.TIQuery
The heading for the 'most expressed in' column.
COLUMN_MOST_EXPRESSED_IN - Static variable in class edu.mssm.crover.tools.tissue.TIQuerySql
The heading for the 'most expressed in' column.
COLUMN_NAME_ID_REF - Static variable in class edu.mssm.crover.tables.readers.GeoDataSetReader
 
ColumnFilter - Class in edu.mssm.crover.tables
 
ColumnFilter() - Constructor for class edu.mssm.crover.tables.ColumnFilter
 
ColumnIdentifierLengthException - Exception in edu.mssm.crover.tools.tissue
Thrown when the column identifier is greater than 30 characters.
ColumnIdentifierLengthException(String) - Constructor for exception edu.mssm.crover.tools.tissue.ColumnIdentifierLengthException
Associates a detailed message with this exception.
columnIndices - Variable in class edu.mssm.crover.tables.RowProcessor
 
ColumnTypeException - Exception in edu.mssm.crover.tables
Thrown when a string is presented to an appender of a specific type and this appender is unable to parse the string to a type of the elements it is supposed to append.
ColumnTypeException(String) - Constructor for exception edu.mssm.crover.tables.ColumnTypeException
 
ColumnTypeException(String, String) - Constructor for exception edu.mssm.crover.tables.ColumnTypeException
 
CombinePathways - Class in edu.cornell.med.icb.tissueinfo.similarity.clustering
Combine files in the pathway format used by DAVMode.
CombinePathways() - Constructor for class edu.cornell.med.icb.tissueinfo.similarity.clustering.CombinePathways
 
CommandNotInstalled - Exception in edu.mssm.crover.tools
 
CommandNotInstalled(String) - Constructor for exception edu.mssm.crover.tools.CommandNotInstalled
 
CommandNotInstalled(String, String) - Constructor for exception edu.mssm.crover.tools.CommandNotInstalled
 
compareTo(Object) - Method in class edu.mssm.crover.tools.tissue.TissueSelection
Compares two TissueSelection objects.
CompositionTableTreatment - Class in edu.mssm.crover.tables.treatments
 
CompositionTableTreatment(Object) - Constructor for class edu.mssm.crover.tables.treatments.CompositionTableTreatment
 
CompositionTableTreatmentParameter - Class in edu.mssm.crover.tables.treatments
 
CompositionTableTreatmentParameter(String, char, Table) - Constructor for class edu.mssm.crover.tables.treatments.CompositionTableTreatmentParameter
 
compute(double[], double[]) - Static method in class edu.cornell.med.icb.stat.MinMaxCalculator
 
compute(double[], double[], int) - Static method in class edu.cornell.med.icb.stat.MinMaxCalculator
Compute the min/max statistics.
cones - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
confidence(int) - Method in class edu.cornell.med.icb.tissueinfo.similarity.scorers.ExpressionConfidenceScorer
 
conn - Variable in class edu.mssm.crover.tables.AddToTable
The connection to the database used by this instance.
conn - Variable in class edu.mssm.crover.tables.JDBCTable
 
conn - Variable in class edu.mssm.crover.tables.QueryTable
 
conn - Variable in class edu.mssm.crover.tables.TableActivityWatcher
The connectin to the database used by this instance.
ConnectionPool - Class in edu.mssm.crover.db.relational
Pool of JDBC connections.
ConnectionPool(String, String, String, String, int, int) - Constructor for class edu.mssm.crover.db.relational.ConnectionPool
Constructs a connection pool.
connective_tissue - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
contains(String) - Method in class edu.cornell.med.icb.tissueinfo.similarity.clustering.Cluster
 
contains(String) - Method in class edu.mssm.crover.tools.tissue.CuratedDevStage
Returns whether a particular tissue element is present in the library.
contains(String) - Method in class edu.mssm.crover.tools.tissue.CuratedTissue
Returns whether a particular tissue element is present in the library.
contains(CuratedTissue, String) - Method in class edu.mssm.crover.tools.tissue.Hierarchy
Tests whether any of the tissues in tissues are contained in queryTissue.
contains(String, String) - Method in class edu.mssm.crover.tools.tissue.Hierarchy
Tests whether the tissue_part tissue is a part of the tissue_whole tissue.
contains(CuratedTissue, String) - Method in class edu.mssm.crover.tools.tissue.QueryTissueSummary
Determines if the queryTissue is, or is a subset of, any of the tissues in the CuratedTissue ct.
contains(CuratedTissue, String) - Method in class edu.mssm.crover.tools.tissue.TissueSummary
Determines if the queryTissue is, or is a subset of, any of the tissues in the CuratedTissue ct.
convert(String, TissueInfo, TissueESTCountsWriter, String[]) - Method in interface edu.cornell.med.icb.tissueinfo.similarity.EstMatch2Counts
Write tissue EST counts to the writer, for each tissue/condition pair.
convert(String, TissueInfo, TissueESTCountsWriter, String[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.EstMatch2CuratedCancerTissueCounts
 
convert(String, TissueInfo, TissueESTCountsWriter, String[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.EstMatch2CuratedCancerTissueOnlyCounts
 
convert(String, TissueInfo, TissueESTCountsWriter, String[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.EstMatch2CuratedNormalTissueOnlyCounts
 
convert(String, TissueInfo, TissueESTCountsWriter, String[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.EstMatch2CuratedTissueCounts
 
convert(String, TissueInfo, TissueESTCountsWriter, String[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.EstMatch2RawTissueCounts
Gets the number of counts for each tissue for the given accession code.
convert(Object, int) - Method in class edu.mssm.crover.tables.ArrayTable.ColumnDescription.booleanStringConverter
 
convert(Object, int) - Method in class edu.mssm.crover.tables.ArrayTable.ColumnDescription.charStringConverter
 
convert(Object, int) - Method in class edu.mssm.crover.tables.ArrayTable.ColumnDescription.doubleStringConverter
 
convert(Object, int) - Method in class edu.mssm.crover.tables.ArrayTable.ColumnDescription.floatStringConverter
 
convert(Object, int) - Method in class edu.mssm.crover.tables.ArrayTable.ColumnDescription.intStringConverter
 
convert(Object, int) - Method in class edu.mssm.crover.tables.ArrayTable.ColumnDescription.ObjectStringConverter
 
convert(Object, int) - Method in interface edu.mssm.crover.tables.StringConverter
Converts the element of the array to a String.
convert(BlastResult) - Method in class edu.mssm.crover.tools.blast.ExtractAC
calls a convert() method to extract the accession numbers from the BLAST output file.
convert(BlastResult) - Method in class edu.mssm.crover.tools.blast.ExtractAcIdentity
 
copy(Object, int, Object, int) - Method in class edu.mssm.crover.tables.ArrayTable.ColumnDescription.booleanCopier
Copy the boolean value from the source position to the destination position.
copy(Object, int, Object, int) - Method in class edu.mssm.crover.tables.ArrayTable.ColumnDescription.charCopier
Copy the char value from the source position to the destination position.
copy(Object, int, Object, int) - Method in class edu.mssm.crover.tables.ArrayTable.ColumnDescription.doubleCopier
Copy the char value from the source position to the destination position.
copy(Object, int, Object, int) - Method in class edu.mssm.crover.tables.ArrayTable.ColumnDescription.floatCopier
Copy the float value from the source position to the destination position.
copy(Object, int, Object, int) - Method in class edu.mssm.crover.tables.ArrayTable.ColumnDescription.intCopier
Copy the int value from the source position to the destination position.
copy(Object, int, Object, int) - Method in class edu.mssm.crover.tables.ArrayTable.ColumnDescription.objectCopier
Copy the Object value from the source position to the destination position.
copy() - Method in class edu.mssm.crover.tables.ArrayTable
 
copy(RowFilter) - Method in class edu.mssm.crover.tables.ArrayTable
 
copy(RowFilter, ColumnFilter) - Method in class edu.mssm.crover.tables.ArrayTable
 
copy(Table, int, Table.RowIterator, Table, int, Table.RowIterator) - Method in class edu.mssm.crover.tables.ArrayTable
Copy the value at position sourceTable(column, source) to the position destTable(column, dest).
copy(int, Table.RowIterator, int, Table.RowIterator) - Method in class edu.mssm.crover.tables.ArrayTable
Copy the value at position (column, source) to the position (column, dest).
copy() - Method in class edu.mssm.crover.tables.ArrayTable.RowIterator
 
copy() - Method in interface edu.mssm.crover.tables.Table
 
copy(RowFilter) - Method in interface edu.mssm.crover.tables.Table
 
copy(RowFilter, ColumnFilter) - Method in interface edu.mssm.crover.tables.Table
 
copy(Table, int, Table.RowIterator, Table, int, Table.RowIterator) - Method in interface edu.mssm.crover.tables.Table
Copy the value at position sourceTable(column, source) to the position destTable(column, dest).
copy(int, Table.RowIterator, int, Table.RowIterator) - Method in interface edu.mssm.crover.tables.Table
Copy the value at position (column, source) to the position (column, dest).
copy(Object, int, Object, int) - Method in interface edu.mssm.crover.tables.ValueCopier
Copy the value from the source position to the destination position.
copy(InputStream, File) - Method in class edu.mssm.crover.tools.blast.BlastCommand
 
copy(File, File) - Method in class edu.mssm.crover.tools.blast.BlastCommand
 
cornea - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
CORONAL - Static variable in class edu.cornell.med.icb.allen.xml.types.PlaneType
The instance of the coronal type
CORONAL_TYPE - Static variable in class edu.cornell.med.icb.allen.xml.types.PlaneType
The coronal type
corpora_quadrigemina - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
corpus_callosum - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
corpus_luteum - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
corpus_striatum - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
count() - Method in class edu.cornell.med.icb.stat.ZScoreCalculator
 
CountPreprocessor - Interface in edu.cornell.med.icb.tissueinfo.similarity.preprocessors
An interface to preprocess counts before scoring happens.
cranial_nerves - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
cranium - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
createBlastResult(StringReader) - Method in class edu.mssm.crover.tools.blast.BlastCommand
Creates a BlastResult from a StringReader.
crossValidationFoldNumber - Variable in class edu.cornell.med.icb.tissueinfo.similarity.TiSimOptions
 
CrossValidationMode - Class in edu.cornell.med.icb.tissueinfo.similarity
Splits a dataset into a number of categories and performs cross validation with forward mode.
CrossValidationMode() - Constructor for class edu.cornell.med.icb.tissueinfo.similarity.CrossValidationMode
 
CSVReader - Class in edu.mssm.crover.tables.readers
 
CSVReader() - Constructor for class edu.mssm.crover.tables.readers.CSVReader
 
CTISSUE_COLNUM - Static variable in class edu.mssm.crover.tools.tissue.DumpNullsTissueInfo
Column number for curated tissue.
CTISSUE_COLNUM - Static variable in class edu.mssm.crover.tools.tissue.TissueInfoNullsJDBCImpl
The column index for the curated tissue.
CuratedDevStage - Class in edu.mssm.crover.tools.tissue
Storage class for tissue information.
CuratedDevStage(String) - Constructor for class edu.mssm.crover.tools.tissue.CuratedDevStage
Parses the curated tissues and assigns its descriptors.
CuratedTissue - Class in edu.mssm.crover.tools.tissue
Storage class for tissue information.
CuratedTissue(String) - Constructor for class edu.mssm.crover.tools.tissue.CuratedTissue
Parses the curated tissues and assigns its descriptors.
currentShuffledLabelIndex - Variable in class edu.mssm.crover.tables.writers.SVMLightWriter
 

D

DatabaseErrorException - Exception in edu.mssm.crover.db
 
DatabaseErrorException(Exception) - Constructor for exception edu.mssm.crover.db.DatabaseErrorException
 
DatabaseErrorException(String) - Constructor for exception edu.mssm.crover.db.DatabaseErrorException
 
DatabaseNotFound - Exception in edu.mssm.crover.tools.blast
 
DatabaseNotFound(String, String) - Constructor for exception edu.mssm.crover.tools.blast.DatabaseNotFound
 
DbestParser - Class in edu.mssm.crover.tools.tissue
Parses dbEST and extract tissue information.
DbestParser() - Constructor for class edu.mssm.crover.tools.tissue.DbestParser
 
deactivate() - Method in class edu.mssm.crover.db.relational.ConnectionPool
Force the finalization and flag this object as inactive.
DEBUG - Variable in class edu.mssm.crover.db.relational.ConnectionPool
DEBUG flag.
DEFAULT_HIERARCHY_PACKAGE - Static variable in class edu.mssm.crover.tools.tissue.Hierarchy
The default location of the hierarchy package, i.e., the location of the interfaces that define the hierarchy.
DefineColumnFromRow - Class in edu.mssm.crover.tables
 
DefineColumnFromRow(int) - Constructor for class edu.mssm.crover.tables.DefineColumnFromRow
 
defineColumnsFrom(Table) - Method in class edu.mssm.crover.tables.ArrayTable
Defines the columns of this table from the columns in source.
defineColumnsFrom(Table, ColumnFilter) - Method in class edu.mssm.crover.tables.ArrayTable
Defines the columns of this table from the columns in source.
defineColumnsFrom(Table) - Method in interface edu.mssm.crover.tables.Table
Defines the columns of this table from the columns in source.
defineOptions(JSAP) - Method in class edu.cornell.med.icb.tissueinfo.similarity.AnnotateClustersMode
 
defineOptions(JSAP) - Method in class edu.cornell.med.icb.tissueinfo.similarity.BackwardMode
 
defineOptions(JSAP) - Method in class edu.cornell.med.icb.tissueinfo.similarity.ClusterMode
 
defineOptions(JSAP) - Method in class edu.cornell.med.icb.tissueinfo.similarity.CrossValidationMode
 
defineOptions(JSAP) - Method in class edu.cornell.med.icb.tissueinfo.similarity.ForwardMode
 
defineOptions(JSAP) - Method in class edu.cornell.med.icb.tissueinfo.similarity.LeaveOneOutMode
 
defineOptions(JSAP) - Method in class edu.cornell.med.icb.tissueinfo.similarity.ListSearchMode
 
defineOptions(JSAP) - Method in class edu.cornell.med.icb.tissueinfo.similarity.PairSearchMode
 
defineOptions(JSAP) - Method in class edu.cornell.med.icb.tissueinfo.similarity.SimpleSearchMode
 
defineOptions(JSAP) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TallyScoreSearchMode
 
defineOptions(JSAP) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TiSimMode
 
defineOptions(JSAP) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TranscriptListMode
 
defineRocOptions(JSAP) - Static method in class edu.cornell.med.icb.tissueinfo.similarity.LeaveOneOutMode
 
deleteBlastOutput_queryLen() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.BlastOutput
 
deleteBValue() - Method in class edu.mssm.crover.tools.tissue.xml.BlastHits
 
deleteExpectationValue() - Method in class edu.mssm.crover.tools.tissue.xml.BlastHits
 
deleteHit_len() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HitType
 
deleteHit_num() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HitType
 
deleteHsp_alignLen() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
 
deleteHsp_evalue() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
 
deleteHsp_gaps() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
 
deleteHsp_hitFrame() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
 
deleteHsp_hitFrom() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
 
deleteHsp_hitTo() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
 
deleteHsp_identity() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
 
deleteHsp_num() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
 
deleteHsp_positive() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
 
deleteHsp_queryFrame() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
 
deleteHsp_queryFrom() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
 
deleteHsp_queryTo() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
 
deleteHsp_score() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
 
deleteId() - Method in class edu.mssm.crover.tools.tissue.xml.Tokey
 
deleteIteration_iterNum() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.IterationType
 
deleteIteration_queryLen() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.IterationType
 
deleteMaxErrorRate() - Method in class edu.mssm.crover.tools.tissue.xml.BlastHits
 
deleteMinimumLength() - Method in class edu.mssm.crover.tools.tissue.xml.BlastHits
 
deleteParameters_expect() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.ParametersType
 
deleteParameters_gapExtend() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.ParametersType
 
deleteParameters_gapOpen() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.ParametersType
 
deleteParameters_scMatch() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.ParametersType
 
deleteParameters_scMismatch() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.ParametersType
 
deleteProjectcode() - Method in class edu.cornell.med.icb.allen.xml.GeneExpression
 
deleteStatistics_dbLen() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.StatisticsType
 
deleteStatistics_dbNum() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.StatisticsType
 
deleteStatistics_hspLen() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.StatisticsType
 
deleteTokey() - Method in class edu.mssm.crover.tools.tissue.xml.Hit
 
deleteVValue() - Method in class edu.mssm.crover.tools.tissue.xml.BlastHits
 
dendrite - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
dequeue() - Method in class edu.cornell.med.icb.tissueinfo.similarity.ScoredTranscriptBoundedSizeQueue
Dequeues a document from the queue, returning an instance of TranscriptScore.
descending_colon - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
describesResidue(int) - Method in interface edu.mssm.crover.representation.BiologicalAnnotation
Returns whether the position is described by this annotation.
describesResidue(int) - Method in class edu.mssm.crover.representation.Mutation_Annotation
 
describesResidue(int) - Method in class edu.mssm.crover.representation.SequenceOrigin_Annotation
This annotation does not describe independant residues.
describesResidue(int) - Method in class edu.mssm.crover.representation.URL_Annotation
 
describeTable(String) - Method in class edu.mssm.crover.tables.AddToTable
Uses SQL to describe the table, and puts the column headings into a HashSet.
Description - Interface in edu.mssm.crover.representation
 
destroy() - Method in class edu.mssm.crover.db.relational.RDB
Deactivates connections to the database.
destroy() - Method in class edu.mssm.crover.tables.JDBCTable
Destroy all tables.
destroy() - Method in interface edu.mssm.crover.tools.tissue.TissueInfo
Destroy all TissueInfo data and tables.
destroy() - Method in class edu.mssm.crover.tools.tissue.TissueInfoCacheImpl
Destroy all TissueInfo data and tables.
destroy() - Method in class edu.mssm.crover.tools.tissue.TissueInfoJDBCImpl
Destroy all TissueInfo data and tables.
destroy() - Method in class edu.mssm.crover.tools.tissue.TissueInfoMemoryImpl
Destroy all TissueInfo data and tables.
destroy() - Method in class edu.mssm.crover.tools.tissue.TissueInfoMemoryImpl2
Destroy all TissueInfo data and tables.
destroy() - Method in class edu.mssm.crover.tools.tissue.TissueInfoNullsJDBCImpl
Destroy all TissueInfo data and tables.
destroy() - Method in interface edu.mssm.crover.tools.tissue.TIWeb
Destroy all TissueInfo data and tables.
destroy() - Method in class edu.mssm.crover.tools.tissue.TIWebJDBCImpl
Destroy all tables.
determineEffectiveNumberOfGenes(GeneTranscriptRelationships, TiSimOptions) - Static method in class edu.cornell.med.icb.tissueinfo.similarity.LeaveOneOutMode
 
DevStageCuration - Class in edu.mssm.crover.tools.tissue
Stores all the manual curation for every raw tissue string extracted from dbEST.
DevStageCuration(String) - Constructor for class edu.mssm.crover.tools.tissue.DevStageCuration
This constructor tries to obtain curated developmental stages from a file.
DevStageCuration(Reader) - Constructor for class edu.mssm.crover.tools.tissue.DevStageCuration
Reads curated developmental stage information from a reader.
DevStageCuration() - Constructor for class edu.mssm.crover.tools.tissue.DevStageCuration
Default constructor.
devStageTimesExpressed() - Method in class edu.mssm.crover.tools.tissue.QueryTissueSummary
Counts the number of times the query has a hit to each developmental stage.
devStageTimesExpressed() - Method in class edu.mssm.crover.tools.tissue.TissueSummary
Counts the number of times the query has a hit to each developmental stage.
diaphragm - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
diencephalon - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
digestive - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
dispose(File) - Method in class edu.mssm.crover.tools.blast.BlastCommand
 
divideLibraries() - Method in class edu.mssm.crover.tools.tissue.LibraryDivision
Divides the libraries using time as a random seed.
divideLibraries(long) - Method in class edu.mssm.crover.tools.tissue.LibraryDivision
Divides the libraries using a user-defined seed.
divideLibraries(Map<String, Integer>) - Method in class edu.mssm.crover.tools.tissue.LibraryDivision
Divide the libraries using time as a random seed.
divideLibraries(Map<String, Integer>, long) - Method in class edu.mssm.crover.tools.tissue.LibraryDivision
Divide the libraries using a user-defined seed.
divideLibraries(Collection<Integer>, long) - Method in class edu.mssm.crover.tools.tissue.LibraryDivision
Divides up the libraries randomly into two groups, and calculates the number of accession numbers coming from each group.
doNotAggregate(String) - Method in class edu.mssm.crover.tables.treatments.Aggregation
 
doNotGroupBy(String) - Method in class edu.mssm.crover.tables.treatments.Aggregation
 
doNotRemove(String) - Method in class edu.mssm.crover.tables.treatments.Aggregation
 
dorsal_raphe - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
dorsal_root_ganglion - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
DoubleArraySizer - Class in edu.mssm.crover.tables
 
DoubleArraySizer() - Constructor for class edu.mssm.crover.tables.DoubleArraySizer
 
DSSPTableReader - Class in edu.mssm.crover.tables.readers
Reads a DSSP (W.
DSSPTableReader() - Constructor for class edu.mssm.crover.tables.readers.DSSPTableReader
 
dump(TissueInfo, String, String, String[], String) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TiDumpTissueCounts
 
dump(String[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TiDumpTissueCounts
 
dump(String) - Method in class edu.mssm.crover.tools.tissue.DumpNullsTissueInfo
Return the organism associated with a sequence accession code.
dump(String, String, String) - Method in class edu.mssm.crover.tools.tissue.DumpTissueInfo
Return the organism associated with a sequence accession code.
dumpAc(PrintWriter) - Method in class edu.mssm.crover.tools.tissue.DumpTissueInfo
Prints the rows from the TI_SEQ table.
dumpDev(PrintWriter) - Method in class edu.mssm.crover.tools.tissue.DumpTissueInfo
Prints the rows from the TI_DEV table.
dumpNulls(PrintWriter) - Method in class edu.mssm.crover.tools.tissue.DumpNullsTissueInfo
Prints the rows from the TI_NULL table.
DumpNullsTissueInfo - Class in edu.mssm.crover.tools.tissue
Dumps information from the TissueInfo null table.
DumpTissueInfo - Class in edu.mssm.crover.tools.tissue
Dumps TissueInfo to files.
dumpTO(PrintWriter) - Method in class edu.mssm.crover.tools.tissue.DumpTissueInfo
Prints the rows from the TI_TO table.
duodenum - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
dura_mater - Interface in edu.mssm.crover.tools.tissue.hierarchy
 

E

ear - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
ectoderm - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
edu.cornell.med.icb.allen.xml - package edu.cornell.med.icb.allen.xml
 
edu.cornell.med.icb.allen.xml.descriptors - package edu.cornell.med.icb.allen.xml.descriptors
 
edu.cornell.med.icb.allen.xml.types - package edu.cornell.med.icb.allen.xml.types
 
edu.cornell.med.icb.allen.xml.types.descriptors - package edu.cornell.med.icb.allen.xml.types.descriptors
 
edu.cornell.med.icb.stat - package edu.cornell.med.icb.stat
 
edu.cornell.med.icb.tissueinfo.annotations - package edu.cornell.med.icb.tissueinfo.annotations
 
edu.cornell.med.icb.tissueinfo.owl - package edu.cornell.med.icb.tissueinfo.owl
Provides support for exporting the ontologies in the OWL format.
edu.cornell.med.icb.tissueinfo.similarity - package edu.cornell.med.icb.tissueinfo.similarity
Tools to calculate tissue expression profile similarity.
edu.cornell.med.icb.tissueinfo.similarity.clustering - package edu.cornell.med.icb.tissueinfo.similarity.clustering
 
edu.cornell.med.icb.tissueinfo.similarity.preprocessors - package edu.cornell.med.icb.tissueinfo.similarity.preprocessors
 
edu.cornell.med.icb.tissueinfo.similarity.scorers - package edu.cornell.med.icb.tissueinfo.similarity.scorers
 
edu.cornell.med.icb.tools - package edu.cornell.med.icb.tools
 
edu.mssm.crover.db - package edu.mssm.crover.db
 
edu.mssm.crover.db.relational - package edu.mssm.crover.db.relational
Provides configuration and connection pool for a relational database through JDBC.
edu.mssm.crover.imports - package edu.mssm.crover.imports
Provides for the import of sequences from files.
edu.mssm.crover.representation - package edu.mssm.crover.representation
Provides for the representation of biological objects.
edu.mssm.crover.tables - package edu.mssm.crover.tables
Provides for table data structures, algorithms, readers and writers.
edu.mssm.crover.tables.readers - package edu.mssm.crover.tables.readers
Provides table readers.
edu.mssm.crover.tables.treatments - package edu.mssm.crover.tables.treatments
Provides table treatments.
edu.mssm.crover.tables.writers - package edu.mssm.crover.tables.writers
Provides table writers.
edu.mssm.crover.tools - package edu.mssm.crover.tools
Provides API to access bioinformatics tools.
edu.mssm.crover.tools.blast - package edu.mssm.crover.tools.blast
Provides an API to access BLAST from Java.
edu.mssm.crover.tools.blast.parsers - package edu.mssm.crover.tools.blast.parsers
Provides parsers for the XML version of the BLAST oupput.
edu.mssm.crover.tools.blast.parsers.xml.v3 - package edu.mssm.crover.tools.blast.parsers.xml.v3
 
edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors - package edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors
 
edu.mssm.crover.tools.tissue - package edu.mssm.crover.tools.tissue
TissueInfo command line tools and classes.
edu.mssm.crover.tools.tissue.hierarchy - package edu.mssm.crover.tools.tissue.hierarchy
Default hierarchy of tissue developed for TissueInfo.
edu.mssm.crover.tools.tissue.plugins - package edu.mssm.crover.tools.tissue.plugins
TissueInfo plugins.
edu.mssm.crover.tools.tissue.xml - package edu.mssm.crover.tools.tissue.xml
 
edu.mssm.crover.tools.tissue.xml.descriptors - package edu.mssm.crover.tools.tissue.xml.descriptors
 
edu.mssm.crover.util - package edu.mssm.crover.util
Provides various tools and APIs.
elementToString(int) - Method in class edu.mssm.crover.tables.ArrayTable.ColumnDescription
 
elementToString(int, Table.RowIterator) - Method in class edu.mssm.crover.tables.ArrayTable
 
elementToString(int, Table.RowIterator) - Method in interface edu.mssm.crover.tables.Table
 
empty() - Method in class edu.mssm.crover.tables.JDBCTable
Empty table.
empty() - Method in interface edu.mssm.crover.tools.tissue.TissueInfo
Empty TissueInfo.
empty() - Method in class edu.mssm.crover.tools.tissue.TissueInfoCacheImpl
Empty TissueInfo.
empty() - Method in class edu.mssm.crover.tools.tissue.TissueInfoJDBCImpl
Empty TissueInfo.
empty() - Method in class edu.mssm.crover.tools.tissue.TissueInfoMemoryImpl
Empty TissueInfo.
empty() - Method in class edu.mssm.crover.tools.tissue.TissueInfoMemoryImpl2
Empty TissueInfo.
empty() - Method in class edu.mssm.crover.tools.tissue.TissueInfoNullsJDBCImpl
Empty TissueInfo.
empty() - Method in interface edu.mssm.crover.tools.tissue.TIWeb
Empty TissueInfo.
empty() - Method in class edu.mssm.crover.tools.tissue.TIWebJDBCImpl
Empty table.
end() - Method in class edu.mssm.crover.tables.AddToTable
Notifies this class that a batch of interaction now ends.
end() - Method in class edu.mssm.crover.tables.ArrayTable.RowIterator
Returns true when the last row has been passed, false when the row pointed to by the iterator is valid.
end() - Method in class edu.mssm.crover.tables.JDBCTable
Notifies this class that a batch of interaction now ends.
end() - Method in class edu.mssm.crover.tables.QueryTable
Notifies this class that a batch of interaction now ends.
end() - Method in interface edu.mssm.crover.tables.Table.RowIterator
Returns true when the last row has been passed, false when the row pointed to by the iterator is valid.
end() - Method in class edu.mssm.crover.tables.TableActivityWatcher
Notifies this class that a batch of interaction now ends.
end(Table, Table) - Method in class edu.mssm.crover.tables.treatments.Aggregation
Invoked after every row has been processed.
end(Table) - Method in class edu.mssm.crover.tables.treatments.CompositionTableTreatment
 
end(Object) - Method in class edu.mssm.crover.tables.treatments.TableTreatment
 
end(Table) - Method in class edu.mssm.crover.tables.treatments.TableTreatment
 
end() - Method in class edu.mssm.crover.tools.tissue.DumpNullsTissueInfo
Notifies this class that a batch of interaction now ends.
end() - Method in class edu.mssm.crover.tools.tissue.DumpTissueInfo
Notifies this class that a batch of interaction now ends.
end() - Method in interface edu.mssm.crover.tools.tissue.TissueInfo
Notifies this class that a batch of interaction now ends.
end() - Method in class edu.mssm.crover.tools.tissue.TissueInfoCacheImpl
Notifies this class that a batch of interaction now ends.
end() - Method in class edu.mssm.crover.tools.tissue.TissueInfoJDBCImpl
Notifies this class that a batch of interaction now ends.
end() - Method in class edu.mssm.crover.tools.tissue.TissueInfoMemoryImpl
Notifies this class that a batch of interaction now ends.
end() - Method in class edu.mssm.crover.tools.tissue.TissueInfoMemoryImpl2
Notifies this class that a batch of interaction now ends.
end() - Method in class edu.mssm.crover.tools.tissue.TissueInfoNullsJDBCImpl
Notifies this class that a batch of interaction now ends.
end() - Method in interface edu.mssm.crover.tools.tissue.TIWeb
Notifies this class that a batch of interaction now ends.
end() - Method in class edu.mssm.crover.tools.tissue.TIWebJDBCImpl
Notifies this class that a batch of interaction now ends.
endIndex - Variable in class edu.cornell.med.icb.tissueinfo.similarity.TiSimOptions
 
endocrine - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
endoderm - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
endometrium - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
engine - Variable in class edu.cornell.med.icb.tissueinfo.similarity.TiSimOptions
 
enqueue(int, double) - Method in class edu.cornell.med.icb.tissueinfo.similarity.ScoredTranscriptBoundedSizeQueue
Enqueues a transcript with given score and info.
enqueue(TranscriptScore) - Method in class edu.cornell.med.icb.tissueinfo.similarity.ScoredTranscriptBoundedSizeQueue
 
enteric_NS - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
entorhinal_cortex - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
Entrezgeneid - Class in edu.cornell.med.icb.allen.xml
Class Entrezgeneid.
Entrezgeneid() - Constructor for class edu.cornell.med.icb.allen.xml.Entrezgeneid
 
EntrezgeneidDescriptor - Class in edu.cornell.med.icb.allen.xml.descriptors
Class EntrezgeneidDescriptor.
EntrezgeneidDescriptor() - Constructor for class edu.cornell.med.icb.allen.xml.descriptors.EntrezgeneidDescriptor
 
EntrezgeneidTypeType - Class in edu.cornell.med.icb.allen.xml.types
Class EntrezgeneidTypeType.
EntrezgeneidTypeTypeDescriptor - Class in edu.cornell.med.icb.allen.xml.types.descriptors
Class EntrezgeneidTypeTypeDescriptor.
EntrezgeneidTypeTypeDescriptor() - Constructor for class edu.cornell.med.icb.allen.xml.types.descriptors.EntrezgeneidTypeTypeDescriptor
 
enumerate() - Static method in class edu.cornell.med.icb.allen.xml.types.AgeTypeType
Method enumerate.Returns an enumeration of all possible instances of AgeTypeType
enumerate() - Static method in class edu.cornell.med.icb.allen.xml.types.AvgdensityTypeType
Method enumerate.Returns an enumeration of all possible instances of AvgdensityTypeType
enumerate() - Static method in class edu.cornell.med.icb.allen.xml.types.AvglevelTypeType
Method enumerate.Returns an enumeration of all possible instances of AvglevelTypeType
enumerate() - Static method in class edu.cornell.med.icb.allen.xml.types.EntrezgeneidTypeType
Method enumerate.Returns an enumeration of all possible instances of EntrezgeneidTypeType
enumerate() - Static method in class edu.cornell.med.icb.allen.xml.types.GeneidTypeType
Method enumerate.Returns an enumeration of all possible instances of GeneidTypeType
enumerate() - Static method in class edu.cornell.med.icb.allen.xml.types.ImageseriesidTypeType
Method enumerate.Returns an enumeration of all possible instances of ImageseriesidTypeType
enumerate() - Static method in class edu.cornell.med.icb.allen.xml.types.OrganismType
Method enumerate.Returns an enumeration of all possible instances of OrganismType
enumerate() - Static method in class edu.cornell.med.icb.allen.xml.types.PlaneType
Method enumerate.Returns an enumeration of all possible instances of PlaneType
enumerate() - Static method in class edu.cornell.med.icb.allen.xml.types.SexType
Method enumerate.Returns an enumeration of all possible instances of SexType
enumerate() - Static method in class edu.cornell.med.icb.allen.xml.types.StructureidTypeType
Method enumerate.Returns an enumeration of all possible instances of StructureidTypeType
enumerate() - Static method in class edu.cornell.med.icb.allen.xml.types.T_age
Method enumerate.Returns an enumeration of all possible instances of T_age
enumerate() - Static method in class edu.cornell.med.icb.allen.xml.types.TemplateidTypeType
Method enumerate.Returns an enumeration of all possible instances of TemplateidTypeType
enumerate() - Static method in class edu.cornell.med.icb.allen.xml.types.TranscriptgiTypeType
Method enumerate.Returns an enumeration of all possible instances of TranscriptgiTypeType
enumerate() - Static method in class edu.cornell.med.icb.allen.xml.types.TranscriptidTypeType
Method enumerate.Returns an enumeration of all possible instances of TranscriptidTypeType
enumerate() - Static method in class edu.cornell.med.icb.allen.xml.types.TreatmenttypeType
Method enumerate.Returns an enumeration of all possible instances of TreatmenttypeType
enumerateGene() - Method in class edu.cornell.med.icb.allen.xml.Genes
Method enumerateGene.
enumerateGeneExpression() - Method in class edu.cornell.med.icb.allen.xml.GeneExpressions
Method enumerateGeneExpression.
enumerateHit() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Iteration_hitsType
Method enumerateHit.
enumerateHit() - Method in class edu.mssm.crover.tools.tissue.xml.QuerySequence
Method enumerateHit.
enumerateHsp() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Hit_hspsType
Method enumerateHsp.
enumerateImageSeries() - Method in class edu.cornell.med.icb.allen.xml.ImageSeries
Method enumerateImageSeries.
enumerateQuerySequence() - Method in class edu.mssm.crover.tools.tissue.xml.BlastHits
Method enumerateQuerySequence.
enumerateTokey() - Method in class edu.mssm.crover.tools.tissue.xml.TissueInfo
Method enumerateTokey.
eosinophil - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
epidermis - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
epididymis - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
epithalamus - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
epithelium - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
equalOnColumns(Table.RowIterator, int[]) - Method in class edu.mssm.crover.tables.ArrayTable.RowIterator
Compares this iterator instance to another iterator instance.
equalOnColumns(Table, Table.RowIterator, int[]) - Method in class edu.mssm.crover.tables.ArrayTable.RowIterator
 
equalOnColumns(Table.RowIterator, int[]) - Method in interface edu.mssm.crover.tables.Table.RowIterator
Compares this iterator instance to another iterator instance.
equals(FastaReaderType) - Method in class edu.mssm.crover.imports.FastaReaderType
 
equals(Object, int, Object, int) - Method in class edu.mssm.crover.tables.ArrayTable.ColumnDescription.booleanComparator
 
equals(Object, int, Object, int) - Method in class edu.mssm.crover.tables.ArrayTable.ColumnDescription.charComparator
 
equals(Object, int, Object, int) - Method in class edu.mssm.crover.tables.ArrayTable.ColumnDescription.doubleComparator
 
equals(Object, int, Object, int) - Method in class edu.mssm.crover.tables.ArrayTable.ColumnDescription.floatComparator
 
equals(Object, int, Object, int) - Method in class edu.mssm.crover.tables.ArrayTable.ColumnDescription.intComparator
 
equals(Object, int, Object, int) - Method in class edu.mssm.crover.tables.ArrayTable.ColumnDescription.objectComparator
 
equals(Object) - Method in class edu.mssm.crover.tables.ArrayTable
Compare this ArrayTable with another table.
equals(Object, int, Object, int) - Method in interface edu.mssm.crover.tables.ValueComparator
Returns true when the value at index1 of array1 equals the value at index2 of array2.
esophagus - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
EstMatch2Counts - Interface in edu.cornell.med.icb.tissueinfo.similarity
 
EstMatch2CuratedCancerTissueCounts - Class in edu.cornell.med.icb.tissueinfo.similarity
 
EstMatch2CuratedCancerTissueCounts() - Constructor for class edu.cornell.med.icb.tissueinfo.similarity.EstMatch2CuratedCancerTissueCounts
 
EstMatch2CuratedCancerTissueOnlyCounts - Class in edu.cornell.med.icb.tissueinfo.similarity
 
EstMatch2CuratedCancerTissueOnlyCounts() - Constructor for class edu.cornell.med.icb.tissueinfo.similarity.EstMatch2CuratedCancerTissueOnlyCounts
 
EstMatch2CuratedNormalTissueOnlyCounts - Class in edu.cornell.med.icb.tissueinfo.similarity
 
EstMatch2CuratedNormalTissueOnlyCounts() - Constructor for class edu.cornell.med.icb.tissueinfo.similarity.EstMatch2CuratedNormalTissueOnlyCounts
 
EstMatch2CuratedTissueCounts - Class in edu.cornell.med.icb.tissueinfo.similarity
 
EstMatch2CuratedTissueCounts() - Constructor for class edu.cornell.med.icb.tissueinfo.similarity.EstMatch2CuratedTissueCounts
 
EstMatch2RawTissueCounts - Class in edu.cornell.med.icb.tissueinfo.similarity
 
EstMatch2RawTissueCounts() - Constructor for class edu.cornell.med.icb.tissueinfo.similarity.EstMatch2RawTissueCounts
 
EstRepresentationScorer - Class in edu.cornell.med.icb.tissueinfo.similarity.scorers
Same as RawESTScorer, but divides raw counts by the number of EST in the particular tissue plus one.
EstRepresentationScorer() - Constructor for class edu.cornell.med.icb.tissueinfo.similarity.scorers.EstRepresentationScorer
 
evaluateAccuracy(double, double[], double[]) - Method in class edu.cornell.med.icb.stat.AccuracyCalculator
Evaluate the accuracy for a given decision function threshold.
evaluateContingencyTable(double, double[], double[]) - Method in class edu.cornell.med.icb.stat.PredictionStatisticCalculator
Evaluate the contingency table at a specific threshold.
evaluateMCC(double, double[], double[]) - Method in class edu.cornell.med.icb.stat.MatthewsCorrelationCalculator
Evaluate the Mathews Correlation coefficient for a given decision function threshold.
evaluateSensitivity(double, double[], double[]) - Method in class edu.cornell.med.icb.stat.SensitivityCalculator
Evaluate the sensitivity of predictions at a given decision function threshold.
evaluateSpecificity(double, double[], double[]) - Method in class edu.cornell.med.icb.stat.SpecificityCalculator
Evaluate the specificity of predictions at a given decision function threshold.
evaluateStatistic(double[], double[]) - Method in class edu.cornell.med.icb.stat.AreaUnderTheRocCurveCalculator
 
evaluateStatisticAtThreshold(double, double[], double[]) - Method in class edu.cornell.med.icb.stat.AccuracyCalculator
 
evaluateStatisticAtThreshold(double, double[], double[]) - Method in class edu.cornell.med.icb.stat.AreaUnderTheRocCurveCalculator
 
evaluateStatisticAtThreshold(double, double[], double[]) - Method in class edu.cornell.med.icb.stat.MatthewsCorrelationCalculator
 
evaluateStatisticAtThreshold(double, ObjectList<double[]>, ObjectList<double[]>) - Method in class edu.cornell.med.icb.stat.PredictionStatisticCalculator
 
evaluateStatisticAtThreshold(double, double[], double[]) - Method in class edu.cornell.med.icb.stat.PredictionStatisticCalculator
Evaluate the statistic for a given decision function threshold.
evaluateStatisticAtThreshold(double, double[], double[]) - Method in class edu.cornell.med.icb.stat.RootMeanSquaredErrorCalculator
 
evaluateStatisticAtThreshold(double, double[], double[]) - Method in class edu.cornell.med.icb.stat.SensitivityCalculator
 
evaluateStatisticAtThreshold(double, double[], double[]) - Method in class edu.cornell.med.icb.stat.SpecificityCalculator
 
execute() - Static method in class edu.cornell.med.icb.tissueinfo.owl.ExportOntology
Required by the Protege OWL methods, but is rarely (if ever) called.
exocrine - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
expected - Variable in exception edu.mssm.crover.tables.treatments.InadequateBindingException
 
export(String) - Method in class edu.cornell.med.icb.tissueinfo.owl.ExportOntology
Exports the OWL ontology.
ExportOntology - Class in edu.cornell.med.icb.tissueinfo.owl
Exports the tissue info hierarchy as an OWL ontology.
ExportOntology() - Constructor for class edu.cornell.med.icb.tissueinfo.owl.ExportOntology
Creates a new exporter.
expressedIn() - Method in class edu.mssm.crover.tools.tissue.QueryTissueSummary
Returns an array of the tissues in which the ESTs associated with the given accession numbers are expressed.
expressedIn() - Method in class edu.mssm.crover.tools.tissue.TissueSummary
Returns an array of the tissues in which the ESTs associated with the given accession numbers are expressed.
expressedInDevStage() - Method in class edu.mssm.crover.tools.tissue.QueryTissueSummary
Returns an array of the developmental stages in which the ESTs associated with the given accession numbers are expressed.
expressedInDevStage() - Method in class edu.mssm.crover.tools.tissue.TissueSummary
Returns an array of the developmental stages in which the ESTs associated with the given accession numbers are expressed.
expressedInRawTissues() - Method in class edu.mssm.crover.tools.tissue.TissueSummary
Returns an array of the raw tissues in which the ESTs associated with the given accession numbers are expressed.
ExpressionConfidenceScorer - Class in edu.cornell.med.icb.tissueinfo.similarity.scorers
Implements the scorer described in http://icb.med.cornell.edu/wiki/uploads/math/c/2/8/c280e1c6b3550fcff8e2dc01676f923a.png.
ExpressionConfidenceScorer() - Constructor for class edu.cornell.med.icb.tissueinfo.similarity.scorers.ExpressionConfidenceScorer
 
ExpressionProfileSimilarityScorer - Interface in edu.cornell.med.icb.tissueinfo.similarity.scorers
Implementations of this interface can be used to score the similarity of two expression profiles.
extract(BlastResult) - Method in class edu.mssm.crover.tools.blast.ExtractDefLine
calls an extract() method to extract the hit information from the first HSP from the first hit of the BLAST output file.
ExtractAC - Class in edu.mssm.crover.tools.blast
Extracts the accession numbers from the definition line of a BLAST output.
ExtractAC() - Constructor for class edu.mssm.crover.tools.blast.ExtractAC
 
ExtractAcIdentity - Class in edu.mssm.crover.tools.blast
Extracts the accession numbers from the definition line of a BLAST output.
ExtractAcIdentity() - Constructor for class edu.mssm.crover.tools.blast.ExtractAcIdentity
 
ExtractDefLine - Class in edu.mssm.crover.tools.blast
Extracts the definition line from the first hit of a BLAST output.
ExtractDefLine() - Constructor for class edu.mssm.crover.tools.blast.ExtractDefLine
 
eye - Interface in edu.mssm.crover.tools.tissue.hierarchy
 

F

F - Static variable in class edu.cornell.med.icb.allen.xml.types.SexType
The instance of the F type
F_TYPE - Static variable in class edu.cornell.med.icb.allen.xml.types.SexType
The F type
facial_nerve - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
fallopian_tube - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
FASTA - Static variable in class edu.mssm.crover.imports.FastaReader
 
FastaReader - Class in edu.mssm.crover.imports
The fasta reader is very simple and cannot do a lot of error checking (because the FASTA format does not provide enough information to cross check).
FastaReader() - Constructor for class edu.mssm.crover.imports.FastaReader
 
FastaReaderType - Class in edu.mssm.crover.imports
 
FastaReaderType() - Constructor for class edu.mssm.crover.imports.FastaReaderType
 
FastExpressionConfidenceScorer - Class in edu.cornell.med.icb.tissueinfo.similarity.scorers
Optimized version of ExpressionConfidenceScorer with fixed confidence thresholds.
FastExpressionConfidenceScorer() - Constructor for class edu.cornell.med.icb.tissueinfo.similarity.scorers.FastExpressionConfidenceScorer
 
FEMALE - Static variable in class edu.cornell.med.icb.allen.xml.types.SexType
The instance of the female type
FEMALE_TYPE - Static variable in class edu.cornell.med.icb.allen.xml.types.SexType
The female type
fibroblast - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
Filter - Interface in edu.mssm.crover.tables
Interface for table filters.
FilterClusters - Class in edu.cornell.med.icb.tissueinfo.similarity.clustering
Filters clusters to keep only transcripts in a cluster that appear in a specified list of transcripts.
FilterClusters() - Constructor for class edu.cornell.med.icb.tissueinfo.similarity.clustering.FilterClusters
 
FilterTransposeGenotypeTable - Class in edu.cornell.med.icb.tools
 
FilterTransposeGenotypeTable() - Constructor for class edu.cornell.med.icb.tools.FilterTransposeGenotypeTable
 
finalize() - Method in class edu.mssm.crover.db.relational.ConnectionPool
 
finalize() - Method in class edu.mssm.crover.tables.JDBCTable
 
finalize() - Method in class edu.mssm.crover.tools.tissue.TissueInfoJDBCImpl
Clean up.
finalize() - Method in class edu.mssm.crover.tools.tissue.TissueInfoNullsJDBCImpl
Clean up.
finalize() - Method in class edu.mssm.crover.tools.tissue.TIWebJDBCImpl
Cleans up.
findAnnotation(Class) - Method in class edu.mssm.crover.representation.Annotations
Finds and return an annotation according to its class.
findAnnotation(Class, int) - Method in class edu.mssm.crover.representation.Annotations
Finds and return an annotation about a residue, according to its class.
findAnnotation(Class) - Method in interface edu.mssm.crover.representation.BiologicalAnnotations
Finds the annotation that supports the interface annotation_class.
findCancer(String[]) - Method in class edu.mssm.crover.tools.tissue.GetCuratedTissue
Returns whether to print out all the tissues which come from tumor tissue.
findComment(BufferedReader, BiologicalSequence) - Method in class edu.mssm.crover.imports.FastaReader
 
findCuratedDevStages(String, String) - Method in class edu.mssm.crover.tools.tissue.GetCuratedDevStage
Reads each line from the file containing the tissues.
findCuratedTissues(String, boolean, boolean, String) - Method in class edu.mssm.crover.tools.tissue.GetCuratedTissue
Reads each line from the file containing the tissues.
findParents(String[]) - Method in class edu.mssm.crover.tools.tissue.GetCuratedTissue
Returns whether to print out two levels of parent interfaces of the curated tissues.
findReaderTypeFromExtension(String) - Method in class edu.mssm.crover.imports.SequenceReaderFactoryImpl
 
firstRow() - Method in class edu.mssm.crover.tables.ArrayTable
Returns an iterator that reference the first instance of this table.
firstRow() - Method in interface edu.mssm.crover.tables.Table
Returns an iterator that reference the first instance of this table.
Fisher - Class in gominer
An implementation of the Fishers's Exact algorithm Adapted from Oyvind Langsrud's Javascript implementation http://www.matforsk.no/ola/fisher.htm
Fisher() - Constructor for class gominer.Fisher
 
fisher(int, int, int, int) - Method in class gominer.Fisher
Calculates the 2-tailed gominer.Fisher p value, using the counts that are expected to be readily available in the system
fixRowNumber(int) - Method in class edu.mssm.crover.tables.ArrayTable
Enforce the number of row of the table to be at least equal to the provided number of element of the column.
FLOAT - Static variable in class edu.cornell.med.icb.allen.xml.types.AvgdensityTypeType
The instance of the float type
FLOAT - Static variable in class edu.cornell.med.icb.allen.xml.types.AvglevelTypeType
The instance of the float type
FLOAT_TYPE - Static variable in class edu.cornell.med.icb.allen.xml.types.AvgdensityTypeType
The float type
FLOAT_TYPE - Static variable in class edu.cornell.med.icb.allen.xml.types.AvglevelTypeType
The float type
FloatArraySizer - Class in edu.mssm.crover.tables
 
FloatArraySizer() - Constructor for class edu.mssm.crover.tables.FloatArraySizer
 
focusGroup - Variable in class edu.cornell.med.icb.tissueinfo.similarity.TiSimOptions
 
ForwardMode - Class in edu.cornell.med.icb.tissueinfo.similarity
 
ForwardMode() - Constructor for class edu.cornell.med.icb.tissueinfo.similarity.ForwardMode
 
frontal_cortex - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
frontal_lobe - Interface in edu.mssm.crover.tools.tissue.hierarchy
 

G

gall_bladder - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
ganglion - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
gastrocolic_omentum - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
Gene - Class in edu.cornell.med.icb.allen.xml
Class Gene.
Gene() - Constructor for class edu.cornell.med.icb.allen.xml.Gene
 
gene2Transcripts(IntSet) - Method in class edu.cornell.med.icb.tissueinfo.similarity.GeneTranscriptRelationships
Converts a set of genes to a set of transcripts.
GeneDescriptor - Class in edu.cornell.med.icb.allen.xml.descriptors
Class GeneDescriptor.
GeneDescriptor() - Constructor for class edu.cornell.med.icb.allen.xml.descriptors.GeneDescriptor
 
GeneExpression - Class in edu.cornell.med.icb.allen.xml
Class GeneExpression.
GeneExpression() - Constructor for class edu.cornell.med.icb.allen.xml.GeneExpression
 
GeneExpressionDescriptor - Class in edu.cornell.med.icb.allen.xml.descriptors
Class GeneExpressionDescriptor.
GeneExpressionDescriptor() - Constructor for class edu.cornell.med.icb.allen.xml.descriptors.GeneExpressionDescriptor
 
GeneExpressions - Class in edu.cornell.med.icb.allen.xml
Class GeneExpressions.
GeneExpressions() - Constructor for class edu.cornell.med.icb.allen.xml.GeneExpressions
 
GeneExpressionsDescriptor - Class in edu.cornell.med.icb.allen.xml.descriptors
Class GeneExpressionsDescriptor.
GeneExpressionsDescriptor() - Constructor for class edu.cornell.med.icb.allen.xml.descriptors.GeneExpressionsDescriptor
 
Geneid - Class in edu.cornell.med.icb.allen.xml
Class Geneid.
Geneid() - Constructor for class edu.cornell.med.icb.allen.xml.Geneid
 
geneId2Index - Variable in class edu.cornell.med.icb.tissueinfo.similarity.GeneTranscriptRelationships
 
GeneidDescriptor - Class in edu.cornell.med.icb.allen.xml.descriptors
Class GeneidDescriptor.
GeneidDescriptor() - Constructor for class edu.cornell.med.icb.allen.xml.descriptors.GeneidDescriptor
 
GeneidTypeType - Class in edu.cornell.med.icb.allen.xml.types
Class GeneidTypeType.
GeneidTypeTypeDescriptor - Class in edu.cornell.med.icb.allen.xml.types.descriptors
Class GeneidTypeTypeDescriptor.
GeneidTypeTypeDescriptor() - Constructor for class edu.cornell.med.icb.allen.xml.types.descriptors.GeneidTypeTypeDescriptor
 
GenericArraySizer - Class in edu.mssm.crover.tables
 
GenericArraySizer() - Constructor for class edu.mssm.crover.tables.GenericArraySizer
 
Genes - Class in edu.cornell.med.icb.allen.xml
Class Genes.
Genes() - Constructor for class edu.cornell.med.icb.allen.xml.Genes
 
GenesDescriptor - Class in edu.cornell.med.icb.allen.xml.descriptors
Class GenesDescriptor.
GenesDescriptor() - Constructor for class edu.cornell.med.icb.allen.xml.descriptors.GenesDescriptor
 
GeneTranscriptRelationships - Class in edu.cornell.med.icb.tissueinfo.similarity
 
GeneTranscriptRelationships() - Constructor for class edu.cornell.med.icb.tissueinfo.similarity.GeneTranscriptRelationships
 
GeneTranscriptRelationships(IndexedIdentifier) - Constructor for class edu.cornell.med.icb.tissueinfo.similarity.GeneTranscriptRelationships
 
GeoDataSetReader - Class in edu.mssm.crover.tables.readers
Reads a Gene Expression Omnibus GEO dataset.
GeoDataSetReader() - Constructor for class edu.mssm.crover.tables.readers.GeoDataSetReader
 
GeoPlatformFileReader - Class in edu.mssm.crover.tables.readers
User: campagne Date: Sep 16, 2005 Time: 2:17:19 PM
GeoPlatformFileReader() - Constructor for class edu.mssm.crover.tables.readers.GeoPlatformFileReader
 
getAC(String) - Static method in class edu.mssm.crover.tools.blast.MegablastHSIterator
Method to parse the unique accession number from a gi identifier.
getAC(String) - Method in class edu.mssm.crover.tools.tissue.TImegablast
Cleans the accession code.
getAC(String) - Method in class edu.mssm.crover.tools.tissue.TIMegablastSql
Cleans the accession code.
getAc() - Method in class edu.mssm.crover.tools.tissue.TissueDetails
Getter method for the EST accession code.
getAc() - Method in class edu.mssm.crover.tools.tissue.xml.Hit
Returns the value of field 'ac'.
getAc() - Method in class edu.mssm.crover.tools.tissue.xml.QuerySequence
Returns the value of field 'ac'.
getAccessionCode() - Method in interface edu.mssm.crover.representation.BiologicalOrigin
Returns the accession code inside the origin database.
getAccessionCode() - Method in class edu.mssm.crover.representation.Origin
 
getAccessionFile(String[]) - Static method in class edu.mssm.crover.tools.tissue.GetNulls
Returns the name of the input file.
getAccessMode() - Method in class edu.cornell.med.icb.allen.xml.descriptors.AgeDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.allen.xml.descriptors.AvgdensityDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.allen.xml.descriptors.AvglevelDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.allen.xml.descriptors.EntrezgeneidDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.allen.xml.descriptors.GeneDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.allen.xml.descriptors.GeneExpressionDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.allen.xml.descriptors.GeneExpressionsDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.allen.xml.descriptors.GeneidDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.allen.xml.descriptors.GenesDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.allen.xml.descriptors.ImageSeriesDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.allen.xml.descriptors.ImageseriesidDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.allen.xml.descriptors.ImageSeriesSequenceDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.allen.xml.descriptors.StructureidDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.allen.xml.descriptors.TemplateidDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.allen.xml.descriptors.TranscriptgiDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.allen.xml.descriptors.TranscriptidDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.allen.xml.descriptors.TranscriptnameDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.AgeTypeTypeDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.AvgdensityTypeTypeDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.AvglevelTypeTypeDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.EntrezgeneidTypeTypeDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.GeneidTypeTypeDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.ImageseriesidTypeTypeDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.OrganismTypeDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.PlaneTypeDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.SexTypeDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.StructureidTypeTypeDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.T_ageDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.TemplateidTypeTypeDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.TranscriptgiTypeTypeDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.TranscriptidTypeTypeDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.TreatmenttypeTypeDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutput_iterationsDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutput_iterationsTypeDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutput_paramDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutput_paramTypeDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutputDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Hit_hspsDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Hit_hspsTypeDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.HitDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.HitTypeDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.HspDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.HspTypeDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Iteration_hitsDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Iteration_hitsTypeDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Iteration_statDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Iteration_statTypeDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.IterationDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.IterationTypeDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.ParametersDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.ParametersTypeDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.StatisticsDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.StatisticsTypeDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.mssm.crover.tools.tissue.xml.descriptors.BlastHitsDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.mssm.crover.tools.tissue.xml.descriptors.HitDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.mssm.crover.tools.tissue.xml.descriptors.QuerySequenceDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.mssm.crover.tools.tissue.xml.descriptors.TissueInfoDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.mssm.crover.tools.tissue.xml.descriptors.TokeyDescriptor
Method getAccessMode.
getAcs(String) - Method in interface edu.mssm.crover.tools.tissue.TIWeb
Return an iterator of accession numbers.
getAcs(String) - Method in class edu.mssm.crover.tools.tissue.TIWebJDBCImpl
Return the accession codes associated with a particular tissue profile.
getActiveTable(String) - Method in class edu.mssm.crover.tables.TableActivityWatcher
Gets the name of the active tale corresponding to a specified key.
getAge() - Method in class edu.cornell.med.icb.allen.xml.ImageSeriesSequence
Returns the value of field 'age'.
getAlignLength() - Method in class edu.mssm.crover.tools.tissue.HSP
Getter method for the length of the match.
getAllInfoForQuery(String) - Method in class edu.mssm.crover.tools.tissue.TissueInfoJDBCImpl
Queries the database with the query accession code, and return all tissues associated with any EST accession codes that the query is associated with.
getAllInfoForQuery(String, String) - Method in class edu.mssm.crover.tools.tissue.TissueInfoJDBCImpl
Query the database with the query accession code and organism.
getAnnotations(int, int) - Method in class edu.cornell.med.icb.tissueinfo.annotations.AnnotationSet
 
getAnnotations(int) - Method in class edu.cornell.med.icb.tissueinfo.annotations.AnnotationType
Returns the annotations associated with this sample.
getAnnotations() - Method in class edu.mssm.crover.representation.Annotations
Returns these annotations as an array of BiologicalAnnotation.
getAnnotations() - Method in interface edu.mssm.crover.representation.AnnotationSupport
Returns the annotations associated with an instance.
getAnnotations() - Method in interface edu.mssm.crover.representation.BiologicalAnnotations
Returns the annotations in a array.
getAnnotations() - Method in class edu.mssm.crover.representation.Sequence
 
getAnnotationType(int) - Method in class edu.cornell.med.icb.tissueinfo.annotations.AnnotationSet
Get an annotation type.
getAnnotationTypeIndex(String) - Method in class edu.cornell.med.icb.tissueinfo.annotations.AnnotationSet
 
getAnnotationTypeIndex(MutableString) - Method in class edu.cornell.med.icb.tissueinfo.annotations.AnnotationSet
 
getAvgdensity() - Method in class edu.cornell.med.icb.allen.xml.GeneExpression
Returns the value of field 'avgdensity'.
getAvglevel() - Method in class edu.cornell.med.icb.allen.xml.GeneExpression
Returns the value of field 'avglevel'.
getBlastOutput() - Method in class edu.mssm.crover.tools.blast.BlastResult
Obtains a reference to a BlastOutput instance.
getBlastOutput_db() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.BlastOutput
Returns the value of field 'blastOutput_db'.
getBlastOutput_iterations() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.BlastOutput
Returns the value of field 'blastOutput_iterations'.
getBlastOutput_param() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.BlastOutput
Returns the value of field 'blastOutput_param'.
getBlastOutput_program() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.BlastOutput
Returns the value of field 'blastOutput_program'.
getBlastOutput_queryDef() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.BlastOutput
Returns the value of field 'blastOutput_queryDef'.
getBlastOutput_queryID() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.BlastOutput
Returns the value of field 'blastOutput_queryID'.
getBlastOutput_queryLen() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.BlastOutput
Returns the value of field 'blastOutput_queryLen'.
getBlastOutput_reference() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.BlastOutput
Returns the value of field 'blastOutput_reference'.
getBlastOutput_version() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.BlastOutput
Returns the value of field 'blastOutput_version'.
getBlastType(int, String) - Method in class edu.mssm.crover.tools.blast.BlastCommand
Predicts the BLAST program to be used depending on the sequence type (DNA or protein) and the type of sequence in the database.
getBooleanValue(int, Table.RowIterator) - Method in class edu.mssm.crover.tables.ArrayTable
Returns the value stored in this position as an boolean, when appropriate.
getBooleanValue(int, Table.RowIterator) - Method in interface edu.mssm.crover.tables.Table
Returns the value stored in this position as an boolean, when appropriate.
getBValue() - Method in class edu.mssm.crover.tools.blast.BlastContext
 
getBValue(String[]) - Static method in class edu.mssm.crover.tools.tissue.TISearch
Reads the number of alignments to be returned from BLAST.
getBValue() - Method in class edu.mssm.crover.tools.tissue.xml.BlastHits
Returns the value of field 'bValue'.
getCharValue(int, Table.RowIterator) - Method in class edu.mssm.crover.tables.ArrayTable
Returns the value stored in this position as an int, when appropriate.
getCharValue(int, Table.RowIterator) - Method in interface edu.mssm.crover.tables.Table
Returns the value stored in this position as a char, when appropriate.
getChoiceValue() - Method in class edu.cornell.med.icb.allen.xml.ImageSeries
Returns the value of field 'choiceValue'.
getChromosome() - Method in class edu.cornell.med.icb.allen.xml.Gene
Returns the value of field 'chromosome'.
getCollectRank() - Method in class edu.cornell.med.icb.tissueinfo.similarity.ForwardMode
 
getCollectSumInvRanks() - Method in class edu.cornell.med.icb.tissueinfo.similarity.ForwardMode
 
getCollectSumOfScores() - Method in class edu.cornell.med.icb.tissueinfo.similarity.ForwardMode
 
getColumnIndex(String) - Method in class edu.mssm.crover.tables.ArrayTable
Returns the column index associated with this identifier.
getColumnIndex(String) - Method in interface edu.mssm.crover.tables.Table
Returns the column index associated with this identifier.
getColumnIndexOrDefault(String) - Method in class edu.mssm.crover.tables.ArrayTable
Returns the column index associated with this identifier, or -1 if the column does not exist.
getColumnName() - Method in exception edu.mssm.crover.tables.ColumnTypeException
 
getColumnNumber() - Method in class edu.mssm.crover.tables.ArrayTable
Returns the number of columns of this table.
getColumnNumber() - Method in interface edu.mssm.crover.tables.Table
Returns the number of columns of this table.
getColumnValues(int) - Method in class edu.mssm.crover.tables.ArrayTable
 
getColumnValues(int) - Method in interface edu.mssm.crover.tables.Table
 
getComparator() - Method in class edu.mssm.crover.tables.ArrayTable.ColumnDescription
 
getConnection() - Method in class edu.mssm.crover.db.relational.ConnectionPool
 
getConnection() - Method in class edu.mssm.crover.db.relational.RDB
Obtain a connection from the pool.
getConnectionNumber() - Method in class edu.mssm.crover.db.relational.ConnectionPool
Returns the current number of open connections.
getConnectionNumber() - Method in class edu.mssm.crover.db.relational.RDB
Returns the current number of open connections.
getContent() - Method in class edu.cornell.med.icb.allen.xml.Age
Returns the value of field 'content'.
getContent() - Method in class edu.cornell.med.icb.allen.xml.Avgdensity
Returns the value of field 'content'.
getContent() - Method in class edu.cornell.med.icb.allen.xml.Avglevel
Returns the value of field 'content'.
getContent() - Method in class edu.cornell.med.icb.allen.xml.Entrezgeneid
Returns the value of field 'content'.
getContent() - Method in class edu.cornell.med.icb.allen.xml.Geneid
Returns the value of field 'content'.
getContent() - Method in class edu.cornell.med.icb.allen.xml.Imageseriesid
Returns the value of field 'content'.
getContent() - Method in class edu.cornell.med.icb.allen.xml.Structureid
Returns the value of field 'content'.
getContent() - Method in class edu.cornell.med.icb.allen.xml.Templateid
Returns the value of field 'content'.
getContent() - Method in class edu.cornell.med.icb.allen.xml.Transcriptgi
Returns the value of field 'content'.
getContent() - Method in class edu.cornell.med.icb.allen.xml.Transcriptid
Returns the value of field 'content'.
getContext() - Method in class edu.mssm.crover.tools.blast.BlastCommand
 
getCorrelationCoefficient() - Method in class edu.cornell.med.icb.stat.LinearRegression
Obtain the correlation coefficient.
getCountsDataFilename(String) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TissueESTCountsHelper
 
getCuratedDevStage(String) - Method in class edu.mssm.crover.tools.tissue.DevStageCuration
Gets a curated developmental stage corresponding to a raw developmental stage.
GetCuratedDevStage - Class in edu.mssm.crover.tools.tissue
Reads a file of raw tissues and checks whether a CuratedDevStage exists for that raw tissue.
GetCuratedDevStage() - Constructor for class edu.mssm.crover.tools.tissue.GetCuratedDevStage
 
getCuratedDevStage() - Method in class edu.mssm.crover.tools.tissue.TissueDetails
Getter method for the curated developmental stage.
GetCuratedTissue - Class in edu.mssm.crover.tools.tissue
Reads a file of raw tissues and checks whether a CuratedTissue exists for that raw tissue.
GetCuratedTissue() - Constructor for class edu.mssm.crover.tools.tissue.GetCuratedTissue
 
getCuratedTissue() - Method in class edu.mssm.crover.tools.tissue.NullTissueDetails
Getter method for the curated tissue.
getCuratedTissue(String) - Method in class edu.mssm.crover.tools.tissue.TissueCuration
Gets a curated tissue corresponding to a raw tissue.
getCuratedTissue() - Method in class edu.mssm.crover.tools.tissue.TissueDetails
Getter method for the curated tissue.
getCuratedTissue(String) - Method in class edu.mssm.crover.tools.tissue.TissueInfoNullsJDBCImpl
Return the tissue information associated with a sequence accession code.
getCuratedTissue() - Method in class edu.mssm.crover.tools.tissue.TissueSelection
Returns the curated tissue associated with this instance.
getCuratedTissues(String[]) - Method in class edu.mssm.crover.tools.tissue.TissueInfoNullsJDBCImpl
Return the tissue information associated with a set of sequence accession codes.
getDatabase(String[]) - Static method in class edu.mssm.crover.tools.tissue.TISearch
Reads the name of the database to be searched from the command line.
getDatabase() - Method in class edu.mssm.crover.tools.tissue.xml.BlastHits
Returns the value of field 'database'.
getDataBaseName() - Method in interface edu.mssm.crover.representation.BiologicalOrigin
Returns the name of the database which curates this information.
getDataBaseName() - Method in class edu.mssm.crover.representation.Origin
 
getDefaultBValue() - Method in class edu.mssm.crover.tools.blast.BlastContext
 
getDefaultDefLine() - Method in class edu.mssm.crover.tools.blast.HitSummary
 
getDefaultEValue() - Method in class edu.mssm.crover.tools.blast.BlastContext
 
getDefaultEValue() - Method in class edu.mssm.crover.tools.blast.HitSummary
 
getDefaultHierarchyPackage() - Method in class edu.mssm.crover.tools.tissue.Hierarchy
Getter method for the default location of the hierarchy package.
getDefaultHitLength() - Method in class edu.mssm.crover.tools.blast.HitSummary
 
getDefaultLabelValue() - Method in class edu.mssm.crover.tables.readers.GeoDataSetReader
 
getDefaultMinLength() - Method in class edu.mssm.crover.tools.blast.ExtractAcIdentity
 
getDefaultPercentId() - Method in class edu.mssm.crover.tools.blast.HitSummary
 
getDefaultPercentIdentity() - Method in class edu.mssm.crover.tools.blast.ExtractAcIdentity
 
getDefaultPurity() - Method in class edu.mssm.crover.tools.tissue.QueryTissueSummary
Gets the default value for the minimum percent identity that a match must have to be considered valid.
getDefaultPurity() - Method in class edu.mssm.crover.tools.tissue.TissueSummary
Gets the default value for the minimum percent identity that a match must have to be considered valid.
getDefaultQueryId() - Method in class edu.mssm.crover.tools.blast.HitSummary
 
getDefaultQueryLen() - Method in class edu.mssm.crover.tools.blast.HitSummary
 
getDefaultScore() - Method in class edu.mssm.crover.tools.blast.HitSummary
 
getDefaultSplitPrefix() - Method in class edu.mssm.crover.util.MultiplePartFileIterator
 
getDefaultSubjId() - Method in class edu.mssm.crover.tools.blast.HitSummary
 
getDefaultVValue() - Method in class edu.mssm.crover.tools.blast.BlastContext
 
getDefLine() - Method in class edu.mssm.crover.tools.blast.HitSummary
 
getDefLine(String) - Method in class edu.mssm.crover.util.NCBISequences
Gets the definition line for an accession number.
getDefLine(String, String) - Method in class edu.mssm.crover.util.NCBISequences
Uses the UNIX fastacmd command to find the accession number ac in the database.
getDescription() - Method in class edu.mssm.crover.tables.readers.DSSPTableReader
 
getDescription() - Method in class edu.mssm.crover.tables.readers.LocusLinkTableReader
 
getDescription() - Method in class edu.mssm.crover.tables.readers.MinesetTableReader
 
getDescription() - Method in class edu.mssm.crover.tables.readers.TIWebMinesetReader
 
getDetails(String) - Method in interface edu.mssm.crover.tools.tissue.TissueInfo
Return the tissue information associated with a sequence accession code.
getDetails(String) - Method in class edu.mssm.crover.tools.tissue.TissueInfoCacheImpl
Return the tissue information associated with a sequence accession code.
getDetails(String) - Method in class edu.mssm.crover.tools.tissue.TissueInfoJDBCImpl
Return the tissue information associated with a sequence accession code.
getDetails(String) - Method in class edu.mssm.crover.tools.tissue.TissueInfoMemoryImpl
Return the tissue information associated with a sequence accession code.
getDetails(String) - Method in class edu.mssm.crover.tools.tissue.TissueInfoMemoryImpl2
Return the tissue information associated with a sequence accession code.
getDetails(String) - Method in class edu.mssm.crover.tools.tissue.TissueInfoNullsJDBCImpl
Return the tissue information associated with a sequence accession code.
getDevStage(String) - Method in interface edu.mssm.crover.tools.tissue.TissueInfo
Return the developmental stage information associated with a sequence accession code.
getDevStage(String) - Method in class edu.mssm.crover.tools.tissue.TissueInfoCacheImpl
Return the devstage information associated with a sequence accession code.
getDevStage(String) - Method in class edu.mssm.crover.tools.tissue.TissueInfoJDBCImpl
Return the dev stage information associated with a sequence accession code.
getDevStage(String) - Method in class edu.mssm.crover.tools.tissue.TissueInfoMemoryImpl
Return the devstage information associated with a sequence accession code.
getDevStage(String) - Method in class edu.mssm.crover.tools.tissue.TissueInfoMemoryImpl2
Return the devstage information associated with a sequence accession code.
getDevStageFile(String[]) - Method in class edu.mssm.crover.tools.tissue.GetCuratedDevStage
Returns the name of the input file.
getDoubles() - Method in class edu.mssm.crover.tables.ArrayTable.ColumnDescription
Get the array value as double[].
getDoubles(String) - Method in class edu.mssm.crover.tables.ArrayTable
Get the doubles for a particular column id.
getDoubles(String) - Method in interface edu.mssm.crover.tables.Table
Get the doubles for a particular column id.
getDoubleValue(int, Table.RowIterator) - Method in class edu.mssm.crover.tables.ArrayTable
Returns the value stored in this position as an double, when appropriate.
getDoubleValue(int, Table.RowIterator) - Method in interface edu.mssm.crover.tables.Table
Returns the value stored in this position as an double, when appropriate.
getElement(int) - Method in class edu.mssm.crover.tools.tissue.CuratedDevStage
Gets the tissue element at the specified index from library, if present.
getElement(int) - Method in class edu.mssm.crover.tools.tissue.CuratedTissue
Gets the tissue element at the specified index from library, if present.
getElementNumber() - Method in class edu.mssm.crover.tools.tissue.CuratedDevStage
Returns the number of tissue elements present in the library.
getElementNumber() - Method in class edu.mssm.crover.tools.tissue.CuratedTissue
Returns the number of tissue elements present in the library.
getEntrezgeneid() - Method in class edu.cornell.med.icb.allen.xml.Gene
Returns the value of field 'entrezgeneid'.
getEstCountForQuery(String) - Method in class edu.mssm.crover.tools.tissue.TissueInfoJDBCImpl
Query the database for the number of EST accession codes associated with a query.
getEstDetails() - Method in class edu.mssm.crover.tools.tissue.QueryTissueSummary
Returns all the TissueDetails for all ESTs matching a query sequence.
getEValue() - Method in class edu.mssm.crover.tools.blast.BlastContext
 
getEValue() - Method in class edu.mssm.crover.tools.blast.HitSummary
 
getEValue(String[]) - Static method in class edu.mssm.crover.tools.tissue.TISearch
Reads the minimum expectation value that a match must have to be kept.
getExpectationValue() - Method in class edu.mssm.crover.tools.tissue.xml.BlastHits
Returns the value of field 'expectationValue'.
getExtensions() - Method in class edu.mssm.crover.imports.FastaReaderType
 
getExtensions() - Method in interface edu.mssm.crover.imports.ReaderType
Returns the filename extensions the ReaderType uses to guess if it can handle an InputStream.
getFileFragment(String) - Method in class edu.mssm.crover.tables.QueryTable
 
getFloatValue(int, Table.RowIterator) - Method in class edu.mssm.crover.tables.ArrayTable
Returns the value stored in this position as a float, when appropriate.
getFloatValue(int, Table.RowIterator) - Method in interface edu.mssm.crover.tables.Table
Returns the value stored in this position as a float, when appropriate.
getGene(int) - Method in class edu.cornell.med.icb.allen.xml.Genes
Method getGene.
getGene() - Method in class edu.cornell.med.icb.allen.xml.Genes
Method getGene.Returns the contents of the collection in an Array.
getGeneCount() - Method in class edu.cornell.med.icb.allen.xml.Genes
Method getGeneCount.
getGeneExpression(int) - Method in class edu.cornell.med.icb.allen.xml.GeneExpressions
Method getGeneExpression.
getGeneExpression() - Method in class edu.cornell.med.icb.allen.xml.GeneExpressions
Method getGeneExpression.Returns the contents of the collection in an Array.
getGeneExpressionCount() - Method in class edu.cornell.med.icb.allen.xml.GeneExpressions
Method getGeneExpressionCount.
getGeneExpressions() - Method in class edu.cornell.med.icb.allen.xml.Gene
Returns the value of field 'geneExpressions'.
getGeneid() - Method in class edu.cornell.med.icb.allen.xml.Gene
Returns the value of field 'geneid'.
getGeneid() - Method in class edu.cornell.med.icb.allen.xml.GeneExpression
Returns the value of field 'geneid'.
getGeneid() - Method in class edu.cornell.med.icb.allen.xml.ImageSeriesSequence
Returns the value of field 'geneid'.
getGeneId(int) - Method in class edu.cornell.med.icb.tissueinfo.similarity.GeneTranscriptRelationships
Obtains the gene id from a gene index.
getGeneIndex(MutableString) - Method in class edu.cornell.med.icb.tissueinfo.similarity.GeneTranscriptRelationships
Get the index of a gene.
getGenename() - Method in class edu.cornell.med.icb.allen.xml.Gene
Returns the value of field 'genename'.
getGenesymbol() - Method in class edu.cornell.med.icb.allen.xml.Gene
Returns the value of field 'genesymbol'.
getGenomeFilter() - Method in class edu.cornell.med.icb.tissueinfo.similarity.TiSimilaritySearchEngine
 
getGensatid() - Method in class edu.cornell.med.icb.allen.xml.Gene
Returns the value of field 'gensatid'.
getGlobalBitsForCounts() - Method in class edu.cornell.med.icb.tissueinfo.similarity.TissueESTCountsWriter
 
getGlobalTissueRepresentationArray() - Method in class edu.cornell.med.icb.tissueinfo.similarity.TissueESTCountsReader
 
getGlobalTissueRepresentationCount(int) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TissueESTCountsReader
Return n, the number of ESTs from the tissue which matched a query sequence in the tiac files used to create the compressed tissue EST count data.
getHashtable() - Method in class edu.mssm.crover.tools.tissue.HierarchyKeywords
Splits interface names into keywords.
getHeading(String[]) - Static method in class edu.mssm.crover.tables.AddToTable
Returns the name of the headings in the table to which the data are to be added.
getHierarchyPackage() - Method in class edu.mssm.crover.tools.tissue.Hierarchy
Getter method for the location of the hierarchy package.
getHit(int) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Iteration_hitsType
Method getHit.
getHit() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Iteration_hitsType
Method getHit.Returns the contents of the collection in an Array.
getHit(int) - Method in class edu.mssm.crover.tools.tissue.xml.QuerySequence
Method getHit.
getHit() - Method in class edu.mssm.crover.tools.tissue.xml.QuerySequence
Method getHit.Returns the contents of the collection in an Array.
getHit_accession() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HitType
Returns the value of field 'hit_accession'.
getHit_def() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HitType
Returns the value of field 'hit_def'.
getHit_hsps() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HitType
Returns the value of field 'hit_hsps'.
getHit_id() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HitType
Returns the value of field 'hit_id'.
getHit_len() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HitType
Returns the value of field 'hit_len'.
getHit_num() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HitType
Returns the value of field 'hit_num'.
getHitCount() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Iteration_hitsType
Method getHitCount.
getHitCount() - Method in class edu.mssm.crover.tools.tissue.xml.QuerySequence
Method getHitCount.
getHitLength() - Method in class edu.mssm.crover.tools.blast.HitSummary
 
getHsp(int) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Hit_hspsType
Method getHsp.
getHsp() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Hit_hspsType
Method getHsp.Returns the contents of the collection in an Array.
getHsp_alignLen() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
Returns the value of field 'hsp_alignLen'.
getHsp_bitScore() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
Returns the value of field 'hsp_bitScore'.
getHsp_evalue() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
Returns the value of field 'hsp_evalue'.
getHsp_gaps() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
Returns the value of field 'hsp_gaps'.
getHsp_hitFrame() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
Returns the value of field 'hsp_hitFrame'.
getHsp_hitFrom() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
Returns the value of field 'hsp_hitFrom'.
getHsp_hitTo() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
Returns the value of field 'hsp_hitTo'.
getHsp_hseq() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
Returns the value of field 'hsp_hseq'.
getHsp_identity() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
Returns the value of field 'hsp_identity'.
getHsp_midline() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
Returns the value of field 'hsp_midline'.
getHsp_num() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
Returns the value of field 'hsp_num'.
getHsp_positive() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
Returns the value of field 'hsp_positive'.
getHsp_qseq() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
Returns the value of field 'hsp_qseq'.
getHsp_queryFrame() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
Returns the value of field 'hsp_queryFrame'.
getHsp_queryFrom() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
Returns the value of field 'hsp_queryFrom'.
getHsp_queryTo() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
Returns the value of field 'hsp_queryTo'.
getHsp_score() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
Returns the value of field 'hsp_score'.
getHspCount() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Hit_hspsType
Method getHspCount.
getId() - Method in class edu.mssm.crover.tools.tissue.xml.Tokey
Returns the value of field 'id'.
getIdentifier(int) - Method in class edu.mssm.crover.tables.ArrayTable
Returns the identifier associated with this column index.
getIdentifier(int) - Method in interface edu.mssm.crover.tables.Table
Returns the identifier associated with this column index.
getIdentity() - Method in class edu.cornell.med.icb.allen.xml.descriptors.AgeDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.allen.xml.descriptors.AvgdensityDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.allen.xml.descriptors.AvglevelDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.allen.xml.descriptors.EntrezgeneidDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.allen.xml.descriptors.GeneDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.allen.xml.descriptors.GeneExpressionDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.allen.xml.descriptors.GeneExpressionsDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.allen.xml.descriptors.GeneidDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.allen.xml.descriptors.GenesDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.allen.xml.descriptors.ImageSeriesDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.allen.xml.descriptors.ImageseriesidDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.allen.xml.descriptors.ImageSeriesSequenceDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.allen.xml.descriptors.StructureidDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.allen.xml.descriptors.TemplateidDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.allen.xml.descriptors.TranscriptgiDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.allen.xml.descriptors.TranscriptidDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.allen.xml.descriptors.TranscriptnameDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.AgeTypeTypeDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.AvgdensityTypeTypeDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.AvglevelTypeTypeDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.EntrezgeneidTypeTypeDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.GeneidTypeTypeDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.ImageseriesidTypeTypeDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.OrganismTypeDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.PlaneTypeDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.SexTypeDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.StructureidTypeTypeDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.T_ageDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.TemplateidTypeTypeDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.TranscriptgiTypeTypeDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.TranscriptidTypeTypeDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.TreatmenttypeTypeDescriptor
Method getIdentity.
getIdentity() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutput_iterationsDescriptor
Method getIdentity.
getIdentity() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutput_iterationsTypeDescriptor
Method getIdentity.
getIdentity() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutput_paramDescriptor
Method getIdentity.
getIdentity() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutput_paramTypeDescriptor
Method getIdentity.
getIdentity() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutputDescriptor
Method getIdentity.
getIdentity() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Hit_hspsDescriptor
Method getIdentity.
getIdentity() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Hit_hspsTypeDescriptor
Method getIdentity.
getIdentity() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.HitDescriptor
Method getIdentity.
getIdentity() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.HitTypeDescriptor
Method getIdentity.
getIdentity() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.HspDescriptor
Method getIdentity.
getIdentity() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.HspTypeDescriptor
Method getIdentity.
getIdentity() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Iteration_hitsDescriptor
Method getIdentity.
getIdentity() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Iteration_hitsTypeDescriptor
Method getIdentity.
getIdentity() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Iteration_statDescriptor
Method getIdentity.
getIdentity() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Iteration_statTypeDescriptor
Method getIdentity.
getIdentity() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.IterationDescriptor
Method getIdentity.
getIdentity() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.IterationTypeDescriptor
Method getIdentity.
getIdentity() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.ParametersDescriptor
Method getIdentity.
getIdentity() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.ParametersTypeDescriptor
Method getIdentity.
getIdentity() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.StatisticsDescriptor
Method getIdentity.
getIdentity() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.StatisticsTypeDescriptor
Method getIdentity.
getIdentity() - Method in class edu.mssm.crover.tools.tissue.HSP
Getter method for the percent identity of the match.
getIdentity() - Method in class edu.mssm.crover.tools.tissue.xml.descriptors.BlastHitsDescriptor
Method getIdentity.
getIdentity() - Method in class edu.mssm.crover.tools.tissue.xml.descriptors.HitDescriptor
Method getIdentity.
getIdentity() - Method in class edu.mssm.crover.tools.tissue.xml.descriptors.QuerySequenceDescriptor
Method getIdentity.
getIdentity() - Method in class edu.mssm.crover.tools.tissue.xml.descriptors.TissueInfoDescriptor
Method getIdentity.
getIdentity() - Method in class edu.mssm.crover.tools.tissue.xml.descriptors.TokeyDescriptor
Method getIdentity.
getImageSeries() - Method in class edu.cornell.med.icb.allen.xml.Gene
Returns the value of field 'imageSeries'.
getImageSeries(int) - Method in class edu.cornell.med.icb.allen.xml.ImageSeries
Method getImageSeries.
getImageSeries() - Method in class edu.cornell.med.icb.allen.xml.ImageSeries
Method getImageSeries.Returns the contents of the collection in an Array.
getImageSeriesCount() - Method in class edu.cornell.med.icb.allen.xml.ImageSeries
Method getImageSeriesCount.
getImageseriesdisplayname() - Method in class edu.cornell.med.icb.allen.xml.ImageSeriesSequence
Returns the value of field 'imageseriesdisplayname'.
getImageseriesid() - Method in class edu.cornell.med.icb.allen.xml.ImageSeriesSequence
Returns the value of field 'imageseriesid'.
getImageSeriesSequence() - Method in class edu.cornell.med.icb.allen.xml.ImageSeries
Returns the value of field 'imageSeriesSequence'.
getImpl() - Method in class edu.mssm.crover.tables.ArrayTable.RowIterator
 
getImpl() - Method in interface edu.mssm.crover.tables.Table.RowIterator
Returns the iterator implementation that matches the table implementation.
getInactiveTable(String) - Method in class edu.mssm.crover.tables.TableActivityWatcher
Gets the name of the inactive tale corresponding to a specified key.
getIndex(String[]) - Static method in class edu.mssm.crover.tables.JDBCTable
Returns the column number on which the index is to be created.
getIndex(String[]) - Static method in class edu.mssm.crover.tables.TableActivityWatcher
Returns the column number on which the index is to be created.
getIndexColumn(String[]) - Static method in class edu.mssm.crover.tables.AddToTable
Returns the name of the column to be used as an identifier.
getIndexDescription(int) - Method in class edu.cornell.med.icb.tissueinfo.annotations.Projection
Provides a human readable description of a projected index.
getInfo() - Method in class edu.mssm.crover.imports.FastaReaderType
 
getInfo() - Method in interface edu.mssm.crover.imports.ReaderType
Returns detailled information about the format parsed by this ReaderType.
getInfo() - Method in class edu.mssm.crover.representation.Annotation
 
getInfo() - Method in interface edu.mssm.crover.representation.BiologicalAnnotation
Returns a consise text that describes the nature of this annotation.
getInfo() - Method in class edu.mssm.crover.representation.Mutation_Annotation
 
getInfo() - Method in class edu.mssm.crover.representation.SequenceOrigin_Annotation
 
getInfo() - Method in class edu.mssm.crover.representation.URL_Annotation
 
getInformation() - Method in class edu.mssm.crover.representation.Mutation_Annotation
Get the URL od the document that describes this mutation.
getInformation() - Method in class edu.mssm.crover.representation.URL_Annotation
 
getInputFile(String[]) - Static method in class edu.mssm.crover.tables.AddToTable
Returns the name of the input file.
getInputFile(String[]) - Static method in class edu.mssm.crover.tools.tissue.ReportParser
Returns the name of the input file.
getInstance() - Static method in class edu.mssm.crover.db.relational.RDB
Returns the only instance of RDB available in the system (one per JVM, or zone when used in JServ).
getInstance(String, String, String, String) - Static method in class edu.mssm.crover.db.relational.RDB
Returns the only instance of RDB available in the system (one per JVM, or zone when used in JServ).
getInstance(String, String, String[], String) - Static method in class edu.mssm.crover.tables.AddToTable
Gets an instance of this class.
getInstance(String, int, String) - Static method in class edu.mssm.crover.tables.JDBCTable
 
getInstance() - Static method in class edu.mssm.crover.tables.QueryTable
 
getInstance() - Static method in class edu.mssm.crover.tools.tissue.TissueInfoJDBCImpl
Gets an instance of this class.
getInstance() - Static method in class edu.mssm.crover.tools.tissue.TissueInfoMemoryImpl
Instantiates this class.
getInstance(String[]) - Static method in class edu.mssm.crover.tools.tissue.TissueInfoMemoryImpl
Obtains the singleton instance.
getInstance(String, String, String) - Static method in class edu.mssm.crover.tools.tissue.TissueInfoMemoryImpl
Obtain the singleton instance.
getInstance(String, String, String, String[]) - Static method in class edu.mssm.crover.tools.tissue.TissueInfoMemoryImpl
Obtain the singleton instance.
getInstance(BufferedReader, BufferedReader, BufferedReader, String[]) - Static method in class edu.mssm.crover.tools.tissue.TissueInfoMemoryImpl
Obtain the singleton instance.
getInstance() - Static method in class edu.mssm.crover.tools.tissue.TissueInfoMemoryImpl2
Instantiates this class.
getInstance(String[]) - Static method in class edu.mssm.crover.tools.tissue.TissueInfoMemoryImpl2
Obtains the singleton instance.
getInstance(String, String) - Static method in class edu.mssm.crover.tools.tissue.TissueInfoMemoryImpl2
Obtain the singleton instance.
getInstance(String, String, String[]) - Static method in class edu.mssm.crover.tools.tissue.TissueInfoMemoryImpl2
Obtain the singleton instance.
getInstance(BufferedReader, BufferedReader, String[]) - Static method in class edu.mssm.crover.tools.tissue.TissueInfoMemoryImpl2
Obtain the singleton instance.
getInstance() - Static method in class edu.mssm.crover.tools.tissue.TissueInfoNullsJDBCImpl
Gets an instance of this class.
getInstance(String, int, String) - Static method in class edu.mssm.crover.tools.tissue.TIWebJDBCImpl
Gets an instance of this class.
getInstance() - Static method in class edu.mssm.crover.tools.tissue.TIWebJDBCImpl
Gets an instance of this class.
getIntValue(int, Table.RowIterator) - Method in class edu.mssm.crover.tables.ArrayTable
Returns the value stored in this position as an int, when appropriate.
getIntValue(int, Table.RowIterator) - Method in interface edu.mssm.crover.tables.Table
Returns the value stored in this position as an int, when appropriate.
getIteration() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.BlastOutput_iterationsType
Returns the value of field 'iteration'.
getIteration_hits() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.IterationType
Returns the value of field 'iteration_hits'.
getIteration_iterNum() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.IterationType
Returns the value of field 'iteration_iterNum'.
getIteration_message() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.IterationType
Returns the value of field 'iteration_message'.
getIteration_queryDef() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.IterationType
Returns the value of field 'iteration_queryDef'.
getIteration_queryID() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.IterationType
Returns the value of field 'iteration_queryID'.
getIteration_queryLen() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.IterationType
Returns the value of field 'iteration_queryLen'.
getIteration_stat() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.IterationType
Returns the value of field 'iteration_stat'.
getJavaClass() - Method in class edu.cornell.med.icb.allen.xml.descriptors.AgeDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.allen.xml.descriptors.AvgdensityDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.allen.xml.descriptors.AvglevelDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.allen.xml.descriptors.EntrezgeneidDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.allen.xml.descriptors.GeneDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.allen.xml.descriptors.GeneExpressionDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.allen.xml.descriptors.GeneExpressionsDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.allen.xml.descriptors.GeneidDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.allen.xml.descriptors.GenesDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.allen.xml.descriptors.ImageSeriesDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.allen.xml.descriptors.ImageseriesidDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.allen.xml.descriptors.ImageSeriesSequenceDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.allen.xml.descriptors.StructureidDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.allen.xml.descriptors.TemplateidDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.allen.xml.descriptors.TranscriptgiDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.allen.xml.descriptors.TranscriptidDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.allen.xml.descriptors.TranscriptnameDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.AgeTypeTypeDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.AvgdensityTypeTypeDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.AvglevelTypeTypeDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.EntrezgeneidTypeTypeDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.GeneidTypeTypeDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.ImageseriesidTypeTypeDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.OrganismTypeDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.PlaneTypeDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.SexTypeDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.StructureidTypeTypeDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.T_ageDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.TemplateidTypeTypeDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.TranscriptgiTypeTypeDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.TranscriptidTypeTypeDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.TreatmenttypeTypeDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutput_iterationsDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutput_iterationsTypeDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutput_paramDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutput_paramTypeDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutputDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Hit_hspsDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Hit_hspsTypeDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.HitDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.HitTypeDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.HspDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.HspTypeDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Iteration_hitsDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Iteration_hitsTypeDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Iteration_statDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Iteration_statTypeDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.IterationDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.IterationTypeDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.ParametersDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.ParametersTypeDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.StatisticsDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.StatisticsTypeDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.mssm.crover.tools.tissue.xml.descriptors.BlastHitsDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.mssm.crover.tools.tissue.xml.descriptors.HitDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.mssm.crover.tools.tissue.xml.descriptors.QuerySequenceDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.mssm.crover.tools.tissue.xml.descriptors.TissueInfoDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.mssm.crover.tools.tissue.xml.descriptors.TokeyDescriptor
Method getJavaClass.
getLeft() - Method in class gominer.Fisher
Accessor
getLength() - Method in interface edu.mssm.crover.representation.BiologicalSequence
Returns the length of this sequence.
getLength() - Method in class edu.mssm.crover.representation.Sequence
Returns the length of the sequence.
getLibraries() - Method in class edu.mssm.crover.tools.tissue.LibraryDivision
Getter method for the (raw tissue) libraries and the number of times they occur.
getLibraryCount1() - Method in class edu.mssm.crover.tools.tissue.LibraryDivision
Returns the number of ESTs in the first group of libraries.
getLibraryCount2() - Method in class edu.mssm.crover.tools.tissue.LibraryDivision
Returns the number of ESTs in the second group of libraries.
getLowerCaseList(boolean) - Method in class edu.mssm.crover.tools.tissue.TissueCuration
Converts the default list to using lowercase for all raw tissues.
getLowerCaseList() - Method in class edu.mssm.crover.tools.tissue.TissueCuration
Converts the raw tissues in the default table to lowercase.
getMaxErrorRate() - Method in class edu.mssm.crover.tools.tissue.xml.BlastHits
Returns the value of field 'maxErrorRate'.
getMaxProjectedIndex() - Method in class edu.cornell.med.icb.tissueinfo.annotations.Projection
Return the number of projected index that were generated by this projection.
getMeasureName() - Method in class edu.cornell.med.icb.stat.AccuracyCalculator
 
getMeasureName() - Method in class edu.cornell.med.icb.stat.AreaUnderTheRocCurveCalculator
 
getMeasureName() - Method in class edu.cornell.med.icb.stat.MatthewsCorrelationCalculator
 
getMeasureName() - Method in class edu.cornell.med.icb.stat.PredictionStatisticCalculator
 
getMeasureName() - Method in class edu.cornell.med.icb.stat.RootMeanSquaredErrorCalculator
 
getMeasureName() - Method in class edu.cornell.med.icb.stat.SensitivityCalculator
 
getMeasureName() - Method in class edu.cornell.med.icb.stat.SpecificityCalculator
 
getMessage() - Method in exception edu.mssm.crover.imports.SyntaxErrorException
 
getMessage() - Method in exception edu.mssm.crover.imports.UnsupportedFileFormatException
 
getMessage() - Method in exception edu.mssm.crover.representation.NoSuchResidue
 
getMgimarkeraccessionid() - Method in class edu.cornell.med.icb.allen.xml.Gene
Returns the value of field 'mgimarkeraccessionid'.
getMinimumLength(String[]) - Static method in class edu.mssm.crover.tools.tissue.TISearch
Reads the minimum length required for a HSP to be considered.
getMinimumLength() - Method in class edu.mssm.crover.tools.tissue.xml.BlastHits
Returns the value of field 'minimumLength'.
getMinLength() - Method in class edu.mssm.crover.tools.blast.ExtractAcIdentity
 
getMissingTissues() - Method in class edu.cornell.med.icb.tissueinfo.similarity.TissueESTCountsHelper
 
getN11_() - Method in class gominer.Fisher
Accessor
getN12_() - Method in class gominer.Fisher
Accessor
getN21_() - Method in class gominer.Fisher
Accessor
getN22_() - Method in class gominer.Fisher
Accessor
getNameSpacePrefix() - Method in class edu.cornell.med.icb.allen.xml.descriptors.AgeDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.allen.xml.descriptors.AvgdensityDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.allen.xml.descriptors.AvglevelDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.allen.xml.descriptors.EntrezgeneidDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.allen.xml.descriptors.GeneDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.allen.xml.descriptors.GeneExpressionDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.allen.xml.descriptors.GeneExpressionsDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.allen.xml.descriptors.GeneidDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.allen.xml.descriptors.GenesDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.allen.xml.descriptors.ImageSeriesDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.allen.xml.descriptors.ImageseriesidDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.allen.xml.descriptors.ImageSeriesSequenceDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.allen.xml.descriptors.StructureidDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.allen.xml.descriptors.TemplateidDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.allen.xml.descriptors.TranscriptgiDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.allen.xml.descriptors.TranscriptidDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.allen.xml.descriptors.TranscriptnameDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.AgeTypeTypeDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.AvgdensityTypeTypeDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.AvglevelTypeTypeDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.EntrezgeneidTypeTypeDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.GeneidTypeTypeDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.ImageseriesidTypeTypeDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.OrganismTypeDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.PlaneTypeDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.SexTypeDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.StructureidTypeTypeDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.T_ageDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.TemplateidTypeTypeDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.TranscriptgiTypeTypeDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.TranscriptidTypeTypeDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.TreatmenttypeTypeDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutput_iterationsDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutput_iterationsTypeDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutput_paramDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutput_paramTypeDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutputDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Hit_hspsDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Hit_hspsTypeDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.HitDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.HitTypeDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.HspDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.HspTypeDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Iteration_hitsDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Iteration_hitsTypeDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Iteration_statDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Iteration_statTypeDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.IterationDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.IterationTypeDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.ParametersDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.ParametersTypeDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.StatisticsDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.StatisticsTypeDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.mssm.crover.tools.tissue.xml.descriptors.BlastHitsDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.mssm.crover.tools.tissue.xml.descriptors.HitDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.mssm.crover.tools.tissue.xml.descriptors.QuerySequenceDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.mssm.crover.tools.tissue.xml.descriptors.TissueInfoDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.mssm.crover.tools.tissue.xml.descriptors.TokeyDescriptor
Method getNameSpacePrefix.
getNameSpaceURI() - Method in class edu.cornell.med.icb.allen.xml.descriptors.AgeDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.allen.xml.descriptors.AvgdensityDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.allen.xml.descriptors.AvglevelDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.allen.xml.descriptors.EntrezgeneidDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.allen.xml.descriptors.GeneDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.allen.xml.descriptors.GeneExpressionDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.allen.xml.descriptors.GeneExpressionsDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.allen.xml.descriptors.GeneidDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.allen.xml.descriptors.GenesDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.allen.xml.descriptors.ImageSeriesDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.allen.xml.descriptors.ImageseriesidDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.allen.xml.descriptors.ImageSeriesSequenceDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.allen.xml.descriptors.StructureidDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.allen.xml.descriptors.TemplateidDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.allen.xml.descriptors.TranscriptgiDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.allen.xml.descriptors.TranscriptidDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.allen.xml.descriptors.TranscriptnameDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.AgeTypeTypeDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.AvgdensityTypeTypeDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.AvglevelTypeTypeDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.EntrezgeneidTypeTypeDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.GeneidTypeTypeDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.ImageseriesidTypeTypeDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.OrganismTypeDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.PlaneTypeDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.SexTypeDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.StructureidTypeTypeDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.T_ageDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.TemplateidTypeTypeDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.TranscriptgiTypeTypeDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.TranscriptidTypeTypeDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.TreatmenttypeTypeDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutput_iterationsDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutput_iterationsTypeDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutput_paramDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutput_paramTypeDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutputDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Hit_hspsDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Hit_hspsTypeDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.HitDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.HitTypeDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.HspDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.HspTypeDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Iteration_hitsDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Iteration_hitsTypeDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Iteration_statDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Iteration_statTypeDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.IterationDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.IterationTypeDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.ParametersDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.ParametersTypeDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.StatisticsDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.StatisticsTypeDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.mssm.crover.tools.tissue.xml.descriptors.BlastHitsDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.mssm.crover.tools.tissue.xml.descriptors.HitDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.mssm.crover.tools.tissue.xml.descriptors.QuerySequenceDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.mssm.crover.tools.tissue.xml.descriptors.TissueInfoDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.mssm.crover.tools.tissue.xml.descriptors.TokeyDescriptor
Method getNameSpaceURI.
getNcbiaccessionnumber() - Method in class edu.cornell.med.icb.allen.xml.ImageSeriesSequence
Returns the value of field 'ncbiaccessionnumber'.
getNewColumnNameIndex() - Method in class edu.mssm.crover.tables.DefineColumnFromRow
 
getNullCount() - Method in class edu.mssm.crover.tools.tissue.QueryTissueSummary
Calculates the number of null hits.
getNullCount() - Method in class edu.mssm.crover.tools.tissue.TissueSummary
Calculates the number of null hits.
GetNulls - Class in edu.mssm.crover.tools.tissue
Checks whether the accession code exists in the table.
getNumAcsFromNulls() - Method in class edu.mssm.crover.tools.tissue.TissueSummary
Calculates the number of hits from entries that were marked as null.
getNumAcsKept() - Method in class edu.mssm.crover.tools.tissue.QueryTissueSummary
Calculates the number of hits kept after filtering, etc.
getNumAcsKept() - Method in class edu.mssm.crover.tools.tissue.TissueSummary
Calculates the number of hits kept after filtering, etc.
getNumberOfGenes() - Method in class edu.cornell.med.icb.tissueinfo.similarity.GeneTranscriptRelationships
Returns the number of genes associated with transcripts.
getNumberOfSamples() - Method in class edu.cornell.med.icb.tissueinfo.annotations.AnnotationSet
 
getNumberOfValues(int) - Method in class edu.cornell.med.icb.tissueinfo.annotations.AnnotationSet
Returns the number of distinct value identifiers for the annotation type.
getNumberOfValues() - Method in class edu.cornell.med.icb.tissueinfo.annotations.AnnotationType
Returns the number of distinct value identifiers for this type.
getNumberQuerySequencesWritten() - Method in class edu.cornell.med.icb.tissueinfo.similarity.TissueESTCountsWriter
Returns the number of query sequences written.
getNumLibraries() - Method in class edu.mssm.crover.tools.tissue.LibraryDivision
Gets the number of different libraries found in this set of accession numbers.
getOffsetFilename(String) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TissueESTCountsHelper
 
getOrganism() - Method in class edu.cornell.med.icb.allen.xml.Gene
Returns the value of field 'organism'.
getOrganism() - Method in class edu.mssm.crover.tools.tissue.NullTissueDetails
Getter method for the organism.
getOrganism() - Method in class edu.mssm.crover.tools.tissue.TissueDetails
Getter method for the organism.
getOrganism(String) - Method in interface edu.mssm.crover.tools.tissue.TissueInfo
Return the organism associated with a sequence accession code.
getOrganism(String) - Method in class edu.mssm.crover.tools.tissue.TissueInfoCacheImpl
Return the organism associated with a sequence accession code.
getOrganism(String) - Method in class edu.mssm.crover.tools.tissue.TissueInfoJDBCImpl
Return the organism associated with a sequence accession code.
getOrganism(String) - Method in class edu.mssm.crover.tools.tissue.TissueInfoMemoryImpl
Return the organism associated with a sequence accession code.
getOrganism(String) - Method in class edu.mssm.crover.tools.tissue.TissueInfoMemoryImpl2
Return the organism associated with a sequence accession code.
getOrganism(String) - Method in class edu.mssm.crover.tools.tissue.TissueInfoNullsJDBCImpl
Return the organism associated with a sequence accession code.
getOrganism() - Method in class edu.mssm.crover.tools.tissue.xml.Tokey
Returns the value of field 'organism'.
getOrigin() - Method in class edu.mssm.crover.representation.Annotation
Returns the origin of this sequence.
getOrigin() - Method in interface edu.mssm.crover.representation.BiologicalAnnotation
Obtain the origin of this annotation.
getOutFile(String[]) - Method in class edu.mssm.crover.tools.tissue.GetCuratedDevStage
Returns the name of the output file.
getOutFile(String[]) - Method in class edu.mssm.crover.tools.tissue.GetCuratedTissue
Returns the name of the output file.
getOutFilename(String[]) - Static method in class edu.mssm.crover.tools.tissue.TISearch
Returns the name of the file to which to output accession numbers.
getOutputFile(String[]) - Static method in class edu.mssm.crover.tools.tissue.ReportParser
Returns the name of the output file.
getPackageContents() - Method in class edu.cornell.med.icb.tissueinfo.owl.PackageInspector
Reads the package contents of the package specified in packageName.
getPackageName() - Method in class edu.cornell.med.icb.tissueinfo.owl.PackageInspector
Getter for package name.
getParallelTeam() - Method in class edu.cornell.med.icb.tissueinfo.similarity.PairSearchMode
 
getParallelTeam() - Method in class edu.cornell.med.icb.tissueinfo.similarity.TiSimilaritySearchEngine
 
getParameter() - Method in class edu.mssm.crover.tables.treatments.Aggregation
Returns the parameter passed at construction time.
getParameter() - Method in class edu.mssm.crover.tables.treatments.TableTreatment
Returns a parameter that could have been initialized when the treatment was created.
getParameter() - Method in interface edu.mssm.crover.tables.treatments.Treatment
Returns a parameter that could have been initialized when the treatment was created.
getParameters() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.BlastOutput_paramType
Returns the value of field 'parameters'.
getParameters_expect() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.ParametersType
Returns the value of field 'parameters_expect'.
getParameters_filter() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.ParametersType
Returns the value of field 'parameters_filter'.
getParameters_gapExtend() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.ParametersType
Returns the value of field 'parameters_gapExtend'.
getParameters_gapOpen() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.ParametersType
Returns the value of field 'parameters_gapOpen'.
getParameters_matrix() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.ParametersType
Returns the value of field 'parameters_matrix'.
getParameters_scMatch() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.ParametersType
Returns the value of field 'parameters_scMatch'.
getParameters_scMismatch() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.ParametersType
Returns the value of field 'parameters_scMismatch'.
getPercentId() - Method in class edu.mssm.crover.tools.blast.HitSummary
 
getPercentIdentity() - Method in class edu.mssm.crover.tools.blast.ExtractAcIdentity
 
getPercentIdentity(String[]) - Static method in class edu.mssm.crover.tools.tissue.TISearch
Reads the maximum allowed sequencing error rate.
getPlane() - Method in class edu.cornell.med.icb.allen.xml.ImageSeriesSequence
Returns the value of field 'plane'.
getPrefix(String[]) - Static method in class edu.mssm.crover.tables.JDBCTable
Returns the prefix for the schema and data files.
getPrefix(String[]) - Static method in class edu.mssm.crover.tables.TableActivityWatcher
Returns the prefix for the schema and data files.
getPrefix(String[]) - Static method in class edu.mssm.crover.tools.tissue.ReportParser
Returns the prefix which partitions the file.
getProbeorientation() - Method in class edu.cornell.med.icb.allen.xml.ImageSeriesSequence
Returns the value of field 'probeorientation'.
getProjectcode() - Method in class edu.cornell.med.icb.allen.xml.GeneExpression
Returns the value of field 'projectcode'.
getProjectedIndex(MutableString...) - Method in class edu.cornell.med.icb.tissueinfo.annotations.Projection
Returns the projected index for the ordered set of values.
getProjectedIndex(int...) - Method in class edu.cornell.med.icb.tissueinfo.annotations.Projection
 
getProjectname() - Method in class edu.cornell.med.icb.allen.xml.Gene
Returns the value of field 'projectname'.
getProjectname() - Method in class edu.cornell.med.icb.allen.xml.ImageSeriesSequence
Returns the value of field 'projectname'.
getPropertiesFilename(String) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TissueESTCountsHelper
 
getPurity() - Method in class edu.mssm.crover.tools.tissue.QueryTissueSummary
Getter method for the minimum percent identity that a match must have to be considered valid.
getPurity(String[]) - Static method in class edu.mssm.crover.tools.tissue.QueryTissueSummary
Reads from the command line the minimum percent identity that a match must have to be considered valid.
getPurity() - Method in class edu.mssm.crover.tools.tissue.TissueSummary
Getter method for the minimum percent identity that a match must have to be considered valid.
getPurity(String[]) - Static method in class edu.mssm.crover.tools.tissue.TissueSummary
Reads from the command line the minimum percent identity that a match must have to be considered valid.
getQuery() - Method in class edu.mssm.crover.tools.tissue.HSP
Getter method for the identity of the query sequence.
getQueryId() - Method in class edu.mssm.crover.tools.blast.HitSummary
 
getQueryLen() - Method in class edu.mssm.crover.tools.blast.HitSummary
 
getQuerySequence(int) - Method in class edu.mssm.crover.tools.tissue.xml.BlastHits
Method getQuerySequence.
getQuerySequence() - Method in class edu.mssm.crover.tools.tissue.xml.BlastHits
Method getQuerySequence.Returns the contents of the collection in an Array.
getQuerySequenceCount() - Method in class edu.mssm.crover.tools.tissue.xml.BlastHits
Method getQuerySequenceCount.
getQuerySequenceToOffsetFilename(String) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TissueESTCountsHelper
 
getRawDevStage() - Method in class edu.mssm.crover.tools.tissue.TissueDetails
Getter method for the raw developmental stage.
getRawTissue() - Method in class edu.mssm.crover.tools.tissue.NullTissueDetails
Getter method for the raw tissue.
getRawTissue() - Method in class edu.mssm.crover.tools.tissue.TissueDetails
Getter method for the raw tissue.
getRawTissue(String) - Method in class edu.mssm.crover.tools.tissue.TissueInfoNullsJDBCImpl
Return the tissue information associated with a sequence accession code.
getRawTissue() - Method in class edu.mssm.crover.tools.tissue.xml.Tokey
Returns the value of field 'rawTissue'.
getRawTissues(String[]) - Method in class edu.mssm.crover.tools.tissue.TissueInfoNullsJDBCImpl
Return the tissue information associated with a set of sequence accession codes.
getRawTissueText() - Method in class edu.mssm.crover.tools.tissue.CuratedTissue
Returns the English language representation of the tissue.
getReader() - Method in class edu.cornell.med.icb.tissueinfo.similarity.TiSimilaritySearchEngine
 
getReport(String) - Method in interface edu.mssm.crover.tools.tissue.TIWeb
Return a report form for the accession number.
getReport(String) - Method in class edu.mssm.crover.tools.tissue.TIWebJDBCImpl
Returns the report for that accession number.
getReport(String, String) - Method in class edu.mssm.crover.tools.tissue.TIWebJDBCImpl
Returns the report for that accession number from a specific table.
getResidueCodes() - Method in interface edu.mssm.crover.representation.BiologicalSequence
Returns the residue codes of the sequence.
getResidueCodes() - Method in class edu.mssm.crover.representation.Sequence
Get the residue codes of the sequence.
getResidueCodes() - Method in class edu.mssm.crover.tools.tissue.xml.QuerySequence
Returns the value of field 'residueCodes'.
getResidueNumber() - Method in class edu.mssm.crover.representation.Mutation_Annotation
Get the index of the residue which is described by this mutation.
getResidueNumber() - Method in class edu.mssm.crover.representation.URL_Annotation
 
getResidueURL(int) - Method in class edu.mssm.crover.representation.Annotations
Returns the URL anchored to the residue at the index position.
getResidueURL(int) - Method in interface edu.mssm.crover.representation.BiologicalAnnotations
Returns the URL anchored to the index position.
getRgb() - Method in class edu.cornell.med.icb.allen.xml.GeneExpression
Returns the value of field 'rgb'.
getRiboprobename() - Method in class edu.cornell.med.icb.allen.xml.ImageSeriesSequence
Returns the value of field 'riboprobename'.
getRight() - Method in class gominer.Fisher
Accessor
getRowIteratorArray() - Method in class edu.mssm.crover.tables.treatments.Aggregation.Aggregate
Returns the RowIterators that are part of this aggregate.
getRowNumber() - Method in class edu.mssm.crover.tables.ArrayTable
Returns the number of rows of this table.
getRowNumber() - Method in interface edu.mssm.crover.tables.Table
Returns the number of row of this table.
getSampleIndex(String) - Method in class edu.cornell.med.icb.tissueinfo.annotations.AnnotationSet
 
getSampleIndex(MutableString) - Method in class edu.cornell.med.icb.tissueinfo.annotations.AnnotationSet
 
getScore() - Method in class edu.mssm.crover.tools.blast.HitSummary
 
getSearchDate() - Method in class edu.mssm.crover.tools.tissue.xml.BlastHits
Returns the value of field 'searchDate'.
getSentence() - Method in class edu.mssm.crover.tools.tissue.TissueSelection
Gets the sentence associated with this instance.
getSeqFilename(String[]) - Static method in class edu.mssm.crover.tools.tissue.TISearch
Reads the name of the query sequence input file.
getSeqType(String[]) - Static method in class edu.mssm.crover.tools.tissue.TISearch
Returns the type of sequence that will be used as query.
getSequenceCount() - Method in class edu.cornell.med.icb.tissueinfo.similarity.TissueESTCountsReader
 
getSequenceOrigin() - Method in class edu.mssm.crover.representation.SequenceOrigin_Annotation
Returns the origin that describes from where this sequence was obtained.
getSex() - Method in class edu.cornell.med.icb.allen.xml.ImageSeriesSequence
Returns the value of field 'sex'.
getShortName() - Method in class edu.mssm.crover.imports.FastaReaderType
 
getShortName() - Method in interface edu.mssm.crover.imports.ReaderType
Returns the shortname of this ReaderType.
getShortName() - Method in interface edu.mssm.crover.representation.BiologicalOrigin
Returns the shortname for this origin.
getShortName() - Method in interface edu.mssm.crover.representation.BiologicalSequence
Returns the short name of this sequence.
getShortName() - Method in class edu.mssm.crover.representation.Origin
 
getShortName() - Method in class edu.mssm.crover.representation.Sequence
 
getShortName() - Method in class edu.mssm.crover.tables.readers.DSSPTableReader
 
getShortName() - Method in class edu.mssm.crover.tables.readers.LocusLinkTableReader
 
getShortName() - Method in class edu.mssm.crover.tables.readers.MinesetTableReader
 
getShortName() - Method in class edu.mssm.crover.tables.readers.TIWebMinesetReader
 
getShuffledLabels() - Method in class edu.mssm.crover.tables.writers.SVMLightWriter
 
getSlope() - Method in class edu.cornell.med.icb.stat.LinearRegression
Obtain the slope.
getSpecimenid() - Method in class edu.cornell.med.icb.allen.xml.ImageSeriesSequence
Returns the value of field 'specimenid'.
getSplitPrefix() - Method in class edu.mssm.crover.util.MultiplePartFileIterator
 
getStatistics() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Iteration_statType
Returns the value of field 'statistics'.
getStatistics_dbLen() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.StatisticsType
Returns the value of field 'statistics_dbLen'.
getStatistics_dbNum() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.StatisticsType
Returns the value of field 'statistics_dbNum'.
getStatistics_effSpace() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.StatisticsType
Returns the value of field 'statistics_effSpace'.
getStatistics_entropy() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.StatisticsType
Returns the value of field 'statistics_entropy'.
getStatistics_hspLen() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.StatisticsType
Returns the value of field 'statistics_hspLen'.
getStatistics_kappa() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.StatisticsType
Returns the value of field 'statistics_kappa'.
getStatistics_lambda() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.StatisticsType
Returns the value of field 'statistics_lambda'.
getStrain() - Method in class edu.cornell.med.icb.allen.xml.ImageSeriesSequence
Returns the value of field 'strain'.
getStrings() - Method in class edu.mssm.crover.tables.ArrayTable.ColumnDescription
Get the array value as String[].
getStrings(String) - Method in class edu.mssm.crover.tables.ArrayTable
Get athe array of strings for a particular column id.
getStrings(String) - Method in interface edu.mssm.crover.tables.Table
Get the strings for a particular column id.
getStructureid() - Method in class edu.cornell.med.icb.allen.xml.GeneExpression
Returns the value of field 'structureid'.
getStructurelabel() - Method in class edu.cornell.med.icb.allen.xml.GeneExpression
Returns the value of field 'structurelabel'.
getStructurename() - Method in class edu.cornell.med.icb.allen.xml.GeneExpression
Returns the value of field 'structurename'.
getSubject() - Method in class edu.mssm.crover.tools.tissue.HSP
Getter method for the identity of the subject sequence.
getSubjId() - Method in class edu.mssm.crover.tools.blast.HitSummary
 
getSumForColumn(int) - Method in class edu.mssm.crover.tables.RowSumCalculator
 
getSumOfSquares() - Method in class edu.mssm.crover.tables.SumOfSquaresCalculatorRowProcessor
Get the sum of squares over each record.
getSupportedType() - Method in class edu.mssm.crover.imports.FastaReader
 
getSupportedType() - Method in interface edu.mssm.crover.imports.SequenceReader
 
getSupportedTypes() - Method in interface edu.mssm.crover.imports.SequenceReaderFactory
Returns the ReaderTypes supported by this factory implementation.
getSupportedTypes() - Method in class edu.mssm.crover.imports.SequenceReaderFactoryImpl
 
getTableName(String[]) - Static method in class edu.mssm.crover.tables.AddToTable
Returns the name of the table to which the data are to be added.
getTablename(String[]) - Static method in class edu.mssm.crover.tables.JDBCTable
Returns the prefix for the schema and data files.
getTablename() - Method in class edu.mssm.crover.tables.QueryTable
 
getTemplateid() - Method in class edu.cornell.med.icb.allen.xml.ImageSeriesSequence
Returns the value of field 'templateid'.
getTissue(String) - Method in interface edu.mssm.crover.tools.tissue.TissueInfo
Return the tissue information associated with a sequence accession code.
getTissue(String) - Method in class edu.mssm.crover.tools.tissue.TissueInfoCacheImpl
Return the tissue information associated with a sequence accession code.
getTissue(String) - Method in class edu.mssm.crover.tools.tissue.TissueInfoJDBCImpl
Return the tissue information associated with a sequence accession code.
getTissue(String) - Method in class edu.mssm.crover.tools.tissue.TissueInfoMemoryImpl
Return the tissue information associated with a sequence accession code.
getTissue(String) - Method in class edu.mssm.crover.tools.tissue.TissueInfoMemoryImpl2
Return the tissue information associated with a sequence accession code.
getTissueCount(int) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TiSimilaritySearchEngine
Returns tissue expression counts for a given sequence.
getTissueCount() - Method in class edu.cornell.med.icb.tissueinfo.similarity.TissueESTCountsHelper
Returns the number of tissues registered with this helper.
getTissueCountsNumber() - Method in class edu.cornell.med.icb.tissueinfo.similarity.TissueESTCountsReader
 
getTissueEstMatchCounts(String) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TissueESTCountsHelper
 
getTissueFile(String[]) - Static method in class edu.mssm.crover.tools.sumColumns
Returns the name of the input file.
getTissueFile(String[]) - Static method in class edu.mssm.crover.tools.tissue.CheckLibrary
Returns the name of the input file.
getTissueFile(String[]) - Method in class edu.mssm.crover.tools.tissue.GetCuratedTissue
Returns the name of the input file.
getTissueFile(String[]) - Static method in class edu.mssm.crover.tools.tissue.ReplaceRawTissue
Returns the name of the input file.
getTissueIndex(String) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TissueESTCountsHelper
Get the index corresponding to the tissue.
getTissueIndicesFilename(String) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TissueESTCountsHelper
 
getTissueList(String) - Method in interface edu.mssm.crover.tools.tissue.TIWeb
Return the list of raw tissues associated with an organism.
getTissueList(String) - Method in class edu.mssm.crover.tools.tissue.TIWebJDBCImpl
Return the list of raw tissues associated with an organism.
getTissues(String[]) - Method in interface edu.mssm.crover.tools.tissue.TissueInfo
Return the tissue information associated with several sequence accession codes.
getTissues(String[]) - Method in class edu.mssm.crover.tools.tissue.TissueInfoCacheImpl
Return the tissue information associated with several sequence accession codes.
getTissues(String[]) - Method in class edu.mssm.crover.tools.tissue.TissueInfoJDBCImpl
Return the tissue information associated with each sequence accession code in an array.
getTissues(String[]) - Method in class edu.mssm.crover.tools.tissue.TissueInfoMemoryImpl
Return the tissue information associated with several sequence accession codes.
getTissues(String[]) - Method in class edu.mssm.crover.tools.tissue.TissueInfoMemoryImpl2
Return the tissue information associated with several sequence accession codes.
getTissueType(int) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TissueESTCountsHelper
 
getTokey() - Method in class edu.mssm.crover.tools.tissue.xml.Hit
Returns the value of field 'tokey'.
getTokey(int) - Method in class edu.mssm.crover.tools.tissue.xml.TissueInfo
Method getTokey.
getTokey() - Method in class edu.mssm.crover.tools.tissue.xml.TissueInfo
Method getTokey.Returns the contents of the collection in an Array.
getTokeyCount() - Method in class edu.mssm.crover.tools.tissue.xml.TissueInfo
Method getTokeyCount.
getTranscriptCounts() - Method in class edu.cornell.med.icb.tissueinfo.similarity.TiSimilaritySearchEngine
 
getTranscriptgi() - Method in class edu.cornell.med.icb.allen.xml.ImageSeriesSequence
Returns the value of field 'transcriptgi'.
getTranscriptid() - Method in class edu.cornell.med.icb.allen.xml.ImageSeriesSequence
Returns the value of field 'transcriptid'.
getTranscriptId(int) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TiSimilaritySearchEngine
 
getTranscriptIds() - Method in class edu.cornell.med.icb.tissueinfo.similarity.clustering.Cluster
 
getTranscriptIndex(String) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TiSimilaritySearchEngine
Obtain the index of a transcript.
getTranscriptIndex(String) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TissueESTCountsReader
Obtain the index of a transcript.
getTranscriptname() - Method in class edu.cornell.med.icb.allen.xml.ImageSeriesSequence
Returns the value of field 'transcriptname'.
getTranscriptSet(MutableString) - Method in class edu.cornell.med.icb.tissueinfo.similarity.GeneTranscriptRelationships
Get the set of transcript indices for that that gene.
getTranscriptSet(int) - Method in class edu.cornell.med.icb.tissueinfo.similarity.GeneTranscriptRelationships
Get the set of transcript indices for that that gene.
getTransformation() - Method in class edu.cornell.med.icb.allen.xml.Genes
Returns the value of field 'transformation'.
getTreatmenttype() - Method in class edu.cornell.med.icb.allen.xml.ImageSeriesSequence
Returns the value of field 'treatmenttype'.
getTS(String) - Method in interface edu.mssm.crover.tools.tissue.TIWeb
Return a string of tissues.
getTS(String) - Method in class edu.mssm.crover.tools.tissue.TIWebJDBCImpl
Return the tissue summary associated with a GenBank accession number.
getTwotail() - Method in class gominer.Fisher
Accessor
getType() - Method in class edu.cornell.med.icb.allen.xml.Age
Returns the value of field 'type'.
getType() - Method in class edu.cornell.med.icb.allen.xml.Avgdensity
Returns the value of field 'type'.
getType() - Method in class edu.cornell.med.icb.allen.xml.Avglevel
Returns the value of field 'type'.
getType() - Method in class edu.cornell.med.icb.allen.xml.Entrezgeneid
Returns the value of field 'type'.
getType() - Method in class edu.cornell.med.icb.allen.xml.Geneid
Returns the value of field 'type'.
getType() - Method in class edu.cornell.med.icb.allen.xml.Imageseriesid
Returns the value of field 'type'.
getType() - Method in class edu.cornell.med.icb.allen.xml.Structureid
Returns the value of field 'type'.
getType() - Method in class edu.cornell.med.icb.allen.xml.Templateid
Returns the value of field 'type'.
getType() - Method in class edu.cornell.med.icb.allen.xml.Transcriptgi
Returns the value of field 'type'.
getType() - Method in class edu.cornell.med.icb.allen.xml.Transcriptid
Returns the value of field 'type'.
getType() - Method in class edu.cornell.med.icb.allen.xml.types.AgeTypeType
Method getType.Returns the type of this AgeTypeType
getType() - Method in class edu.cornell.med.icb.allen.xml.types.AvgdensityTypeType
Method getType.Returns the type of this AvgdensityTypeType
getType() - Method in class edu.cornell.med.icb.allen.xml.types.AvglevelTypeType
Method getType.Returns the type of this AvglevelTypeType
getType() - Method in class edu.cornell.med.icb.allen.xml.types.EntrezgeneidTypeType
Method getType.Returns the type of this EntrezgeneidTypeType
getType() - Method in class edu.cornell.med.icb.allen.xml.types.GeneidTypeType
Method getType.Returns the type of this GeneidTypeType
getType() - Method in class edu.cornell.med.icb.allen.xml.types.ImageseriesidTypeType
Method getType.Returns the type of this ImageseriesidTypeType
getType() - Method in class edu.cornell.med.icb.allen.xml.types.OrganismType
Method getType.Returns the type of this OrganismType
getType() - Method in class edu.cornell.med.icb.allen.xml.types.PlaneType
Method getType.Returns the type of this PlaneType
getType() - Method in class edu.cornell.med.icb.allen.xml.types.SexType
Method getType.Returns the type of this SexType
getType() - Method in class edu.cornell.med.icb.allen.xml.types.StructureidTypeType
Method getType.Returns the type of this StructureidTypeType
getType() - Method in class edu.cornell.med.icb.allen.xml.types.T_age
Method getType.Returns the type of this T_age
getType() - Method in class edu.cornell.med.icb.allen.xml.types.TemplateidTypeType
Method getType.Returns the type of this TemplateidTypeType
getType() - Method in class edu.cornell.med.icb.allen.xml.types.TranscriptgiTypeType
Method getType.Returns the type of this TranscriptgiTypeType
getType() - Method in class edu.cornell.med.icb.allen.xml.types.TranscriptidTypeType
Method getType.Returns the type of this TranscriptidTypeType
getType() - Method in class edu.cornell.med.icb.allen.xml.types.TreatmenttypeType
Method getType.Returns the type of this TreatmenttypeType
getType() - Method in class edu.cornell.med.icb.tissueinfo.annotations.AnnotationType
 
getType(int) - Method in class edu.mssm.crover.tables.ArrayTable
Returns the type of the column which index is passed as argument.
getType(int) - Method in interface edu.mssm.crover.tables.Table
Returns the type of the column which index is passed as argument.
getType() - Method in class edu.mssm.crover.tools.tissue.xml.QuerySequence
Returns the value of field 'type'.
getUnspecifiedOrigin() - Static method in class edu.mssm.crover.representation.OriginFactory
Returns an unspecified origin instance.
getValidator() - Method in class edu.cornell.med.icb.allen.xml.descriptors.AgeDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.allen.xml.descriptors.AvgdensityDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.allen.xml.descriptors.AvglevelDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.allen.xml.descriptors.EntrezgeneidDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.allen.xml.descriptors.GeneDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.allen.xml.descriptors.GeneExpressionDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.allen.xml.descriptors.GeneExpressionsDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.allen.xml.descriptors.GeneidDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.allen.xml.descriptors.GenesDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.allen.xml.descriptors.ImageSeriesDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.allen.xml.descriptors.ImageseriesidDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.allen.xml.descriptors.ImageSeriesSequenceDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.allen.xml.descriptors.StructureidDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.allen.xml.descriptors.TemplateidDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.allen.xml.descriptors.TranscriptgiDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.allen.xml.descriptors.TranscriptidDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.allen.xml.descriptors.TranscriptnameDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.AgeTypeTypeDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.AvgdensityTypeTypeDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.AvglevelTypeTypeDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.EntrezgeneidTypeTypeDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.GeneidTypeTypeDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.ImageseriesidTypeTypeDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.OrganismTypeDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.PlaneTypeDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.SexTypeDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.StructureidTypeTypeDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.T_ageDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.TemplateidTypeTypeDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.TranscriptgiTypeTypeDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.TranscriptidTypeTypeDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.TreatmenttypeTypeDescriptor
Method getValidator.
getValidator() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutput_iterationsDescriptor
Method getValidator.
getValidator() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutput_iterationsTypeDescriptor
Method getValidator.
getValidator() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutput_paramDescriptor
Method getValidator.
getValidator() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutput_paramTypeDescriptor
Method getValidator.
getValidator() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutputDescriptor
Method getValidator.
getValidator() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Hit_hspsDescriptor
Method getValidator.
getValidator() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Hit_hspsTypeDescriptor
Method getValidator.
getValidator() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.HitDescriptor
Method getValidator.
getValidator() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.HitTypeDescriptor
Method getValidator.
getValidator() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.HspDescriptor
Method getValidator.
getValidator() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.HspTypeDescriptor
Method getValidator.
getValidator() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Iteration_hitsDescriptor
Method getValidator.
getValidator() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Iteration_hitsTypeDescriptor
Method getValidator.
getValidator() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Iteration_statDescriptor
Method getValidator.
getValidator() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Iteration_statTypeDescriptor
Method getValidator.
getValidator() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.IterationDescriptor
Method getValidator.
getValidator() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.IterationTypeDescriptor
Method getValidator.
getValidator() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.ParametersDescriptor
Method getValidator.
getValidator() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.ParametersTypeDescriptor
Method getValidator.
getValidator() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.StatisticsDescriptor
Method getValidator.
getValidator() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.StatisticsTypeDescriptor
Method getValidator.
getValidator() - Method in class edu.mssm.crover.tools.tissue.xml.descriptors.BlastHitsDescriptor
Method getValidator.
getValidator() - Method in class edu.mssm.crover.tools.tissue.xml.descriptors.HitDescriptor
Method getValidator.
getValidator() - Method in class edu.mssm.crover.tools.tissue.xml.descriptors.QuerySequenceDescriptor
Method getValidator.
getValidator() - Method in class edu.mssm.crover.tools.tissue.xml.descriptors.TissueInfoDescriptor
Method getValidator.
getValidator() - Method in class edu.mssm.crover.tools.tissue.xml.descriptors.TokeyDescriptor
Method getValidator.
getValue(int) - Method in class edu.cornell.med.icb.tissueinfo.annotations.AnnotationType
 
getValue(int, Table.RowIterator) - Method in class edu.mssm.crover.tables.ArrayTable
Returns the value stored in this position as an Object, when appropriate.
getValue() - Method in exception edu.mssm.crover.tables.ColumnTypeException
 
getValue(int, Table.RowIterator) - Method in interface edu.mssm.crover.tables.Table
Returns the value stored in this position as an Object, when appropriate.
getValueIndex(int, MutableString) - Method in class edu.cornell.med.icb.tissueinfo.annotations.AnnotationSet
 
getValueIndex(int, String) - Method in class edu.cornell.med.icb.tissueinfo.annotations.AnnotationSet
 
getValueIndex(MutableString) - Method in class edu.cornell.med.icb.tissueinfo.annotations.AnnotationType
Return the value that represents this value identifier in the annotation sets.
getVersion() - Method in class edu.mssm.crover.tools.blast.BlastResult
Returns the version of BlastOutput contained in this BlastResult.
getVValue() - Method in class edu.mssm.crover.tools.blast.BlastContext
 
getVValue(String[]) - Static method in class edu.mssm.crover.tools.tissue.TISearch
Reads the number of descriptions to be returned from BLAST.
getVValue() - Method in class edu.mssm.crover.tools.tissue.xml.BlastHits
Returns the value of field 'vValue'.
getXIntercept() - Method in class edu.cornell.med.icb.stat.LinearRegression
Obtain the x-intercept.
getXMLFilename(String[]) - Static method in class edu.mssm.crover.tools.tissue.TISearch
Reads the name of the XML BLAST input file.
getXMLName() - Method in class edu.cornell.med.icb.allen.xml.descriptors.AgeDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.allen.xml.descriptors.AvgdensityDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.allen.xml.descriptors.AvglevelDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.allen.xml.descriptors.EntrezgeneidDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.allen.xml.descriptors.GeneDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.allen.xml.descriptors.GeneExpressionDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.allen.xml.descriptors.GeneExpressionsDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.allen.xml.descriptors.GeneidDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.allen.xml.descriptors.GenesDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.allen.xml.descriptors.ImageSeriesDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.allen.xml.descriptors.ImageseriesidDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.allen.xml.descriptors.ImageSeriesSequenceDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.allen.xml.descriptors.StructureidDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.allen.xml.descriptors.TemplateidDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.allen.xml.descriptors.TranscriptgiDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.allen.xml.descriptors.TranscriptidDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.allen.xml.descriptors.TranscriptnameDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.AgeTypeTypeDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.AvgdensityTypeTypeDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.AvglevelTypeTypeDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.EntrezgeneidTypeTypeDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.GeneidTypeTypeDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.ImageseriesidTypeTypeDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.OrganismTypeDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.PlaneTypeDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.SexTypeDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.StructureidTypeTypeDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.T_ageDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.TemplateidTypeTypeDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.TranscriptgiTypeTypeDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.TranscriptidTypeTypeDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.TreatmenttypeTypeDescriptor
Method getXMLName.
getXMLName() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutput_iterationsDescriptor
Method getXMLName.
getXMLName() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutput_iterationsTypeDescriptor
Method getXMLName.
getXMLName() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutput_paramDescriptor
Method getXMLName.
getXMLName() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutput_paramTypeDescriptor
Method getXMLName.
getXMLName() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutputDescriptor
Method getXMLName.
getXMLName() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Hit_hspsDescriptor
Method getXMLName.
getXMLName() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Hit_hspsTypeDescriptor
Method getXMLName.
getXMLName() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.HitDescriptor
Method getXMLName.
getXMLName() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.HitTypeDescriptor
Method getXMLName.
getXMLName() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.HspDescriptor
Method getXMLName.
getXMLName() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.HspTypeDescriptor
Method getXMLName.
getXMLName() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Iteration_hitsDescriptor
Method getXMLName.
getXMLName() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Iteration_hitsTypeDescriptor
Method getXMLName.
getXMLName() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Iteration_statDescriptor
Method getXMLName.
getXMLName() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Iteration_statTypeDescriptor
Method getXMLName.
getXMLName() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.IterationDescriptor
Method getXMLName.
getXMLName() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.IterationTypeDescriptor
Method getXMLName.
getXMLName() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.ParametersDescriptor
Method getXMLName.
getXMLName() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.ParametersTypeDescriptor
Method getXMLName.
getXMLName() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.StatisticsDescriptor
Method getXMLName.
getXMLName() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.StatisticsTypeDescriptor
Method getXMLName.
getXMLName() - Method in class edu.mssm.crover.tools.tissue.xml.descriptors.BlastHitsDescriptor
Method getXMLName.
getXMLName() - Method in class edu.mssm.crover.tools.tissue.xml.descriptors.HitDescriptor
Method getXMLName.
getXMLName() - Method in class edu.mssm.crover.tools.tissue.xml.descriptors.QuerySequenceDescriptor
Method getXMLName.
getXMLName() - Method in class edu.mssm.crover.tools.tissue.xml.descriptors.TissueInfoDescriptor
Method getXMLName.
getXMLName() - Method in class edu.mssm.crover.tools.tissue.xml.descriptors.TokeyDescriptor
Method getXMLName.
getYIntercept() - Method in class edu.cornell.med.icb.stat.LinearRegression
Obtain the y-intercept.
gland - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
glia - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
glomerulus - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
glossopharyngeal_nerve - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
gominer - package gominer
 
gonad - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
granulocyte - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
groupBy(String) - Method in class edu.mssm.crover.tables.treatments.Aggregation
 
GroupScoringMode - Class in edu.cornell.med.icb.tissueinfo.similarity
 
GroupScoringMode() - Constructor for class edu.cornell.med.icb.tissueinfo.similarity.GroupScoringMode
 
guessReaderType(String) - Method in interface edu.mssm.crover.imports.SequenceReaderFactory
Return a ReaderType supported by this factory that is guessed to be able to handle a file named filename.
guessReaderType(String) - Method in class edu.mssm.crover.imports.SequenceReaderFactoryImpl
Attempt to determine a ReaderType suitable to parse the sequence encoding from a filename extension.
gum - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
gut - Interface in edu.mssm.crover.tools.tissue.hierarchy
 

H

harderian_gland - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
hasBlastOutput_queryLen() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.BlastOutput
Method hasBlastOutput_queryLen.
hasBValue() - Method in class edu.mssm.crover.tools.tissue.xml.BlastHits
Method hasBValue.
hasExpectationValue() - Method in class edu.mssm.crover.tools.tissue.xml.BlastHits
Method hasExpectationValue.
hashCode() - Method in class edu.mssm.crover.imports.FastaReaderType
Two ReaderType that have the same shortName are said to be equal (for the purpose of Hashtable insertion.
hasHit_len() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HitType
Method hasHit_len.
hasHit_num() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HitType
Method hasHit_num.
hasHsp_alignLen() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
Method hasHsp_alignLen.
hasHsp_evalue() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
Method hasHsp_evalue.
hasHsp_gaps() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
Method hasHsp_gaps.
hasHsp_hitFrame() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
Method hasHsp_hitFrame.
hasHsp_hitFrom() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
Method hasHsp_hitFrom.
hasHsp_hitTo() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
Method hasHsp_hitTo.
hasHsp_identity() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
Method hasHsp_identity.
hasHsp_num() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
Method hasHsp_num.
hasHsp_positive() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
Method hasHsp_positive.
hasHsp_queryFrame() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
Method hasHsp_queryFrame.
hasHsp_queryFrom() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
Method hasHsp_queryFrom.
hasHsp_queryTo() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
Method hasHsp_queryTo.
hasHsp_score() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
Method hasHsp_score.
hasId() - Method in class edu.mssm.crover.tools.tissue.xml.Tokey
Method hasId.
hasInterface(Object, Class) - Static method in class edu.mssm.crover.util.Inspect
Returns whether the instance a supports the interface described by c.
hasInterface(Class, Class) - Static method in class edu.mssm.crover.util.Inspect
Returns whether the class child supports the interface described by parent.
hasIteration_iterNum() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.IterationType
Method hasIteration_iterNum.
hasIteration_queryLen() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.IterationType
Method hasIteration_queryLen.
hasMaxErrorRate() - Method in class edu.mssm.crover.tools.tissue.xml.BlastHits
Method hasMaxErrorRate.
hasMinimumLength() - Method in class edu.mssm.crover.tools.tissue.xml.BlastHits
Method hasMinimumLength.
hasMoreTokens() - Method in class edu.mssm.crover.tables.readers.TabTokenizer
Are there more tokens in the string?
hasNext() - Method in class edu.cornell.med.icb.tissueinfo.annotations.ArraysIterator
 
hasNext() - Method in class edu.mssm.crover.tools.blast.MegablastHSIterator
Returns true if the iteration has more HitSummaries.
hasNext() - Method in class edu.mssm.crover.tools.blast.XMLBlastHSIterator
Returns true if the iteration has more HitSummaries.
hasNext() - Method in class edu.mssm.crover.util.MultiplePartFileIterator
Looks for a split prefix in the input file, starting either from the beginning of the file, or from the last line of the file that has been read.
hasPair(int, int) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TiSimOptions
 
hasParameters_expect() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.ParametersType
Method hasParameters_expect.
hasParameters_gapExtend() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.ParametersType
Method hasParameters_gapExtend.
hasParameters_gapOpen() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.ParametersType
Method hasParameters_gapOpen.
hasParameters_scMatch() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.ParametersType
Method hasParameters_scMatch.
hasParameters_scMismatch() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.ParametersType
Method hasParameters_scMismatch.
hasProjectcode() - Method in class edu.cornell.med.icb.allen.xml.GeneExpression
Method hasProjectcode.
hasSequence(String) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TissueESTCountsReader
Check if a sequence accession code exists in the compressed EST count data.
hasStatistics_dbLen() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.StatisticsType
Method hasStatistics_dbLen.
hasStatistics_dbNum() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.StatisticsType
Method hasStatistics_dbNum.
hasStatistics_hspLen() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.StatisticsType
Method hasStatistics_hspLen.
hasTissueType(String) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TissueESTCountsHelper
Returns true if the tissue has been registered with this writer.
hasTokey() - Method in class edu.mssm.crover.tools.tissue.xml.Hit
Method hasTokey.
hasVValue() - Method in class edu.mssm.crover.tools.tissue.xml.BlastHits
Method hasVValue.
head - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
heart - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
Hierarchy - Class in edu.mssm.crover.tools.tissue
This class determines the relationships between tissue classes.
Hierarchy() - Constructor for class edu.mssm.crover.tools.tissue.Hierarchy
Constructor.
HIERARCHY_PACKAGE - Static variable in class edu.mssm.crover.tools.tissue.GetCuratedTissue
The hierarchy package in which to look for the parents of the curated tissues.
HierarchyKeywords - Class in edu.mssm.crover.tools.tissue
Splits the hierarchy interface names up into keywords.
HierarchyKeywords() - Constructor for class edu.mssm.crover.tools.tissue.HierarchyKeywords
 
highestStatisticIsBest - Variable in class edu.cornell.med.icb.stat.PredictionStatisticCalculator
Indicates that a larger statistic represents a better predictor performance.
hippocampus - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
histiocyte - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
Hit - Class in edu.mssm.crover.tools.blast.parsers.xml.v3
Class Hit.
Hit() - Constructor for class edu.mssm.crover.tools.blast.parsers.xml.v3.Hit
 
Hit - Class in edu.mssm.crover.tools.tissue.xml
Class Hit.
Hit() - Constructor for class edu.mssm.crover.tools.tissue.xml.Hit
 
Hit_hsps - Class in edu.mssm.crover.tools.blast.parsers.xml.v3
Class Hit_hsps.
Hit_hsps() - Constructor for class edu.mssm.crover.tools.blast.parsers.xml.v3.Hit_hsps
 
Hit_hspsDescriptor - Class in edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors
Class Hit_hspsDescriptor.
Hit_hspsDescriptor() - Constructor for class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Hit_hspsDescriptor
 
Hit_hspsType - Class in edu.mssm.crover.tools.blast.parsers.xml.v3
Class Hit_hspsType.
Hit_hspsType() - Constructor for class edu.mssm.crover.tools.blast.parsers.xml.v3.Hit_hspsType
 
Hit_hspsTypeDescriptor - Class in edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors
Class Hit_hspsTypeDescriptor.
Hit_hspsTypeDescriptor() - Constructor for class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Hit_hspsTypeDescriptor
 
HitDescriptor - Class in edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors
Class HitDescriptor.
HitDescriptor() - Constructor for class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.HitDescriptor
 
HitDescriptor - Class in edu.mssm.crover.tools.tissue.xml.descriptors
Class HitDescriptor.
HitDescriptor() - Constructor for class edu.mssm.crover.tools.tissue.xml.descriptors.HitDescriptor
 
hitsFromNonTumor() - Method in class edu.mssm.crover.tools.tissue.QueryTissueSummary
Calculate the number of hits from non tumor tissue.
hitsFromNonTumor() - Method in class edu.mssm.crover.tools.tissue.TissueSummary
Calculate the number of hits from non tumor tissue.
hitsFromTumor() - Method in class edu.mssm.crover.tools.tissue.QueryTissueSummary
Return the number of hits from tumor tissue.
hitsFromTumor() - Method in class edu.mssm.crover.tools.tissue.TissueSummary
Return the number of hits from tumor tissue.
HitSummary - Class in edu.mssm.crover.tools.blast
Stores the query sequence definition (queryId), the length of the query sequence (queryLen), the definition of the hit (subjId), the long definition of the hit (defLine), the percentage similarity between the query sequence and the hit HSP (percentId, between 0 and 1, not 0 and 100), the e-value of the hit HSP (eValue), and the length of the HSP (hitLength).
HitSummary() - Constructor for class edu.mssm.crover.tools.blast.HitSummary
 
HitType - Class in edu.mssm.crover.tools.blast.parsers.xml.v3
Class HitType.
HitType() - Constructor for class edu.mssm.crover.tools.blast.parsers.xml.v3.HitType
 
HitTypeDescriptor - Class in edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors
Class HitTypeDescriptor.
HitTypeDescriptor() - Constructor for class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.HitTypeDescriptor
 
Hsp - Class in edu.mssm.crover.tools.blast.parsers.xml.v3
Class Hsp.
Hsp() - Constructor for class edu.mssm.crover.tools.blast.parsers.xml.v3.Hsp
 
HSP - Class in edu.mssm.crover.tools.tissue
Storage class for information an HSP.
HSP(String, String, int, float) - Constructor for class edu.mssm.crover.tools.tissue.HSP
Constructor.
HspDescriptor - Class in edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors
Class HspDescriptor.
HspDescriptor() - Constructor for class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.HspDescriptor
 
HspType - Class in edu.mssm.crover.tools.blast.parsers.xml.v3
Class HspType.
HspType() - Constructor for class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
 
HspTypeDescriptor - Class in edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors
Class HspTypeDescriptor.
HspTypeDescriptor() - Constructor for class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.HspTypeDescriptor
 
hypoglossal_nerve - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
hypothalamus - Interface in edu.mssm.crover.tools.tissue.hierarchy
 

I

IconixReader - Class in edu.mssm.crover.tables.readers
original file:
IconixReader() - Constructor for class edu.mssm.crover.tables.readers.IconixReader
 
identifier - Variable in class edu.mssm.crover.tables.ArrayTable.ColumnDescription
 
IdentifierSetRowFilter - Class in edu.mssm.crover.tables
Filter rows based on the value in an 'identifier' column.
IdentifierSetRowFilter(Set<String>, int) - Constructor for class edu.mssm.crover.tables.IdentifierSetRowFilter
 
ileum - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
ImageSeries - Class in edu.cornell.med.icb.allen.xml
Class ImageSeries.
ImageSeries() - Constructor for class edu.cornell.med.icb.allen.xml.ImageSeries
 
ImageSeriesDescriptor - Class in edu.cornell.med.icb.allen.xml.descriptors
Class ImageSeriesDescriptor.
ImageSeriesDescriptor() - Constructor for class edu.cornell.med.icb.allen.xml.descriptors.ImageSeriesDescriptor
 
Imageseriesid - Class in edu.cornell.med.icb.allen.xml
Class Imageseriesid.
Imageseriesid() - Constructor for class edu.cornell.med.icb.allen.xml.Imageseriesid
 
ImageseriesidDescriptor - Class in edu.cornell.med.icb.allen.xml.descriptors
Class ImageseriesidDescriptor.
ImageseriesidDescriptor() - Constructor for class edu.cornell.med.icb.allen.xml.descriptors.ImageseriesidDescriptor
 
ImageseriesidTypeType - Class in edu.cornell.med.icb.allen.xml.types
Class ImageseriesidTypeType.
ImageseriesidTypeTypeDescriptor - Class in edu.cornell.med.icb.allen.xml.types.descriptors
Class ImageseriesidTypeTypeDescriptor.
ImageseriesidTypeTypeDescriptor() - Constructor for class edu.cornell.med.icb.allen.xml.types.descriptors.ImageseriesidTypeTypeDescriptor
 
ImageSeriesSequence - Class in edu.cornell.med.icb.allen.xml
Class ImageSeriesSequence.
ImageSeriesSequence() - Constructor for class edu.cornell.med.icb.allen.xml.ImageSeriesSequence
 
ImageSeriesSequenceDescriptor - Class in edu.cornell.med.icb.allen.xml.descriptors
Class ImageSeriesSequenceDescriptor.
ImageSeriesSequenceDescriptor() - Constructor for class edu.cornell.med.icb.allen.xml.descriptors.ImageSeriesSequenceDescriptor
 
inadequate - Variable in exception edu.mssm.crover.tables.treatments.InadequateBindingException
 
InadequateBindingException - Exception in edu.mssm.crover.tables.treatments
Super-class for the binding exceptions.
InadequateBindingException(Class, Class, Class, String) - Constructor for exception edu.mssm.crover.tables.treatments.InadequateBindingException
 
InadequateDestinationException - Exception in edu.mssm.crover.tables.treatments
Thrown when an attempt is made to bind a treatment to a destination that is inadequate (the treatment, as implemented, requires a specific destination that is not provided).
InadequateSourceException - Exception in edu.mssm.crover.tables.treatments
Thrown when an attempt is made to bind a treatment to a source that is inadequate (the treatment, as implemented, requires a specific source that is not provided).
incrementRowNumber() - Method in class edu.mssm.crover.tables.ArrayTable
 
incrementRowNumber() - Method in interface edu.mssm.crover.tables.Table
 
inferior_parathyroid - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
init(Table) - Method in interface edu.mssm.crover.tables.Filter
initializes this filter with the table.
init(Table) - Method in class edu.mssm.crover.tables.KeepAllFilter
initializes this filter with the table.
init(Table) - Method in class edu.mssm.crover.tables.readers.LocusLinkFilter
Initializes this filter with the table.
initConnection() - Method in class edu.mssm.crover.tables.AddToTable
Makes sure a connection is available.
initConnection() - Method in class edu.mssm.crover.tables.JDBCTable
Makes sure a connection is available.
initConnection() - Method in class edu.mssm.crover.tables.QueryTable
Makes sure a connection is available.
initConnection() - Method in class edu.mssm.crover.tables.TableActivityWatcher
Makes sure a connection is available.
initConnection() - Method in class edu.mssm.crover.tools.tissue.TIWebJDBCImpl
Makes sure a connection is available.
INITIAL_LENGTH - Variable in class edu.mssm.crover.tables.ArrayTable
 
initializeScoreCollection(TiSimilaritySearchEngine) - Method in class edu.cornell.med.icb.tissueinfo.similarity.PairScoreOnlyMode
 
InsightfulMinerTableWriter - Class in edu.mssm.crover.tables.writers
Writes the schema and data from a table in a Insightful Miner like format.
InsightfulMinerTableWriter() - Constructor for class edu.mssm.crover.tables.writers.InsightfulMinerTableWriter
 
Inspect - Class in edu.mssm.crover.util
Inspect a class with the reflection API.
Inspect() - Constructor for class edu.mssm.crover.util.Inspect
 
installed(String, String) - Method in class edu.mssm.crover.tools.blast.BlastCommand
Checks if the command is installed on this machine.
IntArraySizer - Class in edu.mssm.crover.tables
 
IntArraySizer() - Constructor for class edu.mssm.crover.tables.IntArraySizer
 
INTEGER - Static variable in class edu.cornell.med.icb.allen.xml.types.AgeTypeType
The instance of the integer type
INTEGER - Static variable in class edu.cornell.med.icb.allen.xml.types.EntrezgeneidTypeType
The instance of the integer type
INTEGER - Static variable in class edu.cornell.med.icb.allen.xml.types.GeneidTypeType
The instance of the integer type
INTEGER - Static variable in class edu.cornell.med.icb.allen.xml.types.ImageseriesidTypeType
The instance of the integer type
INTEGER - Static variable in class edu.cornell.med.icb.allen.xml.types.StructureidTypeType
The instance of the integer type
INTEGER - Static variable in class edu.cornell.med.icb.allen.xml.types.TemplateidTypeType
The instance of the integer type
INTEGER - Static variable in class edu.cornell.med.icb.allen.xml.types.TranscriptgiTypeType
The instance of the integer type
INTEGER - Static variable in class edu.cornell.med.icb.allen.xml.types.TranscriptidTypeType
The instance of the integer type
INTEGER_TYPE - Static variable in class edu.cornell.med.icb.allen.xml.types.AgeTypeType
The integer type
INTEGER_TYPE - Static variable in class edu.cornell.med.icb.allen.xml.types.EntrezgeneidTypeType
The integer type
INTEGER_TYPE - Static variable in class edu.cornell.med.icb.allen.xml.types.GeneidTypeType
The integer type
INTEGER_TYPE - Static variable in class edu.cornell.med.icb.allen.xml.types.ImageseriesidTypeType
The integer type
INTEGER_TYPE - Static variable in class edu.cornell.med.icb.allen.xml.types.StructureidTypeType
The integer type
INTEGER_TYPE - Static variable in class edu.cornell.med.icb.allen.xml.types.TemplateidTypeType
The integer type
INTEGER_TYPE - Static variable in class edu.cornell.med.icb.allen.xml.types.TranscriptgiTypeType
The integer type
INTEGER_TYPE - Static variable in class edu.cornell.med.icb.allen.xml.types.TranscriptidTypeType
The integer type
interneuron - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
interpretArguments(JSAP, JSAPResult, TiSimOptions) - Method in class edu.cornell.med.icb.tissueinfo.similarity.AnnotateClustersMode
 
interpretArguments(JSAP, JSAPResult, TiSimOptions) - Method in class edu.cornell.med.icb.tissueinfo.similarity.BackwardMode
 
interpretArguments(JSAP, JSAPResult, TiSimOptions) - Method in class edu.cornell.med.icb.tissueinfo.similarity.ClusterMode
 
interpretArguments(JSAP, JSAPResult, TiSimOptions) - Method in class edu.cornell.med.icb.tissueinfo.similarity.CrossValidationMode
 
interpretArguments(JSAP, JSAPResult, TiSimOptions) - Method in class edu.cornell.med.icb.tissueinfo.similarity.ForwardMode
 
interpretArguments(JSAP, JSAPResult, TiSimOptions) - Method in class edu.cornell.med.icb.tissueinfo.similarity.LeaveOneOutMode
 
interpretArguments(JSAP, JSAPResult, TiSimOptions) - Method in class edu.cornell.med.icb.tissueinfo.similarity.ListSearchMode
 
interpretArguments(JSAP, JSAPResult, TiSimOptions) - Method in class edu.cornell.med.icb.tissueinfo.similarity.PairSearchMode
 
interpretArguments(JSAP, JSAPResult, TiSimOptions) - Method in class edu.cornell.med.icb.tissueinfo.similarity.SimpleSearchMode
 
interpretArguments(JSAP, JSAPResult, TiSimOptions) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TallyScoreSearchMode
 
interpretArguments(JSAP, JSAPResult, TiSimOptions) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TiSimMode
 
interpretArguments(JSAP, JSAPResult, TiSimOptions) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TranscriptListMode
 
InvalidColumnException - Exception in edu.mssm.crover.tables
Thrown when the column the client tries to access does not exist in this table.
InvalidColumnException(int) - Constructor for exception edu.mssm.crover.tables.InvalidColumnException
Create a new exeception with the given column.
InvalidColumnException(String) - Constructor for exception edu.mssm.crover.tables.InvalidColumnException
Create a new exeception with the given column.
InvalidFieldLimits - Exception in edu.mssm.crover.imports
Thrown when the field limits were incorrectly specified.
InvalidFieldLimits(String) - Constructor for exception edu.mssm.crover.imports.InvalidFieldLimits
 
iris - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
isAggregateColumn(String) - Method in class edu.mssm.crover.tables.treatments.Aggregation
 
isAll() - Method in class edu.mssm.crover.tools.tissue.CuratedTissue
Whether this instance is marked as non-specific (taken from the whole organism).
isAnnotationFile(String[]) - Static method in class edu.mssm.crover.tools.tissue.CheckLibrary
 
isBeta(Table, Table.RowIterator, int) - Static method in class edu.mssm.crover.tables.treatments.CompositionTableTreatment
 
isCancer() - Method in class edu.mssm.crover.tools.tissue.CuratedTissue
Whether this instance is marked as coming from tumour tissue.
isCancer() - Method in class edu.mssm.crover.tools.tissue.QueryTissueSummary
Determines whether or not all the accession numbers for the EST are found in tumor tissue, with the usual contamination parameter.
isCancer() - Method in class edu.mssm.crover.tools.tissue.TissueSummary
Determines whether or not all the accession numbers for the EST are found in tumor tissue, with the usual contamination parameter.
isColumn(String) - Method in class edu.mssm.crover.tables.ArrayTable
Returns true when the identifier designate a column of this column.
isColumn(String) - Method in interface edu.mssm.crover.tables.Table
Returns true when the identifier designate a column of this column.
isElementDefinition() - Method in class edu.cornell.med.icb.allen.xml.descriptors.AgeDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.allen.xml.descriptors.AvgdensityDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.allen.xml.descriptors.AvglevelDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.allen.xml.descriptors.EntrezgeneidDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.allen.xml.descriptors.GeneDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.allen.xml.descriptors.GeneExpressionDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.allen.xml.descriptors.GeneExpressionsDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.allen.xml.descriptors.GeneidDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.allen.xml.descriptors.GenesDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.allen.xml.descriptors.ImageSeriesDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.allen.xml.descriptors.ImageseriesidDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.allen.xml.descriptors.ImageSeriesSequenceDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.allen.xml.descriptors.StructureidDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.allen.xml.descriptors.TemplateidDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.allen.xml.descriptors.TranscriptgiDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.allen.xml.descriptors.TranscriptidDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.allen.xml.descriptors.TranscriptnameDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.AgeTypeTypeDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.AvgdensityTypeTypeDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.AvglevelTypeTypeDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.EntrezgeneidTypeTypeDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.GeneidTypeTypeDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.ImageseriesidTypeTypeDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.OrganismTypeDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.PlaneTypeDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.SexTypeDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.StructureidTypeTypeDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.T_ageDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.TemplateidTypeTypeDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.TranscriptgiTypeTypeDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.TranscriptidTypeTypeDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.allen.xml.types.descriptors.TreatmenttypeTypeDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutput_iterationsDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutput_iterationsTypeDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutput_paramDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutput_paramTypeDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.BlastOutputDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Hit_hspsDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Hit_hspsTypeDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.HitDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.HitTypeDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.HspDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.HspTypeDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Iteration_hitsDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Iteration_hitsTypeDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Iteration_statDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Iteration_statTypeDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.IterationDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.IterationTypeDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.ParametersDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.ParametersTypeDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.StatisticsDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.StatisticsTypeDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.mssm.crover.tools.tissue.xml.descriptors.BlastHitsDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.mssm.crover.tools.tissue.xml.descriptors.HitDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.mssm.crover.tools.tissue.xml.descriptors.QuerySequenceDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.mssm.crover.tools.tissue.xml.descriptors.TissueInfoDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.mssm.crover.tools.tissue.xml.descriptors.TokeyDescriptor
Method isElementDefinition.
isEmpty() - Method in class edu.cornell.med.icb.tissueinfo.similarity.ScoredTranscriptBoundedSizeQueue
 
isExpressedIn(String) - Method in class edu.mssm.crover.tools.tissue.QueryTissueSummary
Determines whether the ESTs associated with the given accession numbers are expressed in the specified tissue.
isExpressedIn(String) - Method in class edu.mssm.crover.tools.tissue.TissueSummary
Determines whether the ESTs associated with the given accession numbers are expressed in the specified tissue.
isExpressedInDevStage(String) - Method in class edu.mssm.crover.tools.tissue.QueryTissueSummary
Determines whether the ESTs associated with the given accession numbers are expressed in the specified tissue.
isExpressedInDevStage(String) - Method in class edu.mssm.crover.tools.tissue.TissueSummary
Determines whether the ESTs associated with the given accession numbers are expressed in the specified tissue.
isExpressedInRawTissue(String) - Method in class edu.mssm.crover.tools.tissue.TissueSummary
Determines whether the ESTs associated with the given accession numbers are expressed in the specified tissue.
isGroupByColumn(String) - Method in class edu.mssm.crover.tables.treatments.Aggregation
 
ISH - Static variable in class edu.cornell.med.icb.allen.xml.types.TreatmenttypeType
The instance of the ISH type
ISH_TYPE - Static variable in class edu.cornell.med.icb.allen.xml.types.TreatmenttypeType
The ISH type
isInGroup(String, String[]) - Method in class edu.mssm.crover.tables.treatments.Aggregation
 
isNonSpecific() - Method in class edu.mssm.crover.tools.tissue.QueryTissueSummary
Specifies whether the ESTs associated with the accession numbers are expressed in a specific (localized expression pattern) way, or not.
isNonSpecific() - Method in class edu.mssm.crover.tools.tissue.TissueSummary
Specifies whether the ESTs associated with the accession numbers are expressed in a specific (localized expression pattern) way, or not.
isPartOfAggregate(Table, Table.RowIterator) - Method in class edu.mssm.crover.tables.treatments.Aggregation.Aggregate
Determines wether this source instance is part of this aggregate, or not.
isPlant() - Method in class edu.mssm.crover.tools.tissue.CuratedTissue
Whether this instance is marked as coming from plant tissue.
isRaw() - Method in class edu.mssm.crover.tools.tissue.CuratedTissue
Whether the tissue is a raw String, i.e., not yet represented in TissueCuration.
isRemoveColumn(String) - Method in class edu.mssm.crover.tables.treatments.Aggregation
 
isUnknown() - Method in class edu.mssm.crover.tools.tissue.CuratedDevStage
Whether the developmental stage is unknown.
isValid() - Method in class edu.cornell.med.icb.allen.xml.Age
Method isValid.
isValid() - Method in class edu.cornell.med.icb.allen.xml.Avgdensity
Method isValid.
isValid() - Method in class edu.cornell.med.icb.allen.xml.Avglevel
Method isValid.
isValid() - Method in class edu.cornell.med.icb.allen.xml.Entrezgeneid
Method isValid.
isValid() - Method in class edu.cornell.med.icb.allen.xml.Gene
Method isValid.
isValid() - Method in class edu.cornell.med.icb.allen.xml.GeneExpression
Method isValid.
isValid() - Method in class edu.cornell.med.icb.allen.xml.GeneExpressions
Method isValid.
isValid() - Method in class edu.cornell.med.icb.allen.xml.Geneid
Method isValid.
isValid() - Method in class edu.cornell.med.icb.allen.xml.Genes
Method isValid.
isValid() - Method in class edu.cornell.med.icb.allen.xml.ImageSeries
Method isValid.
isValid() - Method in class edu.cornell.med.icb.allen.xml.Imageseriesid
Method isValid.
isValid() - Method in class edu.cornell.med.icb.allen.xml.ImageSeriesSequence
Method isValid.
isValid() - Method in class edu.cornell.med.icb.allen.xml.Structureid
Method isValid.
isValid() - Method in class edu.cornell.med.icb.allen.xml.Templateid
Method isValid.
isValid() - Method in class edu.cornell.med.icb.allen.xml.Transcriptgi
Method isValid.
isValid() - Method in class edu.cornell.med.icb.allen.xml.Transcriptid
Method isValid.
isValid() - Method in class edu.cornell.med.icb.allen.xml.Transcriptname
Method isValid.
isValid() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.BlastOutput
Method isValid.
isValid() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.BlastOutput_iterations
Method isValid.
isValid() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.BlastOutput_iterationsType
Method isValid.
isValid() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.BlastOutput_param
Method isValid.
isValid() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.BlastOutput_paramType
Method isValid.
isValid() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Hit
Method isValid.
isValid() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Hit_hsps
Method isValid.
isValid() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Hit_hspsType
Method isValid.
isValid() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HitType
Method isValid.
isValid() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Hsp
Method isValid.
isValid() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
Method isValid.
isValid() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Iteration
Method isValid.
isValid() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Iteration_hits
Method isValid.
isValid() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Iteration_hitsType
Method isValid.
isValid() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Iteration_stat
Method isValid.
isValid() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Iteration_statType
Method isValid.
isValid() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.IterationType
Method isValid.
isValid() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Parameters
Method isValid.
isValid() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.ParametersType
Method isValid.
isValid() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Statistics
Method isValid.
isValid() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.StatisticsType
Method isValid.
isValid() - Method in class edu.mssm.crover.tools.tissue.xml.BlastHits
Method isValid.
isValid() - Method in class edu.mssm.crover.tools.tissue.xml.Hit
Method isValid.
isValid() - Method in class edu.mssm.crover.tools.tissue.xml.QuerySequence
Method isValid.
isValid() - Method in class edu.mssm.crover.tools.tissue.xml.TissueInfo
Method isValid.
isValid() - Method in class edu.mssm.crover.tools.tissue.xml.Tokey
Method isValid.
iterateGene() - Method in class edu.cornell.med.icb.allen.xml.Genes
Method iterateGene.
iterateGeneExpression() - Method in class edu.cornell.med.icb.allen.xml.GeneExpressions
Method iterateGeneExpression.
iterateHit() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Iteration_hitsType
Method iterateHit.
iterateHit() - Method in class edu.mssm.crover.tools.tissue.xml.QuerySequence
Method iterateHit.
iterateHsp() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Hit_hspsType
Method iterateHsp.
iterateImageSeries() - Method in class edu.cornell.med.icb.allen.xml.ImageSeries
Method iterateImageSeries.
iterateQuerySequence() - Method in class edu.mssm.crover.tools.tissue.xml.BlastHits
Method iterateQuerySequence.
iterateTokey() - Method in class edu.mssm.crover.tools.tissue.xml.TissueInfo
Method iterateTokey.
Iteration - Class in edu.mssm.crover.tools.blast.parsers.xml.v3
Class Iteration.
Iteration() - Constructor for class edu.mssm.crover.tools.blast.parsers.xml.v3.Iteration
 
Iteration_hits - Class in edu.mssm.crover.tools.blast.parsers.xml.v3
Class Iteration_hits.
Iteration_hits() - Constructor for class edu.mssm.crover.tools.blast.parsers.xml.v3.Iteration_hits
 
Iteration_hitsDescriptor - Class in edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors
Class Iteration_hitsDescriptor.
Iteration_hitsDescriptor() - Constructor for class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Iteration_hitsDescriptor
 
Iteration_hitsType - Class in edu.mssm.crover.tools.blast.parsers.xml.v3
Class Iteration_hitsType.
Iteration_hitsType() - Constructor for class edu.mssm.crover.tools.blast.parsers.xml.v3.Iteration_hitsType
 
Iteration_hitsTypeDescriptor - Class in edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors
Class Iteration_hitsTypeDescriptor.
Iteration_hitsTypeDescriptor() - Constructor for class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Iteration_hitsTypeDescriptor
 
Iteration_stat - Class in edu.mssm.crover.tools.blast.parsers.xml.v3
Class Iteration_stat.
Iteration_stat() - Constructor for class edu.mssm.crover.tools.blast.parsers.xml.v3.Iteration_stat
 
Iteration_statDescriptor - Class in edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors
Class Iteration_statDescriptor.
Iteration_statDescriptor() - Constructor for class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Iteration_statDescriptor
 
Iteration_statType - Class in edu.mssm.crover.tools.blast.parsers.xml.v3
Class Iteration_statType.
Iteration_statType() - Constructor for class edu.mssm.crover.tools.blast.parsers.xml.v3.Iteration_statType
 
Iteration_statTypeDescriptor - Class in edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors
Class Iteration_statTypeDescriptor.
Iteration_statTypeDescriptor() - Constructor for class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.Iteration_statTypeDescriptor
 
IterationDescriptor - Class in edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors
Class IterationDescriptor.
IterationDescriptor() - Constructor for class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.IterationDescriptor
 
IterationType - Class in edu.mssm.crover.tools.blast.parsers.xml.v3
Class IterationType.
IterationType() - Constructor for class edu.mssm.crover.tools.blast.parsers.xml.v3.IterationType
 
IterationTypeDescriptor - Class in edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors
Class IterationTypeDescriptor.
IterationTypeDescriptor() - Constructor for class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.IterationTypeDescriptor
 

J

JDBCTable - Class in edu.mssm.crover.tables
Creates and fills an ORACLE table from Mineset schema and data files.
JDBCTable() - Constructor for class edu.mssm.crover.tables.JDBCTable
 
JDBCTable(String, int, String) - Constructor for class edu.mssm.crover.tables.JDBCTable
 
jejunum - Interface in edu.mssm.crover.tools.tissue.hierarchy
 

K

k - Variable in class edu.cornell.med.icb.tissueinfo.similarity.TiSimOptions
 
KeepAllFilter - Class in edu.mssm.crover.tables
Dummy filter that keeps every row.
KeepAllFilter() - Constructor for class edu.mssm.crover.tables.KeepAllFilter
 
keepRow(Table.RowIterator) - Method in interface edu.mssm.crover.tables.Filter
Should this row be kept by the filter? The row referenced by the iterator is evaluated by this method.
keepRow(Table.RowIterator) - Method in class edu.mssm.crover.tables.KeepAllFilter
Always return true.
keepRow(Table.RowIterator) - Method in class edu.mssm.crover.tables.readers.LocusLinkFilter
 
KeepSubSetColumnFilter - Class in edu.mssm.crover.tables
Keep columns if they match a subset of pre-determined subset of column identifiers.
KeepSubSetColumnFilter(Set<String>) - Constructor for class edu.mssm.crover.tables.KeepSubSetColumnFilter
 
KendallTauScorer - Class in edu.cornell.med.icb.tissueinfo.similarity.scorers
Scores two transcript by calculating the Kendall's tau measure between their tissue expression profiles.
KendallTauScorer() - Constructor for class edu.cornell.med.icb.tissueinfo.similarity.scorers.KendallTauScorer
 
kidney - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
kupffer_cell - Interface in edu.mssm.crover.tools.tissue.hierarchy
 

L

labelColumnGroup(double, Set<String>) - Method in class edu.mssm.crover.tables.readers.GeoDataSetReader
Label a group of columns.
labelColumnIndex - Variable in class edu.mssm.crover.tables.writers.SVMLightWriter
 
lacrimal_gland - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
large_intestine - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
larynx - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
lastRow() - Method in class edu.mssm.crover.tables.ArrayTable
Returns an iterator that reference the last instance of this table.
lastRow() - Method in interface edu.mssm.crover.tables.Table
Returns an iterator that reference the last instance of this table.
LeaveOneOutMode - Class in edu.cornell.med.icb.tissueinfo.similarity
Performs leave-one-out with forward mode.
LeaveOneOutMode() - Constructor for class edu.cornell.med.icb.tissueinfo.similarity.LeaveOneOutMode
 
lens - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
leptomeninges - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
leukocyte - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
LibraryDivision - Class in edu.mssm.crover.tools.tissue
Gets the raw tissue library information for each accession number.
LibraryDivision() - Constructor for class edu.mssm.crover.tools.tissue.LibraryDivision
Empty constructor.
LibraryDivision(String[], TissueInfo) - Constructor for class edu.mssm.crover.tools.tissue.LibraryDivision
Retrieves the raw tissue library for each accession number.
LibraryDivision(String[], TissueInfo, String) - Constructor for class edu.mssm.crover.tools.tissue.LibraryDivision
Retrieves the raw tissue library for each accession number.
LinearRegression - Class in edu.cornell.med.icb.stat
This class performs a Linear Regression.
LinearRegression() - Constructor for class edu.cornell.med.icb.stat.LinearRegression
Create a linear regression calculator.
ListSearchMode - Class in edu.cornell.med.icb.tissueinfo.similarity
Scan a list of accession codes.
ListSearchMode() - Constructor for class edu.cornell.med.icb.tissueinfo.similarity.ListSearchMode
 
liver - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
load(String) - Method in class edu.cornell.med.icb.tissueinfo.similarity.GeneTranscriptRelationships
Loads the relationships from a tab delimited file.
loadTiDev(BufferedReader) - Method in class edu.mssm.crover.tools.tissue.TissueInfoMemoryImpl
Loads a file representation of TissueInfo.
loadTiSeq(BufferedReader) - Method in class edu.mssm.crover.tools.tissue.TissueInfoMemoryImpl
Loads a file representation of TissueInfo.
loadTiSeq(BufferedReader) - Method in class edu.mssm.crover.tools.tissue.TissueInfoMemoryImpl2
Loads a file representation of TissueInfo.
loadTiTo(BufferedReader) - Method in class edu.mssm.crover.tools.tissue.TissueInfoMemoryImpl
Loads a file representation of TissueInfo.
loadTiTo(BufferedReader) - Method in class edu.mssm.crover.tools.tissue.TissueInfoMemoryImpl2
Loads a file representation of TissueInfo.
LocusLinkFilter - Class in edu.mssm.crover.tables.readers
 
LocusLinkFilter() - Constructor for class edu.mssm.crover.tables.readers.LocusLinkFilter
 
LocusLinkTableReader - Class in edu.mssm.crover.tables.readers
Reads LocusLink LL.out ascii table format.
LocusLinkTableReader() - Constructor for class edu.mssm.crover.tables.readers.LocusLinkTableReader
 
LOG - Static variable in class edu.cornell.med.icb.stat.MinMaxCalculator
The logger to use.
Log10Preprocessor - Class in edu.cornell.med.icb.tissueinfo.similarity.preprocessors
Transform count values to log10(count).
Log10Preprocessor() - Constructor for class edu.cornell.med.icb.tissueinfo.similarity.preprocessors.Log10Preprocessor
 
lung - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
lymph - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
lymph_node - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
lymphatic - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
lymphocyte - Interface in edu.mssm.crover.tools.tissue.hierarchy
 

M

M - Static variable in class edu.cornell.med.icb.allen.xml.types.SexType
The instance of the M type
M_TYPE - Static variable in class edu.cornell.med.icb.allen.xml.types.SexType
The M type
macrophage - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
main(String[]) - Static method in class edu.cornell.med.icb.stat.MinMaxCalculator
 
main(String[]) - Static method in class edu.cornell.med.icb.tissueinfo.owl.ExportOntology
Runs the exporter and handles any errors.
main(String[]) - Static method in class edu.cornell.med.icb.tissueinfo.similarity.AllenGeneAtlas2Counts
 
main(String[]) - Static method in class edu.cornell.med.icb.tissueinfo.similarity.clustering.CombinePathways
 
main(String[]) - Static method in class edu.cornell.med.icb.tissueinfo.similarity.clustering.FilterClusters
 
main(String[]) - Static method in class edu.cornell.med.icb.tissueinfo.similarity.clustering.TransformClusters
 
main(String[]) - Static method in class edu.cornell.med.icb.tissueinfo.similarity.TiDumpTissueCounts
 
main(String[]) - Static method in class edu.cornell.med.icb.tissueinfo.similarity.TiSimilarity
 
main(String[]) - Static method in class edu.cornell.med.icb.tissueinfo.similarity.TiSimilarityLocalCopy
 
main(String[]) - Static method in class edu.cornell.med.icb.tissueinfo.similarity.TissueESTCountsReader
 
main(String[]) - Static method in class edu.cornell.med.icb.tools.FilterTransposeGenotypeTable
 
main(String[]) - Static method in class edu.mssm.crover.db.relational.RDB
Tests and demonstrates this class behaviour.
main(String[]) - Static method in class edu.mssm.crover.imports.FastaReader
 
main(String[]) - Static method in class edu.mssm.crover.imports.SequenceReaderFactoryImpl
Test of the factory implementation.
main(String[]) - Static method in class edu.mssm.crover.representation.Annotations
Tests various features of this class.
main(String[]) - Static method in class edu.mssm.crover.tables.AddToTable
Main method.
main(String[]) - Static method in class edu.mssm.crover.tables.JDBCTable
 
main(String[]) - Static method in class edu.mssm.crover.tables.QueryTable
 
main(String[]) - Static method in class edu.mssm.crover.tables.readers.DSSPTableReader
 
main(String[]) - Static method in class edu.mssm.crover.tables.readers.LocusLinkTableReader
 
main(String[]) - Static method in class edu.mssm.crover.tables.readers.MinesetTableReader
 
main(String[]) - Static method in class edu.mssm.crover.tables.readers.TIWebMinesetReader
 
main(String[]) - Static method in class edu.mssm.crover.tables.TableActivityWatcher
Main method.
main(String[]) - Static method in class edu.mssm.crover.tables.treatments.Aggregation
Example and test of use for this class.
main(String[]) - Static method in class edu.mssm.crover.tables.writers.InsightfulMinerTableWriter
 
main(String[]) - Static method in class edu.mssm.crover.tables.writers.MinesetTableWriter
 
main(String[]) - Static method in class edu.mssm.crover.tools.blast.BlastCommand
 
main(String[]) - Static method in class edu.mssm.crover.tools.blast.BlastContext
 
main(String[]) - Static method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Parser
 
main(String[]) - Static method in class edu.mssm.crover.tools.sumColumns
Reads a file of which contains two (tab-delimited) columns: an integer and a tissue.
main(String[]) - Static method in class edu.mssm.crover.tools.tissue.CheckLibrary
Checks whether a CuratedTissue exists for the list of raw tissues given in the input file.
main(String[]) - Static method in class edu.mssm.crover.tools.tissue.CuratedDevStage
Main method.
main(String[]) - Static method in class edu.mssm.crover.tools.tissue.CuratedTissue
Main method.
main(String[]) - Static method in class edu.mssm.crover.tools.tissue.DevStageCuration
Main method.
main(String[]) - Static method in class edu.mssm.crover.tools.tissue.DumpNullsTissueInfo
Main method.
main(String[]) - Static method in class edu.mssm.crover.tools.tissue.DumpTissueInfo
Main method.
main(String[]) - Static method in class edu.mssm.crover.tools.tissue.GetCuratedDevStage
Main method.
main(String[]) - Static method in class edu.mssm.crover.tools.tissue.GetCuratedTissue
Main method.
main(String[]) - Static method in class edu.mssm.crover.tools.tissue.GetNulls
Main method.
main(String[]) - Static method in class edu.mssm.crover.tools.tissue.Hierarchy
Main method.
main(String[]) - Static method in class edu.mssm.crover.tools.tissue.HierarchyKeywords
Main method.
main(String[]) - Static method in class edu.mssm.crover.tools.tissue.LibraryDivision
Main method.
main(String[]) - Static method in class edu.mssm.crover.tools.tissue.NullParser
Main method.
main(String[]) - Static method in class edu.mssm.crover.tools.tissue.ReplaceRawTissue
Reads a file which contains two (tab-delimited) columns: an integer and a raw tissue.
main(String[]) - Static method in class edu.mssm.crover.tools.tissue.ReportParser
Main method.
main(String[]) - Static method in class edu.mssm.crover.tools.tissue.TIimport
Main method.
main(String[]) - Static method in class edu.mssm.crover.tools.tissue.TImegablast
Main method.
main(String[]) - Static method in class edu.mssm.crover.tools.tissue.TIMegablastSql
Main method.
main(String[]) - Static method in class edu.mssm.crover.tools.tissue.TINullImport
Main method.
main(String[]) - Static method in class edu.mssm.crover.tools.tissue.TIQuery
Main method.
main(String[]) - Static method in class edu.mssm.crover.tools.tissue.TIQuerySql
Main method.
main(String[]) - Static method in class edu.mssm.crover.tools.tissue.TISearch
Main method.
main(String[]) - Static method in class edu.mssm.crover.tools.tissue.TissueCuration
Main method.
main(String[]) - Static method in class edu.mssm.crover.tools.tissue.TissueInfoJDBCImpl
Main method.
main(String[]) - Static method in class edu.mssm.crover.tools.tissue.TissueInfoMemoryImpl
Main method.
main(String[]) - Static method in class edu.mssm.crover.tools.tissue.TissueInfoMemoryImpl2
Main method.
main(String[]) - Static method in class edu.mssm.crover.tools.tissue.TissueInfoNullsJDBCImpl
Main method.
main(String[]) - Static method in class edu.mssm.crover.tools.tissue.TissueSelectionHelper
Main method.
main(String[]) - Static method in class edu.mssm.crover.tools.tissue.TissueSummary
Main method.
main(String[]) - Static method in class edu.mssm.crover.tools.tissue.TIWebJDBCImpl
Main method.
main(String[]) - Static method in class edu.mssm.crover.util.NCBISequences
 
main(String[]) - Static method in class gominer.Fisher
This is for testing and debugging purposes.
makeId(String) - Method in class edu.mssm.crover.tables.JDBCTable
 
makeId(String) - Method in class edu.mssm.crover.tools.tissue.TIWebJDBCImpl
Creates a non-weird character-containing column name.
makeRawTissueText(String) - Method in class edu.mssm.crover.tools.tissue.CuratedTissue
Creates the English language representation of the tissue which has already been curated.
MALE - Static variable in class edu.cornell.med.icb.allen.xml.types.SexType
The instance of the male type
MALE_TYPE - Static variable in class edu.cornell.med.icb.allen.xml.types.SexType
The male type
mammary_gland - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
marshal(Writer) - Method in class edu.cornell.med.icb.allen.xml.Age
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.allen.xml.Age
 
marshal(Writer) - Method in class edu.cornell.med.icb.allen.xml.Avgdensity
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.allen.xml.Avgdensity
 
marshal(Writer) - Method in class edu.cornell.med.icb.allen.xml.Avglevel
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.allen.xml.Avglevel
 
marshal(Writer) - Method in class edu.cornell.med.icb.allen.xml.Entrezgeneid
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.allen.xml.Entrezgeneid
 
marshal(Writer) - Method in class edu.cornell.med.icb.allen.xml.Gene
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.allen.xml.Gene
 
marshal(Writer) - Method in class edu.cornell.med.icb.allen.xml.GeneExpression
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.allen.xml.GeneExpression
 
marshal(Writer) - Method in class edu.cornell.med.icb.allen.xml.GeneExpressions
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.allen.xml.GeneExpressions
 
marshal(Writer) - Method in class edu.cornell.med.icb.allen.xml.Geneid
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.allen.xml.Geneid
 
marshal(Writer) - Method in class edu.cornell.med.icb.allen.xml.Genes
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.allen.xml.Genes
 
marshal(Writer) - Method in class edu.cornell.med.icb.allen.xml.ImageSeries
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.allen.xml.ImageSeries
 
marshal(Writer) - Method in class edu.cornell.med.icb.allen.xml.Imageseriesid
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.allen.xml.Imageseriesid
 
marshal(Writer) - Method in class edu.cornell.med.icb.allen.xml.ImageSeriesSequence
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.allen.xml.ImageSeriesSequence
 
marshal(Writer) - Method in class edu.cornell.med.icb.allen.xml.Structureid
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.allen.xml.Structureid
 
marshal(Writer) - Method in class edu.cornell.med.icb.allen.xml.Templateid
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.allen.xml.Templateid
 
marshal(Writer) - Method in class edu.cornell.med.icb.allen.xml.Transcriptgi
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.allen.xml.Transcriptgi
 
marshal(Writer) - Method in class edu.cornell.med.icb.allen.xml.Transcriptid
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.allen.xml.Transcriptid
 
marshal(Writer) - Method in class edu.cornell.med.icb.allen.xml.Transcriptname
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.allen.xml.Transcriptname
 
marshal(Writer) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.BlastOutput
 
marshal(ContentHandler) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.BlastOutput
 
marshal(Writer) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.BlastOutput_iterations
 
marshal(ContentHandler) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.BlastOutput_iterations
 
marshal(Writer) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.BlastOutput_iterationsType
 
marshal(ContentHandler) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.BlastOutput_iterationsType
 
marshal(Writer) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.BlastOutput_param
 
marshal(ContentHandler) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.BlastOutput_param
 
marshal(Writer) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.BlastOutput_paramType
 
marshal(ContentHandler) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.BlastOutput_paramType
 
marshal(Writer) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Hit
 
marshal(ContentHandler) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Hit
 
marshal(Writer) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Hit_hsps
 
marshal(ContentHandler) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Hit_hsps
 
marshal(Writer) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Hit_hspsType
 
marshal(ContentHandler) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Hit_hspsType
 
marshal(Writer) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HitType
 
marshal(ContentHandler) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HitType
 
marshal(Writer) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Hsp
 
marshal(ContentHandler) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Hsp
 
marshal(Writer) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
 
marshal(ContentHandler) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HspType
 
marshal(Writer) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Iteration
 
marshal(ContentHandler) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Iteration
 
marshal(Writer) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Iteration_hits
 
marshal(ContentHandler) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Iteration_hits
 
marshal(Writer) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Iteration_hitsType
 
marshal(ContentHandler) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Iteration_hitsType
 
marshal(Writer) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Iteration_stat
 
marshal(ContentHandler) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Iteration_stat
 
marshal(Writer) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Iteration_statType
 
marshal(ContentHandler) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Iteration_statType
 
marshal(Writer) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.IterationType
 
marshal(ContentHandler) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.IterationType
 
marshal(Writer) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Parameters
 
marshal(ContentHandler) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Parameters
 
marshal(Writer) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.ParametersType
 
marshal(ContentHandler) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.ParametersType
 
marshal(Writer) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Statistics
 
marshal(ContentHandler) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Statistics
 
marshal(Writer) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.StatisticsType
 
marshal(ContentHandler) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.StatisticsType
 
marshal(Writer) - Method in class edu.mssm.crover.tools.tissue.xml.BlastHits
 
marshal(ContentHandler) - Method in class edu.mssm.crover.tools.tissue.xml.BlastHits
 
marshal(Writer) - Method in class edu.mssm.crover.tools.tissue.xml.Hit
 
marshal(ContentHandler) - Method in class edu.mssm.crover.tools.tissue.xml.Hit
 
marshal(Writer) - Method in class edu.mssm.crover.tools.tissue.xml.QuerySequence
 
marshal(ContentHandler) - Method in class edu.mssm.crover.tools.tissue.xml.QuerySequence
 
marshal(Writer) - Method in class edu.mssm.crover.tools.tissue.xml.TissueInfo
 
marshal(ContentHandler) - Method in class edu.mssm.crover.tools.tissue.xml.TissueInfo
 
marshal(Writer) - Method in class edu.mssm.crover.tools.tissue.xml.Tokey
 
marshal(ContentHandler) - Method in class edu.mssm.crover.tools.tissue.xml.Tokey
 
matchExtension(String) - Method in class edu.mssm.crover.imports.FastaReaderType
This method should be in a superclass common to all the ReaderType implementations.
matchExtension(String) - Method in interface edu.mssm.crover.imports.ReaderType
Returns true when the ReaderType can handle the given extension.
matching(IntSet) - Method in class edu.cornell.med.icb.tissueinfo.annotations.ProjectionRule
 
MatthewsCorrelationCalculator - Class in edu.cornell.med.icb.stat
Calculates the Matthews Correlation coefficient.
MatthewsCorrelationCalculator() - Constructor for class edu.cornell.med.icb.stat.MatthewsCorrelationCalculator
 
max() - Method in class edu.cornell.med.icb.stat.ZScoreCalculator
 
MaxNormalizedConfidenceScorer - Class in edu.cornell.med.icb.tissueinfo.similarity.scorers
Confidence scorer normalized with MaxNormalizedScorer.
MaxNormalizedConfidenceScorer() - Constructor for class edu.cornell.med.icb.tissueinfo.similarity.scorers.MaxNormalizedConfidenceScorer
 
MaxNormalizerScorer - Class in edu.cornell.med.icb.tissueinfo.similarity.scorers
A scorer that normalizes the score produced by another scorer given the maximum score that could be obtained against each of the scored transcripts.
MaxNormalizerScorer(ExpressionProfileSimilarityScorer) - Constructor for class edu.cornell.med.icb.tissueinfo.similarity.scorers.MaxNormalizerScorer
 
maxSequenceIndex - Variable in class edu.cornell.med.icb.tissueinfo.similarity.TiSimOptions
 
maxSize - Variable in class edu.cornell.med.icb.tissueinfo.similarity.ScoredTranscriptBoundedSizeQueue
The maximum number of documents to be ranked.
mbToTiac(String, String, String, double, double, int, boolean, boolean) - Method in class edu.mssm.crover.tools.tissue.TImegablast
Creates a tiac file from the megablast output file.
mbToTiac(String, String, String, double, double, int, boolean, boolean, boolean) - Method in class edu.mssm.crover.tools.tissue.TImegablast
Creates a tiac file from the megablast output file.
mbToTiac(String, String, boolean, double, double, int, boolean, boolean) - Method in class edu.mssm.crover.tools.tissue.TIMegablastSql
Creates a tiac file from the megablast output file.
mbToTiac(String, String, boolean, double, double, int, boolean, boolean, boolean) - Method in class edu.mssm.crover.tools.tissue.TIMegablastSql
Creates a tiac file from the megablast output file.
mean() - Method in class edu.cornell.med.icb.stat.ZScoreCalculator
 
medulla_oblongata - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
MegablastHSIterator - Class in edu.mssm.crover.tools.blast
Iterates through a megablast -D 3 output file, returns HitSummaries.
MegablastHSIterator(File) - Constructor for class edu.mssm.crover.tools.blast.MegablastHSIterator
 
MegablastHSIterator(Reader) - Constructor for class edu.mssm.crover.tools.blast.MegablastHSIterator
 
meninges - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
mesencephalon - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
mesoderm - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
metencephalon - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
microglia - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
min() - Method in class edu.cornell.med.icb.stat.ZScoreCalculator
 
MinesetTableReader - Class in edu.mssm.crover.tables.readers
Reads SGI's MineSet ASCII table format.
MinesetTableReader() - Constructor for class edu.mssm.crover.tables.readers.MinesetTableReader
 
MinesetTableWriter - Class in edu.mssm.crover.tables.writers
Writes the schema and data from a table in a Mineset like format.
MinesetTableWriter() - Constructor for class edu.mssm.crover.tables.writers.MinesetTableWriter
 
minesetType(Class, StringBuffer) - Static method in class edu.mssm.crover.tables.writers.InsightfulMinerTableWriter
 
minesetType(Class, StringBuffer) - Static method in class edu.mssm.crover.tables.writers.MinesetTableWriter
 
MinMaxCalculator - Class in edu.cornell.med.icb.stat
Calculates the Min/Max statistics for a feature.
MinMaxCalculator() - Constructor for class edu.cornell.med.icb.stat.MinMaxCalculator
 
monocyte - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
mostExpressedIn() - Method in class edu.mssm.crover.tools.tissue.QueryTissueSummary
Returns the tissue in which the EST is most expressed.
mostExpressedIn() - Method in class edu.mssm.crover.tools.tissue.TissueSummary
Returns the tissue in which the EST is most expressed.
mostExpressedInDevStage() - Method in class edu.mssm.crover.tools.tissue.QueryTissueSummary
Returns the developmental stage in which the EST is most expressed.
mostExpressedInDevStage() - Method in class edu.mssm.crover.tools.tissue.TissueSummary
Returns the developmental stage in which the EST is most expressed.
motor_neuron - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
MOUSE - Static variable in class edu.cornell.med.icb.allen.xml.types.OrganismType
The instance of the Mouse type
MOUSE_TYPE - Static variable in class edu.cornell.med.icb.allen.xml.types.OrganismType
The Mouse type
mouth - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
MultiplePartFileIterator - Class in edu.mssm.crover.util
Divides a multiple XML BlastOutput into several single BlastResults.
MultiplePartFileIterator(File) - Constructor for class edu.mssm.crover.util.MultiplePartFileIterator
 
MultiplePartFileIterator(Reader) - Constructor for class edu.mssm.crover.util.MultiplePartFileIterator
 
muscle - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
Mutation_Annotation - Class in edu.mssm.crover.representation
Annotates ponctual mutations.
Mutation_Annotation() - Constructor for class edu.mssm.crover.representation.Mutation_Annotation
 
myelencephalon - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
myenteric_plexus - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
myometrium - Interface in edu.mssm.crover.tools.tissue.hierarchy
 

N

NCBISequences - Class in edu.mssm.crover.util
Accesses NCBI formatted sequence databases.
NCBISequences() - Constructor for class edu.mssm.crover.util.NCBISequences
 
neocortex - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
neostriatum - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
nervous_system - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
neural_retina - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
neuron - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
neutrophil - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
next() - Method in class edu.cornell.med.icb.tissueinfo.annotations.ArraysIterator
 
next() - Method in class edu.mssm.crover.tables.ArrayTable.RowIterator
Advances the iterator to the next row of the table.
next() - Method in interface edu.mssm.crover.tables.Table.RowIterator
Advances the iterator to the next row of the table.
next() - Method in class edu.mssm.crover.tools.blast.MegablastHSIterator
Returns the next HitSummary in the interation.
next() - Method in class edu.mssm.crover.tools.blast.XMLBlastHSIterator
Returns the next HitSummary in the interation.
next() - Method in class edu.mssm.crover.util.MultiplePartFileIterator
Returns the next part of the file, from (and including) the split prefix, up to the next split prefix.
next_valid_index - Variable in class edu.mssm.crover.tables.ArrayTable.ColumnDescription
 
nextToken() - Method in class edu.mssm.crover.tables.readers.TabTokenizer
Returns the next token.
nonpigmented_ciliary_epithelium - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
normalize(int[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TissueESTCountsReader
 
NormalizedBinaryScorer - Class in edu.cornell.med.icb.tissueinfo.similarity.scorers
Binary scorer normalized with NormalizedScorer.
NormalizedBinaryScorer() - Constructor for class edu.cornell.med.icb.tissueinfo.similarity.scorers.NormalizedBinaryScorer
 
NormalizedConfidenceScorer - Class in edu.cornell.med.icb.tissueinfo.similarity.scorers
Confidence scorer normalized with NormalizedScorer.
NormalizedConfidenceScorer() - Constructor for class edu.cornell.med.icb.tissueinfo.similarity.scorers.NormalizedConfidenceScorer
 
NormalizeRowProcessor - Class in edu.mssm.crover.tables
 
NormalizeRowProcessor(int[]) - Constructor for class edu.mssm.crover.tables.NormalizeRowProcessor
 
NormalizeRowProcessor(Table, String) - Constructor for class edu.mssm.crover.tables.NormalizeRowProcessor
 
NormalizerScorer - Class in edu.cornell.med.icb.tissueinfo.similarity.scorers
A scorer that normalizes the score produced by another scorer given the number of EST counts that are not zero in the query and target.
NormalizerScorer(ExpressionProfileSimilarityScorer) - Constructor for class edu.cornell.med.icb.tissueinfo.similarity.scorers.NormalizerScorer
 
nose - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
NoSuchResidue - Exception in edu.mssm.crover.representation
 
NoSuchResidue(char) - Constructor for exception edu.mssm.crover.representation.NoSuchResidue
 
notHelical(Table, Table.RowIterator, int) - Static method in class edu.mssm.crover.tables.treatments.CompositionTableTreatment
 
nucleus_accumbens - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
NullParser - Class in edu.mssm.crover.tools.tissue
Parses information for entries marked as null by DbestParser and passed through the Textractor program, and curates the tissue information.
NullParser() - Constructor for class edu.mssm.crover.tools.tissue.NullParser
 
NullTissueDetails - Class in edu.mssm.crover.tools.tissue
Storage class for details associated with ESTs which were originally marked as null, since we could not parse a tissue from their dbEST entry.
NullTissueDetails() - Constructor for class edu.mssm.crover.tools.tissue.NullTissueDetails
 
numberOfGenesWithTranscripts - Variable in class edu.cornell.med.icb.tissueinfo.similarity.TiSimOptions
The number of genes with non-zero count transcripts.
numCancerInTissue(String, boolean) - Method in class edu.mssm.crover.tools.tissue.TissueSummary
Counts the number of times the query matches an EST that comes from a specified tumor tissue.
numExpressedIn(String) - Method in class edu.mssm.crover.tools.tissue.QueryTissueSummary
Returns the number of times an EST is found expressed in a tissue.
numExpressedIn(String) - Method in class edu.mssm.crover.tools.tissue.TissueSummary
Returns the number of times an EST is found expressed in a tissue.
numExpressedInDevStage(String) - Method in class edu.mssm.crover.tools.tissue.QueryTissueSummary
Returns the number of times an EST is found expressed in a tissue.
numExpressedInDevStage(String) - Method in class edu.mssm.crover.tools.tissue.TissueSummary
Returns the number of times an EST is found expressed in a tissue.
numExpressedInDevStageAndTissue(String[], String) - Method in class edu.mssm.crover.tools.tissue.TissueSummary
Returns the number of times a query sequence is found expressed in both a developmental stage and a tissue, concurrently.
numExpressedInRawTissue(String) - Method in class edu.mssm.crover.tools.tissue.TissueSummary
Returns the number of times an EST is found expressed in a raw tissue.
numNegative - Variable in class edu.mssm.crover.tables.writers.SVMLightWriter
 
numPlant() - Method in class edu.mssm.crover.tools.tissue.QueryTissueSummary
Calculates the number of ESTs associated with the gene that are expressed in plant tissue.
numPlant() - Method in class edu.mssm.crover.tools.tissue.TissueSummary
Calculates the number of ESTs associated with the gene that are expressed in plant tissue.
numPositive - Variable in class edu.mssm.crover.tables.writers.SVMLightWriter
 

O

observe(double) - Method in class edu.cornell.med.icb.stat.ZScoreCalculator
 
occipital_lobe - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
ocular_ciliary_epithelium - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
oculomotor_nerve - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
olfactory_nerve - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
oligodendrocyte - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
oneTail(int, int, int, int) - Method in class gominer.Fisher
Calculates the 2-tailed gominer.Fisher p value, using the counts that are expected to be readily available in the system
onlyExpressedIn(String) - Method in class edu.mssm.crover.tools.tissue.QueryTissueSummary
Determines whether the ESTs associated with the given accession numbers are expressed ONLY in the specified tissue.
onlyExpressedIn(String) - Method in class edu.mssm.crover.tools.tissue.TissueSummary
Determines whether the ESTs associated with the given accession numbers are expressed ONLY in the specified tissue.
onlyExpressedInDevStage(String) - Method in class edu.mssm.crover.tools.tissue.QueryTissueSummary
Determines whether the ESTs associated with the given accession numbers are expressed ONLY in the specified developmental stage.
onlyExpressedInDevStage(String) - Method in class edu.mssm.crover.tools.tissue.TissueSummary
Determines whether the ESTs associated with the given accession numbers are expressed ONLY in the specified developmental stage.
optic_nerve - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
optimalThreshold - Variable in class edu.cornell.med.icb.stat.PredictionStatisticCalculator
The value of the threshold where the optimal statistic is obtained.
OptionHandler - Interface in edu.mssm.crover.tools.tissue.plugins
A process.
OrganismType - Class in edu.cornell.med.icb.allen.xml.types
Class OrganismType.
OrganismTypeDescriptor - Class in edu.cornell.med.icb.allen.xml.types.descriptors
Class OrganismTypeDescriptor.
OrganismTypeDescriptor() - Constructor for class edu.cornell.med.icb.allen.xml.types.descriptors.OrganismTypeDescriptor
 
origin - Variable in class edu.mssm.crover.representation.Annotation
 
Origin - Class in edu.mssm.crover.representation
Default implementation of BiologicalOrigin.
Origin() - Constructor for class edu.mssm.crover.representation.Origin
 
origin - Variable in exception edu.mssm.crover.tables.treatments.TreatmentInterrupted
 
OriginFactory - Class in edu.mssm.crover.representation
Factory to return origins of a specific kind.
OriginFactory() - Constructor for class edu.mssm.crover.representation.OriginFactory
 
osteoclast - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
output - Variable in class edu.cornell.med.icb.tissueinfo.similarity.TiSimOptions
 
OUTPUT_PAIRWISE - Static variable in class edu.mssm.crover.tools.blast.BlastCommand
 
OUTPUT_XML - Static variable in class edu.mssm.crover.tools.blast.BlastCommand
Selects the XML Blast output.
ovarian_follicle - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
ovary - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
oviduct - Interface in edu.mssm.crover.tools.tissue.hierarchy
 

P

PackageInspector - Class in edu.cornell.med.icb.tissueinfo.owl
Retrieves a list of classes from a package at run time.
PackageInspector(String) - Constructor for class edu.cornell.med.icb.tissueinfo.owl.PackageInspector
Creates a new PackageInspector and sets the package name.
pairs - Variable in class edu.cornell.med.icb.tissueinfo.similarity.TiSimOptions
 
PairScoreOnlyMode - Class in edu.cornell.med.icb.tissueinfo.similarity
 
PairScoreOnlyMode() - Constructor for class edu.cornell.med.icb.tissueinfo.similarity.PairScoreOnlyMode
 
PairSearchMode - Class in edu.cornell.med.icb.tissueinfo.similarity
 
PairSearchMode() - Constructor for class edu.cornell.med.icb.tissueinfo.similarity.PairSearchMode
 
paleostriatum - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
pancreas - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
pancreatic_islets - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
parameter - Variable in class edu.mssm.crover.tables.treatments.Aggregation
 
parameter - Variable in class edu.mssm.crover.tables.treatments.TableTreatment
Stores the optional treatment parameter.
Parameters - Class in edu.mssm.crover.tools.blast.parsers.xml.v3
Class Parameters.
Parameters() - Constructor for class edu.mssm.crover.tools.blast.parsers.xml.v3.Parameters
 
ParametersDescriptor - Class in edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors
Class ParametersDescriptor.
ParametersDescriptor() - Constructor for class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.ParametersDescriptor
 
ParametersType - Class in edu.mssm.crover.tools.blast.parsers.xml.v3
Class ParametersType.
ParametersType() - Constructor for class edu.mssm.crover.tools.blast.parsers.xml.v3.ParametersType
 
ParametersTypeDescriptor - Class in edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors
Class ParametersTypeDescriptor.
ParametersTypeDescriptor() - Constructor for class edu.mssm.crover.tools.blast.parsers.xml.v3.descriptors.ParametersTypeDescriptor
 
parasympathetic_NS - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
parathyroid - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
parietal_lobe - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
parotid - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
parse(Reader) - Method in class edu.cornell.med.icb.tissueinfo.annotations.AnnotationParser
Parse an extended TissueInfo annotation file.
parse(String) - Method in class edu.cornell.med.icb.tissueinfo.similarity.clustering.ClusterFileParser
 
parse(File) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Parser
Parses BLAST XML output.
parse(BufferedReader, TissueInfo) - Method in class edu.mssm.crover.tools.tissue.DbestParser
Parses GenBank dbEST gzipped files.
parse(BufferedReader, TissueInfoNullsJDBCImpl) - Method in class edu.mssm.crover.tools.tissue.NullParser
Parses GenBank dbEST gzipped files.
parse(File, File, String) - Method in class edu.mssm.crover.tools.tissue.ReportParser
Find the start positions of sections delimited by prefix in the report file and writes those start positions to a file.
parseAppend(int, String) - Method in class edu.mssm.crover.tables.ArrayTable
Append a value passed as a String.
parseAppend(int, String) - Method in interface edu.mssm.crover.tables.Table
Append a value passed as a String.
parseColumnHeader(Table, String, String, Class, int) - Static method in class edu.mssm.crover.tables.readers.MinesetTableReader
 
parseColumnHeader(Table, String, String, Class, int) - Static method in class edu.mssm.crover.tables.readers.TIWebMinesetReader
 
parseLine(Table, String, int, int[]) - Static method in class edu.mssm.crover.tables.readers.DSSPTableReader
 
Parser - Class in edu.mssm.crover.tools.blast.parsers.xml.v3
 
Parser() - Constructor for class edu.mssm.crover.tools.blast.parsers.xml.v3.Parser
 
parseString(String) - Method in class edu.mssm.crover.tools.tissue.TissueSelectionHelper
Converts the raw tissue to an array of tissue keywords that describe that raw tissue.
PearsonScorer - Class in edu.cornell.med.icb.tissueinfo.similarity.scorers
Scores two transcript by calculating the Pearson correlation coefficient between their tissue expression profiles.
PearsonScorer() - Constructor for class edu.cornell.med.icb.tissueinfo.similarity.scorers.PearsonScorer
 
penis - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
percentCancer() - Method in class edu.mssm.crover.tools.tissue.QueryTissueSummary
Calculates the percentage of ESTs associated with the gene that are expressed in tumor tissue.
percentCancer() - Method in class edu.mssm.crover.tools.tissue.TissueSummary
Calculates the percentage of ESTs associated with the gene that are expressed in tumor tissue.
peripheral_NS - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
peritoneal_macrophage - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
peritoneum - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
permutateColumns(String, int) - Method in class edu.mssm.crover.tables.ArrayTable
Permutate the position of columns.
permutateColumns(String, int) - Method in interface edu.mssm.crover.tables.Table
Permutate the position of columns.
peroneal_nerve - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
peyers_patch - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
pharyngeal_gland - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
pharynx - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
pheromone_gland - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
pia_mater - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
pigmented_ciliary_epithelium - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
pigmented_retinal_epithelium - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
pineal_gland - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
pituitary - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
placenta - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
PlaneType - Class in edu.cornell.med.icb.allen.xml.types
Class PlaneType.
PlaneTypeDescriptor - Class in edu.cornell.med.icb.allen.xml.types.descriptors
Class PlaneTypeDescriptor.
PlaneTypeDescriptor() - Constructor for class edu.cornell.med.icb.allen.xml.types.descriptors.PlaneTypeDescriptor
 
plasma - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
platelet - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
pons - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
posterior_pituitary - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
postProcessData(ArrayTable, boolean) - Method in interface edu.mssm.crover.tools.tissue.plugins.OptionHandler
Processes the data.
PrecalculateConfidence - Class in edu.cornell.med.icb.tissueinfo.similarity.preprocessors
Replaces counts with confidence scores.
PrecalculateConfidence() - Constructor for class edu.cornell.med.icb.tissueinfo.similarity.preprocessors.PrecalculateConfidence
 
PredictionStatisticCalculator - Class in edu.cornell.med.icb.stat
 
PredictionStatisticCalculator() - Constructor for class edu.cornell.med.icb.stat.PredictionStatisticCalculator
 
predictivePotential(double) - Method in class edu.cornell.med.icb.stat.PredictionStatisticCalculator
Return a value that is larger when the statistics indicates a larger predictive potential.
preProcessorChain - Variable in class edu.cornell.med.icb.tissueinfo.similarity.TiSimOptions
 
prepuce - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
preputial_gland - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
printHelp() - Static method in class edu.mssm.crover.tables.AddToTable
Prints the help menu.
printHelpFile() - Static method in class edu.mssm.crover.tools.tissue.TISearch
Prints the help file.
printout(String) - Method in class edu.mssm.crover.tools.tissue.GetCuratedDevStage
Prints the String to the writer or stdout.
printout(String) - Method in class edu.mssm.crover.tools.tissue.GetCuratedTissue
Prints the String to the writer or stdout.
printQueryTargetPairScore(MutableString, MutableString, double, int, int, PrintWriter, int, int) - Static method in class edu.cornell.med.icb.tissueinfo.similarity.TiSimilarity
 
process(TiSimOptions) - Method in class edu.cornell.med.icb.tissueinfo.similarity.AnnotateClustersMode
 
process(TiSimOptions) - Method in class edu.cornell.med.icb.tissueinfo.similarity.BackwardMode
 
process(TiSimOptions) - Method in class edu.cornell.med.icb.tissueinfo.similarity.ClusterMode
 
process(TiSimOptions) - Method in class edu.cornell.med.icb.tissueinfo.similarity.CrossValidationMode
 
process(TiSimOptions) - Method in class edu.cornell.med.icb.tissueinfo.similarity.ForwardMode
 
process(TiSimOptions) - Method in class edu.cornell.med.icb.tissueinfo.similarity.GroupScoringMode
 
process(TiSimOptions) - Method in class edu.cornell.med.icb.tissueinfo.similarity.LeaveOneOutMode
 
process(TiSimOptions) - Method in class edu.cornell.med.icb.tissueinfo.similarity.ListSearchMode
 
process(TiSimOptions) - Method in class edu.cornell.med.icb.tissueinfo.similarity.PairSearchMode
 
process(int[]) - Method in interface edu.cornell.med.icb.tissueinfo.similarity.preprocessors.CountPreprocessor
Process the counts in place.
process(int[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.preprocessors.Log10Preprocessor
 
process(int[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.preprocessors.PrecalculateConfidence
 
process(int[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.preprocessors.ShuffleCounts
 
process(TiSimOptions) - Method in class edu.cornell.med.icb.tissueinfo.similarity.SimpleSearchMode
 
process(TiSimOptions) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TallyScoreSearchMode
 
process(TiSimOptions) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TiSimMode
Process with options.
process(TiSimOptions) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TranscriptListMode
 
process(Object) - Method in class edu.mssm.crover.tables.treatments.TableTreatment
In place processing.
process(Table) - Method in class edu.mssm.crover.tables.treatments.TableTreatment
Go through each instance of the table and perform an operation the nature of which is left to a subclass.
process(Object, Object) - Method in class edu.mssm.crover.tables.treatments.TableTreatment
Go through each instance of the table and perform an operation the nature of which is left to a subclass.
process(Object) - Method in interface edu.mssm.crover.tables.treatments.Treatment
In place processing.
processRow(Table, Table.RowIterator) - Method in class edu.mssm.crover.tables.NormalizeRowProcessor
 
processRow(Table, Table.RowIterator) - Method in class edu.mssm.crover.tables.RowFloorAdjustmentCalculator
 
processRow(Table, Table.RowIterator) - Method in class edu.mssm.crover.tables.RowOffsetCalculator
 
processRow(Table, Table.RowIterator) - Method in class edu.mssm.crover.tables.RowProcessor
 
processRow(Table, Table.RowIterator) - Method in class edu.mssm.crover.tables.RowSumCalculator
 
processRow(Table, Table.RowIterator) - Method in class edu.mssm.crover.tables.ScalingRowProcessor
 
processRow(Table, Table.RowIterator) - Method in class edu.mssm.crover.tables.SumOfSquaresCalculatorRowProcessor
 
processRow(Table, Table.RowIterator) - Method in class edu.mssm.crover.tables.writers.SVMLightWriter
 
processRows(RowProcessor) - Method in class edu.mssm.crover.tables.ArrayTable
Process each row of this table with user-defineable operation.
processRows(RowProcessor) - Method in interface edu.mssm.crover.tables.Table
 
project(MutableString, IntSet) - Method in class edu.cornell.med.icb.tissueinfo.annotations.Projection
Returns the indices, in the destination annotation subspace, where this sample projects.
project(int, IntSet) - Method in class edu.cornell.med.icb.tissueinfo.annotations.Projection
 
Projection - Class in edu.cornell.med.icb.tissueinfo.annotations
Project samples into a subspace of the annotation space.
Projection(AnnotationSet) - Constructor for class edu.cornell.med.icb.tissueinfo.annotations.Projection
 
ProjectionRule - Class in edu.cornell.med.icb.tissueinfo.annotations
 
ProjectionRule() - Constructor for class edu.cornell.med.icb.tissueinfo.annotations.ProjectionRule
 
PROPERTY_BASENAME - Static variable in class edu.cornell.med.icb.tissueinfo.similarity.TissueESTCountsHelper
 
PROPERTY_GLOBAL_BITS_FOR_COUNTS - Static variable in class edu.cornell.med.icb.tissueinfo.similarity.TissueESTCountsHelper
 
PROPERTY_QUERY_SEQUENCES_COUNT - Static variable in class edu.cornell.med.icb.tissueinfo.similarity.TissueESTCountsHelper
 
prosencephalon - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
prostate - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
putamen - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
pylorus - Interface in edu.mssm.crover.tools.tissue.hierarchy
 

Q

query(String) - Method in class edu.mssm.crover.tools.tissue.HierarchyKeywords
Checks whether the hashtable of tissues contains the query keyword.
queryAccessionCodeIndices - Variable in class edu.cornell.med.icb.tissueinfo.similarity.TiSimOptions
 
queryAccessionCodes - Variable in class edu.cornell.med.icb.tissueinfo.similarity.TiSimOptions
 
QuerySequence - Class in edu.mssm.crover.tools.tissue.xml
Class QuerySequence.
QuerySequence() - Constructor for class edu.mssm.crover.tools.tissue.xml.QuerySequence
 
QuerySequenceDescriptor - Class in edu.mssm.crover.tools.tissue.xml.descriptors
Class QuerySequenceDescriptor.
QuerySequenceDescriptor() - Constructor for class edu.mssm.crover.tools.tissue.xml.descriptors.QuerySequenceDescriptor
 
QueryTable - Class in edu.mssm.crover.tables
Passes various requests(queries) to a table, using SQL queries.
QueryTable() - Constructor for class edu.mssm.crover.tables.QueryTable
 
QueryTissueSummary - Class in edu.mssm.crover.tools.tissue
Processes the information about a query sequence and calculates a number of attributes for that query sequence.
QueryTissueSummary(String, TissueInfoJDBCImpl) - Constructor for class edu.mssm.crover.tools.tissue.QueryTissueSummary
Creates a CuratedTissue and a CuratedDevStage for each accession number.
QueryTissueSummary(String, TissueInfoJDBCImpl, String[]) - Constructor for class edu.mssm.crover.tools.tissue.QueryTissueSummary
Creates a CuratedTissue and a CuratedDevStage for each accession number which comes from the required organism(s).
queue - Variable in class edu.cornell.med.icb.tissueinfo.similarity.ScoredTranscriptBoundedSizeQueue
The underlying queue.
queueToList(ScoredTranscriptBoundedSizeQueue) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TiSimilaritySearchEngine
 
queueToRankedList(ScoredTranscriptBoundedSizeQueue) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TiSimilaritySearchEngine
Returns a list of results where each item has a rank.
queueToRankedListIgnoreQueryItems(ScoredTranscriptBoundedSizeQueue, IntSet) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TiSimilaritySearchEngine
Returns a list of results where each item has a rank.

R

randomAccess() - Method in class edu.cornell.med.icb.tissueinfo.similarity.TissueESTCountsReader
Prepare this instance for random access.
randomEngine - Variable in class edu.mssm.crover.tables.writers.SVMLightWriter
 
RandomSample - Class in edu.mssm.crover.tables.treatments
 
RandomSample(long) - Constructor for class edu.mssm.crover.tables.treatments.RandomSample
 
randomSeed - Variable in class edu.cornell.med.icb.tissueinfo.similarity.TiSimOptions
 
rank - Variable in class edu.cornell.med.icb.tissueinfo.similarity.TranscriptScore
 
rankByScore - Variable in class edu.cornell.med.icb.tissueinfo.similarity.TiSimOptions
Rank by sum of score if true, by sum of inverse rank if false.
rankFusionWithSpecificityRank - Variable in class edu.cornell.med.icb.tissueinfo.similarity.TiSimOptions
 
rawCounts(int[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TissueESTCountsReader
 
RawEstCountScorer - Class in edu.cornell.med.icb.tissueinfo.similarity.scorers
Implements the scheme described in http://icb.med.cornell.edu/wiki/uploads/math/c/2/8/c280e1c6b3550fcff8e2dc01676f923a.png, but without transforming raw counts into confidence values.
RawEstCountScorer() - Constructor for class edu.cornell.med.icb.tissueinfo.similarity.scorers.RawEstCountScorer
 
RDB - Class in edu.mssm.crover.db.relational
Relational Database access point.
read(Reader) - Method in class edu.mssm.crover.tables.readers.AffymetrixTxtFormatReader
 
read(Reader) - Method in class edu.mssm.crover.tables.readers.CologneReader
Reads the data from the file into a Table.
read(Reader) - Method in class edu.mssm.crover.tables.readers.ColumbiaTmmReader
Reads the data from the file into a Table.
read(Reader) - Method in class edu.mssm.crover.tables.readers.CSVReader
Reads the data from the file into a Table.
read(Reader, InputStream) - Static method in class edu.mssm.crover.tables.readers.DSSPTableReader
 
read(Reader, Reader) - Static method in class edu.mssm.crover.tables.readers.DSSPTableReader
 
read(Reader) - Method in class edu.mssm.crover.tables.readers.GeoDataSetReader
 
read(Reader) - Method in class edu.mssm.crover.tables.readers.GeoPlatformFileReader
 
read(Reader) - Method in class edu.mssm.crover.tables.readers.IconixReader
Reads the data from the file into a Table.
read(InputStream) - Method in class edu.mssm.crover.tables.readers.LocusLinkTableReader
 
read(Reader) - Method in class edu.mssm.crover.tables.readers.LocusLinkTableReader
 
read(Reader, Filter) - Static method in class edu.mssm.crover.tables.readers.LocusLinkTableReader
 
read(Reader, InputStream) - Static method in class edu.mssm.crover.tables.readers.MinesetTableReader
 
read(Reader, Reader) - Static method in class edu.mssm.crover.tables.readers.MinesetTableReader
 
read(Reader) - Method in class edu.mssm.crover.tables.readers.SVMLightReader
 
read(Reader) - Method in interface edu.mssm.crover.tables.readers.TableReader
Parses tabular data and returns the appropriate Table.
read(Reader, InputStream) - Static method in class edu.mssm.crover.tables.readers.TIWebMinesetReader
 
read(Reader, Reader) - Static method in class edu.mssm.crover.tables.readers.TIWebMinesetReader
 
read(Reader) - Method in class edu.mssm.crover.tables.readers.WhiteheadResReader
 
read(InputStream) - Method in class edu.mssm.crover.tools.blast.BlastCommand
 
read(File, long, long) - Method in class edu.mssm.crover.tools.tissue.ReportParser
Returns a section from the file from the given start point to the given end point.
readCounts(String, int[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TissueESTCountsReader
Read count data for the specified query sequence.
readCounts(int, int[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TissueESTCountsReader
Read count data for the specified query sequence.
ReaderType - Interface in edu.mssm.crover.imports
ReaderType encapsulates the information about a sequence "file format".
readFile(InputStream) - Method in class edu.mssm.crover.imports.FastaReader
 
readFile(InputStream) - Method in interface edu.mssm.crover.imports.SequenceReader
 
readNextCounts(MutableString, int[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TissueESTCountsReader
Read count data for the next available sequence in the stream.
readNextCounts(int[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TissueESTCountsReader
Read count data for the next available sequence in the stream.
readResidues(BufferedReader, BiologicalSequence) - Method in class edu.mssm.crover.imports.FastaReader
 
readSequences(InputStream, ReaderType) - Method in interface edu.mssm.crover.imports.SequenceReaderFactory
 
readSequences(InputStream, ReaderType) - Method in class edu.mssm.crover.imports.SequenceReaderFactoryImpl
 
reason - Variable in exception edu.mssm.crover.imports.UnsupportedFileFormatException
 
recodeLabel(Object) - Method in class edu.mssm.crover.tables.writers.SVMLightWriter
 
rectum - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
red_blood_cell - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
registerAnnotationType(MutableString) - Method in class edu.cornell.med.icb.tissueinfo.annotations.AnnotationSet
Associate a annotationType with an annotation type.
registerDefaultValue(MutableString, MutableString) - Method in class edu.cornell.med.icb.tissueinfo.annotations.AnnotationSet
Register a default value for a type.
registerDefaultValue(String, String) - Method in class edu.cornell.med.icb.tissueinfo.annotations.AnnotationSet
Register a default value for a type.
registerDefaultValue(MutableString) - Method in class edu.cornell.med.icb.tissueinfo.annotations.AnnotationType
Register a default value for this type.
registerTissueType(String) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TissueESTCountsWriter
 
regress() - Method in class edu.cornell.med.icb.stat.LinearRegression
Run the regression.
rejectRow(Table.RowIterator) - Method in class edu.mssm.crover.tables.readers.LocusLinkTableReader
 
remove() - Method in class edu.cornell.med.icb.tissueinfo.annotations.ArraysIterator
 
remove(String) - Method in class edu.mssm.crover.tables.treatments.Aggregation
 
removeAllGene() - Method in class edu.cornell.med.icb.allen.xml.Genes
 
removeAllGeneExpression() - Method in class edu.cornell.med.icb.allen.xml.GeneExpressions
 
removeAllHit() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Iteration_hitsType
 
removeAllHit() - Method in class edu.mssm.crover.tools.tissue.xml.QuerySequence
 
removeAllHsp() - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Hit_hspsType
 
removeAllImageSeries() - Method in class edu.cornell.med.icb.allen.xml.ImageSeries
 
removeAllQuerySequence() - Method in class edu.mssm.crover.tools.tissue.xml.BlastHits
 
removeAllTokey() - Method in class edu.mssm.crover.tools.tissue.xml.TissueInfo
 
removeAnnotation(BiologicalAnnotation) - Method in class edu.mssm.crover.representation.Annotations
Removes an annotation from this list.
removeAnnotation(BiologicalAnnotation) - Method in interface edu.mssm.crover.representation.BiologicalAnnotations
Removes an annotation from this list.
removeColumn(String) - Method in class edu.mssm.crover.tables.ArrayTable
Removes a column from this table.
removeColumn(int) - Method in class edu.mssm.crover.tables.ArrayTable
 
removeColumn(String) - Method in interface edu.mssm.crover.tables.Table
Removes a column from this table.
removeColumn(int) - Method in interface edu.mssm.crover.tables.Table
Removes a column from this table.
removeGene(Gene) - Method in class edu.cornell.med.icb.allen.xml.Genes
Method removeGene.
removeGeneAt(int) - Method in class edu.cornell.med.icb.allen.xml.Genes
Method removeGeneAt.
removeGeneExpression(GeneExpression) - Method in class edu.cornell.med.icb.allen.xml.GeneExpressions
Method removeGeneExpression.
removeGeneExpressionAt(int) - Method in class edu.cornell.med.icb.allen.xml.GeneExpressions
Method removeGeneExpressionAt.
removeHit(Hit) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Iteration_hitsType
Method removeHit.
removeHit(Hit) - Method in class edu.mssm.crover.tools.tissue.xml.QuerySequence
Method removeHit.
removeHitAt(int) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Iteration_hitsType
Method removeHitAt.
removeHitAt(int) - Method in class edu.mssm.crover.tools.tissue.xml.QuerySequence
Method removeHitAt.
removeHsp(Hsp) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Hit_hspsType
Method removeHsp.
removeHspAt(int) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Hit_hspsType
Method removeHspAt.
removeImageSeries(ImageSeries) - Method in class edu.cornell.med.icb.allen.xml.ImageSeries
Method removeImageSeries.
removeImageSeriesAt(int) - Method in class edu.cornell.med.icb.allen.xml.ImageSeries
Method removeImageSeriesAt.
removeLastRow() - Method in class edu.mssm.crover.tables.ArrayTable.ColumnDescription
 
removeLastRow() - Method in class edu.mssm.crover.tables.ArrayTable
Removes the last appended row from each column of this table.
removeLastRow() - Method in interface edu.mssm.crover.tables.Table
Removes the last appended row from each column of this table.
removeQuerySequence(QuerySequence) - Method in class edu.mssm.crover.tools.tissue.xml.BlastHits
Method removeQuerySequence.
removeQuerySequenceAt(int) - Method in class edu.mssm.crover.tools.tissue.xml.BlastHits
Method removeQuerySequenceAt.
removeSubstringTissues(String[]) - Method in class edu.mssm.crover.tools.tissue.NullParser
Removes all tissues that are substrings of other tissues in the same set.
removeTokey(Tokey) - Method in class edu.mssm.crover.tools.tissue.xml.TissueInfo
Method removeTokey.
removeTokeyAt(int) - Method in class edu.mssm.crover.tools.tissue.xml.TissueInfo
Method removeTokeyAt.
replaceDoublesWith(double[]) - Method in class edu.mssm.crover.tables.ArrayTable.ColumnDescription
Replace array values with the specified values.
ReplaceRawTissue - Class in edu.mssm.crover.tools.tissue
Replaces a raw tissue with the curated tissue, if it exists in the tissue curation table.
replaceStringsWith(String[]) - Method in class edu.mssm.crover.tables.ArrayTable.ColumnDescription
Replace array values with the specified values.
ReportParser - Class in edu.mssm.crover.tools.tissue
Parses report files from tiquery.
ReportParser() - Constructor for class edu.mssm.crover.tools.tissue.ReportParser
 
reserve(int, int) - Method in class edu.mssm.crover.tables.ArrayTable
Reserve the space for numElements in the given column.
reserve(int, int) - Method in interface edu.mssm.crover.tables.Table
Reserve the space for numElements in the given column.
reset() - Method in class edu.cornell.med.icb.stat.LinearRegression
Prepare for a new regression calculation.
reset() - Method in class edu.cornell.med.icb.stat.ZScoreCalculator
Reset the calculator to a state before any value have been observed.
respiratory - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
result - Variable in class edu.mssm.crover.tables.treatments.CompositionTableTreatmentParameter
 
retina - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
returnConnection(Connection) - Method in class edu.mssm.crover.db.relational.ConnectionPool
 
returnConnection(Connection) - Method in class edu.mssm.crover.db.relational.RDB
Returns a connection to the pool.
rhinencephalon - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
rhombencephalon - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
rods - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
RootMeanSquaredErrorCalculator - Class in edu.cornell.med.icb.stat
Calculates the root mean squared error (RMSE).
RootMeanSquaredErrorCalculator() - Constructor for class edu.cornell.med.icb.stat.RootMeanSquaredErrorCalculator
 
RowFilter - Class in edu.mssm.crover.tables
 
RowFilter() - Constructor for class edu.mssm.crover.tables.RowFilter
 
RowFloorAdjustmentCalculator - Class in edu.mssm.crover.tables
Add an offset to each selected column.
RowFloorAdjustmentCalculator(int[], double, boolean, boolean) - Constructor for class edu.mssm.crover.tables.RowFloorAdjustmentCalculator
For one channel arrays, values are set to the minimum of the floor or the value.
RowOffsetCalculator - Class in edu.mssm.crover.tables
Add an offset to each selected column.
RowOffsetCalculator(int[], Int2DoubleMap) - Constructor for class edu.mssm.crover.tables.RowOffsetCalculator
 
RowProcessor - Class in edu.mssm.crover.tables
 
RowProcessor(int[]) - Constructor for class edu.mssm.crover.tables.RowProcessor
 
RowSumCalculator - Class in edu.mssm.crover.tables
 
RowSumCalculator(int[]) - Constructor for class edu.mssm.crover.tables.RowSumCalculator
 
RTISSUE_COLNUM - Static variable in class edu.mssm.crover.tools.tissue.TissueInfoNullsJDBCImpl
The column index for the raw tissue.
run(String, BiologicalSequence, String) - Method in class edu.mssm.crover.tools.blast.BlastCommand
Run BLAST with a query sequence.
run(int, File, String) - Method in class edu.mssm.crover.tools.blast.BlastCommand
Run BLAST with a (multiple) sequence file.
run(String, File, String, int) - Method in class edu.mssm.crover.tools.blast.BlastCommand
Runs BLAST on the sequences encoded by the sequence(s) in the File seqFile passed as argument.
run(String, BiologicalSequence, String, int) - Method in class edu.mssm.crover.tools.blast.BlastCommand
Predicts the product of the genes encoded by the sequence passed as argument.
runbl2(String, BiologicalSequence, BiologicalSequence) - Method in class edu.mssm.crover.tools.blast.BlastCommand
 

S

SAGITTAL - Static variable in class edu.cornell.med.icb.allen.xml.types.PlaneType
The instance of the sagittal type
SAGITTAL_TYPE - Static variable in class edu.cornell.med.icb.allen.xml.types.PlaneType
The sagittal type
salivary_gland - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
sample(Table) - Method in class edu.mssm.crover.tables.treatments.RandomSample
 
ScalingRowProcessor - Class in edu.mssm.crover.tables
 
ScalingRowProcessor(int[]) - Constructor for class edu.mssm.crover.tables.ScalingRowProcessor
 
ScalingRowProcessor(Table, String) - Constructor for class edu.mssm.crover.tables.ScalingRowProcessor
Scale all columns except the identifier column.
sciatic_nerve - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
score(int[], int[], int[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.scorers.BaselineNormalizedConfidenceScorer
 
score(int[], int[], int[], float[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.scorers.BaselineNormalizedConfidenceScorer
 
score(int[], int[], int[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.scorers.BaselineNormalizerScorer
 
score(int[], int[], int[], float[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.scorers.BaselineNormalizerScorer
 
score(int[], int[], int[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.scorers.BinaryScorer
 
score(int[], int[], int[], float[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.scorers.BinaryScorer
 
score(int[], int[], int[], float[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.scorers.EstRepresentationScorer
 
score(int[], int[], int[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.scorers.EstRepresentationScorer
 
score(int[], int[], int[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.scorers.ExpressionConfidenceScorer
 
score(int[], int[], int[], float[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.scorers.ExpressionConfidenceScorer
 
score(int[], int[], int[]) - Method in interface edu.cornell.med.icb.tissueinfo.similarity.scorers.ExpressionProfileSimilarityScorer
 
score(int[], int[], int[], float[]) - Method in interface edu.cornell.med.icb.tissueinfo.similarity.scorers.ExpressionProfileSimilarityScorer
 
score(int[], int[], int[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.scorers.FastExpressionConfidenceScorer
 
score(int[], int[], int[], float[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.scorers.FastExpressionConfidenceScorer
 
score(int[], int[], int[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.scorers.KendallTauScorer
 
score(int[], int[], int[], float[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.scorers.KendallTauScorer
 
score(int[], int[], int[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.scorers.MaxNormalizedConfidenceScorer
 
score(int[], int[], int[], float[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.scorers.MaxNormalizedConfidenceScorer
 
score(int[], int[], int[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.scorers.MaxNormalizerScorer
 
score(int[], int[], int[], float[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.scorers.MaxNormalizerScorer
 
score(int[], int[], int[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.scorers.NormalizedBinaryScorer
 
score(int[], int[], int[], float[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.scorers.NormalizedBinaryScorer
 
score(int[], int[], int[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.scorers.NormalizedConfidenceScorer
 
score(int[], int[], int[], float[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.scorers.NormalizedConfidenceScorer
 
score(int[], int[], int[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.scorers.NormalizerScorer
 
score(int[], int[], int[], float[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.scorers.NormalizerScorer
 
score(int[], int[], int[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.scorers.PearsonScorer
 
score(int[], int[], int[], float[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.scorers.PearsonScorer
 
score(int[], int[], int[], float[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.scorers.RawEstCountScorer
 
score(int[], int[], int[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.scorers.RawEstCountScorer
 
score(int[], int[], int[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.scorers.ShuffleNormalizedBinaryScorer
 
score(int[], int[], int[], float[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.scorers.ShuffleNormalizedBinaryScorer
 
score(int[], int[], int[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.scorers.ShuffleNormalizedConfidenceScorer
 
score(int[], int[], int[], float[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.scorers.ShuffleNormalizedConfidenceScorer
 
score(int[], int[], int[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.scorers.ShuffleNormalizerScorer
 
score(int[], int[], int[], float[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.scorers.ShuffleNormalizerScorer
 
score(int, int) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TiSimilaritySearchEngine
 
score - Variable in class edu.cornell.med.icb.tissueinfo.similarity.TranscriptScore
 
score1 - Variable in class edu.cornell.med.icb.tissueinfo.similarity.clustering.Cluster
 
score2 - Variable in class edu.cornell.med.icb.tissueinfo.similarity.clustering.Cluster
 
score3 - Variable in class edu.cornell.med.icb.tissueinfo.similarity.clustering.Cluster
 
ScoredTranscriptBoundedSizeQueue - Class in edu.cornell.med.icb.tissueinfo.similarity
This class is an adaptation of MG4J's DocumentScoreBoundedSizeQueue.
ScoredTranscriptBoundedSizeQueue(int) - Constructor for class edu.cornell.med.icb.tissueinfo.similarity.ScoredTranscriptBoundedSizeQueue
Creates a new empty bounded-size queue with a given capacity and natural order as comparator.
scorer - Variable in class edu.cornell.med.icb.tissueinfo.similarity.TiSimOptions
 
searchFullGenome(int, double[], int[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TiSimilaritySearchEngine
Perform a tiSimilarity query, rank and score each transcript of the genome with respect to the query.
searchFullGenome(int, int[], double[], int[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TiSimilaritySearchEngine
Perform a tiSimilarity query, rank and score each transcript of the genome with respect to the query.
searchFullGenome(int, int) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TiSimilaritySearchEngine
Perform a tiSimilarity query.
searchFullGenome(int, int[], int) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TiSimilaritySearchEngine
Perform a tiSimilarity query.
searchQueryIndex(TiSimOptions, PrintWriter, int) - Method in class edu.cornell.med.icb.tissueinfo.similarity.PairScoreOnlyMode
 
searchQueryIndex(TiSimOptions, PrintWriter, int) - Method in class edu.cornell.med.icb.tissueinfo.similarity.PairSearchMode
 
searchWithFocusGroup(int[], double[], double[], int) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TiSimilaritySearchEngine
Perform a tiSimilarity query, rank and score each transcript of the genome with respect to transcripts in a focus group.
searchWithFocusGroup(int[], double[], double[], int, int, int) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TiSimilaritySearchEngine
Perform a tiSimilarity query, rank and score each transcript of the genome with respect to transcripts in a focus group.
searchWithFocusGroup(int[], int[], double[], double[], int) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TiSimilaritySearchEngine
Perform a tiSimilarity query, rank and score each transcript of the genome with respect to transcripts in a focus group.
sebaceous_gland - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
seminal_vesicle - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
seminiferous_tubules - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
SensitivityCalculator - Class in edu.cornell.med.icb.stat
Calculates the specificity of predictions.
SensitivityCalculator() - Constructor for class edu.cornell.med.icb.stat.SensitivityCalculator
 
sensory_neuron - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
sensory_somatic_NS - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
septum - Interface in edu.mssm.crover.tools.tissue.hierarchy
The wall/membrane that separates the two heart ventricules.
Sequence - Class in edu.mssm.crover.representation
Default implementation of BiologicalSequence.
Sequence() - Constructor for class edu.mssm.crover.representation.Sequence
 
Sequence(String, String) - Constructor for class edu.mssm.crover.representation.Sequence
 
sequence - Variable in class edu.mssm.crover.representation.Sequence
 
SequenceOrigin_Annotation - Class in edu.mssm.crover.representation
This annotation describes the origin of the sequence itself.
SequenceOrigin_Annotation(BiologicalOrigin) - Constructor for class edu.mssm.crover.representation.SequenceOrigin_Annotation
 
SequenceReader - Interface in edu.mssm.crover.imports
SequenceReader are used by a SequenceReaderFactory.
SequenceReaderFactory - Interface in edu.mssm.crover.imports
Gives access to specialized Sequence readers.
SequenceReaderFactoryImpl - Class in edu.mssm.crover.imports
This default implementation of SequenceReaderFactory allows to read sequence files in the following formats: FASTA/Pearson PIR SwissProt with some annotations PDB headers with SEQRES and with secondary structure annotations.
SequenceReaderFactoryImpl() - Constructor for class edu.mssm.crover.imports.SequenceReaderFactoryImpl
 
sequentialAccess() - Method in class edu.cornell.med.icb.tissueinfo.similarity.TissueESTCountsReader
Prepare this instance for sequential access.
serum - Interface in edu.mssm.crover.tools.tissue.hierarchy
 
set(BiologicalSequence) - Method in class edu.mssm.crover.representation.Sequence
Transfer information from the source to this instance.
setAc(String) - Method in class edu.mssm.crover.tools.tissue.TissueDetails
Setter method for the EST accession code.
setAc(String) - Method in class edu.mssm.crover.tools.tissue.xml.Hit
Sets the value of field 'ac'.
setAc(String) - Method in class edu.mssm.crover.tools.tissue.xml.QuerySequence
Sets the value of field 'ac'.
setAccessionCode(String) - Method in interface edu.mssm.crover.representation.BiologicalOrigin
Sets the accession code inside the origin database.
setAccessionCode(String) - Method in class edu.mssm.crover.representation.Origin
 
setActiveTable(String) - Method in class edu.mssm.crover.tables.TableActivityWatcher
Sets the name of the active tale corresponding to a specified key.
setAge(Age) - Method in class edu.cornell.med.icb.allen.xml.ImageSeriesSequence
Sets the value of field 'age'.
setAnnotations(BiologicalAnnotations) - Method in interface edu.mssm.crover.representation.AnnotationSupport
Sets the annotations for an instance.
setAnnotations(BiologicalAnnotations) - Method in class edu.mssm.crover.representation.Sequence
 
setAverageL(int) - Method in class edu.cornell.med.icb.tissueinfo.similarity.scorers.ShuffleNormalizerScorer
Set the number of shuffled scores that should be averaged.
setAvgdensity(Avgdensity) - Method in class edu.cornell.med.icb.allen.xml.GeneExpression
Sets the value of field 'avgdensity'.
setAvglevel(Avglevel) - Method in class edu.cornell.med.icb.allen.xml.GeneExpression
Sets the value of field 'avglevel'.
setBlastOutput(Object) - Method in class edu.mssm.crover.tools.blast.BlastResult
 
setBlastOutput_db(String) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.BlastOutput
Sets the value of field 'blastOutput_db'.
setBlastOutput_iterations(BlastOutput_iterations) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.BlastOutput
Sets the value of field 'blastOutput_iterations'.
setBlastOutput_param(BlastOutput_param) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.BlastOutput
Sets the value of field 'blastOutput_param'.
setBlastOutput_program(String) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.BlastOutput
Sets the value of field 'blastOutput_program'.
setBlastOutput_queryDef(String) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.BlastOutput
Sets the value of field 'blastOutput_queryDef'.
setBlastOutput_queryID(String) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.BlastOutput
Sets the value of field 'blastOutput_queryID'.
setBlastOutput_queryLen(int) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.BlastOutput
Sets the value of field 'blastOutput_queryLen'.
setBlastOutput_reference(String) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.BlastOutput
Sets the value of field 'blastOutput_reference'.
setBlastOutput_version(String) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.BlastOutput
Sets the value of field 'blastOutput_version'.
setBValue(int) - Method in class edu.mssm.crover.tools.blast.BlastContext
 
setBValue(int) - Method in class edu.mssm.crover.tools.tissue.xml.BlastHits
Sets the value of field 'bValue'.
setChromosome(String) - Method in class edu.cornell.med.icb.allen.xml.Gene
Sets the value of field 'chromosome'.
setChunk(int) - Method in class edu.mssm.crover.tables.ArrayTable
Set the number of element of a column to expand the size with when the available space is saturated for this column.
setCollectLOOInformation(int) - Method in class edu.cornell.med.icb.tissueinfo.similarity.ForwardMode
 
setCollectLOOInformation(IntSet) - Method in class edu.cornell.med.icb.tissueinfo.similarity.ForwardMode
 
setColumnFilter(Set<String>) - Method in class edu.mssm.crover.tables.readers.CSVReader
 
setColumnFilter(Set<String>) - Method in class edu.mssm.crover.tables.readers.GeoDataSetReader
Set a filter to read only certain columns.
setConfidenceThresholds(int[]) - Method in class edu.cornell.med.icb.tissueinfo.similarity.scorers.ExpressionConfidenceScorer
Define the confidence thresholds and values for scoring.
setContent(BigDecimal) - Method in class edu.cornell.med.icb.allen.xml.Age
Sets the value of field 'content'.
setContent(BigDecimal) - Method in class edu.cornell.med.icb.allen.xml.Avgdensity
Sets the value of field 'content'.
setContent(BigDecimal) - Method in class edu.cornell.med.icb.allen.xml.Avglevel
Sets the value of field 'content'.
setContent(BigDecimal) - Method in class edu.cornell.med.icb.allen.xml.Entrezgeneid
Sets the value of field 'content'.
setContent(BigDecimal) - Method in class edu.cornell.med.icb.allen.xml.Geneid
Sets the value of field 'content'.
setContent(BigDecimal) - Method in class edu.cornell.med.icb.allen.xml.Imageseriesid
Sets the value of field 'content'.
setContent(BigDecimal) - Method in class edu.cornell.med.icb.allen.xml.Structureid
Sets the value of field 'content'.
setContent(BigDecimal) - Method in class edu.cornell.med.icb.allen.xml.Templateid
Sets the value of field 'content'.
setContent(BigDecimal) - Method in class edu.cornell.med.icb.allen.xml.Transcriptgi
Sets the value of field 'content'.
setContent(BigDecimal) - Method in class edu.cornell.med.icb.allen.xml.Transcriptid
Sets the value of field 'content'.
setContext(BlastContext) - Method in class edu.mssm.crover.tools.blast.BlastCommand
 
setCuratedDevStage(CuratedDevStage) - Method in class edu.mssm.crover.tools.tissue.TissueDetails
Setter method for the curated developmental stage.
setCuratedTissue(String) - Method in class edu.mssm.crover.tools.tissue.NullTissueDetails
Setter method for the curated tissue.
setCuratedTissue(CuratedTissue) - Method in class edu.mssm.crover.tools.tissue.TissueDetails
Setter method for the curated tissue.
setCuratedTissue(CuratedTissue) - Method in class edu.mssm.crover.tools.tissue.TissueSelection
Sets both the CuratedTissue and the English language sentence.
setDatabase(String) - Method in class edu.mssm.crover.tools.tissue.xml.BlastHits
Sets the value of field 'database'.
setDataBaseName(String) - Method in interface edu.mssm.crover.representation.BiologicalOrigin
Sets the name of the database which curates this information.
setDataBaseName(String) - Method in class edu.mssm.crover.representation.Origin
 
setDefaultLabelValue(double) - Method in class edu.mssm.crover.tables.readers.GeoDataSetReader
Set the value of the label to use when the column does not match any label column group.
setDefLine(String) - Method in class edu.mssm.crover.tools.blast.HitSummary
 
setDoNotAdd(boolean) - Method in class edu.mssm.crover.tools.tissue.DbestParser
Set the doNotAdd parameter.
setDoNotAdd(boolean) - Method in class edu.mssm.crover.tools.tissue.NullParser
Setter for the doNotAdd parameter.
setEntrezgeneid(Entrezgeneid) - Method in class edu.cornell.med.icb.allen.xml.Gene
Sets the value of field 'entrezgeneid'.
setEValue(double) - Method in class edu.mssm.crover.tools.blast.BlastContext
 
setEValue(double) - Method in class edu.mssm.crover.tools.blast.HitSummary
 
setExpectationValue(double) - Method in class edu.mssm.crover.tools.tissue.xml.BlastHits
Sets the value of field 'expectationValue'.
setFirstPass(boolean) - Method in class edu.mssm.crover.tables.ScalingRowProcessor
 
setGene(int, Gene) - Method in class edu.cornell.med.icb.allen.xml.Genes
 
setGene(Gene[]) - Method in class edu.cornell.med.icb.allen.xml.Genes
 
setGeneExpression(int, GeneExpression) - Method in class edu.cornell.med.icb.allen.xml.GeneExpressions
 
setGeneExpression(GeneExpression[]) - Method in class edu.cornell.med.icb.allen.xml.GeneExpressions
 
setGeneExpressions(GeneExpressions) - Method in class edu.cornell.med.icb.allen.xml.Gene
Sets the value of field 'geneExpressions'.
setGeneid(Geneid) - Method in class edu.cornell.med.icb.allen.xml.Gene
Sets the value of field 'geneid'.
setGeneid(Geneid) - Method in class edu.cornell.med.icb.allen.xml.GeneExpression
Sets the value of field 'geneid'.
setGeneid(Geneid) - Method in class edu.cornell.med.icb.allen.xml.ImageSeriesSequence
Sets the value of field 'geneid'.
setGenename(String) - Method in class edu.cornell.med.icb.allen.xml.Gene
Sets the value of field 'genename'.
setGenesymbol(String) - Method in class edu.cornell.med.icb.allen.xml.Gene
Sets the value of field 'genesymbol'.
setGenomeFilter(IntSet) - Method in class edu.cornell.med.icb.tissueinfo.similarity.TiSimilaritySearchEngine
When genomeFilter is not null, only sequences whose index are in genomeFilter are scored with respect to the query sequence.
setGensatid(String) - Method in class edu.cornell.med.icb.allen.xml.Gene
Sets the value of field 'gensatid'.
setHierarchyPackage(String) - Method in class edu.mssm.crover.tools.tissue.Hierarchy
Setter method for the location of the hierarchy package.
setHit(int, Hit) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Iteration_hitsType
 
setHit(Hit[]) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Iteration_hitsType
 
setHit(int, Hit) - Method in class edu.mssm.crover.tools.tissue.xml.QuerySequence
 
setHit(Hit[]) - Method in class edu.mssm.crover.tools.tissue.xml.QuerySequence
 
setHit_accession(String) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HitType
Sets the value of field 'hit_accession'.
setHit_def(String) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HitType
Sets the value of field 'hit_def'.
setHit_hsps(Hit_hsps) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HitType
Sets the value of field 'hit_hsps'.
setHit_id(String) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HitType
Sets the value of field 'hit_id'.
setHit_len(int) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HitType
Sets the value of field 'hit_len'.
setHit_num(int) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.HitType
Sets the value of field 'hit_num'.
setHitLength(int) - Method in class edu.mssm.crover.tools.blast.HitSummary
 
setHsp(int, Hsp) - Method in class edu.mssm.crover.tools.blast.parsers.xml.v3.Hit_hspsType