icb-utils API icb-utils-182 (20120309094326)
A B C D E F G H I L M N O P R S T U V W X

A

add(E) - Method in class edu.cornell.med.icb.util.BoundedPriorityQueue
Add a element to the queue then ensure then queue isn't larger than maxCapacity.
addAll(Collection<? extends E>) - Method in class edu.cornell.med.icb.util.BoundedPriorityQueue
Add a collection of elements to the queue then ensure the queue isn't larger than maxCapacity.
addColumn(String) - Method in class edu.cornell.med.icb.io.TsvToFromMap
Add a column.
addField(ConditionField) - Method in class edu.cornell.med.icb.io.ConditionsParser
Add a new ConditionField to the parser.
addHelpFlag(JSAP) - Method in class edu.cornell.med.icb.cli.UseModality
 

B

beginParse(Reader) - Method in class edu.cornell.med.icb.io.ConditionsParser
This method is called first to begin parsing condition data.
beginParseAllToBeans(Reader, Class<T>, Map<String, String>) - Method in class edu.cornell.med.icb.io.ConditionsParser
This does complete parsing of the entire file into objects.
beginParseAllToBeans(Reader, T, Map<String, String>) - Method in class edu.cornell.med.icb.io.ConditionsParser
This does complete parsing of the entire file into objects.
BoundedPriorityQueue<E> - Class in edu.cornell.med.icb.util
This class extends the PriorityQueue to implement a Bounded version, a version that will contain no more than maxCapacity elements.
BoundedPriorityQueue(int, Comparator<E>, boolean) - Constructor for class edu.cornell.med.icb.util.BoundedPriorityQueue
Create a BoundedPriorityQueue specifying the max capacity, the comparator to use to order the queue, and if surplus elements should be removed form the head or tail.
BoundedPriorityQueue(int, Comparator<E>) - Constructor for class edu.cornell.med.icb.util.BoundedPriorityQueue
Create a BoundedPriorityQueue specifying the max capacity, the comparator to use to order the queue.
BoundedPriorityQueue(int, boolean) - Constructor for class edu.cornell.med.icb.util.BoundedPriorityQueue
Create a BoundedPriorityQueue specifying the max capacity.
BoundedPriorityQueue(int) - Constructor for class edu.cornell.med.icb.util.BoundedPriorityQueue
Create a BoundedPriorityQueue specifying the max capacity.

C

checkPrintHelp(JSAP, JSAPResult) - Static method in class edu.cornell.med.icb.cli.UseModality
Determine whether or not a help message should be displayed.
choose(int) - Method in class edu.cornell.med.icb.util.RandomAdapter
 
choose(int, int) - Method in class edu.cornell.med.icb.util.RandomAdapter
 
cleanStringArray(String[]) - Static method in class edu.cornell.med.icb.util.ICBStringUtils
This will take a String[] and clean it, removing all null or empty strings including strings that would trim to empty.
clearFields() - Method in class edu.cornell.med.icb.io.ConditionsParser
Clear the fields for the parser.
clone() - Method in class edu.cornell.med.icb.identifier.IndexedIdentifier
Creates and returns a copy of this object.
close() - Method in class edu.cornell.med.icb.io.TSVReader
Closes this stream and releases any system resources associated with it.
close() - Method in class edu.cornell.med.icb.iterators.TextFileLineIterator
For either manual or automatic closing.
close() - Method in class edu.cornell.med.icb.iterators.TsvLineIterator
In case we need to close early.
concatPathParts(String...) - Static method in class edu.cornell.med.icb.util.ICBFilenameUtils
This works somewhat differently than Apache Commons FilenameUtils.concat().
ConditionField - Class in edu.cornell.med.icb.io
A condition field for parsing condition files with the ConditionsParser.
ConditionField(ConditionField.FieldType, String) - Constructor for class edu.cornell.med.icb.io.ConditionField
Create a new field, specifying the type and the name.
ConditionField.FieldType - Enum in edu.cornell.med.icb.io
Enum for field type.
ConditionsParser - Class in edu.cornell.med.icb.io
This class is a very glorified TSVReader.
ConditionsParser() - Constructor for class edu.cornell.med.icb.io.ConditionsParser
Create a new ConditionsParser with no fields specified.
ConditionsParser(List<ConditionField>) - Constructor for class edu.cornell.med.icb.io.ConditionsParser
Create a new ConditionsParser with a List[ConditionField] of fields.
ConditionsParsingException - Exception in edu.cornell.med.icb.io
Error with condition parsing.
ConditionsParsingException() - Constructor for exception edu.cornell.med.icb.io.ConditionsParsingException
No args exception.
ConditionsParsingException(String) - Constructor for exception edu.cornell.med.icb.io.ConditionsParsingException
Message only exception.
ConditionsParsingException(String, Throwable) - Constructor for exception edu.cornell.med.icb.io.ConditionsParsingException
Message and throwable exception.
ConditionsParsingException(Throwable) - Constructor for exception edu.cornell.med.icb.io.ConditionsParsingException
Throwable exception (no message).
consoleToHtml(String) - Static method in class edu.cornell.med.icb.util.ICBStringUtils
Format a simple string with spaces, newlines, tabs to simple html.
createFromTsvFile(File) - Static method in class edu.cornell.med.icb.io.TsvToFromMap
Construct a TsvToFromMap based on the columns of a given TSV file.

D

DataObjectInputStream - Class in edu.cornell.med.icb.io
A DataInputStream but with a readObject() method to de-serialize an object from the stream.
DataObjectInputStream(InputStream) - Constructor for class edu.cornell.med.icb.io.DataObjectInputStream
Creates a DataInputStream that uses the specified underlying InputStream.
DataObjectOutputStream - Class in edu.cornell.med.icb.io
A DataOutputStream but with a writeObject(o) method to serialize an object to the stream.
DataObjectOutputStream(OutputStream) - Constructor for class edu.cornell.med.icb.io.DataObjectOutputStream
Creates a new data output stream to write data to the specified underlying output stream.
defineOptions(JSAP) - Method in class edu.cornell.med.icb.cli.UseModality
Define command line options.
DoubleIndexedIdentifier - Class in edu.cornell.med.icb.identifier
Associates identifiers to indices, both ways.
DoubleIndexedIdentifier(IndexedIdentifier) - Constructor for class edu.cornell.med.icb.identifier.DoubleIndexedIdentifier
 

E

edu.cornell.med.icb.cli - package edu.cornell.med.icb.cli
 
edu.cornell.med.icb.identifier - package edu.cornell.med.icb.identifier
 
edu.cornell.med.icb.io - package edu.cornell.med.icb.io
ICB IO Classes.
edu.cornell.med.icb.ip - package edu.cornell.med.icb.ip
ICB IP Classes
edu.cornell.med.icb.iterators - package edu.cornell.med.icb.iterators
ICB iterators.
edu.cornell.med.icb.maps - package edu.cornell.med.icb.maps
 
edu.cornell.med.icb.util - package edu.cornell.med.icb.util
ICB Util Classes.
equals(Object) - Method in class edu.cornell.med.icb.ip.IpAddress
Equals.

F

findResource(String) - Method in class edu.cornell.med.icb.io.ResourceFinder
Obtain a URL for a specified resource.
FlatteningIterator - Class in edu.cornell.med.icb.iterators
This comes from http://snippets.dzone.com/posts/show/3523 The author, David R.
FlatteningIterator(Object...) - Constructor for class edu.cornell.med.icb.iterators.FlatteningIterator
Create a flattening iterator with the given objects.
fromPropertyMap(Map<String, Properties>) - Method in class edu.cornell.med.icb.identifier.IndexedIdentifier
Set the current state of the object from a map of properties.
fromPropertyMap(Map<String, Properties>) - Method in interface edu.cornell.med.icb.identifier.PropertyMappable
Set the current state of the object from a map of properties.

G

generateRandomString() - Static method in class edu.cornell.med.icb.util.ICBStringUtils
Generate a random string of characters A..Z of length RANDOM_STRING_LENGTH_DEFAULT.
generateRandomString(int) - Static method in class edu.cornell.med.icb.util.ICBStringUtils
Generate a random string of characters A..Z of length 'length'.
getClassnameKey() - Method in class edu.cornell.med.icb.io.ConditionField
Get the classnameKey String.
getColumnHeaders() - Method in class edu.cornell.med.icb.io.TsvToFromMap
Obtain a copy of the column headers.
getComment() - Method in class edu.cornell.med.icb.ip.IpAddress
Get comment.
getCommentPrefix() - Method in class edu.cornell.med.icb.io.ConditionsParser
Get the commentPrefix String.
getCommentPrefix() - Method in class edu.cornell.med.icb.io.TSVReader
Get the comment prefix being used.
getCorrelationCoefficient() - Method in class edu.cornell.med.icb.util.ProcessEstimator
Obtain the correlation coefficient.
getCurrentValue() - Method in class edu.cornell.med.icb.io.ConditionField
Get the currentValue of this field.
getDefaultValue() - Method in class edu.cornell.med.icb.io.ConditionField
Get the defaultValue String.
getDouble() - Method in class edu.cornell.med.icb.io.TSVReader
Get the current field as a double.
getDouble(T) - Method in class edu.cornell.med.icb.maps.LinkedHashToMultiTypeMap
Returns the mapped value as a Double or null if the field doesn't exist in the map.
getDoubleArray(T) - Method in class edu.cornell.med.icb.maps.LinkedHashToMultiTypeMap
Returns the mapped value as a double[] or null if the field doesn't exist in the map.
getDoubleArray(T, char) - Method in class edu.cornell.med.icb.maps.LinkedHashToMultiTypeMap
Returns the mapped value as a double[] or null if the field doesn't exist in the map.
getEscapeChar() - Method in class edu.cornell.med.icb.io.ConditionsParser
Get the escape char to use when parsing.
getEscapeChar() - Method in class edu.cornell.med.icb.io.TSVReader
Get the escape character being used.
getExecutedModality() - Method in class edu.cornell.med.icb.cli.UseModality
 
getFieldName() - Method in class edu.cornell.med.icb.io.ConditionField
Get the field name of this field.
getFields() - Method in class edu.cornell.med.icb.io.ConditionsParser
Get the list of fields the parser will use when parsing the file.
getFieldsCount() - Method in class edu.cornell.med.icb.io.ConditionsParser
Get the number of fields the parser will try to retrieve from the file.
getFieldSeparator() - Method in class edu.cornell.med.icb.io.ConditionsParser
Get the fieldSeparator char.
getFieldType() - Method in class edu.cornell.med.icb.io.ConditionField
Get the field type for this field.
getFloat() - Method in class edu.cornell.med.icb.io.TSVReader
Get the current field as a float.
getId(int) - Method in class edu.cornell.med.icb.identifier.DoubleIndexedIdentifier
 
getImplementationVersion(Class<?>) - Static method in class edu.cornell.med.icb.util.VersionUtils
Gets the Implementation-Version attribute from the manifest of the jar file a class is loaded from.
getIndex(MutableString) - Method in class edu.cornell.med.icb.identifier.DoubleIndexedIdentifier
 
getIndex(String) - Method in class edu.cornell.med.icb.identifier.DoubleIndexedIdentifier
 
getInt() - Method in class edu.cornell.med.icb.io.TSVReader
Get the current field as an int.
getInt(T) - Method in class edu.cornell.med.icb.maps.LinkedHashToMultiTypeMap
Returns the mapped value as a Integer or null if the field doesn't exist in the map.
getIntArray(T) - Method in class edu.cornell.med.icb.maps.LinkedHashToMultiTypeMap
Returns the mapped value as a int[] or null if the field doesn't exist in the map.
getIntArray(T, char) - Method in class edu.cornell.med.icb.maps.LinkedHashToMultiTypeMap
Returns the mapped value as a int[] or null if the field doesn't exist in the map.
getIpAddress() - Method in class edu.cornell.med.icb.ip.IpAddress
Get the ip address (InetAddress).
getKeyValueSeparator() - Method in class edu.cornell.med.icb.io.ConditionField
Get the keyValueSeparator char.
getLineNumber() - Method in class edu.cornell.med.icb.io.ConditionsParser
Get the current line number.
getListSeparator() - Method in class edu.cornell.med.icb.io.ConditionField
Get the listSeparator char.
getLong() - Method in class edu.cornell.med.icb.io.TSVReader
Get the current field as a long.
getMaxCapacity() - Method in class edu.cornell.med.icb.util.BoundedPriorityQueue
Get the max capacity of the queue.
getNumColumnHeaders() - Method in class edu.cornell.med.icb.io.TsvToFromMap
Retrieve the number of column headers.
getOriginalArgs() - Method in class edu.cornell.med.icb.cli.UseModality
Get the command line args used to start the program.
getResourceListing(Class) - Method in class edu.cornell.med.icb.io.ResourceFinder
List directory contents for a resource folder that contains the specified class, this list will include the .class file associated with clazz.
getResourceListing(Class, String) - Method in class edu.cornell.med.icb.io.ResourceFinder
List directory contents for a resource folder.
getSearchInClasspath() - Method in class edu.cornell.med.icb.io.ResourceFinder
Get when to search in classpath for the resource (default is SearchInClasspath.BEFORE_LOCAL).
getString() - Method in class edu.cornell.med.icb.io.TSVReader
Get the current field as a String.
getString(T) - Method in class edu.cornell.med.icb.maps.LinkedHashToMultiTypeMap
Synonym for just using get(field).
getTimeSpent() - Method in class edu.cornell.med.icb.util.ProcessEstimator
Return the time milliseconds that the ProcessEstimator has been running while clock was running (not suspended)..
getTotalUnits() - Method in class edu.cornell.med.icb.util.ProcessEstimator
Get the number of total units.
getUnescapeResults() - Method in class edu.cornell.med.icb.io.TSVReader
Get the if the results should be unescaped.
getUnitsCompleted() - Method in class edu.cornell.med.icb.util.ProcessEstimator
The number of completed units of work.
getValueBeanProperty() - Method in class edu.cornell.med.icb.io.ConditionField
Get the defaultValue String.

H

hashCode() - Method in class edu.cornell.med.icb.ip.IpAddress
Get the hash code for this object.
hasNext() - Method in class edu.cornell.med.icb.io.ConditionsParser
Determine if a next condition line is available.
hasNext() - Method in class edu.cornell.med.icb.io.TSVReader
Check if the file has more lines.
hasNext() - Method in class edu.cornell.med.icb.iterators.FlatteningIterator
Returns if there are any objects left to iterate over.
hasNext() - Method in class edu.cornell.med.icb.iterators.PreSortedMergeTextFilesLineIterator
If there is another line to be read.
highlightString(String, String, String, String) - Static method in class edu.cornell.med.icb.util.ICBStringUtils
Highlight occurrences of highlightWords within toHighlight.
highlightStrings(String, String[], String, String) - Static method in class edu.cornell.med.icb.util.ICBStringUtils
Highlight occurrences of highlightWords within toHighlight.
htmlFix(String) - Static method in class edu.cornell.med.icb.util.ICBStringUtils
Fix the incoming string to be safe for HTML <input>, etc..
htmlToConsole(String) - Static method in class edu.cornell.med.icb.util.ICBStringUtils
Format a simple HTML string for the console.
humanMemorySize(long) - Static method in class edu.cornell.med.icb.util.ICBStringUtils
Make byte sizes (such as file or memory sizes) human readable, such as 42,462,614 becomes 40.5 MB.
humanMemorySize(long, int) - Static method in class edu.cornell.med.icb.util.ICBStringUtils
Make byte sizes (such as file or memory sizes) human readable, such as 42,462,614 becomes 40.5 MB.

I

ICBFilenameUtils - Class in edu.cornell.med.icb.util
Utility methods related to filenames.
ICBStringNormalizer - Class in edu.cornell.med.icb.util
Class for normalizing strings, such as removing accents.
ICBStringUtils - Class in edu.cornell.med.icb.util
 
IndexedIdentifier - Class in edu.cornell.med.icb.identifier
Maintains a mapping between identifiers and indices.
IndexedIdentifier(int) - Constructor for class edu.cornell.med.icb.identifier.IndexedIdentifier
Create a new empty IndexedIdentifier with an estimated size.
IndexedIdentifier() - Constructor for class edu.cornell.med.icb.identifier.IndexedIdentifier
Create a new empty IndexedIdentifier.
IndexedIdentifier(Map<String, Properties>) - Constructor for class edu.cornell.med.icb.identifier.IndexedIdentifier
Create a new IndexedIdentifier that is initialized using the data in the supplied map of properties.
inputStreamForResource(String) - Method in class edu.cornell.med.icb.io.ResourceFinder
Return an InputStream for a given resource using the ResourceFinder.
interpretArguments(JSAP, JSAPResult, OptionType) - Method in class edu.cornell.med.icb.cli.UseModality
Transfer arguments from command line arguments to application options.
IpAddress - Class in edu.cornell.med.icb.ip
An ip address and optional associated comment.
IpAddress(InetAddress, String) - Constructor for class edu.cornell.med.icb.ip.IpAddress
Create an IpAddrss with an InetAddress and a comment.
IpAddress(InetAddress) - Constructor for class edu.cornell.med.icb.ip.IpAddress
Create an IpAddrss with an InetAddress but no comment.
ipListContains(List<IpAddress>, String) - Static method in class edu.cornell.med.icb.ip.IpUtils
See if the supplied IpAddress List contains the specified address string.
ipListContains(List<IpAddress>, IpAddress) - Static method in class edu.cornell.med.icb.ip.IpUtils
See if the supplied IpAddress List contains the specified IpAddress, specifically the value from address.getIpAddress() - any comment with address is ignored.
ipListContains(List<IpAddress>, InetAddress) - Static method in class edu.cornell.med.icb.ip.IpUtils
See if the supplied IpAddress List contains the specified InetAddress address.
IpUtils - Class in edu.cornell.med.icb.ip
Utility class for validating ip addresses, reading IpAddress files, etc.
isClassname() - Method in class edu.cornell.med.icb.io.ConditionField
The classname to use.
isCommentLine() - Method in class edu.cornell.med.icb.io.TSVReader
Get if the current line is a comment line.
isEmptyLine() - Method in class edu.cornell.med.icb.io.TSVReader
Return true if the current line is empty.
isHeaderWritten() - Method in class edu.cornell.med.icb.io.TsvToFromMap
Get if the header has already been written for this object.
isLenientColumnCount() - Method in class edu.cornell.med.icb.io.TsvToFromMap
When executing readDataToMap() if the input string has too many or too few columns it will normally throw an exception.
isList() - Method in class edu.cornell.med.icb.io.ConditionField
Get if this field may contain list values, separated by listSeparator.
isRemoveFromFrontSize() - Method in class edu.cornell.med.icb.util.BoundedPriorityQueue
Get if surplus elements should be removed from the front of the queue.
isSkipDuplicates() - Method in class edu.cornell.med.icb.iterators.PreSortedMergeTextFilesLineIterator
Get if duplicates will be skipped.
isSkipEmptyLines() - Method in class edu.cornell.med.icb.iterators.PreSortedMergeTextFilesLineIterator
Get if empty lines will be skipped.
iterator() - Method in class edu.cornell.med.icb.iterators.IteratorIterable
The augmented iterator.
iterator() - Method in class edu.cornell.med.icb.iterators.PreSortedMergeTextFilesLineIterator
This is the one method of the Iterable interface.
iterator() - Method in class edu.cornell.med.icb.iterators.RecursiveFileListIterator
The augmented iterator.
iterator() - Method in class edu.cornell.med.icb.iterators.TextFileLineIterator
This is the one method of the Iterable interface.
iterator() - Method in class edu.cornell.med.icb.iterators.TsvLineIterator
This is the one method of the Iterable interface.
IteratorIterable<T> - Class in edu.cornell.med.icb.iterators
Class that takes an Iterator and makes it Iterable so it can be used with a java foreach loop.
IteratorIterable(Iterator<T>) - Constructor for class edu.cornell.med.icb.iterators.IteratorIterable
Constructor, to convert the iterator.

L

LinkedHashToMultiTypeMap<T> - Class in edu.cornell.med.icb.maps
An extension of LinkedHashMap[T, String].
LinkedHashToMultiTypeMap() - Constructor for class edu.cornell.med.icb.maps.LinkedHashToMultiTypeMap
 

M

makeStringWrappable(String, int, String) - Static method in class edu.cornell.med.icb.util.ICBStringUtils
This will remove redundant whitespace then add sLineBreakString as necessary to help eliminate the problem (primary seen in FireFox) where long names containing no (or very little) whitespace would cause the HTML table to be excessively wide.
millis2hms(long) - Static method in class edu.cornell.med.icb.util.ICBStringUtils
Convert milliseconds to hours, minutes seconds.
modifyFilename(String, String[], String) - Static method in class edu.cornell.med.icb.util.ICBStringUtils
This method tries to append a string (mod) to the end of origFilename but BEFORE the extension.

N

next() - Method in class edu.cornell.med.icb.io.TSVReader
Prepare the line for parsing of fields.
next() - Method in class edu.cornell.med.icb.iterators.FlatteningIterator
Returns the next element in our iteration, throwing a NoSuchElementException if none is found.
next() - Method in class edu.cornell.med.icb.iterators.PreSortedMergeTextFilesLineIterator
Retrieve the next line.
next(int) - Method in class edu.cornell.med.icb.util.RandomAdapter
 
nextBoolean() - Method in class edu.cornell.med.icb.util.RandomAdapter
 
nextBytes(byte[]) - Method in class edu.cornell.med.icb.util.RandomAdapter
 
nextDouble() - Method in class edu.cornell.med.icb.util.RandomAdapter
 
nextFloat() - Method in class edu.cornell.med.icb.util.RandomAdapter
 
nextGaussian() - Method in class edu.cornell.med.icb.util.RandomAdapter
 
nextInt(int) - Method in class edu.cornell.med.icb.util.RandomAdapter
 
nextInt() - Method in class edu.cornell.med.icb.util.RandomAdapter
 
nextLong() - Method in class edu.cornell.med.icb.util.RandomAdapter
 
numTokens() - Method in class edu.cornell.med.icb.io.TSVReader
Get the number of fields on the current line.

O

offer(E) - Method in class edu.cornell.med.icb.util.BoundedPriorityQueue
Offer (add) an element to the queue then ensure then queue isn't larger than maxCapacity.

P

parseAllFieldsBean(Object, Map<String, String>) - Method in class edu.cornell.med.icb.io.ConditionsParser
This is a special case that allows ALL fields to be parsed at once as bean.
parseFieldBean(String, Object, Map<String, String>) - Method in class edu.cornell.med.icb.io.ConditionsParser
Parse the field (should be FieldType of MAP) to bean names and values to be set on targetObject.
parseFieldMap(String) - Method in class edu.cornell.med.icb.io.ConditionsParser
Parse the field to a MAP.
parseFieldValueBoolean(String) - Method in class edu.cornell.med.icb.io.ConditionsParser
Return the boolean value of the field named with fieldName or the default (converted to an boolean) if that field wasn't in the conditions file.
parseFieldValueBooleanArray(String) - Method in class edu.cornell.med.icb.io.ConditionsParser
Return the boolean[] values of the field named with fieldName or the default if that field wasn't in the conditions file.
parseFieldValueDouble(String) - Method in class edu.cornell.med.icb.io.ConditionsParser
Return the double value of the field named with fieldName or the default (converted to an double) if that field wasn't in the conditions file.
parseFieldValueDoubleArray(String) - Method in class edu.cornell.med.icb.io.ConditionsParser
Return the double[] values of the field named with fieldName or the default if that field wasn't in the conditions file.
parseFieldValueInt(String) - Method in class edu.cornell.med.icb.io.ConditionsParser
Return the int value of the field named with fieldName or the default (converted to an int) if that field wasn't in the conditions file.
parseFieldValueIntArray(String) - Method in class edu.cornell.med.icb.io.ConditionsParser
Return the int[] values of the field named with fieldName or the default if that field wasn't in the conditions file.
parseFieldValueString(String) - Method in class edu.cornell.med.icb.io.ConditionsParser
Return the String value of the field named with fieldName or the default if that field wasn't in the conditions file.
parseFieldValueStringArray(String) - Method in class edu.cornell.med.icb.io.ConditionsParser
Return the String[] values of the field named with fieldName or the default if that field wasn't in the conditions file.
PreSortedMergeTextFilesLineIterator - Class in edu.cornell.med.icb.iterators
Take a list of pre-sorted input files and return their lines in sorted order.
PreSortedMergeTextFilesLineIterator(String[]) - Constructor for class edu.cornell.med.icb.iterators.PreSortedMergeTextFilesLineIterator
Constructor with a String array of filenames.
PreSortedMergeTextFilesLineIterator(List) - Constructor for class edu.cornell.med.icb.iterators.PreSortedMergeTextFilesLineIterator
Constructor for filenames OR streams in a list.
PreSortedMergeTextFilesLineIterator(InputStream[]) - Constructor for class edu.cornell.med.icb.iterators.PreSortedMergeTextFilesLineIterator
Constructor for input streams.
printHelp(JSAP) - Method in class edu.cornell.med.icb.cli.UseModality
 
process(String[], OptionType) - Method in class edu.cornell.med.icb.cli.UseModality
Process the command line arguments.
process(OptionType) - Method in class edu.cornell.med.icb.cli.UseModality
Process with options.
ProcessEstimator - Class in edu.cornell.med.icb.util
Assist with estimation of time remaining for a long running process with a known number of units of work.
ProcessEstimator(int) - Constructor for class edu.cornell.med.icb.util.ProcessEstimator
Create a process estimator for a specified number of totalUnits.
PropertyMappable - Interface in edu.cornell.med.icb.identifier
Classes that implement this interface are capable of storing and loading there state to and from property objects.
put(T, Double) - Method in class edu.cornell.med.icb.maps.LinkedHashToMultiTypeMap
Put a Double into the map.
put(T, double[]) - Method in class edu.cornell.med.icb.maps.LinkedHashToMultiTypeMap
Put a double[] into the map.
put(T, Integer) - Method in class edu.cornell.med.icb.maps.LinkedHashToMultiTypeMap
Put an Integer into the map.
put(T, int[]) - Method in class edu.cornell.med.icb.maps.LinkedHashToMultiTypeMap
Put an int[] into the map.

R

RANDOM_STRING_LENGTH_DEFAULT - Static variable in class edu.cornell.med.icb.util.ICBStringUtils
 
RandomAdapter - Class in edu.cornell.med.icb.util
An adapter to use the colt RandomEngine implementations when java.util.Random is expected.
RandomAdapter(RandomEngine) - Constructor for class edu.cornell.med.icb.util.RandomAdapter
 
readDataToMap(String) - Method in class edu.cornell.med.icb.io.TsvToFromMap
Given a line of text, convert it to a Map[columnName, value] of data.
readIpList(InputStream, boolean, boolean) - Static method in class edu.cornell.med.icb.ip.IpUtils
Read a data from a stream (generally a file) that contains ip addresses and/or hostnames and comments.
readObject() - Method in class edu.cornell.med.icb.io.DataObjectInputStream
Read an object from the current stream position.
RecursiveFileListIterator - Class in edu.cornell.med.icb.iterators
This comes from http://snippets.dzone.com/posts/show/3532 The author, David R.
RecursiveFileListIterator(File, FileFilter) - Constructor for class edu.cornell.med.icb.iterators.RecursiveFileListIterator
Create a new RecursiveFileListIterator.
RecursiveFileListIterator(File) - Constructor for class edu.cornell.med.icb.iterators.RecursiveFileListIterator
Create a new RecursiveFileListIterator.
registerIdentifier(MutableString) - Method in class edu.cornell.med.icb.identifier.IndexedIdentifier
 
registerMode(String, Class<? extends UseModality<OptionType>>) - Method in class edu.cornell.med.icb.cli.UseModality
Register a new mode.
remove() - Method in class edu.cornell.med.icb.iterators.FlatteningIterator
Remove, does nothing.
remove() - Method in class edu.cornell.med.icb.iterators.PreSortedMergeTextFilesLineIterator
Remove not supported.
removeAccents(String) - Static method in class edu.cornell.med.icb.util.ICBStringNormalizer
Take a string with (international) access and return the same string but with the accents removed.
resetValueToDefault() - Method in class edu.cornell.med.icb.io.ConditionField
Reset currentValue of this field to default value.
ResourceFinder - Class in edu.cornell.med.icb.io
Help with obtaining resources.
ResourceFinder() - Constructor for class edu.cornell.med.icb.io.ResourceFinder
No extra paths configuration.
ResourceFinder(String...) - Constructor for class edu.cornell.med.icb.io.ResourceFinder
Create a resource finder.
ResourceFinder.SearchInClasspath - Enum in edu.cornell.med.icb.io
When to search the classpath enum.
resumeTimer() - Method in class edu.cornell.med.icb.util.ProcessEstimator
Resume the timer that was suspended with suspendTimer().
reversedList(boolean) - Method in class edu.cornell.med.icb.util.BoundedPriorityQueue
Reverse the queue to a list.

S

safeFilename(String) - Static method in class edu.cornell.med.icb.util.ICBStringUtils
Fixes filenames to be "safe" removing unwanted characters.
searchInClasspath - Variable in class edu.cornell.med.icb.io.ResourceFinder
When to search the classpath.
setClassname(boolean) - Method in class edu.cornell.med.icb.io.ConditionField
If FieldType is VALUE, this specifies that the value is a fully qualified pathname for a class with an no args constructor.
setClassnameKey(String) - Method in class edu.cornell.med.icb.io.ConditionField
When specifying a FieldType BEAN, it is possible to provide a classname and have a new object be created, the value associated with the key specified by classnameKey specifies the full class path of the object that should be created, and when you call parseFieldBean pass a null targetObject.
setCommentPrefix(String) - Method in class edu.cornell.med.icb.io.ConditionsParser
Set the commentPrefix, the String value (normally one or two characters) that specify the line is a comment and should be ignored, treated like a blank line.
setCommentPrefix(String) - Method in class edu.cornell.med.icb.io.TSVReader
Set the comment prefix that will be used to ignore commented lines.
setCurrentValue(String) - Method in class edu.cornell.med.icb.io.ConditionField
Set the currentValue of this field.
setDefaultValue(String) - Method in class edu.cornell.med.icb.io.ConditionField
Set the default value for this field, if no value is provided (or if the field is omitted).
setEscapeChar(Character) - Method in class edu.cornell.med.icb.io.ConditionsParser
Set the escape character that will be used when parsing.
setEscapeChar(Character) - Method in class edu.cornell.med.icb.io.TSVReader
Set the escape character being used.
setFieldSeparator(char) - Method in class edu.cornell.med.icb.io.ConditionsParser
Set the fieldSeparator, the char value that will separate multiple fields in the input.
setHeaderWritten(boolean) - Method in class edu.cornell.med.icb.io.TsvToFromMap
Set if the header has already been written for this object.
setKeyValueSeparator(char) - Method in class edu.cornell.med.icb.io.ConditionField
Set the keyValueSeparator, the char value that will separate key from value, used when FieldType is MAP.
setLenientColumnCount(boolean) - Method in class edu.cornell.med.icb.io.TsvToFromMap
When executing readDataToMap() if the input string has too many or too few columns it will normally throw an exception.
setList(boolean) - Method in class edu.cornell.med.icb.io.ConditionField
Set if this field contains list values, separated by listSeparator.
setListSeparator(char) - Method in class edu.cornell.med.icb.io.ConditionField
Set the listSeparator, the char value that will separate mutliple values for the field.
setMaxCapacity(int) - Method in class edu.cornell.med.icb.util.BoundedPriorityQueue
Set the max capacity of the queue.
setOriginalArgs(String[]) - Method in class edu.cornell.med.icb.cli.UseModality
Set the command line args used to start the program.
setRemoveFromFrontSize(boolean) - Method in class edu.cornell.med.icb.util.BoundedPriorityQueue
Set if surplus elements should be removed from the front of the queue.
setSearchInClasspath(ResourceFinder.SearchInClasspath) - Method in class edu.cornell.med.icb.io.ResourceFinder
Set when to search in classpath for the resource.
setSkipDuplicates(boolean) - Method in class edu.cornell.med.icb.iterators.PreSortedMergeTextFilesLineIterator
Set if duplicates will be skipped.
setSkipEmptyLines(boolean) - Method in class edu.cornell.med.icb.iterators.PreSortedMergeTextFilesLineIterator
Set if empty lines will be skipped.
setTestingMode(boolean) - Method in class edu.cornell.med.icb.cli.UseModality
Indiate that the code is in "test" mode.
setUnescapeResults(boolean) - Method in class edu.cornell.med.icb.io.TSVReader
Set the if the results should be unescaped.
setValueBeanProperty(String) - Method in class edu.cornell.med.icb.io.ConditionField
Set the bean property that will automatically be set if (a) FieldType is VALUE and (b) parsing for the field is done via parseFieldBean.
SimpleChecksum - Class in edu.cornell.med.icb.util
Utility class to add a simple 2 character checksum to a string and a method to validate the string has the correct checksum.
simpleChecksum(String) - Static method in class edu.cornell.med.icb.util.SimpleChecksum
Takes a string and returns a that same string with two additional characters which are a simple checksum, each char will be "A".."Z".
size() - Method in class edu.cornell.med.icb.identifier.DoubleIndexedIdentifier
 
skip() - Method in class edu.cornell.med.icb.io.TSVReader
Skip the current line.
split(String, char, Character) - Static method in class edu.cornell.med.icb.util.ICBStringUtils
Split a string.
startTimer() - Method in class edu.cornell.med.icb.util.ProcessEstimator
Starts the timer, clearing any elapsed time.
stripExtraSpaces(String) - Static method in class edu.cornell.med.icb.util.ICBStringUtils
Remove extra spaces.
suspendTimer() - Method in class edu.cornell.med.icb.util.ProcessEstimator
Suspends the timer, can be resumed with resumeTimer().

T

TextFileLineIterator - Class in edu.cornell.med.icb.iterators
This class allows line-by-line iteration through a text file.
TextFileLineIterator(String) - Constructor for class edu.cornell.med.icb.iterators.TextFileLineIterator
Create the object using a filename.
TextFileLineIterator(File) - Constructor for class edu.cornell.med.icb.iterators.TextFileLineIterator
Create the object using a file.
TextFileLineIterator(InputStream) - Constructor for class edu.cornell.med.icb.iterators.TextFileLineIterator
Create the object using an InputStream.
toPropertyMap() - Method in class edu.cornell.med.icb.identifier.IndexedIdentifier
Store the current state of the object to a map of properties.
toPropertyMap() - Method in interface edu.cornell.med.icb.identifier.PropertyMappable
Store the current state of the object to a map of properties.
TsvLineIterator - Class in edu.cornell.med.icb.iterators
Iterate a tsv file using a specified TsvToFromMap.
TsvLineIterator(String) - Constructor for class edu.cornell.med.icb.iterators.TsvLineIterator
Create the object using a filename.
TsvLineIterator(File) - Constructor for class edu.cornell.med.icb.iterators.TsvLineIterator
Create the object using a file.
TsvLineIterator(String, TsvToFromMap) - Constructor for class edu.cornell.med.icb.iterators.TsvLineIterator
Create the object using a filename.
TsvLineIterator(File, TsvToFromMap) - Constructor for class edu.cornell.med.icb.iterators.TsvLineIterator
Create the object using a file.
TsvLineIterator(InputStream, TsvToFromMap) - Constructor for class edu.cornell.med.icb.iterators.TsvLineIterator
Create the object using an InputStream.
TSVReader - Class in edu.cornell.med.icb.io
Helper class to parse tab/single character delimited file.
TSVReader(Reader) - Constructor for class edu.cornell.med.icb.io.TSVReader
Create a new TSVReader based on the supplied reader with a tab delimiter.
TSVReader(Reader, char) - Constructor for class edu.cornell.med.icb.io.TSVReader
Create a new TSVReader based on the supplied reader with the supplied delimiter.
TsvToFromMap - Class in edu.cornell.med.icb.io
Generic way to read/write TSV files given the column headers.
TsvToFromMap() - Constructor for class edu.cornell.med.icb.io.TsvToFromMap
Create a new TsvToFromMap object with no columns, it is expected that the columns will be added later with addColumn(...).
TsvToFromMap(String...) - Constructor for class edu.cornell.med.icb.io.TsvToFromMap
Create a new TsvToFromMap object given an array of columnHeader labels.

U

unescape(String[], Character) - Static method in class edu.cornell.med.icb.util.ICBStringUtils
Unescape an array of Strings.
unescape(String, Character) - Static method in class edu.cornell.med.icb.util.ICBStringUtils
Unescape a String.
unitCompleted() - Method in class edu.cornell.med.icb.util.ProcessEstimator
Call when a unit of work has been completed.
urlFix(String) - Static method in class edu.cornell.med.icb.util.ICBStringUtils
Fix a URL, encode special characters to hex values.
UseModality<OptionType> - Class in edu.cornell.med.icb.cli
Regroups parsing of command line options and processing for modular command line interface definition.
UseModality() - Constructor for class edu.cornell.med.icb.cli.UseModality
 

V

validate(String) - Static method in class edu.cornell.med.icb.util.SimpleChecksum
Take a string that contains a simple checksum and validate the that checksum is correct.
validateIpAddress(String) - Static method in class edu.cornell.med.icb.ip.IpUtils
Attempt to validate an IP address or hostname with optional comment.
valueOf(String) - Static method in enum edu.cornell.med.icb.io.ConditionField.FieldType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum edu.cornell.med.icb.io.ResourceFinder.SearchInClasspath
Returns the enum constant of this type with the specified name.
values() - Static method in enum edu.cornell.med.icb.io.ConditionField.FieldType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum edu.cornell.med.icb.io.ResourceFinder.SearchInClasspath
Returns an array containing the constants of this enum type, in the order they are declared.
VersionUtils - Class in edu.cornell.med.icb.util
Utilities to deal with version numbers of source code.

W

writeDataFromMap(PrintWriter, Map<String, String>) - Method in class edu.cornell.med.icb.io.TsvToFromMap
Write the Map[columnHeader, value] of data to the PrintWriter out.
writeHeader(PrintWriter) - Method in class edu.cornell.med.icb.io.TsvToFromMap
Write the header.
writeObject(Object) - Method in class edu.cornell.med.icb.io.DataObjectOutputStream
Write an object to the current stream position.

X

xmlFix(String) - Static method in class edu.cornell.med.icb.util.ICBStringUtils
Fix the incoming string to be safe for HTML <input>, etc..

A B C D E F G H I L M N O P R S T U V W X
icb-utils API icb-utils-182 (20120309094326)

Copyright © 2005-2012 Institute for Computational Biomedicine, All Rights Reserved.