edu.cornell.med.icb.tissueinfo.annotations
Class AnnotationType

java.lang.Object
  edu.cornell.med.icb.tissueinfo.annotations.AnnotationType

public class AnnotationType
extends Object

Author:

Fabien Campagne Date: Sep 5, 2007 Time: 10:40:51 AM

Constructor Summary

AnnotationType(MutableString type)

Method Summary

void	associate(int sampleId, int value)
void	associate(int sampleId, MutableString value)
IntSet	getAnnotations(int sampleIndex) Returns the annotations associated with this sample.
int	getNumberOfValues() Returns the number of distinct value identifiers for this type.
MutableString	getType()
MutableString	getValue(int valueIndex)
int	getValueIndex(MutableString valueId) Return the value that represents this value identifier in the annotation sets.
void	registerDefaultValue(MutableString annotationValue) Register a default value for this type.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

AnnotationType

public AnnotationType(MutableString type)

Method Detail

getType

public MutableString getType()

associate

public void associate(int sampleId,
                      MutableString value)

associate

public void associate(int sampleId,
                      int value)

getAnnotations

public IntSet getAnnotations(int sampleIndex)

Returns the annotations associated with this sample. If a default value is defined for the type, will return the index of the default value.

Parameters:

sampleIndex - Index of the sample

Returns:

Set of annotation indices.

getValueIndex

public int getValueIndex(MutableString valueId)

Return the value that represents this value identifier in the annotation sets.

Parameters:

valueId - value identifier, such as lung, liver for tissue type annotations.

Returns:

Index of the value used to store the annotation in set returned by getAnnotations.

getNumberOfValues

public int getNumberOfValues()

Returns the number of distinct value identifiers for this type.

Returns:

the number of distinct value identifiers for this type.

getValue

public MutableString getValue(int valueIndex)

registerDefaultValue

public void registerDefaultValue(MutableString annotationValue)

Register a default value for this type. The default value will be returned whenever no value has been associated to the sample for this annotation type.

Parameters:

annotationValue - Default value.