org.coolmap.core.util.bioparser.gseagmt

Class GmtEntry

java.lang.Object

org.coolmap.core.util.bioparser.gseagmt.GmtEntry

public class GmtEntry
extends java.lang.Object

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	GmtEntry.ID_TYPE

Constructor Summary

Constructors

Constructor and Description
GmtEntry(java.lang.String name, GmtEntry.ID_TYPE idType)

Method Summary

Modifier and Type	Method and Description
void	addDescription(java.lang.String genesetString, java.lang.String descriptionString)
void	addEntry(java.lang.String genesetString, java.lang.String geneString)
void	clear(java.lang.String genesetString)
void	clearAll()
java.lang.String	getDescription(java.lang.String genesetString)
java.util.Set<java.lang.String>	getGeneSetGenes(java.lang.String geneSetName)
java.util.Set<java.lang.String>	getGeneSetNames()
static GmtEntry	parse(java.io.InputStream in)
static GmtEntry	parse(java.lang.String name, GmtEntry.ID_TYPE idType, java.io.InputStream in) parse from input stream
void	printStructure()

Methods inherited from class java.lang.Object

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

Constructor Detail

GmtEntry

public GmtEntry(java.lang.String name,
                GmtEntry.ID_TYPE idType)

Method Detail

addEntry

public void addEntry(java.lang.String genesetString,
                     java.lang.String geneString)

clear

public void clear(java.lang.String genesetString)

clearAll

public void clearAll()

addDescription

public void addDescription(java.lang.String genesetString,
                           java.lang.String descriptionString)

getDescription

public java.lang.String getDescription(java.lang.String genesetString)

printStructure

public void printStructure()

getGeneSetNames

public java.util.Set<java.lang.String> getGeneSetNames()

getGeneSetGenes

public java.util.Set<java.lang.String> getGeneSetGenes(java.lang.String geneSetName)

parse

public static GmtEntry parse(java.lang.String name,
                             GmtEntry.ID_TYPE idType,
                             java.io.InputStream in)
                      throws java.io.IOException

parse from input stream

Parameters:

name -

idType -

in -

Returns:

Throws:

java.io.IOException

parse

public static GmtEntry parse(java.io.InputStream in)
                      throws java.io.IOException

Throws:

java.io.IOException