cytoscape.data.synonyms
Class Thesaurus

java.lang.Object
  cytoscape.data.synonyms.Thesaurus

All Implemented Interfaces:

Serializable

public class Thesaurus
extends Object
implements Serializable

todo (pshannon, 25 oct 2002): there may be multiple canonicalNames for the same common name. a good example is from the d16s3098 marker region studied in the ISB's JDRF project: PHEMX -> NM_005705 PHEMX -> NM_139022 PHEMX -> NM_139023 PHEMX -> NM_139024 these are (I believe) mRNA splice variants. what to do?

See Also:

Serialized Form

Constructor Summary

Thesaurus(String species)
Creates a new Thesaurus object.

Method Summary

void	add(String canonicalName, String commonName) DOCUMENT ME!
void	addAlternateCommonName(String canonicalName, String alternateCommonName) DOCUMENT ME!
void	dump() DOCUMENT ME!
String[]	getAllCommonNames(String canonicalName) DOCUMENT ME!
String[]	getAllNamesInGroup(String key) DOCUMENT ME!
String[]	getAlternateCommonNames(String canonicalName) DOCUMENT ME!
String	getCommonName(String canonicalName) DOCUMENT ME!
String	getNodeLabel(String commonName) DOCUMENT ME!
String	getSpecies() DOCUMENT ME!
int	nodeLabelCount() DOCUMENT ME!
void	remove(String canonicalName, String commonName) DOCUMENT ME!
protected void	storeAmongAllCommonNames(String commonName, String canonicalName)
String	toString() DOCUMENT ME!

Methods inherited from class java.lang.Object

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

Constructor Detail

Thesaurus

public Thesaurus(String species)

Creates a new Thesaurus object.

Parameters:

species - DOCUMENT ME!

Method Detail

getSpecies

public String getSpecies()

DOCUMENT ME!

Returns:

DOCUMENT ME!

nodeLabelCount

public int nodeLabelCount()

DOCUMENT ME!

Returns:

DOCUMENT ME!

add

public void add(String canonicalName,
                String commonName)

DOCUMENT ME!

Parameters:

canonicalName - DOCUMENT ME!

commonName - DOCUMENT ME!

remove

public void remove(String canonicalName,
                   String commonName)

DOCUMENT ME!

Parameters:

canonicalName - DOCUMENT ME!

commonName - DOCUMENT ME!

addAlternateCommonName

public void addAlternateCommonName(String canonicalName,
                                   String alternateCommonName)

DOCUMENT ME!

Parameters:

canonicalName - DOCUMENT ME!

alternateCommonName - DOCUMENT ME!

storeAmongAllCommonNames

protected void storeAmongAllCommonNames(String commonName,
                                        String canonicalName)

getCommonName

public String getCommonName(String canonicalName)

DOCUMENT ME!

Parameters:

canonicalName - DOCUMENT ME!

Returns:

DOCUMENT ME!

getNodeLabel

public String getNodeLabel(String commonName)

DOCUMENT ME!

Parameters:

commonName - DOCUMENT ME!

Returns:

DOCUMENT ME!

getAllCommonNames

public String[] getAllCommonNames(String canonicalName)

DOCUMENT ME!

Parameters:

canonicalName - DOCUMENT ME!

Returns:

DOCUMENT ME!

getAlternateCommonNames

public String[] getAlternateCommonNames(String canonicalName)

DOCUMENT ME!

Parameters:

canonicalName - DOCUMENT ME!

Returns:

DOCUMENT ME!

getAllNamesInGroup

public String[] getAllNamesInGroup(String key)

DOCUMENT ME!

Parameters:

key - DOCUMENT ME!

Returns:

DOCUMENT ME!

toString

public String toString()

DOCUMENT ME!

Overrides:

toString in class Object

Returns:

DOCUMENT ME!

dump

public void dump()

DOCUMENT ME!