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)

Method Summary

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

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

Thesaurus

public Thesaurus(String species)

Method Detail

getSpecies

public String getSpecies()

nodeLabelCount

public int nodeLabelCount()

add

public void add(String canonicalName,
                String commonName)

remove

public void remove(String canonicalName,
                   String commonName)

addAlternateCommonName

public void addAlternateCommonName(String canonicalName,
                                   String alternateCommonName)

getCommonName

public String getCommonName(String canonicalName)

getNodeLabel

public String getNodeLabel(String commonName)

getAllCommonNames

public String[] getAllCommonNames(String canonicalName)

getAlternateCommonNames

public String[] getAlternateCommonNames(String canonicalName)

getAllNamesInGroup

public String[] getAllNamesInGroup(String key)

toString

public String toString()

Overrides:

toString in class Object

dump

public void dump()