Cytoscape 2.6.2 (c) 2006,2007 ISB, MSKCC, UCSD

cytoscape.data.synonyms
Class Thesaurus

java.lang.Object
  extended by 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!
 String toString()
          DOCUMENT ME!
 
Methods inherited from class java.lang.Object
equals, 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!

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!


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