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

cytoscape.data.servers
Class BioDataServer

java.lang.Object
  extended by cytoscape.data.servers.BioDataServer

public class BioDataServer
extends Object


Constructor Summary
BioDataServer()
          Creates a new BioDataServer object.
BioDataServer(String serverName)
          serverName is either an RMI URI, or a manifest file which says what files to load into an in-process server; the manifest, the annotations, and the ontologies, may be files on a filesystem, files in a jar, or files retrieved by HTTP Mod. by Kei (9/10/2005): 1.
 
Method Summary
 void addAnnotation(Annotation annotation)
          DOCUMENT ME!
 void addThesaurus(String species, Thesaurus thesaurus)
          DOCUMENT ME!
 void clear()
          DOCUMENT ME!
 String describe()
          DOCUMENT ME!
 String[][] getAllAnnotations(AnnotationDescription description, String entity)
          DOCUMENT ME!
 String[] getAllCommonNames(String species, String commonName)
          DOCUMENT ME!
 Annotation getAnnotation(AnnotationDescription description)
          DOCUMENT ME!
 Annotation getAnnotation(String species, String curator, String type)
          DOCUMENT ME!
 int getAnnotationCount()
          DOCUMENT ME!
 AnnotationDescription[] getAnnotationDescriptions()
          DOCUMENT ME!
 String getCanonicalName(String species, String commonName)
          DOCUMENT ME!
 int[] getClassifications(AnnotationDescription description, String entity)
          DOCUMENT ME!
 int[] getClassifications(String species, String curator, String type, String entity)
          DOCUMENT ME!
 String getCommonName(String species, String canonicalName)
          DOCUMENT ME!
 void loadAnnotationFiles(String[] annotationFilenames, String[] ontologyFilenames)
          DOCUMENT ME!
 void loadObo(String[] annotationFilenames, String[] ontologyFilenames)
          DOCUMENT ME!
 void loadThesaurusFiles(String[] thesaurusFilenames)
          DOCUMENT ME!
 void loadThesaurusFiles2(String[] thesaurusFilenames)
          DOCUMENT ME!
 Ontology[] readOntologyFlatFiles(String[] ontologyFilenames)
          DOCUMENT ME!
 Ontology[] readOntologyFlatFiles2(String[] ontologyFilenames)
          DOCUMENT ME!
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

BioDataServer

public BioDataServer(String serverName)
              throws Exception
serverName is either an RMI URI, or a manifest file which says what files to load into an in-process server; the manifest, the annotations, and the ontologies, may be files on a filesystem, files in a jar, or files retrieved by HTTP Mod. by Kei (9/10/2005): 1. Read new obo file and gene_association file format. 2. Wrote a taxon number <-> taxon name converter. This function is based on the list in the file, users need to put the file in the dir. Bio Data Server manages ontologies mapped onto CyAttributes This can be managed through GO Mapper GUI. kono(4/12/2006)

Throws:
Exception

BioDataServer

public BioDataServer()
              throws Exception
Creates a new BioDataServer object.

Throws:
Exception - DOCUMENT ME!
Method Detail

readOntologyFlatFiles

public Ontology[] readOntologyFlatFiles(String[] ontologyFilenames)
                                 throws Exception
DOCUMENT ME!

Parameters:
ontologyFilenames - DOCUMENT ME!
Returns:
DOCUMENT ME!
Throws:
Exception - DOCUMENT ME!

readOntologyFlatFiles2

public Ontology[] readOntologyFlatFiles2(String[] ontologyFilenames)
                                  throws Exception
DOCUMENT ME!

Parameters:
ontologyFilenames - DOCUMENT ME!
Returns:
DOCUMENT ME!
Throws:
Exception - DOCUMENT ME!

loadObo

public void loadObo(String[] annotationFilenames,
                    String[] ontologyFilenames)
             throws Exception
DOCUMENT ME!

Parameters:
annotationFilenames - DOCUMENT ME!
ontologyFilenames - DOCUMENT ME!
Throws:
Exception - DOCUMENT ME!

loadAnnotationFiles

public void loadAnnotationFiles(String[] annotationFilenames,
                                String[] ontologyFilenames)
                         throws Exception
DOCUMENT ME!

Parameters:
annotationFilenames - DOCUMENT ME!
ontologyFilenames - DOCUMENT ME!
Throws:
Exception - DOCUMENT ME!

loadThesaurusFiles

public void loadThesaurusFiles(String[] thesaurusFilenames)
                        throws Exception
DOCUMENT ME!

Parameters:
thesaurusFilenames - DOCUMENT ME!
Throws:
Exception - DOCUMENT ME!

loadThesaurusFiles2

public void loadThesaurusFiles2(String[] thesaurusFilenames)
                         throws Exception
DOCUMENT ME!

Parameters:
thesaurusFilenames - DOCUMENT ME!
Throws:
Exception - DOCUMENT ME!

clear

public void clear()
DOCUMENT ME!


addAnnotation

public void addAnnotation(Annotation annotation)
DOCUMENT ME!

Parameters:
annotation - DOCUMENT ME!

getAnnotationCount

public int getAnnotationCount()
DOCUMENT ME!

Returns:
DOCUMENT ME!

getAnnotationDescriptions

public AnnotationDescription[] getAnnotationDescriptions()
DOCUMENT ME!

Returns:
DOCUMENT ME!

getAnnotation

public Annotation getAnnotation(String species,
                                String curator,
                                String type)
DOCUMENT ME!

Parameters:
species - DOCUMENT ME!
curator - DOCUMENT ME!
type - DOCUMENT ME!
Returns:
DOCUMENT ME!

getAnnotation

public Annotation getAnnotation(AnnotationDescription description)
DOCUMENT ME!

Parameters:
description - DOCUMENT ME!
Returns:
DOCUMENT ME!

getClassifications

public int[] getClassifications(String species,
                                String curator,
                                String type,
                                String entity)
DOCUMENT ME!

Parameters:
species - DOCUMENT ME!
curator - DOCUMENT ME!
type - DOCUMENT ME!
entity - DOCUMENT ME!
Returns:
DOCUMENT ME!

getClassifications

public int[] getClassifications(AnnotationDescription description,
                                String entity)
DOCUMENT ME!

Parameters:
description - DOCUMENT ME!
entity - DOCUMENT ME!
Returns:
DOCUMENT ME!

getAllAnnotations

public String[][] getAllAnnotations(AnnotationDescription description,
                                    String entity)
DOCUMENT ME!

Parameters:
description - DOCUMENT ME!
entity - DOCUMENT ME!
Returns:
DOCUMENT ME!

describe

public String describe()
DOCUMENT ME!

Returns:
DOCUMENT ME!

addThesaurus

public void addThesaurus(String species,
                         Thesaurus thesaurus)
DOCUMENT ME!

Parameters:
species - DOCUMENT ME!
thesaurus - DOCUMENT ME!

getCanonicalName

public String getCanonicalName(String species,
                               String commonName)
DOCUMENT ME!

Parameters:
species - DOCUMENT ME!
commonName - DOCUMENT ME!
Returns:
DOCUMENT ME!

getAllCommonNames

public String[] getAllCommonNames(String species,
                                  String commonName)
DOCUMENT ME!

Parameters:
species - DOCUMENT ME!
commonName - DOCUMENT ME!
Returns:
DOCUMENT ME!

getCommonName

public String getCommonName(String species,
                            String canonicalName)
DOCUMENT ME!

Parameters:
species - DOCUMENT ME!
canonicalName - DOCUMENT ME!
Returns:
DOCUMENT ME!

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