cytoscape.data.servers
Class BioDataServer

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

public class BioDataServer

extends Object

Constructor Summary

BioDataServer()

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.

Method Summary

void	addAnnotation(cytoscape.data.annotation.Annotation annotation)
void	addThesaurus(String species, cytoscape.data.synonyms.Thesaurus thesaurus)
void	clear()
String	describe()
String[][]	getAllAnnotations(cytoscape.data.annotation.AnnotationDescription description, String entity)
String[]	getAllCommonNames(String species, String commonName)
cytoscape.data.annotation.Annotation	getAnnotation(cytoscape.data.annotation.AnnotationDescription description)
cytoscape.data.annotation.Annotation	getAnnotation(String species, String curator, String type)
int	getAnnotationCount()
cytoscape.data.annotation.AnnotationDescription[]	getAnnotationDescriptions()
String	getCanonicalName(String species, String commonName)
int[]	getClassifications(cytoscape.data.annotation.AnnotationDescription description, String entity)
int[]	getClassifications(String species, String curator, String type, String entity)
String	getCommonName(String species, String canonicalName)
void	loadAnnotationFiles(String[] annotationFilenames, String[] ontologyFilenames)
void	loadObo(String[] annotationFilenames, String[] ontologyFilenames)
void	loadThesaurusFiles(String[] thesaurusFilenames)
void	loadThesaurusFiles2(String[] thesaurusFilenames)
cytoscape.data.annotation.Ontology[]	readOntologyFlatFiles(String[] ontologyFilenames)
cytoscape.data.annotation.Ontology[]	readOntologyFlatFiles2(String[] ontologyFilenames)

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.

BioDataServer

public BioDataServer()
              throws Exception

Method Detail

readOntologyFlatFiles

public cytoscape.data.annotation.Ontology[] readOntologyFlatFiles(String[] ontologyFilenames)
                                                           throws Exception

Throws:

Exception

readOntologyFlatFiles2

public cytoscape.data.annotation.Ontology[] readOntologyFlatFiles2(String[] ontologyFilenames)
                                                            throws Exception

Throws:

Exception

loadObo

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

Throws:

Exception

loadAnnotationFiles

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

Throws:

Exception

loadThesaurusFiles

public void loadThesaurusFiles(String[] thesaurusFilenames)
                        throws Exception

Throws:

Exception

loadThesaurusFiles2

public void loadThesaurusFiles2(String[] thesaurusFilenames)
                         throws Exception

Throws:

Exception

clear

public void clear()

addAnnotation

public void addAnnotation(cytoscape.data.annotation.Annotation annotation)

getAnnotationCount

public int getAnnotationCount()

getAnnotationDescriptions

public cytoscape.data.annotation.AnnotationDescription[] getAnnotationDescriptions()

getAnnotation

public cytoscape.data.annotation.Annotation getAnnotation(String species,
                                                          String curator,
                                                          String type)

getAnnotation

public cytoscape.data.annotation.Annotation getAnnotation(cytoscape.data.annotation.AnnotationDescription description)

getClassifications

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

getClassifications

public int[] getClassifications(cytoscape.data.annotation.AnnotationDescription description,
                                String entity)

getAllAnnotations

public String[][] getAllAnnotations(cytoscape.data.annotation.AnnotationDescription description,
                                    String entity)

describe

public String describe()

addThesaurus

public void addThesaurus(String species,
                         cytoscape.data.synonyms.Thesaurus thesaurus)

getCanonicalName

public String getCanonicalName(String species,
                               String commonName)

getAllCommonNames

public String[] getAllCommonNames(String species,
                                  String commonName)

getCommonName

public String getCommonName(String species,
                            String canonicalName)