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

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	loadThesaurusFiles(String[] thesaurusFilenames)
cytoscape.data.annotation.Ontology[]	readOntologyFlatFiles(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

BioDataServer

public BioDataServer()
              throws Exception

Method Detail

readOntologyFlatFiles

public cytoscape.data.annotation.Ontology[] readOntologyFlatFiles(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

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)