cytoscape.data.servers
Class BioDataServer

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

public class BioDataServer
extends Object

Field Summary

protected BioDataServerInterface

server

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.

Method Summary

void	addAnnotation(Annotation annotation) DOCUMENT ME!
void	addThesaurus(String species, Thesaurus thesaurus) DOCUMENT ME!
protected boolean	checkFileType(BufferedReader br)
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!
protected String[]	parseLoadFile(String filename, String key)
protected Ontology	pickOntology(Ontology[] ontologies, Annotation annotation)
Ontology[]	readOntologyFlatFiles(String[] ontologyFilenames) DOCUMENT ME!
Ontology[]	readOntologyFlatFiles2(String[] ontologyFilenames) DOCUMENT ME!

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

server

protected BioDataServerInterface server

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

checkFileType

protected boolean checkFileType(BufferedReader br)
                         throws IOException

Throws:

IOException

parseLoadFile

protected String[] parseLoadFile(String filename,
                                 String key)

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!

pickOntology

protected Ontology pickOntology(Ontology[] ontologies,
                                Annotation annotation)

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!