cytoscape.data.servers
Class BioDataServerRmi

java.lang.Object
  java.rmi.server.RemoteObject
      java.rmi.server.RemoteServer
          java.rmi.server.UnicastRemoteObject
              cytoscape.data.servers.BioDataServerRmi

All Implemented Interfaces:

BioDataServerInterface, Serializable, Remote

public class BioDataServerRmi
extends UnicastRemoteObject
implements BioDataServerInterface, Serializable

This is the actual class which implements BioDataServer Methods.

Author:

kono 04/19/2006: Old code removed (to resolve naming issue.)

See Also:

Serialized Form

Field Summary

protected HashMap	annotations
protected Date	lastAccessTime
protected Date	startTime
protected HashMap	thesauri

Fields inherited from class java.rmi.server.RemoteObject

ref

Constructor Summary

BioDataServerRmi()
Creates a new BioDataServerRmi object.

Method Summary

void	addAnnotation(Annotation newAnnotation) if the new annotation is to an already annotated species, curator and type, then simply add (with possible overwriting for identical
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!
static void	main(String[] args) DOCUMENT ME!

Methods inherited from class java.rmi.server.UnicastRemoteObject

clone, exportObject, exportObject, exportObject, unexportObject

Methods inherited from class java.rmi.server.RemoteServer

getClientHost, getLog, setLog

Methods inherited from class java.rmi.server.RemoteObject

equals, getRef, hashCode, toString, toStub

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

annotations

protected HashMap annotations

thesauri

protected HashMap thesauri

startTime

protected Date startTime

lastAccessTime

protected Date lastAccessTime

Constructor Detail

BioDataServerRmi

public BioDataServerRmi()
                 throws RemoteException

Creates a new BioDataServerRmi object.

Throws:

RemoteException - DOCUMENT ME!

Method Detail

addAnnotation

public void addAnnotation(Annotation newAnnotation)

if the new annotation is to an already annotated species, curator and type, then simply add (with possible overwriting for identical

Specified by:

addAnnotation in interface BioDataServerInterface

Parameters:

newAnnotation - DOCUMENT ME!

clear

public void clear()

DOCUMENT ME!

Specified by:

clear in interface BioDataServerInterface

getAnnotationCount

public int getAnnotationCount()

DOCUMENT ME!

Specified by:

getAnnotationCount in interface BioDataServerInterface

Returns:

DOCUMENT ME!

getAnnotationDescriptions

public AnnotationDescription[] getAnnotationDescriptions()

DOCUMENT ME!

Specified by:

getAnnotationDescriptions in interface BioDataServerInterface

Returns:

DOCUMENT ME!

getAnnotation

public Annotation getAnnotation(String species,
                                String curator,
                                String type)

DOCUMENT ME!

Specified by:

getAnnotation in interface BioDataServerInterface

Parameters:

species - DOCUMENT ME!

curator - DOCUMENT ME!

type - DOCUMENT ME!

Returns:

DOCUMENT ME!

getAnnotation

public Annotation getAnnotation(AnnotationDescription description)

DOCUMENT ME!

Specified by:

getAnnotation in interface BioDataServerInterface

Parameters:

description - DOCUMENT ME!

Returns:

DOCUMENT ME!

getClassifications

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

DOCUMENT ME!

Specified by:

getClassifications in interface BioDataServerInterface

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!

Specified by:

getClassifications in interface BioDataServerInterface

Parameters:

description - DOCUMENT ME!

entity - DOCUMENT ME!

Returns:

DOCUMENT ME!

getAllAnnotations

public String[][] getAllAnnotations(AnnotationDescription description,
                                    String entity)

DOCUMENT ME!

Specified by:

getAllAnnotations in interface BioDataServerInterface

Parameters:

description - DOCUMENT ME!

entity - DOCUMENT ME!

Returns:

DOCUMENT ME!

describe

public String describe()

DOCUMENT ME!

Specified by:

describe in interface BioDataServerInterface

Returns:

DOCUMENT ME!

addThesaurus

public void addThesaurus(String species,
                         Thesaurus thesaurus)

DOCUMENT ME!

Specified by:

addThesaurus in interface BioDataServerInterface

Parameters:

species - DOCUMENT ME!

thesaurus - DOCUMENT ME!

getCanonicalName

public String getCanonicalName(String species,
                               String commonName)

DOCUMENT ME!

Specified by:

getCanonicalName in interface BioDataServerInterface

Parameters:

species - DOCUMENT ME!

commonName - DOCUMENT ME!

Returns:

DOCUMENT ME!

getAllCommonNames

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

DOCUMENT ME!

Specified by:

getAllCommonNames in interface BioDataServerInterface

Parameters:

species - DOCUMENT ME!

commonName - DOCUMENT ME!

Returns:

DOCUMENT ME!

getCommonName

public String getCommonName(String species,
                            String canonicalName)

DOCUMENT ME!

Specified by:

getCommonName in interface BioDataServerInterface

Parameters:

species - DOCUMENT ME!

canonicalName - DOCUMENT ME!

Returns:

DOCUMENT ME!

main

public static void main(String[] args)

DOCUMENT ME!

Parameters:

args - DOCUMENT ME!