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, Remote, Serializable

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

Constructor Summary

BioDataServerRmi()

Method Summary

void	addAnnotation(cytoscape.data.annotation.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, 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)
static void	main(String[] args)

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

getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

BioDataServerRmi

public BioDataServerRmi()
                 throws RemoteException

Method Detail

addAnnotation

public void addAnnotation(cytoscape.data.annotation.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

clear

public void clear()

Specified by:

clear in interface BioDataServerInterface

getAnnotationCount

public int getAnnotationCount()

Specified by:

getAnnotationCount in interface BioDataServerInterface

getAnnotationDescriptions

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

Specified by:

getAnnotationDescriptions in interface BioDataServerInterface

getAnnotation

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

Specified by:

getAnnotation in interface BioDataServerInterface

getAnnotation

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

Specified by:

getAnnotation in interface BioDataServerInterface

getClassifications

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

Specified by:

getClassifications in interface BioDataServerInterface

getClassifications

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

Specified by:

getClassifications in interface BioDataServerInterface

getAllAnnotations

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

Specified by:

getAllAnnotations in interface BioDataServerInterface

describe

public String describe()

Specified by:

describe in interface BioDataServerInterface

addThesaurus

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

Specified by:

addThesaurus in interface BioDataServerInterface

getCanonicalName

public String getCanonicalName(String species,
                               String commonName)

Specified by:

getCanonicalName in interface BioDataServerInterface

getAllCommonNames

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

Specified by:

getAllCommonNames in interface BioDataServerInterface

getCommonName

public String getCommonName(String species,
                            String canonicalName)

Specified by:

getCommonName in interface BioDataServerInterface

main

public static void main(String[] args)