Cytoscape 2.6.2 (c) 2006,2007 ISB, MSKCC, UCSD

cytoscape.data.servers
Class BioDataServerRmi

java.lang.Object
  extended by java.rmi.server.RemoteObject
      extended by java.rmi.server.RemoteServer
          extended by java.rmi.server.UnicastRemoteObject
              extended by 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

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
getClass, notify, notifyAll, wait, wait, wait
 

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!

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