org.wandora.application.tools.importers

Class GOAImport

java.lang.Object

org.wandora.application.tools.AbstractWandoraTool

org.wandora.application.tools.importers.AbstractImportTool

org.wandora.application.tools.importers.GOAImport

All Implemented Interfaces:

java.io.Serializable, java.lang.Runnable, WandoraTool, WandoraToolLogger, TopicMapLogger

public class GOAImport
extends AbstractImportTool
implements WandoraTool

Gene Ontology Annotation file format import. See http://www.geneontology.org/GO.format.annotation.shtml

Author:

akivela

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	GOAImport.GOAParser OBOParser class implements parser for OBO flat file format.

Field Summary

Fields inherited from class org.wandora.application.tools.importers.AbstractImportTool

ASK_SOURCE, askSource, CLOSE_LOGS, closeLogs, CUSTOM_IMPORTER, directMerge, FILE_DIALOG_TITLE_TEXT, FILE_IMPORTER, forceFiles, newLayer, RAW_IMPORTER, resetWandoraFirst, TOPICMAP_DIRECT_MERGE, TOPICMAP_MAKE_NEW_LAYER, TOPICMAP_RESET_FIRST, URL_DIALOG_MESSAGE_TEXT, URL_IMPORTER, WEB_IMPORT, webImport

Fields inherited from interface org.wandora.application.WandoraToolLogger

CLOSE, EXECUTE, INVISIBLE, VISIBLE, WAIT

Constructor Summary

Constructors

Constructor and Description
GOAImport()

Method Summary

Modifier and Type	Method and Description
java.lang.String	getDescription() AdminToolManager views tool descriptions while user browses available tools and build user customizable GUI elements such as Tools menu.
java.lang.String	getGUIText(int textType)
javax.swing.Icon	getIcon() All tools may have identifying graphic icon used within tool GUI elements.
java.lang.String	getName() Tools name represent the tool in UI unless the tool has been given explicitly another GUI name.
void	importGOA(java.io.InputStream in, TopicMap map)
void	importStream(Wandora wandora, java.lang.String streamName, java.io.InputStream inputStream)

Methods inherited from class org.wandora.application.tools.importers.AbstractImportTool

createNewLayer, execute, finalizeImport, getLayerNameFor, getOptions, getType, importFile, importFiles, importUrl, initializeImport, requestImports, setOptions

Methods inherited from class org.wandora.application.tools.AbstractWandoraTool

addUndoMarker, addUndoMarker, allowMultipleInvocations, clearAllThreads, clearThreads, clearThreads, clearToolLock, clearToolLock, clearToolLocks, configure, execute, execute, forceStop, forceStop, getContext, getCurrentLogger, getDefaultLogger, getHistory, getLastLogger, getState, getThreads, getThreads, getToolMenuItem, getToolMenuItem, getTopicName, hlog, initialize, interruptAllThreads, interruptThreads, interruptThreads, isConfigurable, isRunning, isRunning, lockLog, log, log, log, log, requiresRefresh, run, runInOwnThread, setContext, setDefaultLogger, setLogTitle, setProgress, setProgressMax, setState, setToolLogger, singleLog, singleLog, singleLog, solveContextTopicMap, solveNameForTopicMap, writeOptions

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.wandora.application.WandoraTool

configure, execute, execute, execute, getContext, getToolMenuItem, getType, hlog, initialize, isConfigurable, isRunning, log, log, log, log, requiresRefresh, setContext, setToolLogger, writeOptions

Methods inherited from interface org.wandora.application.WandoraToolLogger

forceStop, getHistory, getState, lockLog, setLogTitle, setProgress, setProgressMax, setState

Constructor Detail

GOAImport

public GOAImport()

Method Detail

getName

public java.lang.String getName()

Description copied from class: AbstractWandoraTool

Tools name represent the tool in UI unless the tool has been given explicitly another GUI name. All tools should override this method and return a valid string representing name of the tool.

Specified by:

getName in interface WandoraTool

Overrides:

getName in class AbstractWandoraTool

Returns:

String representing tool's name.

getDescription

public java.lang.String getDescription()

Description copied from class: AbstractWandoraTool

AdminToolManager views tool descriptions while user browses available tools and build user customizable GUI elements such as Tools menu. By default description equals the tool name. All tools should override this method.

Specified by:

getDescription in interface WandoraTool

Overrides:

getDescription in class AbstractWandoraTool

Returns:

String representing tool's description.

getIcon

public javax.swing.Icon getIcon()

Description copied from class: AbstractWandoraTool

All tools may have identifying graphic icon used within tool GUI elements. getIcon should return Icon object of the tool.

Specified by:

getIcon in interface WandoraTool

Overrides:

getIcon in class AbstractImportTool

Returns:

icon for the tool.

importStream

public void importStream(Wandora wandora,
                         java.lang.String streamName,
                         java.io.InputStream inputStream)

Specified by:

importStream in class AbstractImportTool

importGOA

public void importGOA(java.io.InputStream in,
                      TopicMap map)

getGUIText

public java.lang.String getGUIText(int textType)

Overrides:

getGUIText in class AbstractImportTool