Author: pwang
Date: 2010-10-21 17:03:55 -0700 (Thu, 21 Oct 2010)
New Revision: 22342
Modified:
core3/io-api/trunk/src/main/java/org/cytoscape/io/read/CyNetworkViewReader.java
core3/io-api/trunk/src/main/java/org/cytoscape/io/read/CyNetworkViewReaderManager.java
core3/io-api/trunk/src/main/java/org/cytoscape/io/read/CyPropertyReader.java
core3/io-api/trunk/src/main/java/org/cytoscape/io/read/CyPropertyReaderManager.java
core3/io-api/trunk/src/main/java/org/cytoscape/io/read/CySessionReader.java
core3/io-api/trunk/src/main/java/org/cytoscape/io/read/CySessionReaderManager.java
core3/io-api/trunk/src/main/java/org/cytoscape/io/read/CyTableReader.java
core3/io-api/trunk/src/main/java/org/cytoscape/io/read/CyTableReaderManager.java
core3/io-api/trunk/src/main/java/org/cytoscape/io/read/InputStreamTaskFactory.java
core3/io-api/trunk/src/main/java/org/cytoscape/io/util/StreamUtil.java
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/AbstractCyWriter.java
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CyNetworkViewWriter.java
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CyNetworkViewWriterFactory.java
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CyNetworkViewWriterManager.java
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CyTableWriter.java
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CyTableWriterFactory.java
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CyTableWriterManager.java
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CyWriterFactory.java
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CyWriterManager.java
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/PropertyWriterFactory.java
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/PropertyWriterManager.java
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/SessionWriter.java
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/SessionWriterFactory.java
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/SessionWriterManager.java
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/ViewWriter.java
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/ViewWriterFactory.java
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/ViewWriterManager.java
Log:
Update doc
Modified:
core3/io-api/trunk/src/main/java/org/cytoscape/io/read/CyNetworkViewReader.java
===================================================================
---
core3/io-api/trunk/src/main/java/org/cytoscape/io/read/CyNetworkViewReader.java
2010-10-21 23:32:45 UTC (rev 22341)
+++
core3/io-api/trunk/src/main/java/org/cytoscape/io/read/CyNetworkViewReader.java
2010-10-22 00:03:55 UTC (rev 22342)
@@ -1,32 +1,30 @@
package org.cytoscape.io.read;
-import java.io.InputStream;
-
import org.cytoscape.view.vizmap.VisualStyle;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.work.Task;
/**
* An extension of the Task interface that returns an array of
- * {...@link CyNetworkView} objects as well as optional
- * {...@link VisualStyle} objects that are read as part of the Task.
+ * {...@link org.cytoscape.view.model.CyNetworkView} objects as well as
optional
+ * {...@link org.cytoscape.view.vizmap.VisualStyle} objects that are read as
part of the Task.
* Instances of this interface are created by InputStreamTaskFactory
* objects registered as OSGi services, which are in turn processed
* by associated reader manager objects that distinguish
* InputStreamTaskFactories based on the DataCategory associated with
- * the CyFileFilter.
+ * the {...@link org.cytoscape.io.CyFileFilter}.
*/
public interface CyNetworkViewReader extends Task {
/**
- * Return an array of CyNetworkView objects
- * @return An array of CyNetworkView objects.
+ * Return an array of {...@link org.cytoscape.view.model.CyNetworkView}
objects
+ * @return An array of {...@link
org.cytoscape.view.model.CyNetworkView} objects.
*/
CyNetworkView[] getNetworkViews();
/**
- * Return an array of VisualStyle objects.
- * @return An array of VisualStyle objects. The list may be
+ * Return an array of {...@link org.cytoscape.view.vizmap.VisualStyle}
objects.
+ * @return An array of {...@link org.cytoscape.view.vizmap.VisualStyle}
objects. The list may be
* empty if no VisualStyle is defined by the input being
* read.
*/
Modified:
core3/io-api/trunk/src/main/java/org/cytoscape/io/read/CyNetworkViewReaderManager.java
===================================================================
---
core3/io-api/trunk/src/main/java/org/cytoscape/io/read/CyNetworkViewReaderManager.java
2010-10-21 23:32:45 UTC (rev 22341)
+++
core3/io-api/trunk/src/main/java/org/cytoscape/io/read/CyNetworkViewReaderManager.java
2010-10-22 00:03:55 UTC (rev 22342)
@@ -30,15 +30,12 @@
import java.io.InputStream;
import java.net.URI;
-import java.util.Map;
-import org.cytoscape.work.TaskIterator;
-
/**
* An object that registers all InputStreamReaderFactory singletons,
* processes specified input to determine the appropriate factory to
- * use and then returns an instance of the correct CyNetworkViewReader
+ * use and then returns an instance of the correct {...@link
org.cytoscape.io.read.CyNetworkViewReader}
* for the input.
*/
public interface CyNetworkViewReaderManager {
Modified:
core3/io-api/trunk/src/main/java/org/cytoscape/io/read/CyPropertyReader.java
===================================================================
---
core3/io-api/trunk/src/main/java/org/cytoscape/io/read/CyPropertyReader.java
2010-10-21 23:32:45 UTC (rev 22341)
+++
core3/io-api/trunk/src/main/java/org/cytoscape/io/read/CyPropertyReader.java
2010-10-22 00:03:55 UTC (rev 22342)
@@ -9,14 +9,14 @@
* {...@link java.util.Properties},
* {...@link org.cytoscape.property.bookmark.Bookmarks},
* {...@link org.cytoscape.property.session.Cysession}. The system
- * determines the specific object type based on the CyFileFilter
+ * determines the specific object type based on the {...@link
org.cytoscape.io.CyFileFilter}
* associated with the InputStreamTaskFactory service that
* produces this reader.
* Instances of this interface are created by InputStreamTaskFactory
* objects registered as OSGi services, which are in turn processed
* by associated reader manager objects that distinguish
* InputStreamTaskFactories based on the DataCategory associated with
- * the CyFileFilter.
+ * the {...@link org.cytoscape.io.CyFileFilter}.
*/
public interface CyPropertyReader extends Task {
Modified:
core3/io-api/trunk/src/main/java/org/cytoscape/io/read/CyPropertyReaderManager.java
===================================================================
---
core3/io-api/trunk/src/main/java/org/cytoscape/io/read/CyPropertyReaderManager.java
2010-10-21 23:32:45 UTC (rev 22341)
+++
core3/io-api/trunk/src/main/java/org/cytoscape/io/read/CyPropertyReaderManager.java
2010-10-22 00:03:55 UTC (rev 22342)
@@ -6,14 +6,14 @@
/**
* An object that registers all InputStreamReaderFactory singletons,
* processes specified input to determine the appropriate factory to
- * use and then returns an instance of the correct CyPropertyReader
+ * use and then returns an instance of the correct {...@link
org.cytoscape.io.read.CyPropertyReader}
* for the input.
*/
public interface CyPropertyReaderManager {
/**
* Given a URI this method will attempt to find a InputStreamReaderFactory
* that can read the URI, will set the InputStream for the factory and
- * will return the reader task.
+ * will return the reader.
* @param uri The URI we're attempting to read.
* @return A reader than can read the specified URI. Will return null if
* no reader can be found.
@@ -23,7 +23,7 @@
/**
* Given an InputStream this method will attempt to find a
InputStreamReaderFactory
* that can read the stream, will set the InputStream for the factory and
- * will return the reader task.
+ * will return the reader.
* @param stream The input stream we're attempting to read.
* @return A reader than can read the specified stream. Will return null if
* no reader can be found.
Modified:
core3/io-api/trunk/src/main/java/org/cytoscape/io/read/CySessionReader.java
===================================================================
--- core3/io-api/trunk/src/main/java/org/cytoscape/io/read/CySessionReader.java
2010-10-21 23:32:45 UTC (rev 22341)
+++ core3/io-api/trunk/src/main/java/org/cytoscape/io/read/CySessionReader.java
2010-10-22 00:03:55 UTC (rev 22342)
@@ -5,21 +5,21 @@
/**
* An extension of the Task interface that returns a
- * {...@link CySession} object. The reader does nothing
- * beyond create the CySession object and does NOT
- * use the CySession object to define the state of
+ * {...@link org.cytoscape.property.session.Cysession} object. The reader does
nothing
+ * beyond create the {...@link org.cytoscape.property.session.Cysession}
object and does NOT
+ * use the {...@link org.cytoscape.property.session.Cysession} object to
define the state of
* Cytoscape - that is managed by the CySessionManager.
- * Instances of this interface are created by InputStreamTaskFactory
+ * Instances of this interface are created by {...@link
org.cytoscape.io.read.InputStreamTaskFactory}
* objects registered as OSGi services, which are in turn processed
* by associated reader manager objects that distinguish
- * InputStreamTaskFactories based on the DataCategory associated with
- * the CyFileFilter.
+ * InputStreamTaskFactories based on the {...@link
org.cytoscape.io.DataCategory} associated with
+ * the {...@link org.cytoscape.io.CyFileFilter}.
*/
public interface CySessionReader extends Task {
/**
- * return a session object
- * @return A {...@link CySession} object.
+ * return a {...@link org.cytoscape.session.CySession} object
+ * @return A {...@link org.cytoscape.session.CySession} object.
*/
CySession getCySession();
}
Modified:
core3/io-api/trunk/src/main/java/org/cytoscape/io/read/CySessionReaderManager.java
===================================================================
---
core3/io-api/trunk/src/main/java/org/cytoscape/io/read/CySessionReaderManager.java
2010-10-21 23:32:45 UTC (rev 22341)
+++
core3/io-api/trunk/src/main/java/org/cytoscape/io/read/CySessionReaderManager.java
2010-10-22 00:03:55 UTC (rev 22342)
@@ -6,14 +6,14 @@
/**
* An object that registers all InputStreamReaderFactory singletons,
* processes specified input to determine the appropriate factory to
- * use and then returns an instance of the correct CySessionReader
+ * use and then returns an instance of the correct {...@link
org.cytoscape.io.read.CySessionReader}
* for the input.
*/
public interface CySessionReaderManager {
/**
* Given a URI this method will attempt to find a InputStreamReaderFactory
* that can read the URI, will set the InputStream for the factory and
- * will return the reader task.
+ * will return the reader.
* @param uri The URI we're attempting to read.
* @return A reader than can read the specified URI. Will return null if
* no reader can be found.
@@ -21,9 +21,9 @@
CySessionReader getReader(URI uri);
/**
- * Given an InputStream this method will attempt to find a
InputStreamReaderFactory
+ * Given an {...@link java.io.InputStream} this method will attempt to
find a InputStreamReaderFactory
* that can read the stream, will set the InputStream for the factory and
- * will return the reader task.
+ * will return the reader.
* @param stream The input stream we're attempting to read.
* @return A reader than can read the specified stream. Will return null if
* no reader can be found.
Modified:
core3/io-api/trunk/src/main/java/org/cytoscape/io/read/CyTableReader.java
===================================================================
--- core3/io-api/trunk/src/main/java/org/cytoscape/io/read/CyTableReader.java
2010-10-21 23:32:45 UTC (rev 22341)
+++ core3/io-api/trunk/src/main/java/org/cytoscape/io/read/CyTableReader.java
2010-10-22 00:03:55 UTC (rev 22342)
@@ -5,18 +5,18 @@
/**
* An extension of the Task interface that returns an array of
- * {...@link CyTable} objects.
- * Instances of this interface are created by InputStreamTaskFactory
+ * {...@link org.cytoscape.model.CyTable} objects.
+ * Instances of this interface are created by {...@link
org.cytoscape.io.read.InputStreamTaskFactory}
* objects registered as OSGi services, which are in turn processed
* by associated reader manager objects that distinguish
- * InputStreamTaskFactories based on the DataCategory associated with
- * the CyFileFilter.
+ * InputStreamTaskFactories based on the {...@link
org.cytoscape.io.DataCategory} associated with
+ * the {...@link org.cytoscape.io.CyFileFilter}.
*/
public interface CyTableReader extends Task{
/**
- * Return an array of CyTable objects.
- * @return An array of CyTable objects.
+ * Return an array of {...@link org.cytoscape.model.CyTable} objects.
+ * @return An array of {...@link org.cytoscape.model.CyTable} objects.
*/
public CyTable[] getCyDataTables();
}
Modified:
core3/io-api/trunk/src/main/java/org/cytoscape/io/read/CyTableReaderManager.java
===================================================================
---
core3/io-api/trunk/src/main/java/org/cytoscape/io/read/CyTableReaderManager.java
2010-10-21 23:32:45 UTC (rev 22341)
+++
core3/io-api/trunk/src/main/java/org/cytoscape/io/read/CyTableReaderManager.java
2010-10-22 00:03:55 UTC (rev 22342)
@@ -30,13 +30,12 @@
import java.io.InputStream;
import java.net.URI;
-import org.cytoscape.work.TaskIterator;
/**
* An object that registers all InputStreamReaderFactory singletons,
* processes specified input to determine the appropriate factory to
- * use and then returns an instance of the correct CyTableReader
+ * use and then returns an instance of the correct {...@link
org.cytoscape.io.read.CyTableReader}
* for the input.
*/
public interface CyTableReaderManager {
@@ -44,7 +43,7 @@
/**
* Given a URI this method will attempt to find a
InputStreamReaderFactory
* that can read the URI, will set the InputStream for the factory and
- * will return the reader task.
+ * will return the reader.
* @param uri The URI we're attempting to read.
* @return A reader than can read the specified URI. Will return null
* if no reader can be found.
@@ -52,9 +51,9 @@
CyTableReader getReader(URI uri);
/**
- * Given an InputStream this method will attempt to find a
InputStreamReaderFactory
+ * Given an {...@link java.io.InputStream} this method will attempt to
find a InputStreamReaderFactory
* that can read the stream, will set the InputStream for the factory
and
- * will return the reader task.
+ * will return the reader.
* @param stream The input stream we're attempting to read.
* @return A reader than can read the specified stream. Will return null
* if no reader can be found.
Modified:
core3/io-api/trunk/src/main/java/org/cytoscape/io/read/InputStreamTaskFactory.java
===================================================================
---
core3/io-api/trunk/src/main/java/org/cytoscape/io/read/InputStreamTaskFactory.java
2010-10-21 23:32:45 UTC (rev 22341)
+++
core3/io-api/trunk/src/main/java/org/cytoscape/io/read/InputStreamTaskFactory.java
2010-10-22 00:03:55 UTC (rev 22342)
@@ -14,7 +14,7 @@
/**
* Sets the input stream that will be read by the Reader created from
* this factory.
- * @param is The InputStream to be read.
+ * @param is The {...@link java.io.InputStream} to be read.
*/
void setInputStream(InputStream is);
}
Modified: core3/io-api/trunk/src/main/java/org/cytoscape/io/util/StreamUtil.java
===================================================================
--- core3/io-api/trunk/src/main/java/org/cytoscape/io/util/StreamUtil.java
2010-10-21 23:32:45 UTC (rev 22341)
+++ core3/io-api/trunk/src/main/java/org/cytoscape/io/util/StreamUtil.java
2010-10-22 00:03:55 UTC (rev 22342)
@@ -13,18 +13,24 @@
// TODO what's the difference between these two methods?
/**
+ * Gets the input stream from given {...@link java.net.URL}.
* @param source The URL from which to generate the InputStream.
* @return An input stream from the specified URL.
*/
public InputStream getInputStream(URL source) throws IOException;
/**
+ * Obtain an InputStream for a given URL. Ensure proxy servers and an
input
+ * stream to the real URL source is created--not a locally cached and
out of
+ * date source. Proxy servers and other characteristics can cause pages
to
+ * be cached.
* @param source The URL from which to generate the InputStream.
* @return An input stream from the specified URL.
*/
public InputStream getBasicInputStream(URL source) throws IOException;
/**
+ * Obtain a {...@link java.net.URLConnectio} for a given {...@link
java.net.URL}.
* @param source The URL from which to generate the URLConnection.
* @return An URLConnection from the specified URL.
*/
Modified:
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/AbstractCyWriter.java
===================================================================
---
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/AbstractCyWriter.java
2010-10-21 23:32:45 UTC (rev 22341)
+++
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/AbstractCyWriter.java
2010-10-22 00:03:55 UTC (rev 22342)
@@ -16,7 +16,7 @@
* An abstract utility implementation of a Task that writes a user defined
* file to a file type determined by a provided writer manager. This class
* is meant to be extended for specific file types such that the appropriate
- * CyWriter can be identified.
+ * {...@link org.cytoscape.io.write.CyWriter} can be identified.
*/
public abstract class AbstractCyWriter<T extends CyWriterManager> extends
AbstractTask
implements CyWriter {
@@ -25,7 +25,7 @@
/**
* The method sets the file to be written. This field should not
- * be called directly, but rather handled by the {...@link Tunable}
+ * be called directly, but rather handled by the {...@link
org.cytoscape.work.Tunable}
* processing. This method is the "setter" portion of a
* getter/setter tunable method pair.
* @param f The file to be written.
@@ -37,7 +37,7 @@
/**
* This method gets the file to be written. This method should not
- * be called directly, but rather handled by the {...@link Tunable}
+ * be called directly, but rather handled by the {...@link
org.cytoscape.work.Tunable}
* processing. This method is the "getter" portion of a
* getter/setter tunable method pair.
* @return The file to be written.
@@ -50,7 +50,7 @@
/**
* The list of file type options generated by the file types
* available from the CyWriterManager. This field should not
- * be set directly, but rather handled by the {...@link Tunable}
+ * be set directly, but rather handled by the {...@link
org.cytoscape.work.Tunable}
* processing.
*/
@Tunable(description = "Select the export file format")
@@ -65,7 +65,7 @@
/**
* @param writerManager The CyWriterManager to be used to determine
which
- * CyWriter to be used to write the file chosen by the user.
+ * {...@link org.cytoscape.io.write.CyWriter} to be used to write the
file chosen by the user.
*/
public AbstractCyWriter(T writerManager) {
if ( writerManager == null )
@@ -80,9 +80,9 @@
}
/**
- * This method processes the chosesn input file and output type and
attempts
+ * This method processes the chosen input file and output type and
attempts
* to write the file.
- * @param tm The TaskMonitor provided by the TaskManager execution
environment.
+ * @param tm The {...@link org.cytoscape.work.TaskMonitor} provided by
the TaskManager execution environment.
*/
public final void run(TaskMonitor tm) throws Exception {
if ( outputFile == null )
@@ -104,7 +104,7 @@
}
/**
- * Should return a CyWriter object for writing the specified file of
the specified type.
+ * Should return a {...@link org.cytoscape.io.write.CyWriter} object
for writing the specified file of the specified type.
* @param filter The specific type of file to be written.
* @param out The file that will be written.
*/
Modified:
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CyNetworkViewWriter.java
===================================================================
---
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CyNetworkViewWriter.java
2010-10-21 23:32:45 UTC (rev 22341)
+++
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CyNetworkViewWriter.java
2010-10-22 00:03:55 UTC (rev 22342)
@@ -6,7 +6,7 @@
import java.io.File;
/**
- * A utility Task implementation specifically for writing a CyNetworkView.
+ * A utility Task implementation specifically for writing a {...@link
org.cytoscape.view.model.CyNetworkView}.
*/
public final class CyNetworkViewWriter extends
AbstractCyWriter<CyNetworkViewWriterManager> {
@@ -14,9 +14,9 @@
private final CyNetworkView view;
/**
- * @param writerManager The CyNetworkViewWriterManager used to
determine which
- * CyNetworkViewWriterFactory to use to write the file.
- * @param view The CyNetworkView to be written out.
+ * @param writerManager The {...@link
org.cytoscape.io.write.CyNetworkViewWriterManager} used to determine which
+ * {...@link org.cytoscape.io.write.CyNetworkViewWriterFactory} to use
to write the file.
+ * @param view The {...@link org.cytoscape.view.model.CyNetworkView} to
be written out.
*/
public CyNetworkViewWriter(CyNetworkViewWriterManager writerManager,
CyNetworkView view ) {
super(writerManager);
Modified:
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CyNetworkViewWriterFactory.java
===================================================================
---
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CyNetworkViewWriterFactory.java
2010-10-21 23:32:45 UTC (rev 22341)
+++
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CyNetworkViewWriterFactory.java
2010-10-22 00:03:55 UTC (rev 22342)
@@ -1,21 +1,20 @@
package org.cytoscape.io.write;
-import java.io.IOException;
-
-import org.cytoscape.io.FileIOFactory;
import org.cytoscape.view.model.CyNetworkView;
/**
- * A specialization of CyWriterFactory that allows a CyNetworkView to
+ * A specialization of {...@link org.cytoscape.io.write.CyWriterFactory} that
allows a
+ * {...@link org.cytoscape.view.model.CyNetworkView} to
* be specified and written.
*/
public interface CyNetworkViewWriterFactory extends CyWriterFactory {
/**
- * Specifies the CyNetworkView to be written by the CyWriter Task
+ * Specifies the {...@link org.cytoscape.view.model.CyNetworkView} to
be written by the
+ * {...@link org.cytoscaoe.io.write.CyWriter} Task
* generated by this factory. This method must be called
* prior to calling the getWriter() method.
- * @param view The CyNetworkView to be written.
+ * @param view The {...@link org.cytoscape.view.model.CyNetworkView} to
be written.
*/
void setNetworkView(CyNetworkView view);
}
Modified:
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CyNetworkViewWriterManager.java
===================================================================
---
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CyNetworkViewWriterManager.java
2010-10-21 23:32:45 UTC (rev 22341)
+++
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CyNetworkViewWriterManager.java
2010-10-22 00:03:55 UTC (rev 22342)
@@ -40,24 +40,25 @@
import java.io.OutputStream;
/**
- * A CyWriterManager specific to writing CyNetworkView objects.
+ * A {...@link org.cytoscape.io.write.CyWriterManager} specific to writing
+ * {...@link org.cytoscape.view.model.CyNetworkView} objects.
*/
public interface CyNetworkViewWriterManager extends CyWriterManager {
/**
- * @param view The CyNetworkView to be written.
- * @param filter The CyFileFilter that defines the type of file to be
written.
+ * @param view The {...@link org.cytoscape.view.model.CyNetworkView} to
be written.
+ * @param filter The {...@link org.cytoscape.io.CyFileFilter} that
defines the type of file to be written.
* @param file The file to be written.
- * @return The CyWriter Task that will attempt to write the specified
view to the
+ * @return The {...@link org.cytoscape.io.write.CyWriter} Task that
will attempt to write the specified view to the
* specified file of the specified file type.
*/
CyWriter getWriter(CyNetworkView view, CyFileFilter filter, File file)
throws Exception;
/**
- * @param view The CyNetworkView to be written.
- * @param filter The CyFileFilter that defines the type of file to be
written.
+ * @param view The {...@link org.cytoscape.view.model.CyNetworkView} to
be written.
+ * @param filter The {...@link org.cytoscape.io.CyFileFilter} that
defines the type of file to be written.
* @param os The output steam to be written.
- * @return The CyWriter Task that will attempt to write the specified
view to the
+ * @return The {...@link CyWriter} Task that will attempt to write the
specified view to the
* specified output steam of the specified file type.
*/
CyWriter getWriter(CyNetworkView view, CyFileFilter filter,
OutputStream os) throws Exception;
Modified:
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CyTableWriter.java
===================================================================
--- core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CyTableWriter.java
2010-10-21 23:32:45 UTC (rev 22341)
+++ core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CyTableWriter.java
2010-10-22 00:03:55 UTC (rev 22342)
@@ -6,16 +6,16 @@
import java.io.File;
/**
- * A utility Task implementation specifically for writing CyTable objects.
+ * A utility Task implementation specifically for writing {...@link
org.cytoscape.model.CyTable} objects.
*/
public final class CyTableWriter extends
AbstractCyWriter<CyTableWriterManager> {
private final CyTable table;
/**
- * @param writerManager The CyTableWriterManager used to determine
which
- * CyTableWriterFactory to use to write the file.
- * @param table The CyTable to be written out.
+ * @param writerManager The {...@link
org.cytoscape.io.write.CyTableWriterManager} used to determine which
+ * {...@link org.cytoscape.io.write.CyTableWriterFactory} to use to
write the file.
+ * @param table The {...@link org.cytoscape.model.CyTable} to be
written out.
*/
public CyTableWriter(CyTableWriterManager writerManager, CyTable table ) {
super(writerManager);
Modified:
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CyTableWriterFactory.java
===================================================================
---
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CyTableWriterFactory.java
2010-10-21 23:32:45 UTC (rev 22341)
+++
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CyTableWriterFactory.java
2010-10-22 00:03:55 UTC (rev 22342)
@@ -1,21 +1,18 @@
package org.cytoscape.io.write;
-import java.io.IOException;
-
-import org.cytoscape.io.FileIOFactory;
import org.cytoscape.model.CyTable;
/**
- * A specialization of CyWriterFactory that allows a CyTable to
+ * A specialization of {...@link CyWriterFactory} that allows a {...@link
org.cytoscape.model.CyTable} to
* be specified and written.
*/
public interface CyTableWriterFactory extends CyWriterFactory {
/**
- * Specifies the CyTable to be written by the CyWriter Task
+ * Specifies the {...@link org.cytoscape.model.CyTable} to be written
by the {...@link CyWriter} Task
* generated by this factory. This method must be called
* prior to calling the getWriter() method.
- * @param table The CyTable to be written.
+ * @param table The {...@link org.cytoscape.model.CyTable} to be
written.
*/
void setTable(CyTable table);
}
Modified:
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CyTableWriterManager.java
===================================================================
---
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CyTableWriterManager.java
2010-10-21 23:32:45 UTC (rev 22341)
+++
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CyTableWriterManager.java
2010-10-22 00:03:55 UTC (rev 22342)
@@ -40,24 +40,24 @@
import java.io.OutputStream;
/**
- * A CyWriterManager specific to writing CyTable objects.
+ * A {...@link CyWriterManager} specific to writing {...@link
org.cytoscape.model.CyTable} objects.
*/
public interface CyTableWriterManager extends CyWriterManager {
/**
- * @param table The CyTable to be written.
- * @param filter The CyFileFilter that defines the type of file to be
written.
+ * @param table The {...@link org.cytoscape.model.CyTable} to be
written.
+ * @param filter The {...@link org.cytoscape.io.CyFileFilter} that
defines the type of file to be written.
* @param file The file to be written.
- * @return The CyWriter Task that will attempt to write the specified
table to the
+ * @return The {...@link CyWriter} Task that will attempt to write the
specified table to the
* specified file of the specified file type.
*/
CyWriter getWriter(CyTable table, CyFileFilter filter, File file)
throws Exception;
/**
- * @param table The CyTable to be written.
- * @param filter The CyFileFilter that defines the type of file to be
written.
+ * @param table The {...@link org.cytoscape.model.CyTable} to be
written.
+ * @param filter The {...@link org.cytoscape.io.CyFileFilter} that
defines the type of file to be written.
* @param os The output stream to be written.
- * @return The CyWriter Task that will attempt to write the specified
table to the
+ * @return The {...@link CyWriter} Task that will attempt to write the
specified table to the
* specified output stream of the specified file type.
*/
CyWriter getWriter(CyTable table, CyFileFilter filter, OutputStream os)
throws Exception;
Modified:
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CyWriterFactory.java
===================================================================
---
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CyWriterFactory.java
2010-10-21 23:32:45 UTC (rev 22341)
+++
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CyWriterFactory.java
2010-10-22 00:03:55 UTC (rev 22342)
@@ -1,6 +1,5 @@
package org.cytoscape.io.write;
-import java.io.File;
import java.io.OutputStream;
import org.cytoscape.io.FileIOFactory;
@@ -14,15 +13,15 @@
public interface CyWriterFactory extends FileIOFactory {
/**
- * This method defines where the generated CyWriter Task should
+ * This method defines where the generated {...@link CyWriter} Task
should
* write its data to. This method is meant to be called prior
* to calling getWriter().
- * @param os The OutputStream to be written to.
+ * @param os The {...@link java.io.OutputStream} to be written to.
*/
void setOutputStream(OutputStream os);
/**
- * @return A CyWriter Task suitable for writing to the specified
+ * @return A {...@link CyWriter} Task suitable for writing to the
specified
* output stream.
*/
CyWriter getWriter();
Modified:
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CyWriterManager.java
===================================================================
---
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CyWriterManager.java
2010-10-21 23:32:45 UTC (rev 22341)
+++
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CyWriterManager.java
2010-10-22 00:03:55 UTC (rev 22342)
@@ -40,14 +40,14 @@
import org.cytoscape.io.CyFileFilter;
/**
- * A CyWriterManager aggregates CyWriterFactory services for specific
DataCategories
- * and provides a mechanism for choosing the CyWriterFactory given a particular
+ * A CyWriterManager aggregates {...@link CyWriterFactory} services for
specific DataCategories
+ * and provides a mechanism for choosing the {...@link CyWriterFactory} given
a particular
* file type.
*/
public interface CyWriterManager {
/**
- * @return A list of the available CyFileFilters that define the
available
+ * @return A list of the available {...@link
org.cytoscape.io.CyFileFilters} that define the available
* output types.
*/
List<CyFileFilter> getAvailableWriters();
@@ -55,9 +55,9 @@
/**
* @param filter The filter used to determine the type of file written.
- * @param os The OutputStream that will be written to by the CyWriter
- * generated by the CyWriterFactory.
- * @return A CyWriterFactory for the appropriate filter.
+ * @param os The {...@link java.io.OutputStream} that will be written
to by the {...@link CyWriter}
+ * generated by the {...@link CyWriterFactory}.
+ * @return A {...@link CyWriterFactory} for the appropriate filter.
*/
public CyWriterFactory getMatchingFactory(CyFileFilter filter,
OutputStream os);
}
Modified:
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/PropertyWriterFactory.java
===================================================================
---
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/PropertyWriterFactory.java
2010-10-21 23:32:45 UTC (rev 22341)
+++
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/PropertyWriterFactory.java
2010-10-22 00:03:55 UTC (rev 22342)
@@ -2,14 +2,14 @@
/**
- * A specialization of CyWriterFactory that allows a property Object to
+ * A specialization of {...@link CyWriterFactory} that allows a property
Object to
* be specified and written. See {...@link org.cytoscape.property.CyProperty}
* for details on the type of Object.
*/
public interface PropertyWriterFactory extends CyWriterFactory {
/**
- * Specifies the property object to be written by the CyWriter Task
+ * Specifies the property object to be written by the {...@link
CyWriter} Task
* generated by this factory. This method must be called
* prior to calling the getWriter() method.
* @param property The property object to be written. In general
Modified:
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/PropertyWriterManager.java
===================================================================
---
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/PropertyWriterManager.java
2010-10-21 23:32:45 UTC (rev 22341)
+++
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/PropertyWriterManager.java
2010-10-22 00:03:55 UTC (rev 22342)
@@ -39,7 +39,7 @@
import java.io.OutputStream;
/**
- * A CyWriterManager specific to writing property objects. See
+ * A {...@link CyWriterManager} specific to writing property objects. See
* {...@link org.cytoscape.property.CyProperty} for information on
* types of object expected.
*/
@@ -47,18 +47,18 @@
/**
* @param property The property object to be written.
- * @param filter The CyFileFilter that defines the type of file to be
written.
+ * @param filter The {...@link org.cytoscape.io.CyFileFilter} that
defines the type of file to be written.
* @param file The file to be written.
- * @return The CyWriter Task that will attempt to write the specified
property
+ * @return The {...@link CyWriter} Task that will attempt to write the
specified property
* object to the specified file of the specified file type.
*/
CyWriter getWriter(Object property, CyFileFilter filter, File file)
throws Exception;
/**
* @param property The property object to be written.
- * @param filter The CyFileFilter that defines the type of file to be
written.
+ * @param filter The {...@link CyFileFilter} that defines the type of
file to be written.
* @param os The output stream to be written.
- * @return The CyWriter Task that will attempt to write the specified
property
+ * @return The {...@link CyWriter} Task that will attempt to write the
specified property
* object to the specified output stream of the specified file type.
*/
CyWriter getWriter(Object property, CyFileFilter filter, OutputStream
os) throws Exception;
Modified:
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/SessionWriter.java
===================================================================
--- core3/io-api/trunk/src/main/java/org/cytoscape/io/write/SessionWriter.java
2010-10-21 23:32:45 UTC (rev 22341)
+++ core3/io-api/trunk/src/main/java/org/cytoscape/io/write/SessionWriter.java
2010-10-22 00:03:55 UTC (rev 22342)
@@ -9,7 +9,7 @@
import java.util.List;
/**
- * A utility Task implementation that writes a CySession to a file.
+ * A utility Task implementation that writes a {...@link
org.cytoscape.session.CySession} to a file.
*/
public final class SessionWriter extends AbstractTask implements CyWriter {
@@ -18,10 +18,10 @@
private final File outputFile;
/**
- * @param writerMgr The SessionWriterManager contains single expected
- * SessionWriterFactory to use to write the file.
- * @param session The CySession to be written out.
- * @param outputFile The file the CySession should be written to.
+ * @param writerMgr The {...@link
org.cytoscape.io.write.SessionWriterManager} contains single expected
+ * {...@link org.cytoscape.io.write.SessionWriterFactory} to use to
write the file.
+ * @param session The {...@link org.cytoscape.session.CySession} to be
written out.
+ * @param outputFile The file the {...@link
org.cytoscape.session.CySession} should be written to.
*/
public SessionWriter(SessionWriterManager writerMgr, CySession session,
File outputFile) {
@@ -41,7 +41,7 @@
/**
* The method that will actually write the specified session to the
specified
* file.
- * @param tm The TaskMonitor provided by the TaskManager execution
environment.
+ * @param tm The {...@link org.cytoscape.work.TaskMonitor} provided by
the TaskManager execution environment.
*/
public final void run(TaskMonitor tm) throws Exception {
Modified:
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/SessionWriterFactory.java
===================================================================
---
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/SessionWriterFactory.java
2010-10-21 23:32:45 UTC (rev 22341)
+++
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/SessionWriterFactory.java
2010-10-22 00:03:55 UTC (rev 22342)
@@ -4,16 +4,16 @@
import org.cytoscape.session.CySession;
/**
- * A specialization of CyWriterFactory that allows a CySession to
+ * A specialization of {...@link CyWriterFactory} that allows a {...@link
org.cytoscape.session.CySession} to
* be specified and written.
*/
public interface SessionWriterFactory extends CyWriterFactory {
/**
- * Specifies the CySession to be written by the CyWriter Task
+ * Specifies the {...@link org.cytoscape.session.CySession} to be
written by the {...@link CyWriter} Task
* generated by this factory. This method must be called
* prior to calling the getWriter() method.
- * @param session The CySession to be written.
+ * @param session The {...@link org.cytoscape.session.CySession} to be
written.
*/
void setSession(CySession session);
}
Modified:
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/SessionWriterManager.java
===================================================================
---
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/SessionWriterManager.java
2010-10-21 23:32:45 UTC (rev 22341)
+++
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/SessionWriterManager.java
2010-10-22 00:03:55 UTC (rev 22342)
@@ -40,24 +40,24 @@
import java.io.OutputStream;
/**
- * A CyWriterManager specific to writing CySession objects.
+ * A {...@link CyWriterManager} specific to writing {...@link
org.cytoscape.session.CySession} objects.
*/
public interface SessionWriterManager extends CyWriterManager {
/**
- * @param session The CySession to be written.
- * @param filter The CyFileFilter that defines the type of file to be
written.
+ * @param session The {...@link org.cytoscape.session.CySession} to be
written.
+ * @param filter The {...@link org.cytoscape.io.CyFileFilter} that
defines the type of file to be written.
* @param file The file to be written.
- * @return The CyWriter Task that will attempt to write the specified
session to the
+ * @return The {...@link CyWriter} Task that will attempt to write the
specified session to the
* specified file of the specified file type.
*/
CyWriter getWriter(CySession session, CyFileFilter filter, File file)
throws Exception;
/**
- * @param session The CySession to be written.
- * @param filter The CyFileFilter that defines the type of file to be
written.
+ * @param session The {...@link org.cytoscape.session.CySession} to be
written.
+ * @param filter The {...@link org.cytoscape.io.CyFileFilter} that
defines the type of file to be written.
* @param os The output stream to be written.
- * @return The CyWriter Task that will attempt to write the specified
session to the
+ * @return The {...@link CyWriter} Task that will attempt to write the
specified session to the
* specified output stream of the specified file type.
*/
CyWriter getWriter(CySession session, CyFileFilter filter, OutputStream
os) throws Exception;
Modified:
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/ViewWriter.java
===================================================================
--- core3/io-api/trunk/src/main/java/org/cytoscape/io/write/ViewWriter.java
2010-10-21 23:32:45 UTC (rev 22341)
+++ core3/io-api/trunk/src/main/java/org/cytoscape/io/write/ViewWriter.java
2010-10-22 00:03:55 UTC (rev 22342)
@@ -16,7 +16,7 @@
private final RenderingEngine re;
/**
- * @param writerManager The ViewWriterManager used to determine which
type of
+ * @param writerManager The {...@link
org.cytoscape.io.write.ViewWriterManager} used to determine which type of
* file should be written.
* @param view The View object to be written to the specified file.
* @param re The RenderingEngine used to generate the image to be
written to the file.
Modified:
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/ViewWriterFactory.java
===================================================================
---
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/ViewWriterFactory.java
2010-10-21 23:32:45 UTC (rev 22341)
+++
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/ViewWriterFactory.java
2010-10-22 00:03:55 UTC (rev 22342)
@@ -5,17 +5,17 @@
import org.cytoscape.view.model.View;
/**
- * A specialization of CyWriterFactory that allows a View to
+ * A specialization of {...@link CyWriterFactory} that allows a View to
* be specified and written.
*/
public interface ViewWriterFactory extends CyWriterFactory {
/**
- * Specifies the View to be written by the CyWriter Task
+ * Specifies the {...@link org.cytoscape.view.model.View} to be written
by the {...@link CyWriter} Task
* generated by this factory. This method must be called
* prior to calling the getWriter() method.
- * @param view The View to be written.
- * @param re The RenderingEngine used to generate the image of the
+ * @param view The {org.cytoscape.view.model.View} to be written.
+ * @param re The {...@link
org.cytoscape.view.presentation.RenderingEngine} used to generate the image of
the
* specified View.
*/
void setViewRenderer(View<?> view, RenderingEngine re);
Modified:
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/ViewWriterManager.java
===================================================================
---
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/ViewWriterManager.java
2010-10-21 23:32:45 UTC (rev 22341)
+++
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/ViewWriterManager.java
2010-10-22 00:03:55 UTC (rev 22342)
@@ -41,26 +41,26 @@
import java.io.OutputStream;
/**
- * A CyWriterManager specific to writing View objects.
+ * A {...@link CyWriterManager} specific to writing View objects.
*/
public interface ViewWriterManager extends CyWriterManager {
/**
- * @param view The View to be written.
- * @param re The RenderingEngine used to generate the image to be
written.
- * @param filter The CyFileFilter that defines the type of file to be
written.
+ * @param view The {...@link org.cytoscape.view.model.View} to be
written.
+ * @param re The {...@link
org.cytoscape.view.presentation.RenderingEngine} used to generate the image to
be written.
+ * @param filter The {...@link org.cytoscape.io.CyFileFilter} that
defines the type of file to be written.
* @param file The file to be written.
- * @return The CyWriter Task that will attempt to write the specified
view to the
+ * @return The {...@link org.cytoscape.io.CyWriter} Task that will
attempt to write the specified view to the
* specified file of the specified file type.
*/
CyWriter getWriter(View<?> view, RenderingEngine re, CyFileFilter
filter, File file) throws Exception;
/**
* @param view The View to be written.
- * @param re The RenderingEngine used to generate the image to be
written.
- * @param filter The CyFileFilter that defines the type of file to be
written.
+ * @param re The {...@link
org.cytoscape.view.presentation.RenderingEngine} used to generate the image to
be written.
+ * @param filter The {...@link org.cytoscape.io.CyFileFilter} that
defines the type of file to be written.
* @param os The output stream to be written.
- * @return The CyWriter Task that will attempt to write the specified
view to the
+ * @return The {...@link CyWriter} Task that will attempt to write the
specified view to the
* specified output stream of the specified file type.
*/
CyWriter getWriter(View<?> view, RenderingEngine re, CyFileFilter
filter, OutputStream os) throws Exception;
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