Author: pwang
Date: 2010-10-25 11:21:17 -0700 (Mon, 25 Oct 2010)
New Revision: 22361
Added:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/io/
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/io/AbstractCyWriter.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/io/CyNetworkViewWriter.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/io/CyTableWriter.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/io/ViewWriter.java
Log:
Moved from io-api bundle
Copied:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/io/AbstractCyWriter.java
(from rev 22342,
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/AbstractCyWriter.java)
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/io/AbstractCyWriter.java
(rev 0)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/io/AbstractCyWriter.java
2010-10-25 18:21:17 UTC (rev 22361)
@@ -0,0 +1,116 @@
+
+package org.cytoscape.task.internal.io;
+
+import org.cytoscape.work.AbstractTask;
+import org.cytoscape.work.TaskMonitor;
+import org.cytoscape.work.Tunable;
+import org.cytoscape.work.util.ListSingleSelection;
+import org.cytoscape.io.CyFileFilter;
+import org.cytoscape.io.write.CyWriter;
+import org.cytoscape.io.write.CyWriterManager;
+
+import java.io.File;
+
+import java.util.Map;
+import java.util.TreeMap;
+import java.util.ArrayList;
+
+/**
+ * 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
+ * {...@link org.cytoscape.io.write.CyWriter} can be identified.
+ */
+public abstract class AbstractCyWriter<T extends CyWriterManager> extends
AbstractTask
+ implements CyWriter {
+
+ private File outputFile;
+
+ /**
+ * The method sets the file to be written. This field should not
+ * 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.
+ */
+ public final void setOutputFile(File f) {
+ if ( f != null )
+ outputFile = f;
+ }
+
+ /**
+ * This method gets the file to be written. This method should not
+ * 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.
+ */
+ @Tunable(description="Select the output file name")
+ public final File getOutputFile() {
+ return outputFile;
+ }
+
+ /**
+ * 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
org.cytoscape.work.Tunable}
+ * processing.
+ */
+ @Tunable(description = "Select the export file format")
+ public final ListSingleSelection<String> options;
+
+ private final Map<String,CyFileFilter> descriptionFilterMap;
+
+ /**
+ * The CyWriterManager specified in the constructor.
+ */
+ protected final T writerManager;
+
+ /**
+ * @param writerManager The CyWriterManager to be used to determine
which
+ * {...@link org.cytoscape.io.write.CyWriter} to be used to write the
file chosen by the user.
+ */
+ public AbstractCyWriter(T writerManager) {
+ if ( writerManager == null )
+ throw new NullPointerException("CyWriterManager is
null");
+ this.writerManager = writerManager;
+
+ descriptionFilterMap = new TreeMap<String,CyFileFilter>();
+ for ( CyFileFilter f : writerManager.getAvailableWriters() )
+ descriptionFilterMap.put( f.getDescription(), f );
+
+ options = new ListSingleSelection<String>( new
ArrayList<String>( descriptionFilterMap.keySet() ) );
+ }
+
+ /**
+ * This method processes the chosen input file and output type and
attempts
+ * to write the file.
+ * @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 )
+ throw new NullPointerException("Output file has not be
specified!");
+
+ String desc = options.getSelectedValue();
+ if ( desc == null )
+ throw new NullPointerException("No file type has been
specified!");
+
+ CyFileFilter filter = descriptionFilterMap.get(desc);
+ if ( filter == null )
+ throw new NullPointerException("No file filter found
for specified file type!");
+
+ CyWriter writer = getWriter(filter,outputFile);
+ if ( writer == null )
+ throw new NullPointerException("No CyWriter found for
specified file type!");
+
+ insertTasksAfterCurrentTask( writer );
+ }
+
+ /**
+ * 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.
+ */
+ protected abstract CyWriter getWriter(CyFileFilter filter, File out)
throws Exception;
+
+}
Copied:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/io/CyNetworkViewWriter.java
(from rev 22342,
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CyNetworkViewWriter.java)
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/io/CyNetworkViewWriter.java
(rev 0)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/io/CyNetworkViewWriter.java
2010-10-25 18:21:17 UTC (rev 22361)
@@ -0,0 +1,38 @@
+
+package org.cytoscape.task.internal.io;
+
+import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.io.CyFileFilter;
+import org.cytoscape.io.write.CyNetworkViewWriterFactory;
+import org.cytoscape.io.write.CyNetworkViewWriterManager;
+import org.cytoscape.io.write.CyWriter;
+
+import java.io.File;
+
+/**
+ * A utility Task implementation specifically for writing a {...@link
org.cytoscape.view.model.CyNetworkView}.
+ */
+public final class CyNetworkViewWriter extends
AbstractCyWriter<CyNetworkViewWriterManager> {
+
+ // the view to be written
+ private final CyNetworkView view;
+
+ /**
+ * @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);
+ if ( view == null )
+ throw new NullPointerException("View is null");
+ this.view = view;
+ }
+
+ /**
+ * {...@inheritdoc}
+ */
+ protected CyWriter getWriter(CyFileFilter filter, File file) throws
Exception{
+ return writerManager.getWriter(view,filter,file);
+ }
+}
Copied:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/io/CyTableWriter.java
(from rev 22342,
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CyTableWriter.java)
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/io/CyTableWriter.java
(rev 0)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/io/CyTableWriter.java
2010-10-25 18:21:17 UTC (rev 22361)
@@ -0,0 +1,37 @@
+
+package org.cytoscape.task.internal.io;
+
+import org.cytoscape.model.CyTable;
+import org.cytoscape.io.CyFileFilter;
+import org.cytoscape.io.write.CyTableWriterFactory;
+import org.cytoscape.io.write.CyTableWriterManager;
+import org.cytoscape.io.write.CyWriter;
+
+import java.io.File;
+
+/**
+ * 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 {...@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);
+ if ( table == null )
+ throw new NullPointerException("Table is null");
+ this.table = table;
+ }
+
+ /**
+ * {...@inheritdoc}
+ */
+ protected CyWriter getWriter(CyFileFilter filter, File file) throws
Exception{
+ return writerManager.getWriter(table,filter,file);
+ }
+}
Copied:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/io/ViewWriter.java
(from rev 22342,
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/ViewWriter.java)
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/io/ViewWriter.java
(rev 0)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/io/ViewWriter.java
2010-10-25 18:21:17 UTC (rev 22361)
@@ -0,0 +1,45 @@
+
+package org.cytoscape.task.internal.io;
+
+import org.cytoscape.view.model.View;
+import org.cytoscape.view.presentation.RenderingEngine;
+import org.cytoscape.io.CyFileFilter;
+import org.cytoscape.io.write.CyWriter;
+import org.cytoscape.io.write.ViewWriterManager;
+
+import java.io.File;
+
+/**
+ * A utility Task implementation that will write the specified View to the
+ * the specified image file using the specified RenderingEngine.
+ */
+public final class ViewWriter extends AbstractCyWriter<ViewWriterManager> {
+
+ private final View<?> view;
+ private final RenderingEngine re;
+
+ /**
+ * @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.
+ */
+ public ViewWriter(ViewWriterManager writerManager, View<?> view,
RenderingEngine re ) {
+ super(writerManager);
+
+ if ( view == null )
+ throw new NullPointerException("view is null");
+ this.view = view;
+
+ if ( re == null )
+ throw new NullPointerException("rendering engine is
null");
+ this.re = re;
+ }
+
+ /**
+ * {...@inheritdoc}
+ */
+ protected CyWriter getWriter(CyFileFilter filter, File file) throws
Exception {
+ return writerManager.getWriter(view,re,filter,file);
+ }
+}
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