Author: pwang
Date: 2010-10-25 14:52:08 -0700 (Mon, 25 Oct 2010)
New Revision: 22389
Added:
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CyPropertyWriterFactory.java
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CyPropertyWriterManager.java
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CySessionWriter.java
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CySessionWriterFactory.java
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CySessionWriterManager.java
Removed:
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
Log:
Rename classes
Copied:
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CyPropertyWriterFactory.java
(from rev 22368,
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/PropertyWriterFactory.java)
===================================================================
---
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CyPropertyWriterFactory.java
(rev 0)
+++
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CyPropertyWriterFactory.java
2010-10-25 21:52:08 UTC (rev 22389)
@@ -0,0 +1,19 @@
+package org.cytoscape.io.write;
+
+
+/**
+ * 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 CyPropertyWriterFactory extends CyWriterFactory {
+
+ /**
+ * 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
+ * this object should be of types described in {...@link
org.cytoscape.property.CyProperty}.
+ */
+ void setProperty(Object property);
+}
Copied:
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CyPropertyWriterManager.java
(from rev 22368,
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/PropertyWriterManager.java)
===================================================================
---
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CyPropertyWriterManager.java
(rev 0)
+++
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CyPropertyWriterManager.java
2010-10-25 21:52:08 UTC (rev 22389)
@@ -0,0 +1,65 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package org.cytoscape.io.write;
+
+import org.cytoscape.io.CyFileFilter;
+import java.io.File;
+import java.io.OutputStream;
+
+/**
+ * A {...@link CyWriterManager} specific to writing property objects. See
+ * {...@link org.cytoscape.property.CyProperty} for information on
+ * types of object expected.
+ */
+public interface CyPropertyWriterManager extends CyWriterManager {
+
+ /**
+ * @param property The property object 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 {...@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 {...@link CyFileFilter} that defines the type of
file to be written.
+ * @param os The output stream to be written.
+ * @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;
+}
Copied:
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CySessionWriter.java
(from rev 22368,
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/SessionWriter.java)
===================================================================
---
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CySessionWriter.java
(rev 0)
+++
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CySessionWriter.java
2010-10-25 21:52:08 UTC (rev 22389)
@@ -0,0 +1,60 @@
+
+package org.cytoscape.io.write;
+
+import org.cytoscape.session.CySession;
+import org.cytoscape.io.CyFileFilter;
+import org.cytoscape.work.TaskMonitor;
+import org.cytoscape.work.AbstractTask;
+import java.io.File;
+import java.util.List;
+
+/**
+ * A utility Task implementation that writes a {...@link
org.cytoscape.session.CySession} to a file.
+ */
+public final class CySessionWriter extends AbstractTask implements CyWriter {
+
+ private final CySession session;
+ private final CySessionWriterManager writerMgr;
+ private final File outputFile;
+
+ /**
+ * @param writerMgr The {...@link
org.cytoscape.io.write.CySessionWriterManager} contains single expected
+ * {...@link org.cytoscape.io.write.CySessionWriterFactory} 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 CySessionWriter(CySessionWriterManager writerMgr, CySession
session, File outputFile) {
+
+ if ( writerMgr == null )
+ throw new NullPointerException("Writer Manager is
null");
+ this.writerMgr = writerMgr;
+
+ if ( session == null )
+ throw new NullPointerException("Session Manager is
null");
+ this.session = session;
+
+ if ( outputFile == null )
+ throw new NullPointerException("Output File is null");
+ this.outputFile = outputFile;
+ }
+
+ /**
+ * The method that will actually write the specified session to the
specified
+ * file.
+ * @param tm The {...@link org.cytoscape.work.TaskMonitor} provided by
the TaskManager execution environment.
+ */
+ public final void run(TaskMonitor tm) throws Exception {
+
+ List<CyFileFilter> filters = writerMgr.getAvailableWriters();
+ if ( filters == null || filters.size() < 1)
+ throw new NullPointerException("No Session file filters
found");
+ if ( filters.size() > 1 )
+ throw new IllegalArgumentException("Found too many
session filters!");
+
+ CyWriter writer =
writerMgr.getWriter(session,filters.get(0),outputFile);
+ if ( writer == null )
+ throw new NullPointerException("No CyWriter found for
specified file type!");
+
+ insertTasksAfterCurrentTask( writer );
+ }
+}
Copied:
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CySessionWriterFactory.java
(from rev 22368,
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/SessionWriterFactory.java)
===================================================================
---
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CySessionWriterFactory.java
(rev 0)
+++
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CySessionWriterFactory.java
2010-10-25 21:52:08 UTC (rev 22389)
@@ -0,0 +1,19 @@
+package org.cytoscape.io.write;
+
+
+import org.cytoscape.session.CySession;
+
+/**
+ * A specialization of {...@link CyWriterFactory} that allows a {...@link
org.cytoscape.session.CySession} to
+ * be specified and written.
+ */
+public interface CySessionWriterFactory extends CyWriterFactory {
+
+ /**
+ * 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 {...@link org.cytoscape.session.CySession} to be
written.
+ */
+ void setSession(CySession session);
+}
Copied:
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CySessionWriterManager.java
(from rev 22368,
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/SessionWriterManager.java)
===================================================================
---
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CySessionWriterManager.java
(rev 0)
+++
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/CySessionWriterManager.java
2010-10-25 21:52:08 UTC (rev 22389)
@@ -0,0 +1,64 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package org.cytoscape.io.write;
+
+import org.cytoscape.session.CySession;
+import org.cytoscape.io.CyFileFilter;
+import java.io.File;
+import java.io.OutputStream;
+
+/**
+ * A {...@link CyWriterManager} specific to writing {...@link
org.cytoscape.session.CySession} objects.
+ */
+public interface CySessionWriterManager extends CyWriterManager {
+
+ /**
+ * @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 {...@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 {...@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 {...@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;
+}
Deleted:
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
2010-10-25 21:48:31 UTC (rev 22388)
+++
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/PropertyWriterFactory.java
2010-10-25 21:52:08 UTC (rev 22389)
@@ -1,19 +0,0 @@
-package org.cytoscape.io.write;
-
-
-/**
- * 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 {...@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
- * this object should be of types described in {...@link
org.cytoscape.property.CyProperty}.
- */
- void setProperty(Object property);
-}
Deleted:
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
2010-10-25 21:48:31 UTC (rev 22388)
+++
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/PropertyWriterManager.java
2010-10-25 21:52:08 UTC (rev 22389)
@@ -1,65 +0,0 @@
-/*
- Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
-
- The Cytoscape Consortium is:
- - Institute for Systems Biology
- - University of California San Diego
- - Memorial Sloan-Kettering Cancer Center
- - Institut Pasteur
- - Agilent Technologies
-
- This library is free software; you can redistribute it and/or modify it
- under the terms of the GNU Lesser General Public License as published
- by the Free Software Foundation; either version 2.1 of the License, or
- any later version.
-
- This library is distributed in the hope that it will be useful, but
- WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
- MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
- documentation provided hereunder is on an "as is" basis, and the
- Institute for Systems Biology and the Whitehead Institute
- have no obligations to provide maintenance, support,
- updates, enhancements or modifications. In no event shall the
- Institute for Systems Biology and the Whitehead Institute
- be liable to any party for direct, indirect, special,
- incidental or consequential damages, including lost profits, arising
- out of the use of this software and its documentation, even if the
- Institute for Systems Biology and the Whitehead Institute
- have been advised of the possibility of such damage. See
- the GNU Lesser General Public License for more details.
-
- You should have received a copy of the GNU Lesser General Public License
- along with this library; if not, write to the Free Software Foundation,
- Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
- */
-package org.cytoscape.io.write;
-
-import org.cytoscape.io.CyFileFilter;
-import java.io.File;
-import java.io.OutputStream;
-
-/**
- * A {...@link CyWriterManager} specific to writing property objects. See
- * {...@link org.cytoscape.property.CyProperty} for information on
- * types of object expected.
- */
-public interface PropertyWriterManager extends CyWriterManager {
-
- /**
- * @param property The property object 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 {...@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 {...@link CyFileFilter} that defines the type of
file to be written.
- * @param os The output stream to be written.
- * @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;
-}
Deleted:
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
2010-10-25 21:48:31 UTC (rev 22388)
+++ core3/io-api/trunk/src/main/java/org/cytoscape/io/write/SessionWriter.java
2010-10-25 21:52:08 UTC (rev 22389)
@@ -1,60 +0,0 @@
-
-package org.cytoscape.io.write;
-
-import org.cytoscape.session.CySession;
-import org.cytoscape.io.CyFileFilter;
-import org.cytoscape.work.TaskMonitor;
-import org.cytoscape.work.AbstractTask;
-import java.io.File;
-import java.util.List;
-
-/**
- * A utility Task implementation that writes a {...@link
org.cytoscape.session.CySession} to a file.
- */
-public final class SessionWriter extends AbstractTask implements CyWriter {
-
- private final CySession session;
- private final SessionWriterManager writerMgr;
- private final File outputFile;
-
- /**
- * @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) {
-
- if ( writerMgr == null )
- throw new NullPointerException("Writer Manager is
null");
- this.writerMgr = writerMgr;
-
- if ( session == null )
- throw new NullPointerException("Session Manager is
null");
- this.session = session;
-
- if ( outputFile == null )
- throw new NullPointerException("Output File is null");
- this.outputFile = outputFile;
- }
-
- /**
- * The method that will actually write the specified session to the
specified
- * file.
- * @param tm The {...@link org.cytoscape.work.TaskMonitor} provided by
the TaskManager execution environment.
- */
- public final void run(TaskMonitor tm) throws Exception {
-
- List<CyFileFilter> filters = writerMgr.getAvailableWriters();
- if ( filters == null || filters.size() < 1)
- throw new NullPointerException("No Session file filters
found");
- if ( filters.size() > 1 )
- throw new IllegalArgumentException("Found too many
session filters!");
-
- CyWriter writer =
writerMgr.getWriter(session,filters.get(0),outputFile);
- if ( writer == null )
- throw new NullPointerException("No CyWriter found for
specified file type!");
-
- insertTasksAfterCurrentTask( writer );
- }
-}
Deleted:
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
2010-10-25 21:48:31 UTC (rev 22388)
+++
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/SessionWriterFactory.java
2010-10-25 21:52:08 UTC (rev 22389)
@@ -1,19 +0,0 @@
-package org.cytoscape.io.write;
-
-
-import org.cytoscape.session.CySession;
-
-/**
- * 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 {...@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 {...@link org.cytoscape.session.CySession} to be
written.
- */
- void setSession(CySession session);
-}
Deleted:
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
2010-10-25 21:48:31 UTC (rev 22388)
+++
core3/io-api/trunk/src/main/java/org/cytoscape/io/write/SessionWriterManager.java
2010-10-25 21:52:08 UTC (rev 22389)
@@ -1,64 +0,0 @@
-/*
- Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
-
- The Cytoscape Consortium is:
- - Institute for Systems Biology
- - University of California San Diego
- - Memorial Sloan-Kettering Cancer Center
- - Institut Pasteur
- - Agilent Technologies
-
- This library is free software; you can redistribute it and/or modify it
- under the terms of the GNU Lesser General Public License as published
- by the Free Software Foundation; either version 2.1 of the License, or
- any later version.
-
- This library is distributed in the hope that it will be useful, but
- WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
- MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
- documentation provided hereunder is on an "as is" basis, and the
- Institute for Systems Biology and the Whitehead Institute
- have no obligations to provide maintenance, support,
- updates, enhancements or modifications. In no event shall the
- Institute for Systems Biology and the Whitehead Institute
- be liable to any party for direct, indirect, special,
- incidental or consequential damages, including lost profits, arising
- out of the use of this software and its documentation, even if the
- Institute for Systems Biology and the Whitehead Institute
- have been advised of the possibility of such damage. See
- the GNU Lesser General Public License for more details.
-
- You should have received a copy of the GNU Lesser General Public License
- along with this library; if not, write to the Free Software Foundation,
- Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
- */
-package org.cytoscape.io.write;
-
-import org.cytoscape.session.CySession;
-import org.cytoscape.io.CyFileFilter;
-import java.io.File;
-import java.io.OutputStream;
-
-/**
- * A {...@link CyWriterManager} specific to writing {...@link
org.cytoscape.session.CySession} objects.
- */
-public interface SessionWriterManager extends CyWriterManager {
-
- /**
- * @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 {...@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 {...@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 {...@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;
-}
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