Author: jm
Date: 2012-03-27 12:37:00 -0700 (Tue, 27 Mar 2012)
New Revision: 28671
Added:
core3/api/trunk/io-api/src/main/java/org/cytoscape/io/read/AbstractInputStreamTaskFactory.java
Removed:
core3/api/trunk/io-api/src/main/java/org/cytoscape/io/read/SimpleInputStreamTaskFactory.java
Modified:
core3/api/trunk/io-api/src/main/java/org/cytoscape/io/read/InputStreamTaskFactory.java
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxReaderTaskFactory.java
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/CyActivator.java
core3/impl/trunk/graphml-impl/src/main/java/org/cytoscape/io/internal/read/graphml/GraphMLReaderFactory.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/AbstractNetworkReaderFactory.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/AbstractTableReaderFactory.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/CyNetworkReaderManagerImpl.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/CyPropertyReaderManagerImpl.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/CySessionReaderManagerImpl.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/CyTableReaderManagerImpl.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/GenericReaderManager.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/VizmapReaderManagerImpl.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/bookmarks/BookmarkReaderFactory.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/cysession/CysessionReaderFactory.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/datatable/CSVCyReaderFactory.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/properties/PropertiesReaderFactory.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy2SessionReaderFactoryImpl.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy3SessionReaderFactoryImpl.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/vizmap/VizmapPropertiesReaderFactory.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/vizmap/VizmapXMLReaderFactory.java
core3/impl/trunk/psi-mi-impl/impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkViewTaskFactory.java
core3/impl/trunk/psi-mi-impl/impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReaderFactory.java
core3/impl/trunk/sbml-impl/src/main/java/org/cytoscape/sbml/internal/SBMLNetworkViewTaskFactory.java
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/AbstractNetworkReaderFactory.java
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/AbstractTableReaderFactory.java
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/reader/ontology/OBONetworkReaderFactory.java
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/ImportOntologyAndAnnotationTask.java
Log:
Fixes #827: Refactored InputStreamTaskFactory so it doesn't use tunable context
Copied:
core3/api/trunk/io-api/src/main/java/org/cytoscape/io/read/AbstractInputStreamTaskFactory.java
(from rev 28666,
core3/api/trunk/io-api/src/main/java/org/cytoscape/io/read/SimpleInputStreamTaskFactory.java)
===================================================================
---
core3/api/trunk/io-api/src/main/java/org/cytoscape/io/read/AbstractInputStreamTaskFactory.java
(rev 0)
+++
core3/api/trunk/io-api/src/main/java/org/cytoscape/io/read/AbstractInputStreamTaskFactory.java
2012-03-27 19:37:00 UTC (rev 28671)
@@ -0,0 +1,23 @@
+package org.cytoscape.io.read;
+
+import java.io.InputStream;
+
+import org.cytoscape.io.CyFileFilter;
+
+public abstract class AbstractInputStreamTaskFactory implements
InputStreamTaskFactory {
+ private CyFileFilter fileFilter;
+
+ public AbstractInputStreamTaskFactory(CyFileFilter fileFilter) {
+ this.fileFilter = fileFilter;
+ }
+
+ @Override
+ public boolean isReady(InputStream is, String inputName) {
+ return true;
+ }
+
+ @Override
+ public CyFileFilter getFileFilter() {
+ return fileFilter;
+ }
+}
Modified:
core3/api/trunk/io-api/src/main/java/org/cytoscape/io/read/InputStreamTaskFactory.java
===================================================================
---
core3/api/trunk/io-api/src/main/java/org/cytoscape/io/read/InputStreamTaskFactory.java
2012-03-27 19:22:01 UTC (rev 28670)
+++
core3/api/trunk/io-api/src/main/java/org/cytoscape/io/read/InputStreamTaskFactory.java
2012-03-27 19:37:00 UTC (rev 28671)
@@ -11,7 +11,7 @@
* task factories.
* @CyAPI.Spi.Interface
*/
-public interface InputStreamTaskFactory<T> extends CyFileFilterProvider {
+public interface InputStreamTaskFactory extends CyFileFilterProvider {
/**
* Sets the input stream that will be read by the Reader created from
@@ -19,9 +19,7 @@
* @param is The {@link java.io.InputStream} to be read.
* @param inputName The name of the input.
*/
- TaskIterator createTaskIterator(T tunableContext, InputStream is,
String inputName);
+ TaskIterator createTaskIterator(InputStream is, String inputName);
- boolean isReady(T tunableContext, InputStream is, String inputName);
-
- T createTunableContext();
+ boolean isReady(InputStream is, String inputName);
}
Deleted:
core3/api/trunk/io-api/src/main/java/org/cytoscape/io/read/SimpleInputStreamTaskFactory.java
===================================================================
---
core3/api/trunk/io-api/src/main/java/org/cytoscape/io/read/SimpleInputStreamTaskFactory.java
2012-03-27 19:22:01 UTC (rev 28670)
+++
core3/api/trunk/io-api/src/main/java/org/cytoscape/io/read/SimpleInputStreamTaskFactory.java
2012-03-27 19:37:00 UTC (rev 28671)
@@ -1,39 +0,0 @@
-package org.cytoscape.io.read;
-
-import java.io.InputStream;
-
-import org.cytoscape.io.CyFileFilter;
-import org.cytoscape.work.TaskIterator;
-
-public abstract class SimpleInputStreamTaskFactory implements
InputStreamTaskFactory<Object> {
- private CyFileFilter fileFilter;
-
- public SimpleInputStreamTaskFactory(CyFileFilter fileFilter) {
- this.fileFilter = fileFilter;
- }
-
- @Override
- public final TaskIterator createTaskIterator(Object tunableContext,
InputStream is, String inputName) {
- return createTaskIterator(is, inputName);
- }
-
- @Override
- public boolean isReady(Object tunableContext, InputStream is, String
inputName) {
- return isReady(is, inputName);
- }
-
- protected boolean isReady(InputStream is, String inputName) {
- return true;
- }
-
- public Object createTunableContext() {
- return null;
- }
-
- @Override
- public CyFileFilter getFileFilter() {
- return fileFilter;
- }
-
- protected abstract TaskIterator createTaskIterator(InputStream is,
String inputName);
-}
Modified:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxReaderTaskFactory.java
===================================================================
---
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxReaderTaskFactory.java
2012-03-27 19:22:01 UTC (rev 28670)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxReaderTaskFactory.java
2012-03-27 19:37:00 UTC (rev 28671)
@@ -4,16 +4,15 @@
import org.cytoscape.biopax.internal.util.BioPaxVisualStyleUtil;
import org.cytoscape.io.CyFileFilter;
-import org.cytoscape.io.read.InputStreamTaskFactory;
+import org.cytoscape.io.read.AbstractInputStreamTaskFactory;
import org.cytoscape.model.CyNetworkFactory;
import org.cytoscape.session.CyNetworkNaming;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.view.vizmap.VisualMappingManager;
import org.cytoscape.work.TaskIterator;
-public class BioPaxReaderTaskFactory implements InputStreamTaskFactory<Object>
{
+public class BioPaxReaderTaskFactory extends AbstractInputStreamTaskFactory {
- private final CyFileFilter filter;
private final CyNetworkFactory networkFactory;
private final CyNetworkViewFactory viewFactory;
private final CyNetworkNaming naming;
@@ -24,7 +23,7 @@
public BioPaxReaderTaskFactory(CyFileFilter filter, CyNetworkFactory
networkFactory,
CyNetworkViewFactory viewFactory, CyNetworkNaming
naming,
VisualMappingManager mappingManager,
BioPaxVisualStyleUtil bioPaxVisualStyleUtil) {
- this.filter = filter;
+ super(filter);
this.networkFactory = networkFactory;
this.viewFactory = viewFactory;
this.naming = naming;
@@ -34,14 +33,7 @@
@Override
- public CyFileFilter getFileFilter() {
- return filter;
- }
-
-
- @Override
- public TaskIterator createTaskIterator(Object tunableContext,
- InputStream is, String inputName) {
+ public TaskIterator createTaskIterator(InputStream is, String
inputName) {
if(inputName == null)
inputName = "BioPAX_Network"; //default name fallback
@@ -51,15 +43,4 @@
return new TaskIterator(task);
}
- @Override
- public boolean isReady(Object tunableContext, InputStream is,
- String inputName) {
- return true;
- }
-
- @Override
- public Object createTunableContext() {
- return null;
- }
-
}
Modified:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/CyActivator.java
===================================================================
---
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/CyActivator.java
2012-03-27 19:22:01 UTC (rev 28670)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/CyActivator.java
2012-03-27 19:37:00 UTC (rev 28671)
@@ -70,7 +70,7 @@
BioPaxVisualStyleUtil bioPaxVisualStyleUtil = new
BioPaxVisualStyleUtil(visualStyleFactoryRef,visualMappingManagerRef,discreteMappingFunctionFactoryRef,passthroughMappingFunctionFactoryRef);
BioPaxViewTracker bioPaxViewTracker = new
BioPaxViewTracker(bioPaxDetailsPanel,bioPaxContainer, cyApplicationManagerRef,
visualMappingManagerRef, bioPaxVisualStyleUtil);
- InputStreamTaskFactory<?> inputStreamTaskFactory = new
BioPaxReaderTaskFactory(bioPaxFilter,cyNetworkFactoryRef,cyNetworkViewFactoryRef,cyNetworkNamingRef,visualMappingManagerRef,bioPaxVisualStyleUtil);
+ InputStreamTaskFactory inputStreamTaskFactory = new
BioPaxReaderTaskFactory(bioPaxFilter,cyNetworkFactoryRef,cyNetworkViewFactoryRef,cyNetworkNamingRef,visualMappingManagerRef,bioPaxVisualStyleUtil);
CytoPanelComponent cytoPanelComponent = new
BioPaxCytoPanelComponent(bioPaxContainer);
// ExportAsBioPAXAction exportAsBioPAXAction = new
ExportAsBioPAXAction(fileUtilRef, cyApplicationManagerRef, bioPaxFilter,
taskManagerRef);
Modified:
core3/impl/trunk/graphml-impl/src/main/java/org/cytoscape/io/internal/read/graphml/GraphMLReaderFactory.java
===================================================================
---
core3/impl/trunk/graphml-impl/src/main/java/org/cytoscape/io/internal/read/graphml/GraphMLReaderFactory.java
2012-03-27 19:22:01 UTC (rev 28670)
+++
core3/impl/trunk/graphml-impl/src/main/java/org/cytoscape/io/internal/read/graphml/GraphMLReaderFactory.java
2012-03-27 19:37:00 UTC (rev 28671)
@@ -3,14 +3,14 @@
import java.io.InputStream;
import org.cytoscape.io.CyFileFilter;
-import org.cytoscape.io.read.SimpleInputStreamTaskFactory;
+import org.cytoscape.io.read.AbstractInputStreamTaskFactory;
import org.cytoscape.model.CyNetworkFactory;
import org.cytoscape.model.subnetwork.CyRootNetworkManager;
import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.work.TaskIterator;
-public class GraphMLReaderFactory extends SimpleInputStreamTaskFactory {
+public class GraphMLReaderFactory extends AbstractInputStreamTaskFactory {
private final CyNetworkViewFactory cyNetworkViewFactory;
private final CyNetworkFactory cyNetworkFactory;
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/AbstractNetworkReaderFactory.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/AbstractNetworkReaderFactory.java
2012-03-27 19:22:01 UTC (rev 28670)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/AbstractNetworkReaderFactory.java
2012-03-27 19:37:00 UTC (rev 28671)
@@ -28,11 +28,11 @@
package org.cytoscape.io.internal.read;
import org.cytoscape.io.CyFileFilter;
-import org.cytoscape.io.read.SimpleInputStreamTaskFactory;
+import org.cytoscape.io.read.AbstractInputStreamTaskFactory;
import org.cytoscape.model.CyNetworkFactory;
import org.cytoscape.view.model.CyNetworkViewFactory;
-public abstract class AbstractNetworkReaderFactory extends
SimpleInputStreamTaskFactory {
+public abstract class AbstractNetworkReaderFactory extends
AbstractInputStreamTaskFactory {
protected final CyNetworkViewFactory cyNetworkViewFactory;
protected final CyNetworkFactory cyNetworkFactory;
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/AbstractTableReaderFactory.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/AbstractTableReaderFactory.java
2012-03-27 19:22:01 UTC (rev 28670)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/AbstractTableReaderFactory.java
2012-03-27 19:37:00 UTC (rev 28671)
@@ -29,12 +29,12 @@
import org.cytoscape.io.CyFileFilter;
-import org.cytoscape.io.read.SimpleInputStreamTaskFactory;
+import org.cytoscape.io.read.AbstractInputStreamTaskFactory;
import org.cytoscape.model.CyTableFactory;
import org.cytoscape.model.CyTableManager;
-public abstract class AbstractTableReaderFactory extends
SimpleInputStreamTaskFactory {
+public abstract class AbstractTableReaderFactory extends
AbstractInputStreamTaskFactory {
protected final CyTableFactory tableFactory;
protected final CyTableManager tableManager;
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/CyNetworkReaderManagerImpl.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/CyNetworkReaderManagerImpl.java
2012-03-27 19:22:01 UTC (rev 28670)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/CyNetworkReaderManagerImpl.java
2012-03-27 19:37:00 UTC (rev 28671)
@@ -6,7 +6,7 @@
import org.cytoscape.io.read.InputStreamTaskFactory;
import org.cytoscape.io.util.StreamUtil;
-public class CyNetworkReaderManagerImpl extends
GenericReaderManager<InputStreamTaskFactory<?>, CyNetworkReader> implements
+public class CyNetworkReaderManagerImpl extends
GenericReaderManager<InputStreamTaskFactory, CyNetworkReader> implements
CyNetworkReaderManager {
public CyNetworkReaderManagerImpl(final StreamUtil streamUtil) {
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/CyPropertyReaderManagerImpl.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/CyPropertyReaderManagerImpl.java
2012-03-27 19:22:01 UTC (rev 28670)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/CyPropertyReaderManagerImpl.java
2012-03-27 19:37:00 UTC (rev 28671)
@@ -6,7 +6,7 @@
import org.cytoscape.io.read.InputStreamTaskFactory;
import org.cytoscape.io.util.StreamUtil;
-public class CyPropertyReaderManagerImpl extends
GenericReaderManager<InputStreamTaskFactory<?>, CyPropertyReader>
+public class CyPropertyReaderManagerImpl extends
GenericReaderManager<InputStreamTaskFactory, CyPropertyReader>
implements CyPropertyReaderManager {
public CyPropertyReaderManagerImpl(final StreamUtil streamUtil) {
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/CySessionReaderManagerImpl.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/CySessionReaderManagerImpl.java
2012-03-27 19:22:01 UTC (rev 28670)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/CySessionReaderManagerImpl.java
2012-03-27 19:37:00 UTC (rev 28671)
@@ -6,7 +6,7 @@
import org.cytoscape.io.read.InputStreamTaskFactory;
import org.cytoscape.io.util.StreamUtil;
-public class CySessionReaderManagerImpl extends
GenericReaderManager<InputStreamTaskFactory<?>, CySessionReader> implements
+public class CySessionReaderManagerImpl extends
GenericReaderManager<InputStreamTaskFactory, CySessionReader> implements
CySessionReaderManager {
public CySessionReaderManagerImpl(final StreamUtil streamUtil) {
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/CyTableReaderManagerImpl.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/CyTableReaderManagerImpl.java
2012-03-27 19:22:01 UTC (rev 28670)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/CyTableReaderManagerImpl.java
2012-03-27 19:37:00 UTC (rev 28671)
@@ -6,7 +6,7 @@
import org.cytoscape.io.read.InputStreamTaskFactory;
import org.cytoscape.io.util.StreamUtil;
-public class CyTableReaderManagerImpl extends
GenericReaderManager<InputStreamTaskFactory<?>, CyTableReader> implements
+public class CyTableReaderManagerImpl extends
GenericReaderManager<InputStreamTaskFactory, CyTableReader> implements
CyTableReaderManager {
public CyTableReaderManagerImpl(final StreamUtil streamUtil) {
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/GenericReaderManager.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/GenericReaderManager.java
2012-03-27 19:22:01 UTC (rev 28670)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/GenericReaderManager.java
2012-03-27 19:37:00 UTC (rev 28671)
@@ -17,7 +17,7 @@
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
-public class GenericReaderManager<T extends InputStreamTaskFactory<?>, R
extends Task> {
+public class GenericReaderManager<T extends InputStreamTaskFactory, R extends
Task> {
private static final Logger logger = LoggerFactory.getLogger(
GenericReaderManager.class );
@@ -90,7 +90,7 @@
}
- return (R)
factory.createTaskIterator(null, stream, inputName).next();
+ return (R)
factory.createTaskIterator(stream, inputName).next();
} catch (IOException e) {
logger.warn("Error opening stream to
URI: " + uri.toString(), e);
}
@@ -116,7 +116,7 @@
// of the first 2KB rather than the stream
itself.
if
(cff.accepts(CopyInputStream.copyKBytes(stream,1), category)) {
logger.debug("successfully matched
READER " + factory);
- return
(R)factory.createTaskIterator(null, stream, inputName).next();
+ return
(R)factory.createTaskIterator(stream, inputName).next();
}
}
} catch (IOException ioe) {
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/VizmapReaderManagerImpl.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/VizmapReaderManagerImpl.java
2012-03-27 19:22:01 UTC (rev 28670)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/VizmapReaderManagerImpl.java
2012-03-27 19:37:00 UTC (rev 28671)
@@ -6,7 +6,7 @@
import org.cytoscape.io.read.VizmapReaderManager;
import org.cytoscape.io.util.StreamUtil;
-public class VizmapReaderManagerImpl extends
GenericReaderManager<InputStreamTaskFactory<?>, VizmapReader> implements
+public class VizmapReaderManagerImpl extends
GenericReaderManager<InputStreamTaskFactory, VizmapReader> implements
VizmapReaderManager {
public VizmapReaderManagerImpl(final StreamUtil streamUtil) {
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/bookmarks/BookmarkReaderFactory.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/bookmarks/BookmarkReaderFactory.java
2012-03-27 19:22:01 UTC (rev 28670)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/bookmarks/BookmarkReaderFactory.java
2012-03-27 19:37:00 UTC (rev 28671)
@@ -31,11 +31,11 @@
import java.io.InputStream;
import org.cytoscape.io.CyFileFilter;
-import org.cytoscape.io.read.SimpleInputStreamTaskFactory;
+import org.cytoscape.io.read.AbstractInputStreamTaskFactory;
import org.cytoscape.work.TaskIterator;
-public class BookmarkReaderFactory extends SimpleInputStreamTaskFactory {
+public class BookmarkReaderFactory extends AbstractInputStreamTaskFactory {
public BookmarkReaderFactory( CyFileFilter filter ) {
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/cysession/CysessionReaderFactory.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/cysession/CysessionReaderFactory.java
2012-03-27 19:22:01 UTC (rev 28670)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/cysession/CysessionReaderFactory.java
2012-03-27 19:37:00 UTC (rev 28671)
@@ -31,11 +31,11 @@
import java.io.InputStream;
import org.cytoscape.io.CyFileFilter;
-import org.cytoscape.io.read.SimpleInputStreamTaskFactory;
+import org.cytoscape.io.read.AbstractInputStreamTaskFactory;
import org.cytoscape.work.TaskIterator;
-public class CysessionReaderFactory extends SimpleInputStreamTaskFactory {
+public class CysessionReaderFactory extends AbstractInputStreamTaskFactory {
public CysessionReaderFactory( CyFileFilter filter ) {
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/datatable/CSVCyReaderFactory.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/datatable/CSVCyReaderFactory.java
2012-03-27 19:22:01 UTC (rev 28670)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/datatable/CSVCyReaderFactory.java
2012-03-27 19:37:00 UTC (rev 28671)
@@ -5,13 +5,13 @@
import org.cytoscape.equations.EquationCompiler;
import org.cytoscape.io.CyFileFilter;
-import org.cytoscape.io.read.SimpleInputStreamTaskFactory;
+import org.cytoscape.io.read.AbstractInputStreamTaskFactory;
import org.cytoscape.model.CyTableFactory;
import org.cytoscape.model.CyTableManager;
import org.cytoscape.work.TaskIterator;
-public class CSVCyReaderFactory extends SimpleInputStreamTaskFactory {
+public class CSVCyReaderFactory extends AbstractInputStreamTaskFactory {
private final boolean readSchema;
private final boolean handleEquations;
private final CyTableFactory tableFactory;
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/properties/PropertiesReaderFactory.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/properties/PropertiesReaderFactory.java
2012-03-27 19:22:01 UTC (rev 28670)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/properties/PropertiesReaderFactory.java
2012-03-27 19:37:00 UTC (rev 28671)
@@ -31,11 +31,11 @@
import java.io.InputStream;
import org.cytoscape.io.CyFileFilter;
-import org.cytoscape.io.read.SimpleInputStreamTaskFactory;
+import org.cytoscape.io.read.AbstractInputStreamTaskFactory;
import org.cytoscape.work.TaskIterator;
-public class PropertiesReaderFactory extends SimpleInputStreamTaskFactory {
+public class PropertiesReaderFactory extends AbstractInputStreamTaskFactory {
public PropertiesReaderFactory( CyFileFilter filter ) {
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy2SessionReaderFactoryImpl.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy2SessionReaderFactoryImpl.java
2012-03-27 19:22:01 UTC (rev 28670)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy2SessionReaderFactoryImpl.java
2012-03-27 19:37:00 UTC (rev 28671)
@@ -33,12 +33,12 @@
import org.cytoscape.io.internal.util.ReadCache;
import org.cytoscape.io.read.CyNetworkReaderManager;
import org.cytoscape.io.read.CyPropertyReaderManager;
-import org.cytoscape.io.read.SimpleInputStreamTaskFactory;
+import org.cytoscape.io.read.AbstractInputStreamTaskFactory;
import org.cytoscape.io.read.VizmapReaderManager;
import org.cytoscape.model.subnetwork.CyRootNetworkManager;
import org.cytoscape.work.TaskIterator;
-public class Cy2SessionReaderFactoryImpl extends SimpleInputStreamTaskFactory {
+public class Cy2SessionReaderFactoryImpl extends
AbstractInputStreamTaskFactory {
private final CyNetworkReaderManager networkReaderMgr;
private final CyPropertyReaderManager propertyReaderMgr;
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy3SessionReaderFactoryImpl.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy3SessionReaderFactoryImpl.java
2012-03-27 19:22:01 UTC (rev 28670)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy3SessionReaderFactoryImpl.java
2012-03-27 19:37:00 UTC (rev 28671)
@@ -34,13 +34,13 @@
import org.cytoscape.io.internal.util.ReadCache;
import org.cytoscape.io.read.CyNetworkReaderManager;
import org.cytoscape.io.read.CyPropertyReaderManager;
-import org.cytoscape.io.read.SimpleInputStreamTaskFactory;
+import org.cytoscape.io.read.AbstractInputStreamTaskFactory;
import org.cytoscape.io.read.VizmapReaderManager;
import org.cytoscape.model.CyNetworkTableManager;
import org.cytoscape.model.subnetwork.CyRootNetworkManager;
import org.cytoscape.work.TaskIterator;
-public class Cy3SessionReaderFactoryImpl extends SimpleInputStreamTaskFactory {
+public class Cy3SessionReaderFactoryImpl extends
AbstractInputStreamTaskFactory {
private final ReadCache cache;
private final CyNetworkReaderManager networkReaderMgr;
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/vizmap/VizmapPropertiesReaderFactory.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/vizmap/VizmapPropertiesReaderFactory.java
2012-03-27 19:22:01 UTC (rev 28670)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/vizmap/VizmapPropertiesReaderFactory.java
2012-03-27 19:37:00 UTC (rev 28671)
@@ -31,11 +31,11 @@
import org.cytoscape.io.CyFileFilter;
import org.cytoscape.io.internal.util.vizmap.VisualStyleSerializer;
-import org.cytoscape.io.read.SimpleInputStreamTaskFactory;
+import org.cytoscape.io.read.AbstractInputStreamTaskFactory;
import org.cytoscape.work.TaskIterator;
-public class VizmapPropertiesReaderFactory extends
SimpleInputStreamTaskFactory {
+public class VizmapPropertiesReaderFactory extends
AbstractInputStreamTaskFactory {
private final VisualStyleSerializer visualStyleSerializer;
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/vizmap/VizmapXMLReaderFactory.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/vizmap/VizmapXMLReaderFactory.java
2012-03-27 19:22:01 UTC (rev 28670)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/vizmap/VizmapXMLReaderFactory.java
2012-03-27 19:37:00 UTC (rev 28671)
@@ -31,10 +31,10 @@
import org.cytoscape.io.CyFileFilter;
import org.cytoscape.io.internal.util.vizmap.VisualStyleSerializer;
-import org.cytoscape.io.read.SimpleInputStreamTaskFactory;
+import org.cytoscape.io.read.AbstractInputStreamTaskFactory;
import org.cytoscape.work.TaskIterator;
-public class VizmapXMLReaderFactory extends SimpleInputStreamTaskFactory {
+public class VizmapXMLReaderFactory extends AbstractInputStreamTaskFactory {
private final VisualStyleSerializer visualStyleSerializer;
Modified:
core3/impl/trunk/psi-mi-impl/impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkViewTaskFactory.java
===================================================================
---
core3/impl/trunk/psi-mi-impl/impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkViewTaskFactory.java
2012-03-27 19:22:01 UTC (rev 28670)
+++
core3/impl/trunk/psi-mi-impl/impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkViewTaskFactory.java
2012-03-27 19:37:00 UTC (rev 28671)
@@ -3,14 +3,14 @@
import java.io.InputStream;
import org.cytoscape.io.CyFileFilter;
-import org.cytoscape.io.read.SimpleInputStreamTaskFactory;
+import org.cytoscape.io.read.AbstractInputStreamTaskFactory;
import org.cytoscape.model.CyNetworkFactory;
import org.cytoscape.psi_mi.internal.plugin.PsiMiCyFileFilter.PSIMIVersion;
import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.work.TaskIterator;
-public class PsiMiNetworkViewTaskFactory extends SimpleInputStreamTaskFactory
{
+public class PsiMiNetworkViewTaskFactory extends
AbstractInputStreamTaskFactory {
private final CyNetworkViewFactory networkViewFactory;
private final CyNetworkFactory networkFactory;
private final CyLayoutAlgorithmManager layouts;
Modified:
core3/impl/trunk/psi-mi-impl/impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReaderFactory.java
===================================================================
---
core3/impl/trunk/psi-mi-impl/impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReaderFactory.java
2012-03-27 19:22:01 UTC (rev 28670)
+++
core3/impl/trunk/psi-mi-impl/impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReaderFactory.java
2012-03-27 19:37:00 UTC (rev 28671)
@@ -4,14 +4,14 @@
import java.util.Properties;
import org.cytoscape.io.CyFileFilter;
-import org.cytoscape.io.read.SimpleInputStreamTaskFactory;
+import org.cytoscape.io.read.AbstractInputStreamTaskFactory;
import org.cytoscape.model.CyNetworkFactory;
import org.cytoscape.property.CyProperty;
import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.work.TaskIterator;
-public class PsiMiTabReaderFactory extends SimpleInputStreamTaskFactory {
+public class PsiMiTabReaderFactory extends AbstractInputStreamTaskFactory {
private final CyNetworkViewFactory cyNetworkViewFactory;
private final CyNetworkFactory cyNetworkFactory;
Modified:
core3/impl/trunk/sbml-impl/src/main/java/org/cytoscape/sbml/internal/SBMLNetworkViewTaskFactory.java
===================================================================
---
core3/impl/trunk/sbml-impl/src/main/java/org/cytoscape/sbml/internal/SBMLNetworkViewTaskFactory.java
2012-03-27 19:22:01 UTC (rev 28670)
+++
core3/impl/trunk/sbml-impl/src/main/java/org/cytoscape/sbml/internal/SBMLNetworkViewTaskFactory.java
2012-03-27 19:37:00 UTC (rev 28671)
@@ -3,12 +3,12 @@
import java.io.InputStream;
import org.cytoscape.io.CyFileFilter;
-import org.cytoscape.io.read.SimpleInputStreamTaskFactory;
+import org.cytoscape.io.read.AbstractInputStreamTaskFactory;
import org.cytoscape.model.CyNetworkFactory;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.work.TaskIterator;
-public class SBMLNetworkViewTaskFactory extends SimpleInputStreamTaskFactory {
+public class SBMLNetworkViewTaskFactory extends AbstractInputStreamTaskFactory
{
private final CyNetworkFactory networkFactory;
private final CyNetworkViewFactory viewFactory;
Modified:
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/AbstractNetworkReaderFactory.java
===================================================================
---
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/AbstractNetworkReaderFactory.java
2012-03-27 19:22:01 UTC (rev 28670)
+++
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/AbstractNetworkReaderFactory.java
2012-03-27 19:37:00 UTC (rev 28671)
@@ -1,12 +1,12 @@
package org.cytoscape.tableimport.internal;
import org.cytoscape.io.CyFileFilter;
-import org.cytoscape.io.read.SimpleInputStreamTaskFactory;
+import org.cytoscape.io.read.AbstractInputStreamTaskFactory;
import org.cytoscape.model.CyNetworkFactory;
import org.cytoscape.view.model.CyNetworkViewFactory;
// Copy from io-impl
-public abstract class AbstractNetworkReaderFactory extends
SimpleInputStreamTaskFactory {
+public abstract class AbstractNetworkReaderFactory extends
AbstractInputStreamTaskFactory {
protected final CyNetworkViewFactory cyNetworkViewFactory;
protected final CyNetworkFactory cyNetworkFactory;
Modified:
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/AbstractTableReaderFactory.java
===================================================================
---
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/AbstractTableReaderFactory.java
2012-03-27 19:22:01 UTC (rev 28670)
+++
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/AbstractTableReaderFactory.java
2012-03-27 19:37:00 UTC (rev 28671)
@@ -1,11 +1,11 @@
package org.cytoscape.tableimport.internal;
import org.cytoscape.io.CyFileFilter;
-import org.cytoscape.io.read.SimpleInputStreamTaskFactory;
+import org.cytoscape.io.read.AbstractInputStreamTaskFactory;
import org.cytoscape.model.CyTableFactory;
// Copy from io-impl
-public abstract class AbstractTableReaderFactory extends
SimpleInputStreamTaskFactory {
+public abstract class AbstractTableReaderFactory extends
AbstractInputStreamTaskFactory {
protected final CyTableFactory tableFactory;
Modified:
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/reader/ontology/OBONetworkReaderFactory.java
===================================================================
---
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/reader/ontology/OBONetworkReaderFactory.java
2012-03-27 19:22:01 UTC (rev 28670)
+++
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/reader/ontology/OBONetworkReaderFactory.java
2012-03-27 19:37:00 UTC (rev 28671)
@@ -4,13 +4,13 @@
import org.cytoscape.event.CyEventHelper;
import org.cytoscape.io.CyFileFilter;
-import org.cytoscape.io.read.SimpleInputStreamTaskFactory;
+import org.cytoscape.io.read.AbstractInputStreamTaskFactory;
import org.cytoscape.model.CyNetworkFactory;
import org.cytoscape.tableimport.internal.util.CytoscapeServices;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.work.TaskIterator;
-public class OBONetworkReaderFactory extends SimpleInputStreamTaskFactory {
+public class OBONetworkReaderFactory extends AbstractInputStreamTaskFactory {
protected final CyNetworkViewFactory cyNetworkViewFactory;
protected final CyNetworkFactory cyNetworkFactory;
Modified:
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/ImportOntologyAndAnnotationTask.java
===================================================================
---
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/ImportOntologyAndAnnotationTask.java
2012-03-27 19:22:01 UTC (rev 28670)
+++
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/task/ImportOntologyAndAnnotationTask.java
2012-03-27 19:37:00 UTC (rev 28671)
@@ -50,7 +50,7 @@
@Override
public void run(TaskMonitor tm) throws Exception {
logger.debug("Start");
- Task loadOBOTask = factory.createTaskIterator(null, is,
ontologyDagName).next();
+ Task loadOBOTask = factory.createTaskIterator(is,
ontologyDagName).next();
final GeneAssociationReader gaReader =
new GeneAssociationReader(tableFactory,
ontologyDagName, gaStream,
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