Author: mes
Date: 2011-04-29 17:18:58 -0700 (Fri, 29 Apr 2011)
New Revision: 24876
Added:
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/CyLayoutAlgorithmManager.java
Removed:
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/CyLayouts.java
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/layout/ApplyPreferredLayoutTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/layout/ApplyPreferredLayoutTaskFactory.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/ApplyLayoutTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/SubnetworkBuilderUtil.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewReader.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewReaderFactory.java
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/AbstractNetworkViewReaderTester.java
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewReaderTest.java
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewReaderTest.java
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/internal/CyLayoutsImpl.java
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/internal/algorithms/GridNodeLayout.java
core3/layout-prefuse-impl/trunk/src/main/java/org/cytoscape/prefuse/layouts/internal/ForceDirectedLayout.java
core3/psi-mi-impl/trunk/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkViewReader.java
core3/psi-mi-impl/trunk/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkViewTaskFactory.java
core3/psi-mi-impl/trunk/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReader.java
core3/psi-mi-impl/trunk/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReaderFactory.java
core3/psi-mi-impl/trunk/src/test/java/org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkViewReaderTest.java
core3/psi-mi-impl/trunk/src/test/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReaderTest.java
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/layout/ui/LayoutMenuManager.java
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/layout/ui/LayoutSettingsDialog.java
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/layout/ui/SettingsAction.java
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/reader/AbstractGraphReader.java
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/util/CytoscapeServices.java
Log:
Renamed CyLayouts to CyLayoutAlgorithmManager to keep in line with the rest of
the API.
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/layout/ApplyPreferredLayoutTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/layout/ApplyPreferredLayoutTask.java
2011-04-30 00:12:34 UTC (rev 24875)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/layout/ApplyPreferredLayoutTask.java
2011-04-30 00:18:58 UTC (rev 24876)
@@ -31,7 +31,7 @@
import org.cytoscape.task.AbstractNetworkViewTask;
import org.cytoscape.work.TaskMonitor;
import org.cytoscape.view.model.CyNetworkView;
-import org.cytoscape.view.layout.CyLayouts;
+import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.layout.CyLayoutAlgorithm;
import java.util.Properties;
@@ -40,9 +40,9 @@
private static final String DEF_LAYOUT = "force-directed";
private final Properties props;
- private final CyLayouts layouts;
+ private final CyLayoutAlgorithmManager layouts;
- public ApplyPreferredLayoutTask(CyNetworkView v, CyLayouts layouts,
Properties props) {
+ public ApplyPreferredLayoutTask(CyNetworkView v, CyLayoutAlgorithmManager
layouts, Properties props) {
super(v);
this.layouts = layouts;
this.props = props;
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/layout/ApplyPreferredLayoutTaskFactory.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/layout/ApplyPreferredLayoutTaskFactory.java
2011-04-30 00:12:34 UTC (rev 24875)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/layout/ApplyPreferredLayoutTaskFactory.java
2011-04-30 00:18:58 UTC (rev 24876)
@@ -4,15 +4,15 @@
import org.cytoscape.task.AbstractNetworkViewTaskFactory;
import org.cytoscape.work.TaskIterator;
import org.cytoscape.property.CyProperty;
-import org.cytoscape.view.layout.CyLayouts;
+import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import java.util.Properties;
public class ApplyPreferredLayoutTaskFactory extends
AbstractNetworkViewTaskFactory {
- private final CyLayouts layouts;
+ private final CyLayoutAlgorithmManager layouts;
private final Properties props;
- public ApplyPreferredLayoutTaskFactory(CyLayouts layouts,
CyProperty<Properties> p) {
+ public ApplyPreferredLayoutTaskFactory(CyLayoutAlgorithmManager
layouts, CyProperty<Properties> p) {
this.layouts = layouts;
this.props = p.getProperties();
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/ApplyLayoutTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/ApplyLayoutTask.java
2011-04-30 00:12:34 UTC (rev 24875)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/ApplyLayoutTask.java
2011-04-30 00:18:58 UTC (rev 24876)
@@ -1,23 +1,23 @@
package org.cytoscape.task.internal.quickstart.subnetworkbuilder;
import org.cytoscape.view.layout.CyLayoutAlgorithm;
-import org.cytoscape.view.layout.CyLayouts;
+import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.TaskMonitor;
public class ApplyLayoutTask extends AbstractTask {
private final SubnetworkBuilderUtil util;
- private final CyLayouts layouts;
+ private final CyLayoutAlgorithmManager layouts;
- ApplyLayoutTask(final SubnetworkBuilderUtil util, final CyLayouts layouts)
{
+ ApplyLayoutTask(final SubnetworkBuilderUtil util, final
CyLayoutAlgorithmManager layouts) {
this.layouts = layouts;
this.util = util;
}
@Override
public void run(TaskMonitor taskMonitor) throws Exception {
-// final CyLayoutAlgorithm layout =
layouts.getLayout(CyLayouts.DEFAULT_LAYOUT_NAME);
+// final CyLayoutAlgorithm layout =
layouts.getLayout(CyLayoutAlgorithmManager.DEFAULT_LAYOUT_NAME);
final CyLayoutAlgorithm layout = layouts.getDefaultLayout();
layout.setNetworkView(util.appManager.getCurrentNetworkView());
insertTasksAfterCurrentTask(layout.getTaskIterator());
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/SubnetworkBuilderUtil.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/SubnetworkBuilderUtil.java
2011-04-30 00:12:34 UTC (rev 24875)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/SubnetworkBuilderUtil.java
2011-04-30 00:18:58 UTC (rev 24876)
@@ -17,7 +17,7 @@
import org.cytoscape.task.internal.creation.NewNetworkSelectedNodesOnlyTask;
import
org.cytoscape.task.internal.quickstart.ImportNetworkFromPublicDataSetTask;
import
org.cytoscape.task.internal.quickstart.remote.InteractionFilePreprocessor;
-import org.cytoscape.view.layout.CyLayouts;
+import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.view.model.CyNetworkViewManager;
@@ -52,13 +52,13 @@
final VisualStyleFactory vsFactory;
private VisualMappingFunctionFactory discFactory;
private VisualMappingFunctionFactory ptFactory;
- private final CyLayouts layouts;
+ private final CyLayoutAlgorithmManager layouts;
public SubnetworkBuilderUtil(CyNetworkViewReaderManager mgr,
CyNetworkManager netmgr,
final CyNetworkViewManager networkViewManager,
CyProperty<Properties> cyProps,
CyNetworkNaming cyNetworkNaming, StreamUtil streamUtil, final
CyEventHelper eventHelper,
final CyApplicationManager appManager, CyRootNetworkFactory crnf,
CyNetworkViewFactory cnvf,
- VisualMappingManager vmm, final VisualStyleFactory vsFactory, final
CyLayouts layouts) {
+ VisualMappingManager vmm, final VisualStyleFactory vsFactory, final
CyLayoutAlgorithmManager layouts) {
this.mgr = mgr;
this.netmgr = netmgr;
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewReader.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewReader.java
2011-04-30 00:12:34 UTC (rev 24875)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewReader.java
2011-04-30 00:18:58 UTC (rev 24876)
@@ -46,7 +46,7 @@
import org.cytoscape.model.events.RowsAboutToChangeEvent;
import org.cytoscape.model.events.RowsFinishedChangingEvent;
import org.cytoscape.view.layout.CyLayoutAlgorithm;
-import org.cytoscape.view.layout.CyLayouts;
+import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.work.Task;
@@ -68,11 +68,11 @@
private final Set<Interaction> interactions = new HashSet<Interaction>();
private final ReadUtils readUtil;
- private final CyLayouts layouts;
+ private final CyLayoutAlgorithmManager layouts;
private boolean cancelled = false;
- public SIFNetworkViewReader(InputStream is, ReadUtils readUtil, CyLayouts
layouts,
+ public SIFNetworkViewReader(InputStream is, ReadUtils readUtil,
CyLayoutAlgorithmManager layouts,
CyNetworkViewFactory cyNetworkViewFactory, CyNetworkFactory
cyNetworkFactory,
final CyEventHelper eventHelper) {
super(is, cyNetworkViewFactory, cyNetworkFactory);
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewReaderFactory.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewReaderFactory.java
2011-04-30 00:12:34 UTC (rev 24875)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewReaderFactory.java
2011-04-30 00:18:58 UTC (rev 24876)
@@ -32,17 +32,17 @@
import org.cytoscape.io.internal.read.AbstractNetworkViewReaderFactory;
import org.cytoscape.io.internal.util.ReadUtils;
import org.cytoscape.model.CyNetworkFactory;
-import org.cytoscape.view.layout.CyLayouts;
+import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.work.TaskIterator;
public class SIFNetworkViewReaderFactory extends
AbstractNetworkViewReaderFactory {
private final ReadUtils readUtil;
- private final CyLayouts layouts;
+ private final CyLayoutAlgorithmManager layouts;
private final CyEventHelper eventHelper;
- public SIFNetworkViewReaderFactory(ReadUtils readUtil, CyFileFilter
filter, CyLayouts layouts,
+ public SIFNetworkViewReaderFactory(ReadUtils readUtil, CyFileFilter
filter, CyLayoutAlgorithmManager layouts,
CyNetworkViewFactory cyNetworkViewFactory, CyNetworkFactory
cyNetworkFactory,
final CyEventHelper eventHelper) {
super(filter, cyNetworkViewFactory, cyNetworkFactory);
Modified:
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/AbstractNetworkViewReaderTester.java
===================================================================
---
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/AbstractNetworkViewReaderTester.java
2011-04-30 00:12:34 UTC (rev 24875)
+++
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/AbstractNetworkViewReaderTester.java
2011-04-30 00:18:58 UTC (rev 24876)
@@ -30,7 +30,7 @@
import org.cytoscape.model.CyEdge;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewFactory;
-import org.cytoscape.view.layout.CyLayouts;
+import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.layout.CyLayoutAlgorithm;
@@ -44,7 +44,7 @@
protected CyNetworkFactory netFactory;
protected CyNetworkViewFactory viewFactory;
protected ReadUtils readUtil;
- protected CyLayouts layouts;
+ protected CyLayoutAlgorithmManager layouts;
@Before
public void setUp() throws Exception {
@@ -53,7 +53,7 @@
CyLayoutAlgorithm def = mock(CyLayoutAlgorithm.class);
when(def.getTaskIterator()).thenReturn(new TaskIterator(new
SimpleTask()));
- layouts = mock(CyLayouts.class);
+ layouts = mock(CyLayoutAlgorithmManager.class);
when(layouts.getDefaultLayout()).thenReturn(def);
NetworkTestSupport nts = new NetworkTestSupport();
Modified:
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewReaderTest.java
===================================================================
---
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewReaderTest.java
2011-04-30 00:12:34 UTC (rev 24875)
+++
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewReaderTest.java
2011-04-30 00:18:58 UTC (rev 24876)
@@ -29,7 +29,7 @@
import org.cytoscape.model.CyEdge;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewFactory;
-import org.cytoscape.view.layout.CyLayouts;
+import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.layout.CyLayoutAlgorithm;
import org.cytoscape.io.internal.read.AbstractNetworkViewReaderTester;
Modified:
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewReaderTest.java
===================================================================
---
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewReaderTest.java
2011-04-30 00:12:34 UTC (rev 24875)
+++
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewReaderTest.java
2011-04-30 00:18:58 UTC (rev 24876)
@@ -26,7 +26,7 @@
import org.cytoscape.view.vizmap.VisualMappingManager;
import org.cytoscape.view.vizmap.VisualStyleFactory;
import org.cytoscape.view.vizmap.mappings.DiscreteMappingFactory;
-import org.cytoscape.view.layout.CyLayouts;
+import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.layout.CyLayoutAlgorithm;
import org.cytoscape.io.internal.read.xgmml.handler.ReadDataManager;
Copied:
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/CyLayoutAlgorithmManager.java
(from rev 24867,
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/CyLayouts.java)
===================================================================
---
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/CyLayoutAlgorithmManager.java
(rev 0)
+++
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/CyLayoutAlgorithmManager.java
2011-04-30 00:18:58 UTC (rev 24876)
@@ -0,0 +1,52 @@
+/*
+ File: CyLayoutAlgorithmManager.java
+
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ 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.view.layout;
+
+
+import java.util.Collection;
+import java.util.Map;
+
+import org.cytoscape.view.model.CyNetworkView;
+
+
+public interface CyLayoutAlgorithmManager {
+
+ String PREF_MENU_KEY = "preferredMenu";
+ String PREF_MENU_DEFAULT = "Cytoscape Layouts";
+ String DEFAULT_LAYOUT_NAME = "grid";
+
+ CyLayoutAlgorithm getLayout(String name);
+
+ Collection<CyLayoutAlgorithm> getAllLayouts();
+
+ CyLayoutAlgorithm getDefaultLayout();
+
+ String getMenuName(CyLayoutAlgorithm layout);
+}
Deleted:
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/CyLayouts.java
===================================================================
---
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/CyLayouts.java
2011-04-30 00:12:34 UTC (rev 24875)
+++
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/CyLayouts.java
2011-04-30 00:18:58 UTC (rev 24876)
@@ -1,52 +0,0 @@
-/*
- File: CyLayouts.java
-
- Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
-
- 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.view.layout;
-
-
-import java.util.Collection;
-import java.util.Map;
-
-import org.cytoscape.view.model.CyNetworkView;
-
-
-public interface CyLayouts {
-
- String PREF_MENU_KEY = "preferredMenu";
- String PREF_MENU_DEFAULT = "Cytoscape Layouts";
- String DEFAULT_LAYOUT_NAME = "grid";
-
- CyLayoutAlgorithm getLayout(String name);
-
- Collection<CyLayoutAlgorithm> getAllLayouts();
-
- CyLayoutAlgorithm getDefaultLayout();
-
- String getMenuName(CyLayoutAlgorithm layout);
-}
Modified:
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/internal/CyLayoutsImpl.java
===================================================================
---
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/internal/CyLayoutsImpl.java
2011-04-30 00:12:34 UTC (rev 24875)
+++
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/internal/CyLayoutsImpl.java
2011-04-30 00:18:58 UTC (rev 24876)
@@ -30,7 +30,7 @@
package org.cytoscape.view.layout.internal;
-import org.cytoscape.view.layout.CyLayouts;
+import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.layout.CyLayoutAlgorithm;
import org.cytoscape.view.layout.internal.algorithms.GridNodeLayout;
import org.cytoscape.view.model.CyNetworkView;
@@ -44,7 +44,7 @@
* CyLayoutsImpl is a singleton class that is used to register all available
* layout algorithms.
*/
-public class CyLayoutsImpl implements CyLayouts {
+public class CyLayoutsImpl implements CyLayoutAlgorithmManager {
private HashMap<String, CyLayoutAlgorithm> layoutMap;
private HashMap<CyLayoutAlgorithm, String> menuNameMap;
@@ -66,9 +66,9 @@
* @param menu The menu that this should appear under
*/
public void addLayout(CyLayoutAlgorithm layout, Map props) {
- String prefMenu = (String)props.get(CyLayouts.PREF_MENU_KEY);
+ String prefMenu =
(String)props.get(CyLayoutAlgorithmManager.PREF_MENU_KEY);
if ( prefMenu == null || prefMenu.equals("") )
- prefMenu = CyLayouts.PREF_MENU_DEFAULT;
+ prefMenu = CyLayoutAlgorithmManager.PREF_MENU_DEFAULT;
layoutMap.put(layout.getName(),layout);
menuNameMap.put(layout, prefMenu);
@@ -119,7 +119,7 @@
// if ((defaultLayout == null) ||
!layoutMap.containsKey(defaultLayout)) {
// defaultLayout = "grid";
// }
- String defaultLayout = CyLayouts.DEFAULT_LAYOUT_NAME;
+ String defaultLayout =
CyLayoutAlgorithmManager.DEFAULT_LAYOUT_NAME;
CyLayoutAlgorithm l = layoutMap.get(defaultLayout);
return l;
Modified:
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/internal/algorithms/GridNodeLayout.java
===================================================================
---
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/internal/algorithms/GridNodeLayout.java
2011-04-30 00:12:34 UTC (rev 24875)
+++
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/internal/algorithms/GridNodeLayout.java
2011-04-30 00:18:58 UTC (rev 24876)
@@ -38,7 +38,7 @@
import org.cytoscape.model.CyNetwork;
import org.cytoscape.view.layout.AbstractLayoutAlgorithm;
-import org.cytoscape.view.layout.CyLayouts;
+import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.model.View;
import org.cytoscape.view.model.VisualProperty;
@@ -63,7 +63,7 @@
* Creates a new GridNodeLayout object.
*/
public GridNodeLayout(UndoSupport un) {
- super(un,CyLayouts.DEFAULT_LAYOUT_NAME,"Grid Layout");
+ super(un,CyLayoutAlgorithmManager.DEFAULT_LAYOUT_NAME,"Grid
Layout");
}
public boolean tunablesAreValid(final Appendable errMsg) {
Modified:
core3/layout-prefuse-impl/trunk/src/main/java/org/cytoscape/prefuse/layouts/internal/ForceDirectedLayout.java
===================================================================
---
core3/layout-prefuse-impl/trunk/src/main/java/org/cytoscape/prefuse/layouts/internal/ForceDirectedLayout.java
2011-04-30 00:12:34 UTC (rev 24875)
+++
core3/layout-prefuse-impl/trunk/src/main/java/org/cytoscape/prefuse/layouts/internal/ForceDirectedLayout.java
2011-04-30 00:18:58 UTC (rev 24876)
@@ -3,7 +3,7 @@
import java.io.IOException;
import org.cytoscape.view.layout.AbstractLayoutAlgorithm;
-import org.cytoscape.view.layout.CyLayouts;
+import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.work.TaskIterator;
import org.cytoscape.work.Tunable;
import org.cytoscape.work.TunableValidator;
Modified:
core3/psi-mi-impl/trunk/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkViewReader.java
===================================================================
---
core3/psi-mi-impl/trunk/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkViewReader.java
2011-04-30 00:12:34 UTC (rev 24875)
+++
core3/psi-mi-impl/trunk/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkViewReader.java
2011-04-30 00:18:58 UTC (rev 24876)
@@ -15,7 +15,7 @@
import org.cytoscape.psi_mi.internal.data_mapper.MapPsiTwoFiveToInteractions;
import org.cytoscape.psi_mi.internal.model.Interaction;
import org.cytoscape.view.layout.CyLayoutAlgorithm;
-import org.cytoscape.view.layout.CyLayouts;
+import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.view.vizmap.VisualStyle;
@@ -35,9 +35,9 @@
private CyNetworkView networkView;
- private CyLayouts layouts;
+ private CyLayoutAlgorithmManager layouts;
- public PsiMiNetworkViewReader(InputStream inputStream, CyNetworkFactory
networkFactory, CyNetworkViewFactory networkViewFactory, CyLayouts layouts) {
+ public PsiMiNetworkViewReader(InputStream inputStream, CyNetworkFactory
networkFactory, CyNetworkViewFactory networkViewFactory,
CyLayoutAlgorithmManager layouts) {
this.inputStream = inputStream;
this.networkFactory = networkFactory;
this.networkViewFactory = networkViewFactory;
Modified:
core3/psi-mi-impl/trunk/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkViewTaskFactory.java
===================================================================
---
core3/psi-mi-impl/trunk/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkViewTaskFactory.java
2011-04-30 00:12:34 UTC (rev 24875)
+++
core3/psi-mi-impl/trunk/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkViewTaskFactory.java
2011-04-30 00:18:58 UTC (rev 24876)
@@ -5,20 +5,20 @@
import org.cytoscape.io.CyFileFilter;
import org.cytoscape.io.read.InputStreamTaskFactory;
import org.cytoscape.model.CyNetworkFactory;
-import org.cytoscape.view.layout.CyLayouts;
+import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.work.TaskIterator;
public class PsiMiNetworkViewTaskFactory implements InputStreamTaskFactory {
private final CyNetworkViewFactory networkViewFactory;
private final CyNetworkFactory networkFactory;
- private final CyLayouts layouts;
+ private final CyLayoutAlgorithmManager layouts;
private final CyFileFilter filter;
private InputStream inputStream;
private String inputName;
- public PsiMiNetworkViewTaskFactory(CyFileFilter filter,
CyNetworkFactory networkFactory, CyNetworkViewFactory networkViewFactory,
CyLayouts layouts) {
+ public PsiMiNetworkViewTaskFactory(CyFileFilter filter,
CyNetworkFactory networkFactory, CyNetworkViewFactory networkViewFactory,
CyLayoutAlgorithmManager layouts) {
this.filter = filter;
this.networkFactory = networkFactory;
this.networkViewFactory = networkViewFactory;
Modified:
core3/psi-mi-impl/trunk/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReader.java
===================================================================
---
core3/psi-mi-impl/trunk/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReader.java
2011-04-30 00:12:34 UTC (rev 24875)
+++
core3/psi-mi-impl/trunk/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReader.java
2011-04-30 00:18:58 UTC (rev 24876)
@@ -7,7 +7,7 @@
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkFactory;
import org.cytoscape.view.layout.CyLayoutAlgorithm;
-import org.cytoscape.view.layout.CyLayouts;
+import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.view.vizmap.VisualStyle;
@@ -26,13 +26,13 @@
private CyNetworkView[] cyNetworkViews;
private VisualStyle[] visualstyles;
- private final CyLayouts layouts;
+ private final CyLayoutAlgorithmManager layouts;
private final PsiMiTabParser parser;
public PsiMiTabReader(InputStream is,
CyNetworkViewFactory cyNetworkViewFactory,
- CyNetworkFactory cyNetworkFactory, final CyLayouts
layouts) {
+ CyNetworkFactory cyNetworkFactory, final
CyLayoutAlgorithmManager layouts) {
if (is == null)
throw new NullPointerException("Input stream is null");
this.inputStream = is;
Modified:
core3/psi-mi-impl/trunk/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReaderFactory.java
===================================================================
---
core3/psi-mi-impl/trunk/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReaderFactory.java
2011-04-30 00:12:34 UTC (rev 24875)
+++
core3/psi-mi-impl/trunk/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReaderFactory.java
2011-04-30 00:18:58 UTC (rev 24876)
@@ -5,7 +5,7 @@
import org.cytoscape.io.CyFileFilter;
import org.cytoscape.io.read.InputStreamTaskFactory;
import org.cytoscape.model.CyNetworkFactory;
-import org.cytoscape.view.layout.CyLayouts;
+import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.work.TaskIterator;
@@ -15,7 +15,7 @@
private final CyNetworkViewFactory cyNetworkViewFactory;
private final CyNetworkFactory cyNetworkFactory;
- private final CyLayouts layouts;
+ private final CyLayoutAlgorithmManager layouts;
private InputStream inputStream;
private String inputName;
@@ -23,7 +23,7 @@
public PsiMiTabReaderFactory(
CyFileFilter filter,
CyNetworkViewFactory cyNetworkViewFactory,
- CyNetworkFactory cyNetworkFactory, CyLayouts layouts) {
+ CyNetworkFactory cyNetworkFactory,
CyLayoutAlgorithmManager layouts) {
this.cyNetworkFactory = cyNetworkFactory;
this.cyNetworkViewFactory = cyNetworkViewFactory;
this.filter = filter;
Modified:
core3/psi-mi-impl/trunk/src/test/java/org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkViewReaderTest.java
===================================================================
---
core3/psi-mi-impl/trunk/src/test/java/org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkViewReaderTest.java
2011-04-30 00:12:34 UTC (rev 24875)
+++
core3/psi-mi-impl/trunk/src/test/java/org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkViewReaderTest.java
2011-04-30 00:18:58 UTC (rev 24876)
@@ -15,7 +15,7 @@
import org.cytoscape.test.support.NetworkTestSupport;
import org.cytoscape.test.support.NetworkViewTestSupport;
import org.cytoscape.view.layout.CyLayoutAlgorithm;
-import org.cytoscape.view.layout.CyLayouts;
+import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.work.Task;
@@ -27,7 +27,7 @@
import org.mockito.MockitoAnnotations;
public class PsiMiNetworkViewReaderTest {
- @Mock CyLayouts layouts;
+ @Mock CyLayoutAlgorithmManager layouts;
@Mock CyLayoutAlgorithm layout;
@Mock TaskMonitor taskMonitor;
@Mock Task task;
Modified:
core3/psi-mi-impl/trunk/src/test/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReaderTest.java
===================================================================
---
core3/psi-mi-impl/trunk/src/test/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReaderTest.java
2011-04-30 00:12:34 UTC (rev 24875)
+++
core3/psi-mi-impl/trunk/src/test/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReaderTest.java
2011-04-30 00:18:58 UTC (rev 24876)
@@ -15,7 +15,7 @@
import org.cytoscape.test.support.NetworkTestSupport;
import org.cytoscape.test.support.NetworkViewTestSupport;
import org.cytoscape.view.layout.CyLayoutAlgorithm;
-import org.cytoscape.view.layout.CyLayouts;
+import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.work.Task;
@@ -30,7 +30,7 @@
public class PsiMiTabReaderTest {
@Mock
- CyLayouts layouts;
+ CyLayoutAlgorithmManager layouts;
@Mock
CyLayoutAlgorithm layout;
@Mock
Modified:
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/layout/ui/LayoutMenuManager.java
===================================================================
---
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/layout/ui/LayoutMenuManager.java
2011-04-30 00:12:34 UTC (rev 24875)
+++
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/layout/ui/LayoutMenuManager.java
2011-04-30 00:18:58 UTC (rev 24876)
@@ -37,7 +37,7 @@
package org.cytoscape.internal.layout.ui;
import org.cytoscape.view.layout.CyLayoutAlgorithm;
-import org.cytoscape.view.layout.CyLayouts;
+import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.work.TaskManager;
import org.cytoscape.application.swing.CySwingApplication;
import org.cytoscape.session.CyApplicationManager;
@@ -56,13 +56,13 @@
private CyApplicationManager appMgr;
private TaskManager tm;
- private CyLayouts cyLayouts;
+ private CyLayoutAlgorithmManager cyLayoutAlgorithmManager;
- public LayoutMenuManager(CySwingApplication swingApp, CyLayouts
cyLayouts, CyApplicationManager appMgr, TaskManager tm) {
+ public LayoutMenuManager(CySwingApplication swingApp,
CyLayoutAlgorithmManager cyLayoutAlgorithmManager, CyApplicationManager appMgr,
TaskManager tm) {
menuAlgorithmMap = new
HashMap<String,List<CyLayoutAlgorithm>>();
menuMap = new HashMap<String,LayoutMenu>();
existingLayouts = new HashSet<CyLayoutAlgorithm>();
- this.cyLayouts = cyLayouts;
+ this.cyLayoutAlgorithmManager = cyLayoutAlgorithmManager;
this.appMgr = appMgr;
this.tm = tm;
@@ -82,12 +82,12 @@
private void updateMenus(JMenu parentMenu) {
// first add all layouts from cylayouts if they're not already
there
- for ( CyLayoutAlgorithm la : cyLayouts.getAllLayouts() )
+ for ( CyLayoutAlgorithm la :
cyLayoutAlgorithmManager.getAllLayouts() )
if ( !existingLayouts.contains(la) )
addLayout(la);
// now remove any existing layouts that are no longer in
cylayouts
- Set<CyLayoutAlgorithm> newLayouts = new
HashSet<CyLayoutAlgorithm>(cyLayouts.getAllLayouts());
+ Set<CyLayoutAlgorithm> newLayouts = new
HashSet<CyLayoutAlgorithm>(cyLayoutAlgorithmManager.getAllLayouts());
for ( CyLayoutAlgorithm la : existingLayouts )
if ( !newLayouts.contains(la) )
removeLayout(la);
@@ -110,7 +110,7 @@
private void addLayout(CyLayoutAlgorithm layout) {
- String menuName = cyLayouts.getMenuName(layout);
+ String menuName = cyLayoutAlgorithmManager.getMenuName(layout);
if (menuName == null )
return;
Modified:
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/layout/ui/LayoutSettingsDialog.java
===================================================================
---
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/layout/ui/LayoutSettingsDialog.java
2011-04-30 00:12:34 UTC (rev 24875)
+++
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/layout/ui/LayoutSettingsDialog.java
2011-04-30 00:18:58 UTC (rev 24876)
@@ -33,7 +33,7 @@
import org.cytoscape.application.swing.CySwingApplication;
import org.cytoscape.session.CyApplicationManager;
import org.cytoscape.view.layout.CyLayoutAlgorithm;
-import org.cytoscape.view.layout.CyLayouts;
+import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.work.Tunable;
import org.cytoscape.work.swing.GUITaskManager;
@@ -68,7 +68,7 @@
private JComboBox algorithmSelector; // Which algorithm we're using
private JPanel algorithmPanel; // The panel this algorithm uses
- private CyLayouts cyLayouts;
+ private CyLayoutAlgorithmManager cyLayoutAlgorithmManager;
private CySwingApplication desktop;
private LayoutMenuManager menuMgr;
private CyApplicationManager appMgr;
@@ -77,13 +77,13 @@
/**
* Creates a new LayoutSettingsDialog object.
*/
- public LayoutSettingsDialog(final CyLayouts cyLayouts, final
CySwingApplication desktop,
+ public LayoutSettingsDialog(final CyLayoutAlgorithmManager
cyLayoutAlgorithmManager, final CySwingApplication desktop,
final LayoutMenuManager menuMgr, final
CyApplicationManager appMgr,
final GUITaskManager taskManager)
{
super(desktop.getJFrame(), "Layout Settings", false);
initializeOnce(); // Initialize the components we only do once
- this.cyLayouts = cyLayouts;
+ this.cyLayoutAlgorithmManager = cyLayoutAlgorithmManager;
this.desktop = desktop;
this.menuMgr = menuMgr;
this.appMgr = appMgr;
Modified:
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/layout/ui/SettingsAction.java
===================================================================
---
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/layout/ui/SettingsAction.java
2011-04-30 00:12:34 UTC (rev 24875)
+++
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/layout/ui/SettingsAction.java
2011-04-30 00:18:58 UTC (rev 24876)
@@ -33,7 +33,7 @@
import org.cytoscape.application.swing.CySwingApplication;
import org.cytoscape.application.swing.AbstractCyAction;
import org.cytoscape.session.CyApplicationManager;
-import org.cytoscape.view.layout.CyLayouts;
+import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.work.swing.GUITaskManager;
import javax.swing.event.MenuEvent;
@@ -43,12 +43,12 @@
public class SettingsAction extends AbstractCyAction {
private final static long serialVersionUID = 1202339874289357L;
- private CyLayouts cyl;
+ private CyLayoutAlgorithmManager cyl;
private CySwingApplication desk;
private LayoutMenuManager menuMgr;
private GUITaskManager tm;
- public SettingsAction(final CyLayouts cyl, final CySwingApplication
desk, final LayoutMenuManager menuMgr, final CyApplicationManager appMgr, final
GUITaskManager tm)
+ public SettingsAction(final CyLayoutAlgorithmManager cyl, final
CySwingApplication desk, final LayoutMenuManager menuMgr, final
CyApplicationManager appMgr, final GUITaskManager tm)
{
super("Settings...",appMgr);
setPreferredMenu("Layout");
Modified:
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/reader/AbstractGraphReader.java
===================================================================
---
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/reader/AbstractGraphReader.java
2011-04-30 00:12:34 UTC (rev 24875)
+++
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/reader/AbstractGraphReader.java
2011-04-30 00:18:58 UTC (rev 24876)
@@ -7,7 +7,7 @@
import org.cytoscape.model.CyNetwork;
import org.cytoscape.tableimport.internal.util.CytoscapeServices;
import org.cytoscape.view.layout.CyLayoutAlgorithm;
-import org.cytoscape.view.layout.CyLayouts;
+import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
//import cytoscape.task.TaskMonitor;
//import cytoscape.util.CyNetworkNaming;
@@ -98,7 +98,7 @@
* Return the CyLayoutAlgorithm used to layout the graph
*/
//public CyLayoutAlgorithm getLayoutAlgorithm() {
- // return null;//CyLayouts.getDefaultLayout();
+ // return null;//CyLayoutAlgorithmManager.getDefaultLayout();
//}
/**
Modified:
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/util/CytoscapeServices.java
===================================================================
---
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/util/CytoscapeServices.java
2011-04-30 00:12:34 UTC (rev 24875)
+++
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/util/CytoscapeServices.java
2011-04-30 00:18:58 UTC (rev 24876)
@@ -8,7 +8,7 @@
import org.cytoscape.property.CyProperty;
import org.cytoscape.property.bookmark.Bookmarks;
import org.cytoscape.property.bookmark.BookmarksUtil;
-import org.cytoscape.view.layout.CyLayouts;
+import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.view.model.CyNetworkViewManager;
import org.cytoscape.work.swing.GUITaskManager;
@@ -29,7 +29,7 @@
public static FileUtil fileUtil;
public static CyApplicationManager appMgr;
public static CyNetworkManager netMgr;
- public static CyLayouts cyLayoutsServiceRef;
+ public static CyLayoutAlgorithmManager cyLayoutsServiceRef;
public static CyNetworkViewFactory cyNetworkViewFactoryServiceRef;
public static CyNetworkFactory cyNetworkFactoryServiceRef;
public static CyNetworkViewManager networkViewManager;
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