Author: mes
Date: 2011-04-29 16:45:20 -0700 (Fri, 29 Apr 2011)
New Revision: 24874
Added:
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/AbstractLayoutAlgorithm.java
Removed:
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/AbstractLayout.java
Modified:
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/internal/algorithms/GridNodeLayout.java
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/GroupAttributesLayout.java
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/StackedNodeLayout.java
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutAlgorithm.java
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutFRAlgorithm.java
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutFRAlgorithmTask.java
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutKKAlgorithm.java
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/circularLayout/CircularLayoutAlgorithm.java
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/AttributeCircleLayout.java
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/DegreeSortedCircleLayout.java
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/ISOMLayout.java
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithm.java
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithmTask.java
core3/layout-jgraph-impl/trunk/src/main/java/csplugins/layout/JGraphLayoutWrapper.java
core3/layout-prefuse-impl/trunk/src/main/java/org/cytoscape/prefuse/layouts/internal/ForceDirectedLayout.java
Log:
renamed AbstractLayout to AbstractLayoutAlgorithm
Deleted:
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/AbstractLayout.java
===================================================================
---
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/AbstractLayout.java
2011-04-29 23:39:46 UTC (rev 24873)
+++
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/AbstractLayout.java
2011-04-29 23:45:20 UTC (rev 24874)
@@ -1,218 +0,0 @@
-/*
- File: AbstractLayout.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.awt.Dimension;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import org.cytoscape.model.CyNetwork;
-import org.cytoscape.model.CyNode;
-import org.cytoscape.model.CyRow;
-import org.cytoscape.model.CyTableUtil;
-import org.cytoscape.view.model.CyNetworkView;
-import org.cytoscape.view.model.View;
-import org.cytoscape.work.TaskMonitor;
-import org.cytoscape.work.undo.UndoSupport;
-
-
-/**
- * The AbstractLayout provides nice starting point for Layouts
- * written for Cytoscape.
- */
-abstract public class AbstractLayout implements CyLayoutAlgorithm {
- protected CyNetworkView networkView;
-
- // Graph Objects and Views
- protected Set<View<CyNode>> staticNodes;
- protected CyNetwork network;
-
- //
- protected boolean selectedOnly = false;
- protected String edgeAttribute = null;
- protected String nodeAttribute = null;
- protected boolean canceled = false;
- protected Dimension currentSize = new Dimension(20, 20);
- protected HashMap propertyMap = null; // TODO figure out if this is
used in a child somewhere
- protected HashMap savedPropertyMap = null; // TODO figure out if this
is used in a child somewhere
-// private ViewChangeEdit undoableEdit;
-
- // Should definitely be overridden!
- protected String propertyPrefix = "abstract";
- protected UndoSupport undo;
-
- private final String humanName;
- private final String computerName;
-
- /**
- * The Constructor is null
- */
- public AbstractLayout(UndoSupport undo, String computerName, String
humanName) {
- this.staticNodes = new HashSet<View<CyNode>>();
- this.undo = undo;
- this.computerName = computerName;
- this.humanName = humanName;
- }
-
- @Override
- public void setNetworkView(final CyNetworkView networkView) {
- this.networkView = networkView;
- }
-
- /**
- * getName is used to construct property strings
- * for this layout.
- */
- public String getName() {
- return computerName;
- }
-
- /**
- * toString is used to get the user-visible name
- * of the layout
- */
- public String toString() {
- return humanName;
- }
-
- /**
- * These methods should be overridden
- */
- public boolean supportsSelectedOnly() {
- return false;
- }
-
- /**
- * Set the flag that indicates that this algorithm
- * should only operate on the currently selected nodes.
- *
- * @param selectedOnly set to "true" if the algorithm should
- * only apply to selected nodes only
- */
- public void setSelectedOnly(boolean selectedOnly) {
- this.selectedOnly = selectedOnly;
- }
-
- /**
- * Returns the types of node attributes supported by
- * this algorithm. This should be overloaded by the
- * specific algorithm
- *
- * @return the list of supported attribute types, or null
- * if node attributes are not supported
- */
- public Set<Class<?>> supportsNodeAttributes() {
- return new HashSet<Class<?>>();
- }
-
- /**
- * Returns the types of edge attributes supported by
- * this algorithm. This should be overloaded by the
- * specific algorithm
- *
- * @return the list of supported attribute types, or null
- * if edge attributes are not supported
- */
- public Set<Class<?>> supportsEdgeAttributes() {
- return new HashSet<Class<?>>();
- }
-
- /**
- * Set the name of the attribute to use for attribute
- * dependent layout algorithms.
- *
- * @param attributeName The name of the attribute
- */
- public void setLayoutAttribute(String attributeName) {
- if (supportsNodeAttributes().size() > 0) {
- nodeAttribute = attributeName;
- } else if (supportsEdgeAttributes().size() > 0) {
- edgeAttribute = attributeName;
- }
- }
-
- /*
- * Override this if you want to provide a custom attribute
- */
-
- /**
- * This returns the list of "attributes" that are provided
- * by an algorithm for internal purposes. For example,
- * an edge-weighted algorithmn might seed the list of
- * attributes with "unweighted". This should be overloaded
- * by algorithms that intend to return custom attributes.
- *
- * @return A (possibly empty) list of attributes
- */
- public List<String> getInitialAttributeList() {
- return new ArrayList<String>();
- }
-
- /**
- * Initializer, calls <tt>intialize_local</tt> to
- * start construction process.
- */
- public void initialize() {
- double node_count = (double) network.getNodeCount();
- node_count = Math.sqrt(node_count);
- node_count *= 100;
- currentSize = new Dimension((int) node_count, (int) node_count);
- initialize_local();
- }
-
- /**
- * Initializes all local information, and is called immediately
- * within the <tt>initialize()</tt> process.
- * The user is responsible for overriding this method
- * to do any construction that may be necessary:
- * for example, to initialize local per-edge or
- * graph-wide data.
- */
- protected void initialize_local() {
- }
-
- /**
- * Descendents need to call this if they intend to use the
"staticNodes" field.
- */
- public final void initStaticNodes() {
- staticNodes.clear();
- final Set<CyNode> selectedNodes =
- new
HashSet<CyNode>(CyTableUtil.getNodesInState(networkView.getModel(),
-
CyNetwork.SELECTED, true));
- for (final View<CyNode> nodeView : networkView.getNodeViews()) {
- if (!selectedNodes.contains(nodeView.getModel()))
- staticNodes.add(nodeView);
- }
- }
-}
Copied:
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/AbstractLayoutAlgorithm.java
(from rev 24863,
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/AbstractLayout.java)
===================================================================
---
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/AbstractLayoutAlgorithm.java
(rev 0)
+++
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/AbstractLayoutAlgorithm.java
2011-04-29 23:45:20 UTC (rev 24874)
@@ -0,0 +1,218 @@
+/*
+ File: AbstractLayoutAlgorithm.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.awt.Dimension;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNode;
+import org.cytoscape.model.CyRow;
+import org.cytoscape.model.CyTableUtil;
+import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.view.model.View;
+import org.cytoscape.work.TaskMonitor;
+import org.cytoscape.work.undo.UndoSupport;
+
+
+/**
+ * The AbstractLayoutAlgorithm provides nice starting point for Layouts
+ * written for Cytoscape.
+ */
+abstract public class AbstractLayoutAlgorithm implements CyLayoutAlgorithm {
+ protected CyNetworkView networkView;
+
+ // Graph Objects and Views
+ protected Set<View<CyNode>> staticNodes;
+ protected CyNetwork network;
+
+ //
+ protected boolean selectedOnly = false;
+ protected String edgeAttribute = null;
+ protected String nodeAttribute = null;
+ protected boolean canceled = false;
+ protected Dimension currentSize = new Dimension(20, 20);
+ protected HashMap propertyMap = null; // TODO figure out if this is
used in a child somewhere
+ protected HashMap savedPropertyMap = null; // TODO figure out if this
is used in a child somewhere
+// private ViewChangeEdit undoableEdit;
+
+ // Should definitely be overridden!
+ protected String propertyPrefix = "abstract";
+ protected UndoSupport undo;
+
+ private final String humanName;
+ private final String computerName;
+
+ /**
+ * The Constructor is null
+ */
+ public AbstractLayoutAlgorithm(UndoSupport undo, String computerName,
String humanName) {
+ this.staticNodes = new HashSet<View<CyNode>>();
+ this.undo = undo;
+ this.computerName = computerName;
+ this.humanName = humanName;
+ }
+
+ @Override
+ public void setNetworkView(final CyNetworkView networkView) {
+ this.networkView = networkView;
+ }
+
+ /**
+ * getName is used to construct property strings
+ * for this layout.
+ */
+ public String getName() {
+ return computerName;
+ }
+
+ /**
+ * toString is used to get the user-visible name
+ * of the layout
+ */
+ public String toString() {
+ return humanName;
+ }
+
+ /**
+ * These methods should be overridden
+ */
+ public boolean supportsSelectedOnly() {
+ return false;
+ }
+
+ /**
+ * Set the flag that indicates that this algorithm
+ * should only operate on the currently selected nodes.
+ *
+ * @param selectedOnly set to "true" if the algorithm should
+ * only apply to selected nodes only
+ */
+ public void setSelectedOnly(boolean selectedOnly) {
+ this.selectedOnly = selectedOnly;
+ }
+
+ /**
+ * Returns the types of node attributes supported by
+ * this algorithm. This should be overloaded by the
+ * specific algorithm
+ *
+ * @return the list of supported attribute types, or null
+ * if node attributes are not supported
+ */
+ public Set<Class<?>> supportsNodeAttributes() {
+ return new HashSet<Class<?>>();
+ }
+
+ /**
+ * Returns the types of edge attributes supported by
+ * this algorithm. This should be overloaded by the
+ * specific algorithm
+ *
+ * @return the list of supported attribute types, or null
+ * if edge attributes are not supported
+ */
+ public Set<Class<?>> supportsEdgeAttributes() {
+ return new HashSet<Class<?>>();
+ }
+
+ /**
+ * Set the name of the attribute to use for attribute
+ * dependent layout algorithms.
+ *
+ * @param attributeName The name of the attribute
+ */
+ public void setLayoutAttribute(String attributeName) {
+ if (supportsNodeAttributes().size() > 0) {
+ nodeAttribute = attributeName;
+ } else if (supportsEdgeAttributes().size() > 0) {
+ edgeAttribute = attributeName;
+ }
+ }
+
+ /*
+ * Override this if you want to provide a custom attribute
+ */
+
+ /**
+ * This returns the list of "attributes" that are provided
+ * by an algorithm for internal purposes. For example,
+ * an edge-weighted algorithmn might seed the list of
+ * attributes with "unweighted". This should be overloaded
+ * by algorithms that intend to return custom attributes.
+ *
+ * @return A (possibly empty) list of attributes
+ */
+ public List<String> getInitialAttributeList() {
+ return new ArrayList<String>();
+ }
+
+ /**
+ * Initializer, calls <tt>intialize_local</tt> to
+ * start construction process.
+ */
+ public void initialize() {
+ double node_count = (double) network.getNodeCount();
+ node_count = Math.sqrt(node_count);
+ node_count *= 100;
+ currentSize = new Dimension((int) node_count, (int) node_count);
+ initialize_local();
+ }
+
+ /**
+ * Initializes all local information, and is called immediately
+ * within the <tt>initialize()</tt> process.
+ * The user is responsible for overriding this method
+ * to do any construction that may be necessary:
+ * for example, to initialize local per-edge or
+ * graph-wide data.
+ */
+ protected void initialize_local() {
+ }
+
+ /**
+ * Descendents need to call this if they intend to use the
"staticNodes" field.
+ */
+ public final void initStaticNodes() {
+ staticNodes.clear();
+ final Set<CyNode> selectedNodes =
+ new
HashSet<CyNode>(CyTableUtil.getNodesInState(networkView.getModel(),
+
CyNetwork.SELECTED, true));
+ for (final View<CyNode> nodeView : networkView.getNodeViews()) {
+ if (!selectedNodes.contains(nodeView.getModel()))
+ staticNodes.add(nodeView);
+ }
+ }
+}
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
2011-04-29 23:39:46 UTC (rev 24873)
+++
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/internal/algorithms/GridNodeLayout.java
2011-04-29 23:45:20 UTC (rev 24874)
@@ -37,7 +37,7 @@
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyNetwork;
-import org.cytoscape.view.layout.AbstractLayout;
+import org.cytoscape.view.layout.AbstractLayoutAlgorithm;
import org.cytoscape.view.layout.CyLayouts;
import org.cytoscape.view.model.View;
import org.cytoscape.view.model.VisualProperty;
@@ -52,7 +52,7 @@
* The GridNodeLayout provides a very simple layout, suitable as
* the default layout for Cytoscape data readers.
*/
-public class GridNodeLayout extends AbstractLayout implements TunableValidator
{
+public class GridNodeLayout extends AbstractLayoutAlgorithm implements
TunableValidator {
@Tunable(description="Vertical spacing between nodes")
public double nodeVerticalSpacing = 40.0;
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/GroupAttributesLayout.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/GroupAttributesLayout.java
2011-04-29 23:39:46 UTC (rev 24873)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/GroupAttributesLayout.java
2011-04-29 23:45:20 UTC (rev 24874)
@@ -37,7 +37,7 @@
package csplugins.layout.algorithms;
import org.cytoscape.model.CyTableManager;
-import org.cytoscape.view.layout.AbstractLayout;
+import org.cytoscape.view.layout.AbstractLayoutAlgorithm;
import org.cytoscape.work.TaskIterator;
import org.cytoscape.work.Tunable;
import org.cytoscape.work.undo.UndoSupport;
@@ -54,7 +54,7 @@
/**
*
*/
-public class GroupAttributesLayout extends AbstractLayout {
+public class GroupAttributesLayout extends AbstractLayoutAlgorithm {
/*
Layout parameters:
- spacingx: Horizontal spacing (on the x-axis) between two
partitions in a row.
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/StackedNodeLayout.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/StackedNodeLayout.java
2011-04-29 23:39:46 UTC (rev 24873)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/StackedNodeLayout.java
2011-04-29 23:45:20 UTC (rev 24874)
@@ -28,14 +28,14 @@
package csplugins.layout.algorithms;
-import org.cytoscape.view.layout.AbstractLayout;
+import org.cytoscape.view.layout.AbstractLayoutAlgorithm;
import org.cytoscape.work.TaskIterator;
import org.cytoscape.work.Tunable;
import org.cytoscape.work.TunableValidator;
import org.cytoscape.work.undo.UndoSupport;
-public class StackedNodeLayout extends AbstractLayout implements
TunableValidator {
+public class StackedNodeLayout extends AbstractLayoutAlgorithm implements
TunableValidator {
@Tunable(description="x_position")
public double x_position = 10.0;
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutAlgorithm.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutAlgorithm.java
2011-04-29 23:39:46 UTC (rev 24873)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutAlgorithm.java
2011-04-29 23:45:20 UTC (rev 24874)
@@ -150,7 +150,7 @@
* @param value the name of the attribute
*/
public void setSelectedOnly(boolean value) {
- // Inherited by AbstractLayout
+ // Inherited by AbstractLayoutAlgorithm
//selectedOnly = value;
}
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutFRAlgorithm.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutFRAlgorithm.java
2011-04-29 23:39:46 UTC (rev 24873)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutFRAlgorithm.java
2011-04-29 23:45:20 UTC (rev 24874)
@@ -35,7 +35,7 @@
import java.awt.Dimension;
import java.util.ArrayList;
-import org.cytoscape.view.layout.AbstractLayout;
+import org.cytoscape.view.layout.AbstractLayoutAlgorithm;
import org.cytoscape.view.layout.LayoutEdge;
import org.cytoscape.view.layout.LayoutNode;
import org.cytoscape.view.layout.LayoutPartition;
@@ -60,7 +60,7 @@
* @author <a href="mailto:[email protected]";>Scooter Morris</a>
* @version 0.9
*/
-public class BioLayoutFRAlgorithm extends AbstractLayout implements
TunableValidator {
+public class BioLayoutFRAlgorithm extends AbstractLayoutAlgorithm implements
TunableValidator {
/**
* Sets the number of iterations for each update
*/
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutFRAlgorithmTask.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutFRAlgorithmTask.java
2011-04-29 23:39:46 UTC (rev 24873)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutFRAlgorithmTask.java
2011-04-29 23:45:20 UTC (rev 24874)
@@ -137,7 +137,7 @@
}
/**
- * Required methods (and overrides) for AbstractLayout
+ * Required methods (and overrides) for AbstractLayoutAlgorithm
*/
/**
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutKKAlgorithm.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutKKAlgorithm.java
2011-04-29 23:39:46 UTC (rev 24873)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutKKAlgorithm.java
2011-04-29 23:45:20 UTC (rev 24874)
@@ -31,7 +31,7 @@
*/
package csplugins.layout.algorithms.bioLayout;
-import org.cytoscape.view.layout.AbstractLayout;
+import org.cytoscape.view.layout.AbstractLayoutAlgorithm;
import org.cytoscape.work.TaskIterator;
import org.cytoscape.work.Tunable;
@@ -58,7 +58,7 @@
* @author <a href="mailto:[email protected]";>Scooter Morris</a>
* @version 0.9
*/
-public class BioLayoutKKAlgorithm extends AbstractLayout implements
TunableValidator {
+public class BioLayoutKKAlgorithm extends AbstractLayoutAlgorithm implements
TunableValidator {
/**
* The average number of iterations per Node
*/
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/circularLayout/CircularLayoutAlgorithm.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/circularLayout/CircularLayoutAlgorithm.java
2011-04-29 23:39:46 UTC (rev 24873)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/circularLayout/CircularLayoutAlgorithm.java
2011-04-29 23:45:20 UTC (rev 24874)
@@ -5,7 +5,7 @@
import java.util.LinkedList;
import org.cytoscape.model.CyNode;
-import org.cytoscape.view.layout.AbstractLayout;
+import org.cytoscape.view.layout.AbstractLayoutAlgorithm;
import org.cytoscape.view.model.View;
import org.cytoscape.work.TaskIterator;
import org.cytoscape.work.Tunable;
@@ -13,7 +13,7 @@
import org.cytoscape.work.undo.UndoSupport;
-public class CircularLayoutAlgorithm extends AbstractLayout implements
TunableValidator{
+public class CircularLayoutAlgorithm extends AbstractLayoutAlgorithm
implements TunableValidator{
@Tunable(description="Horizontal spacing between nodes")
public int nodeHorizontalSpacing = 64;
@Tunable(description="Vertical spacing between nodes")
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/AttributeCircleLayout.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/AttributeCircleLayout.java
2011-04-29 23:39:46 UTC (rev 24873)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/AttributeCircleLayout.java
2011-04-29 23:45:20 UTC (rev 24874)
@@ -42,7 +42,7 @@
import org.cytoscape.model.CyTableEntry;
import org.cytoscape.model.CyTableEntry.*;
-import org.cytoscape.view.layout.AbstractLayout;
+import org.cytoscape.view.layout.AbstractLayoutAlgorithm;
import org.cytoscape.view.layout.LayoutNode;
import org.cytoscape.work.TaskIterator;
import org.cytoscape.work.Tunable;
@@ -50,7 +50,7 @@
import org.cytoscape.work.undo.UndoSupport;
-public class AttributeCircleLayout extends AbstractLayout implements
TunableValidator {
+public class AttributeCircleLayout extends AbstractLayoutAlgorithm implements
TunableValidator {
@Tunable(description="The attribute to use for the layout")
public String attribute = CyTableEntry.NAME;
@Tunable(description="Circle size")
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/DegreeSortedCircleLayout.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/DegreeSortedCircleLayout.java
2011-04-29 23:39:46 UTC (rev 24873)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/DegreeSortedCircleLayout.java
2011-04-29 23:45:20 UTC (rev 24874)
@@ -11,7 +11,7 @@
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyTableManager;
import org.cytoscape.view.layout.AbstractGraphPartition;
-import org.cytoscape.view.layout.AbstractLayout;
+import org.cytoscape.view.layout.AbstractLayoutAlgorithm;
import org.cytoscape.view.layout.LayoutNode;
import org.cytoscape.view.layout.LayoutPartition;
import org.cytoscape.work.TaskIterator;
@@ -20,7 +20,7 @@
import org.cytoscape.work.undo.UndoSupport;
-public class DegreeSortedCircleLayout extends AbstractLayout implements
TunableValidator {
+public class DegreeSortedCircleLayout extends AbstractLayoutAlgorithm
implements TunableValidator {
private static final String DEGREE_ATTR_NAME = "degree";
private CyTableManager tableMgr;
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/ISOMLayout.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/ISOMLayout.java
2011-04-29 23:39:46 UTC (rev 24873)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/ISOMLayout.java
2011-04-29 23:45:20 UTC (rev 24874)
@@ -6,7 +6,7 @@
import java.util.Iterator;
//import java.util.List;
-import org.cytoscape.view.layout.AbstractLayout;
+import org.cytoscape.view.layout.AbstractLayoutAlgorithm;
import org.cytoscape.work.TaskIterator;
import org.cytoscape.work.Tunable;
import org.cytoscape.work.TunableValidator;
@@ -15,7 +15,7 @@
/**
*
*/
-public class ISOMLayout extends AbstractLayout implements TunableValidator {
+public class ISOMLayout extends AbstractLayoutAlgorithm implements
TunableValidator {
@Tunable(description="Number of iterations")
public int maxEpoch = 5000;
@Tunable(description="Radius constant")
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithm.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithm.java
2011-04-29 23:39:46 UTC (rev 24873)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithm.java
2011-04-29 23:45:20 UTC (rev 24874)
@@ -40,7 +40,7 @@
package csplugins.layout.algorithms.hierarchicalLayout;
-import org.cytoscape.view.layout.AbstractLayout;
+import org.cytoscape.view.layout.AbstractLayoutAlgorithm;
import org.cytoscape.work.TaskIterator;
import org.cytoscape.work.Tunable;
import org.cytoscape.work.TunableValidator;
@@ -70,7 +70,7 @@
* Steps 2 through 6 are performed by calls to methods in the class
* {@link csplugins.hierarchicallayout.Graph}
*/
-public class HierarchicalLayoutAlgorithm extends AbstractLayout implements
TunableValidator {
+public class HierarchicalLayoutAlgorithm extends AbstractLayoutAlgorithm
implements TunableValidator {
@Tunable(description="Horizontal spacing between nodes")
private int nodeHorizontalSpacing = 64;
@Tunable(description="Vertical spacing between nodes")
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithmTask.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithmTask.java
2011-04-29 23:39:46 UTC (rev 24873)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithmTask.java
2011-04-29 23:45:20 UTC (rev 24874)
@@ -88,7 +88,7 @@
*/
/**
- * Main entry point for AbstractLayout classes
+ * Main entry point for AbstractLayoutAlgorithm classes
*/
public void construct() {
taskMonitor.setStatusMessage("Initializing");
Modified:
core3/layout-jgraph-impl/trunk/src/main/java/csplugins/layout/JGraphLayoutWrapper.java
===================================================================
---
core3/layout-jgraph-impl/trunk/src/main/java/csplugins/layout/JGraphLayoutWrapper.java
2011-04-29 23:39:46 UTC (rev 24873)
+++
core3/layout-jgraph-impl/trunk/src/main/java/csplugins/layout/JGraphLayoutWrapper.java
2011-04-29 23:45:20 UTC (rev 24874)
@@ -1,6 +1,6 @@
package csplugins.layout;
-import org.cytoscape.view.layout.AbstractLayout;
+import org.cytoscape.view.layout.AbstractLayoutAlgorithm;
import org.cytoscape.work.TaskIterator;
import org.cytoscape.work.TunableValidator;
import org.cytoscape.work.undo.UndoSupport;
@@ -15,7 +15,7 @@
import org.jgraph.plugins.layouts.SugiyamaLayoutAlgorithm;
import org.jgraph.plugins.layouts.TreeLayoutAlgorithm;
-public class JGraphLayoutWrapper extends AbstractLayout implements
TunableValidator {
+public class JGraphLayoutWrapper extends AbstractLayoutAlgorithm implements
TunableValidator {
public static final int ANNEALING = 0;
public static final int MOEN = 1;
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
2011-04-29 23:39:46 UTC (rev 24873)
+++
core3/layout-prefuse-impl/trunk/src/main/java/org/cytoscape/prefuse/layouts/internal/ForceDirectedLayout.java
2011-04-29 23:45:20 UTC (rev 24874)
@@ -2,7 +2,7 @@
import java.io.IOException;
-import org.cytoscape.view.layout.AbstractLayout;
+import org.cytoscape.view.layout.AbstractLayoutAlgorithm;
import org.cytoscape.view.layout.CyLayouts;
import org.cytoscape.work.TaskIterator;
import org.cytoscape.work.Tunable;
@@ -15,7 +15,7 @@
import prefuse.util.force.Integrator;
import org.cytoscape.work.util.ListSingleSelection;
-public class ForceDirectedLayout extends AbstractLayout implements
TunableValidator {
+public class ForceDirectedLayout extends AbstractLayoutAlgorithm implements
TunableValidator {
@Tunable(description="Number of Iterations", groups="Algorithm
settings")
public int numIterations = 100;
@Tunable(description="Default Spring Coefficient", groups="Algorithm
settings")
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