Author: mes
Date: 2011-05-04 14:32:56 -0700 (Wed, 04 May 2011)
New Revision: 24926
Modified:
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/AbstractBasicLayoutTask.java
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/AbstractLayoutAlgorithm.java
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/AbstractPartitionLayoutTask.java
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/CyLayoutAlgorithm.java
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/PartitionUtil.java
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/BioLayoutFRAlgorithm.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-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:
Added javadoc and other minor reorganization.
Modified:
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/AbstractBasicLayoutTask.java
===================================================================
---
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/AbstractBasicLayoutTask.java
2011-05-04 21:27:32 UTC (rev 24925)
+++
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/AbstractBasicLayoutTask.java
2011-05-04 21:32:56 UTC (rev 24926)
@@ -27,14 +27,38 @@
public abstract class AbstractBasicLayoutTask extends AbstractTask {
private static final Logger logger =
LoggerFactory.getLogger(AbstractBasicLayoutTask.class);
+ private final String name;
+
+ /**
+ * The table column name that provides the layout algorithm name.
+ */
protected static final String LAYOUT_ALGORITHM = "layoutAlgorithm";
+ /**
+ * The network view that the layout will be applied to.
+ */
protected final CyNetworkView networkView;
+
+ /**
+ * The set of nodes whose positions are locked and not meant to change.
+ */
+ protected final Set<View<CyNode>> staticNodes;
+
+ /**
+ * Indicates whether to apply the layout to all nodes or only the
selected nodes.
+ */
protected final boolean selectedOnly;
- protected final Set<View<CyNode>> staticNodes;
- private final String name;
-
+ /**
+ * Constructor.
+ * @param networkView The network view that the layout algorithm will
be applied to.
+ * @param name The name of the algorithm. Used for setting attributes
associated with
+ * this layout.
+ * @param selectedOnly Indicates whether the layout should be applied
to the selected nodes
+ * or not.
+ * @param staticNodes The list of nodes whose positions are meant to be
locked and
+ * not changed.
+ */
public AbstractBasicLayoutTask(final CyNetworkView networkView, final
String name, boolean selectedOnly,
final Set<View<CyNode>> staticNodes)
{
@@ -45,7 +69,7 @@
this.selectedOnly = selectedOnly;
this.staticNodes = staticNodes;
}
-
+
@Override
public final void run(final TaskMonitor taskMonitor) {
final long start = System.currentTimeMillis();
@@ -75,10 +99,19 @@
logger.debug("Layout finished: " +
(System.currentTimeMillis()-start) + " msec.");
}
-
+ /**
+ * Returns true if the specified node view is locked in place, false
otherwise.
+ * @param v The node view to test.
+ * @return True if the specified node view is locked in place, false
otherwise.
+ */
protected boolean isLocked(View<CyNode> v) {
return ((staticNodes != null) && (staticNodes.contains(v)));
}
+ /**
+ * This method is designed to actually encapsulate the layout
algorithm. It will be
+ * called from within the run() method of the task.
+ * @param taskMonitor Provided to allow updates to the task status.
+ */
protected abstract void doLayout(final TaskMonitor taskMonitor);
}
Modified:
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/AbstractLayoutAlgorithm.java
===================================================================
---
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/AbstractLayoutAlgorithm.java
2011-05-04 21:27:32 UTC (rev 24925)
+++
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/AbstractLayoutAlgorithm.java
2011-05-04 21:32:56 UTC (rev 24926)
@@ -48,86 +48,119 @@
/**
- * The AbstractLayoutAlgorithm provides nice starting point for Layouts
- * written for Cytoscape.
+ * The AbstractLayoutAlgorithm provides a basic implementation of a layout
TaskFactory.
*/
abstract public class AbstractLayoutAlgorithm implements CyLayoutAlgorithm {
+
+ /**
+ * The network view that the layout will be applied to.
+ */
protected CyNetworkView networkView;
- // Graph Objects and Views
- protected Set<View<CyNode>> staticNodes;
+ /**
+ * The network model underlying the networkView. This shouldn't be set
directly
+ * by extending classes.
+ */
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
+ /**
+ * The UndoSupport object use for allowing undo of layouts.
+ */
+ protected final UndoSupport undo;
// private ViewChangeEdit undoableEdit;
-
- // Should definitely be overridden!
- protected String propertyPrefix = "abstract";
- protected UndoSupport undo;
-
+
+ /**
+ * The set of nodes that are
+ */
+ protected Set<View<CyNode>> staticNodes = new HashSet<View<CyNode>>();
+
+ /**
+ * Indicates that only selected nodes should be laid out.
+ */
+ protected boolean selectedOnly;
+
+ private final boolean supportsSelectedOnly;
+ private String edgeAttribute = null;
+ private String nodeAttribute = null;
+ private Dimension currentSize = new Dimension(20, 20);
private final String humanName;
private final String computerName;
/**
- * The Constructor is null
+ * The Constructor.
*/
- public AbstractLayoutAlgorithm(UndoSupport undo, String computerName,
String humanName) {
- this.staticNodes = new HashSet<View<CyNode>>();
+ public AbstractLayoutAlgorithm(final UndoSupport undo, final String
computerName, final String humanName, boolean supportsSelectedOnly) {
this.undo = undo;
this.computerName = computerName;
this.humanName = humanName;
+ this.supportsSelectedOnly = supportsSelectedOnly;
}
+ /**
+ * Sets the network view to be laid out.
+ * @param networkView the network view to be laid out.
+ */
@Override
public void setNetworkView(final CyNetworkView networkView) {
this.networkView = networkView;
+ this.network = networkView.getModel();
+ double node_count = (double) network.getNodeCount();
+ node_count = Math.sqrt(node_count);
+ node_count *= 100;
+ currentSize = new Dimension((int) node_count, (int) node_count);
}
+
+ /**
+ * 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;
+ }
+ }
+
+ /**
+ * 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;
+ }
/**
- * getName is used to construct property strings
- * for this layout.
+ * A computer readable name used to construct property strings.
*/
public String getName() {
return computerName;
}
/**
- * toString is used to get the user-visible name
- * of the layout
+ * Used to get the user-visible name of the layout.
*/
public String toString() {
return humanName;
}
/**
- * These methods should be overridden
+ * Indicates whether this algorithm supports applying the layout
+ * only to selected nodes.
*/
- public boolean supportsSelectedOnly() {
- return false;
+ public final boolean supportsSelectedOnly() {
+ return supportsSelectedOnly;
}
/**
- * 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
+ * this algorithm. This should be overridden by the
+ * specific algorithm.
*
* @return the list of supported attribute types, or null
* if node attributes are not supported
@@ -138,8 +171,8 @@
/**
* Returns the types of edge attributes supported by
- * this algorithm. This should be overloaded by the
- * specific algorithm
+ * this algorithm. This should be overridden by the
+ * specific algorithm.
*
* @return the list of supported attribute types, or null
* if edge attributes are not supported
@@ -149,24 +182,6 @@
}
/**
- * 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
@@ -179,31 +194,8 @@
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.
+ * Descendants need to call this if they intend to use the
"staticNodes" field.
*/
public final void initStaticNodes() {
staticNodes.clear();
Modified:
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/AbstractPartitionLayoutTask.java
===================================================================
---
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/AbstractPartitionLayoutTask.java
2011-05-04 21:27:32 UTC (rev 24925)
+++
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/AbstractPartitionLayoutTask.java
2011-05-04 21:32:56 UTC (rev 24926)
@@ -10,6 +10,8 @@
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.View;
import org.cytoscape.work.TaskMonitor;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
/**
* This is a more helpful implementation of a LayoutAlgorithm Task
@@ -20,24 +22,52 @@
* method as an argument.
*/
public abstract class AbstractPartitionLayoutTask extends
AbstractBasicLayoutTask {
+
+ private static Logger logger =
LoggerFactory.getLogger(AbstractPartitionLayoutTask.class);
+
+ /**
+ * The TaskMonitor initially set in the run method of the task.
+ * Used to track the layout progress.
+ */
protected TaskMonitor taskMonitor;
- double incr = 100;
+ /**
+ * The value used for spacing nodes. Defaults to 100.
+ */
+ protected double incr = 100;
+
+ /**
+ * The list of LayoutPartition objects that get laid out.
+ */
protected List <LayoutPartition> partitionList = null;
+
+ /**
+ * The EdgeWeighter used for edge weight calculations.
+ */
protected EdgeWeighter edgeWeighter = null;
- private boolean singlePartition;
+
+ private final boolean singlePartition;
- // Information for taskMonitor
- double current_start = 0; // Starting node number
- double current_size = 0; // Partition size
- double total_nodes = 0; // Total number of nodes
+ /**
+ * Starting node number used for taskMonitor.
+ */
+ protected double current_start = 0;
+
+ /**
+ * Partition size used for taskMonitor.
+ */
+ protected double current_size = 0;
+
+ /**
+ * Total number of nodes used for taskMonitor.
+ */
+ protected double total_nodes = 0;
/**
* Creates a new AbstractPartitionLayoutTask object.
*/
public AbstractPartitionLayoutTask(final CyNetworkView networkView,
final String name,
- final boolean singlePartition,
- final boolean selectedOnly, final
Set<View<CyNode>> staticNodes) {
+ final boolean singlePartition, final
boolean selectedOnly, final Set<View<CyNode>> staticNodes) {
super(networkView, name, selectedOnly, staticNodes);
this.singlePartition = singlePartition;
}
@@ -51,44 +81,25 @@
public abstract void layoutPartion(LayoutPartition partition);
/**
- * DOCUMENT ME!
+ * Returns true if the layout supports only applying the layout to
selected nodes.
*
- * @return DOCUMENT ME!
+ * @return True if the layout supports only applying the layout to
selected nodes.
*/
public boolean supportsSelectedOnly() {
return true;
}
/**
- * Sets the singlePartition flag, which disables partitioning. This
- * can be used by users who do not want to partition their graph for
- * some reason.
+ * Used for
*
- * @param partitioning if false, no paritioning will be done
+ * @param percent The percentage of completion for this partition.
Value must be between 0 and 100.
*/
- public void setPartition(final boolean partitioning) {
- singlePartition = !partitioning;
- }
-
- /**
- * Sets the singlePartition flag, which disables partitioning. This
- * can be used by users who do not want to partition their graph for
- * some reason.
- *
- * @param value if "false", no paritioning will be done
- */
- public void setPartition(String value) {
- Boolean val = new Boolean(value);
- setPartition(val.booleanValue());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param percent The percentage of completion for this partition
- */
protected void setTaskStatus(int percent) {
if (taskMonitor != null) {
+ if ( percent < 0 || percent > 100 ) {
+ logger.warn("invalid percent value set for
layout status (must be between 0 and 100): " + percent);
+ return;
+ }
// Calculate the nodes done for this partition
double nodesDone = current_size*(double)percent/100.;
// Calculate the percent done overall
@@ -99,8 +110,11 @@
}
/**
- * AbstractGraphPartitionLayout implements the constuct method
- * and calls layoutPartion for each partition.
+ * AbstractGraphPartitionLayout implements the doLayout method
+ * of AbstractBasicLayout in which it calls the layoutParition
+ * method on each LayoutPartition object created for the network.
+ * @param taskMonitor the TaskMonitor provided by the run() method
+ * of the Task.
*/
public void doLayout(final TaskMonitor taskMonitor) {
final CyNetwork network = networkView.getModel();
Modified:
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/CyLayoutAlgorithm.java
===================================================================
---
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/CyLayoutAlgorithm.java
2011-05-04 21:27:32 UTC (rev 24925)
+++
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/CyLayoutAlgorithm.java
2011-05-04 21:32:56 UTC (rev 24926)
@@ -40,7 +40,9 @@
import java.util.List;
import java.util.Set;
-
+/**
+ * An extension of NetworkViewTaskFactory specific to layout algorithms.
+ */
public interface CyLayoutAlgorithm extends NetworkViewTaskFactory {
/**
* Tests to see if this layout supports doing a layout on a subset of
the
Modified:
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/PartitionUtil.java
===================================================================
---
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/PartitionUtil.java
2011-05-04 21:27:32 UTC (rev 24925)
+++
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/PartitionUtil.java
2011-05-04 21:32:56 UTC (rev 24926)
@@ -58,8 +58,6 @@
/**
* This class also provides static methods that are used to partition a
network.
- *
- * @author <a href="mailto:[email protected]";>Scooter Morris</a>
*/
public final class PartitionUtil {
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
2011-05-04 21:27:32 UTC (rev 24925)
+++
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/internal/algorithms/GridNodeLayout.java
2011-05-04 21:32:56 UTC (rev 24926)
@@ -63,7 +63,7 @@
* Creates a new GridNodeLayout object.
*/
public GridNodeLayout(UndoSupport un) {
- super(un,CyLayoutAlgorithmManager.DEFAULT_LAYOUT_NAME,"Grid
Layout");
+ super(un,CyLayoutAlgorithmManager.DEFAULT_LAYOUT_NAME,"Grid
Layout", true);
}
public boolean tunablesAreValid(final Appendable errMsg) {
@@ -86,13 +86,4 @@
return new TaskIterator(new GridNodeLayoutTask(networkView,
getName(), selectedOnly, staticNodes,
nodeVerticalSpacing, nodeHorizontalSpacing));
}
-
- /**
- * We do support selected only
- *
- * @return true
- */
- public boolean supportsSelectedOnly() {
- return true;
- }
}
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
2011-05-04 21:27:32 UTC (rev 24925)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/GroupAttributesLayout.java
2011-05-04 21:32:56 UTC (rev 24926)
@@ -85,7 +85,7 @@
* Creates a new GroupAttributesLayout object.
*/
public GroupAttributesLayout(UndoSupport undoSupport, CyTableManager
tableMgr) {
- super(undoSupport, "attributes-layout", "Group Attributes
Layout");
+ super(undoSupport, "attributes-layout", "Group Attributes
Layout", true);
this.tableMgr = tableMgr;
}
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
2011-05-04 21:27:32 UTC (rev 24925)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/StackedNodeLayout.java
2011-05-04 21:32:56 UTC (rev 24926)
@@ -68,7 +68,7 @@
* @param nodes DOCUMENT ME!
*/
public StackedNodeLayout(UndoSupport undoSupport) {
- super(undoSupport, "stacked-node-layout", "Stacked Node
Layout");
+ super(undoSupport, "stacked-node-layout", "Stacked Node
Layout", true);
}
public TaskIterator getTaskIterator() {
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
2011-05-04 21:27:32 UTC (rev 24925)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutFRAlgorithm.java
2011-05-04 21:32:56 UTC (rev 24926)
@@ -1,5 +1,4 @@
/**
- * Copyright (c) 2006 The Regents of the University of California.
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
@@ -122,7 +121,7 @@
*/
public BioLayoutFRAlgorithm(UndoSupport undoSupport, boolean
supportEdgeWeights) {
- super(undoSupport, "fruchterman-rheingold", (supportEdgeWeights
? "Edge-weighted Force directed (BioLayout)" : "Force directed (BioLayout)"));
+ super(undoSupport, "fruchterman-rheingold", (supportEdgeWeights
? "Edge-weighted Force directed (BioLayout)" : "Force directed (BioLayout)"),
true);
supportWeights = supportEdgeWeights;
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
2011-05-04 21:27:32 UTC (rev 24925)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutKKAlgorithm.java
2011-05-04 21:32:56 UTC (rev 24926)
@@ -82,7 +82,8 @@
public BioLayoutKKAlgorithm(UndoSupport un, boolean supportEdgeWeights)
{
super(un, (supportEdgeWeights ? "kamada-kawai" :
"kamada-kawai-noweight"),
- (supportEdgeWeights ? "Edge-weighted Spring
Embedded" : "Spring Embedded") );
+ (supportEdgeWeights ? "Edge-weighted Spring
Embedded" : "Spring Embedded"),
+ true);
supportWeights = supportEdgeWeights;
}
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
2011-05-04 21:27:32 UTC (rev 24925)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/circularLayout/CircularLayoutAlgorithm.java
2011-05-04 21:32:56 UTC (rev 24926)
@@ -31,7 +31,7 @@
* Creates a new Layout object.
*/
public CircularLayoutAlgorithm(UndoSupport un) {
- super(un, "circular", "Circular Layout");
+ super(un, "circular", "Circular Layout", false);
}
//TODO how to validate these values?
@@ -46,13 +46,4 @@
nodeVerticalSpacing,
leftEdge, topEdge,
rightMargin,
singlePartition));
}
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean supportsSelectedOnly() {
- return false;
- }
}
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
2011-05-04 21:27:32 UTC (rev 24925)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/AttributeCircleLayout.java
2011-05-04 21:32:56 UTC (rev 24926)
@@ -68,7 +68,8 @@
public AttributeCircleLayout(final UndoSupport undoSupport, final
boolean supportNodeAttributes)
{
super(undoSupport, (supportNodeAttributes ? "attribute-circle":
"circle"),
- (supportNodeAttributes ? "Attribute Circle
Layout" : "Circle Layout") );
+ (supportNodeAttributes ? "Attribute Circle
Layout" : "Circle Layout"),
+ true);
this.supportNodeAttributes = supportNodeAttributes;
}
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
2011-05-04 21:27:32 UTC (rev 24925)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/DegreeSortedCircleLayout.java
2011-05-04 21:32:56 UTC (rev 24926)
@@ -31,7 +31,7 @@
* Creates a new DegreeSortedCircleLayout object.
*/
public DegreeSortedCircleLayout(UndoSupport undoSupport, CyTableManager
tableMgr) {
- super(undoSupport, "degree-circle", "Degree Sorted Circle
Layout");
+ super(undoSupport, "degree-circle", "Degree Sorted Circle
Layout", true);
this.tableMgr = 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
2011-05-04 21:27:32 UTC (rev 24925)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/ISOMLayout.java
2011-05-04 21:32:56 UTC (rev 24926)
@@ -39,7 +39,7 @@
* Creates a new ISOMLayout object.
*/
public ISOMLayout(UndoSupport undoSupport) {
- super(undoSupport,"isom", "Inverted Self-Organizing Map
Layout");
+ super(undoSupport,"isom", "Inverted Self-Organizing Map
Layout", true);
}
// TODO
@@ -57,13 +57,4 @@
initialAdaptation, minAdaptation,
sizeFactor,
coolingFactor, singlePartition));
}
-
- /**
- * We do support selected only
- *
- * @return true
- */
- public boolean supportsSelectedOnly() {
- return true;
- }
}
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
2011-05-04 21:27:32 UTC (rev 24925)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithm.java
2011-05-04 21:32:56 UTC (rev 24926)
@@ -92,7 +92,7 @@
* Creates a new HierarchicalLayoutAlgorithm object.
*/
public HierarchicalLayoutAlgorithm(UndoSupport undoSupport) {
- super(undoSupport, "hierarchical", "Hierarchical Layout");
+ super(undoSupport, "hierarchical", "Hierarchical Layout",true);
}
// TODO
@@ -107,10 +107,4 @@
nodeHorizontalSpacing, nodeVerticalSpacing,
componentSpacing, bandGap,leftEdge, topEdge,
rightMargin, selected_only));
}
-
- // We do support selected only
- @Override
- public boolean supportsSelectedOnly() {
- return true;
- }
}
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
2011-05-04 21:27:32 UTC (rev 24925)
+++
core3/layout-jgraph-impl/trunk/src/main/java/csplugins/layout/JGraphLayoutWrapper.java
2011-05-04 21:32:56 UTC (rev 24926)
@@ -35,7 +35,7 @@
*/
public JGraphLayoutWrapper(UndoSupport un, int layout_type) {
// names here will be overridden by provided methods
- super(un, "jgraph", "jgraph");
+ super(un, "jgraph", "jgraph", true);
this.layout_type = layout_type;
@@ -164,13 +164,4 @@
return "";
}
-
- /**
- * We do support selected only
- *
- * @return true
- */
- public boolean supportsSelectedOnly() {
- return true;
- }
}
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
2011-05-04 21:27:32 UTC (rev 24925)
+++
core3/layout-prefuse-impl/trunk/src/main/java/org/cytoscape/prefuse/layouts/internal/ForceDirectedLayout.java
2011-05-04 21:32:56 UTC (rev 24926)
@@ -51,7 +51,7 @@
* Creates a new GridNodeLayout object.
*/
public ForceDirectedLayout(UndoSupport un) {
- super(un, "force-directed", "Force Directed Layout");
+ super(un, "force-directed", "Force Directed Layout", true);
}
public boolean tunablesAreValid(final Appendable errMsg) {
@@ -74,13 +74,4 @@
defaultSpringLength,
defaultNodeMass, integrator,
singlePartition));
}
-
- /**
- * We do support selected only
- *
- * @return true
- */
- public boolean supportsSelectedOnly() {
- return true;
- }
}
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