Author: mes
Date: 2011-04-29 15:43:31 -0700 (Fri, 29 Apr 2011)
New Revision: 24861
Added:
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/PartitionUtil.java
Removed:
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/LayoutAdapter.java
Modified:
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/AbstractGraphPartition.java
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/AbstractLayout.java
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/CyLayouts.java
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/EdgeWeighter.java
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/LayoutEdge.java
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/LayoutNode.java
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/LayoutPartition.java
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/LayoutTask.java
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/internal/algorithms/GridNodeLayout.java
Log:
initial layout api cleanup
Modified:
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/AbstractGraphPartition.java
===================================================================
---
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/AbstractGraphPartition.java
2011-04-29 22:33:35 UTC (rev 24860)
+++
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/AbstractGraphPartition.java
2011-04-29 22:43:31 UTC (rev 24861)
@@ -34,8 +34,7 @@
*/
public AbstractGraphPartition(final CyNetworkView networkView, final
String name,
final boolean singlePartition,
- final boolean selectedOnly, final
Set<View<CyNode>> staticNodes)
- {
+ final boolean selectedOnly, final
Set<View<CyNode>> staticNodes) {
super(networkView, name, selectedOnly, staticNodes);
this.singlePartition = singlePartition;
}
@@ -113,7 +112,7 @@
// We still use the partition abstraction, even if we're
// not partitioning. This makes the code further down
// much cleaner
- LayoutPartition partition = new
LayoutPartition(network, networkView, selectedOnly, edgeWeighter);
+ LayoutPartition partition = new
LayoutPartition(networkView, selectedOnly, edgeWeighter);
partition.setTaskMonitor(taskMonitor);
partitionList = new ArrayList(1);
partitionList.add(partition);
@@ -126,11 +125,11 @@
unlockedNodes.add(node);
}
}
- LayoutPartition partition = new
LayoutPartition(network, networkView, unlockedNodes, edgeWeighter);
+ LayoutPartition partition = new
LayoutPartition(networkView, unlockedNodes, edgeWeighter);
partitionList = new ArrayList(1);
partitionList.add(partition);
} else {
- partitionList = LayoutPartition.partition(network,
networkView, false, edgeWeighter);
+ partitionList = PartitionUtil.partition(networkView,
false, edgeWeighter);
}
total_nodes = network.getNodeCount();
Modified:
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 22:33:35 UTC (rev 24860)
+++
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/AbstractLayout.java
2011-04-29 22:43:31 UTC (rev 24861)
@@ -72,12 +72,17 @@
protected String propertyPrefix = "abstract";
protected UndoSupport undo;
+ private final String humanName;
+ private final String computerName;
+
/**
* The Constructor is null
*/
- public AbstractLayout(UndoSupport undo) {
+ public AbstractLayout(UndoSupport undo, String computerName, String
humanName) {
this.staticNodes = new HashSet<View<CyNode>>();
this.undo = undo;
+ this.computerName = computerName;
+ this.humanName = humanName;
}
@Override
@@ -89,13 +94,17 @@
* getName is used to construct property strings
* for this layout.
*/
- public abstract String getName();
+ public String getName() {
+ return computerName;
+ }
/**
* toString is used to get the user-visible name
* of the layout
*/
- public abstract String toString();
+ public String toString() {
+ return humanName;
+ }
/**
* These methods should be overridden
@@ -193,7 +202,8 @@
protected void initialize_local() {
}
- /** Descendents need to call this if they intend to use the
"staticNodes" field.
+ /**
+ * Descendents need to call this if they intend to use the
"staticNodes" field.
*/
public final void initStaticNodes() {
staticNodes.clear();
@@ -204,6 +214,5 @@
if (!selectedNodes.contains(nodeView.getModel()))
staticNodes.add(nodeView);
}
-
}
}
Modified:
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
2011-04-29 22:33:35 UTC (rev 24860)
+++
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/CyLayouts.java
2011-04-29 22:43:31 UTC (rev 24861)
@@ -42,10 +42,6 @@
String PREF_MENU_DEFAULT = "Cytoscape Layouts";
String DEFAULT_LAYOUT_NAME = "grid";
- void addLayout(CyLayoutAlgorithm layout, Map props);
-
- void removeLayout(CyLayoutAlgorithm layout, Map props);
-
CyLayoutAlgorithm getLayout(String name);
Collection<CyLayoutAlgorithm> getAllLayouts();
Modified:
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/EdgeWeighter.java
===================================================================
---
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/EdgeWeighter.java
2011-04-29 22:33:35 UTC (rev 24860)
+++
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/EdgeWeighter.java
2011-04-29 22:43:31 UTC (rev 24861)
@@ -51,41 +51,41 @@
* The EdgeWeighter class. This class is used as a container for information
* about how to interpret weights in an weighted layout.
*/
-public class EdgeWeighter {
+public final class EdgeWeighter {
+
@Tunable(description="How to interpret weight values", groups={"Edge
Weight Settings"})
public WeightTypes type = WeightTypes.GUESS;
+
@Tunable(description="The minimum edge weight to consider",
groups={"Edge Weight Settings"})
public double minWeightCutoff = 0;
+
@Tunable(description="The maximum edge weight to consider",
groups={"Edge Weight Settings"})
public double maxWeightCutoff = Double.MAX_VALUE;
- final static double EPSILON = .001;
+ @Tunable(description="The edge attribute that contains the weights",
groups={"Edge Weight Settings"})
+ public String weightAttribute = null;
+
+
+ private final static double EPSILON = .001;
+
// Default normalization bounds
- final static double LOWER_BOUND = .1f;
- final static double UPPER_BOUND = .9f;
+ private final static double LOWER_BOUND = .1f;
+ private final static double UPPER_BOUND = .9f;
- double lowerBounds = LOWER_BOUND;
- double upperBounds = UPPER_BOUND;
+ private double lowerBounds = LOWER_BOUND;
+ private double upperBounds = UPPER_BOUND;
- double maxWeight = -1000000;
- double minWeight = 1000000;
- double maxLogWeight = -1000000;
- double minLogWeight = 1000000;
+ private double maxWeight = -1000000;
+ private double minWeight = 1000000;
+ private double maxLogWeight = -1000000;
+ private double minLogWeight = 1000000;
- double logWeightCeiling = 1028;
- boolean logOverflow = false;
+ private double logWeightCeiling = 1028;
+ private boolean logOverflow = false;
// These are just here for efficiency reasons
- double normalFactor = Double.MAX_VALUE;
+ private double normalFactor = Double.MAX_VALUE;
- @Tunable(description="The edge attribute that contains the weights",
groups={"Edge Weight Settings"})
- public String weightAttribute = null;
-
- static WeightTypes[] weightChoices = {WeightTypes.GUESS,
- WeightTypes.LOG,
- WeightTypes.DISTANCE,
- WeightTypes.WEIGHT};
-
public void reset() {
maxWeight = -1000000;
minWeight = 1000000;
@@ -174,7 +174,7 @@
weight = normalize(edge.getWeight());
}
break;
- case LOG:
+ case LOG:
// System.out.print("Log: ");
weight = edge.getLogWeight();
// System.out.print("Log weight = "+weight);
@@ -183,12 +183,12 @@
weight = logNormalize(weight);
// System.out.println(" normalized weight = "+weight);
break;
- case DISTANCE:
+ case DISTANCE:
// System.out.println("Distance");
weight = edge.getWeight();
weight = (lowerBounds + upperBounds) -
normalize(weight);
break;
- case WEIGHT:
+ case WEIGHT:
// System.out.println("Weight");
weight = normalize(edge.getWeight());
break;
Deleted:
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/LayoutAdapter.java
===================================================================
---
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/LayoutAdapter.java
2011-04-29 22:33:35 UTC (rev 24860)
+++
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/LayoutAdapter.java
2011-04-29 22:43:31 UTC (rev 24861)
@@ -1,155 +0,0 @@
-/*
- File: LayoutAdapter.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 org.cytoscape.work.TaskMonitor;
-import org.cytoscape.view.model.CyNetworkView;
-import org.cytoscape.view.model.View;
-import org.cytoscape.model.CyNode;
-
-import javax.swing.*;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Set;
-import java.util.HashSet;
-
-
-/**
- * LayoutAdapter provides a *very* minimal interface to implement a layout
- * algorithm. It is meant to be used by graph readers and plugins that provide
- * their own node placement and whose layout approach should not be made
- * available outside of the reader or plugin's context.
- */
-abstract public class LayoutAdapter implements CyLayoutAlgorithm {
-
- /**
- * This method performs the layout on the current network.
- *
- * @param networkView the CyNetworkView on which to perform the layout
- */
- public void doLayout(CyNetworkView networkView) {
- doLayout(networkView, null);
- }
-
- /**
- * This method performs the layout on the current network, but assumes
- * that the layout is part of an existing monitored task
- *
- * @param networkView the CyNetworkView on which to perform the layout
- * @param monitor the task monitor to use
- */
- public abstract void doLayout(CyNetworkView networkView, TaskMonitor
monitor);
-
- /**
- * Get the name of this layout.
- *
- * @return String representing the name of the layout.
- */
- public String getName() {return "LayoutAdaptor";}
-
- /**
- * Tests to see if this layout supports doing a layout on a subset of
the
- * nodes in this network view.
- *
- * @return true if layout supports layouts on a subset of the nodes
- */
- public boolean supportsSelectedOnly() {return false;}
-
- /**
- * Sets the "selectedOnly" flag
- *
- * @param selectedOnly boolean value that tells the layout algorithm
whether to
- * only layout the selected nodes
- */
- public void setSelectedOnly(boolean selectedOnly) {}
-
- /**
- * Tests to see if this layout supports doing a layout based on node
attributes.
- *
- * @return byte array of allowable attribute types or "null" if not
supported. If the
- * first type is "-1", all types are supported
- */
- public Set<Class<?>> supportsNodeAttributes() { return new
HashSet<Class<?>>(); }
-
- /**
- * Tests to see if this layout supports doing a layout based on edge
attributes.
- *
- * @return type array of allowable attribute types or "null" if not
supported. If the
- * first type is "-1", all types are supported
- */
- public Set<Class<?>> supportsEdgeAttributes() { return new
HashSet<Class<?>>(); }
-
- /**
- * Sets the attribute to use for node- or edge- based attribute layouts
- *
- * @param attributeName String with the name of the attribute to use
- */
- public void setLayoutAttribute(String attributeName) {}
-
- /**
- * This returns a (possibly empty) List of Strings that is used for
- * the attribute list in the menu for attribute-based layouts. This
- * allows layout algorithms to provide "special" attributes. For
example,
- * a force directed layout might want to set the list to
["(unweighted)"]
- * to allow the user to perform an unweighted layout. Note that this
value
- * will be set using setLayoutAttribute() just like other attributes,
so the
- * layout algorithm will need to check for it.
- *
- * @return List of Strings
- */
- public List<String> getInitialAttributeList() {return new
ArrayList<String>();}
-
- /**
- * DOCUMENT ME!
- *
- * @param nodes DOCUMENT ME!
- */
- public void lockNodes(View<CyNode>[] nodes) {}
-
- /**
- * DOCUMENT ME!
- *
- * @param v DOCUMENT ME!
- */
- public void lockNode(View<CyNode> v) {}
-
- /**
- * DOCUMENT ME!
- *
- * @param v DOCUMENT ME!
- */
- public void unlockNode(View<CyNode> v) {}
-
- /**
- * DOCUMENT ME!
- */
- public void unlockAllNodes() {}
-}
Modified:
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/LayoutEdge.java
===================================================================
---
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/LayoutEdge.java
2011-04-29 22:33:35 UTC (rev 24860)
+++
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/LayoutEdge.java
2011-04-29 22:43:31 UTC (rev 24861)
@@ -40,7 +40,7 @@
* to information about the weights associated with edges, and pointers to the
* LayoutNodes that are joined by this edge.
*/
-public class LayoutEdge {
+public final class LayoutEdge {
// instance variables
private LayoutNode v1;
private LayoutNode v2;
@@ -49,12 +49,6 @@
private CyEdge edge;
/**
- * An empty constructor
- */
- public LayoutEdge() {
- }
-
- /**
* Create a LayoutEdge that will contain information about this edge.
* Additional information must be filled in later.
*
Modified:
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/LayoutNode.java
===================================================================
---
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/LayoutNode.java
2011-04-29 22:33:35 UTC (rev 24860)
+++
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/LayoutNode.java
2011-04-29 22:43:31 UTC (rev 24861)
@@ -47,9 +47,8 @@
* the methods of this class are wrappers for Node or View<CyNode> methods, and
* these are often wrapped by LayoutPartition methods.
*/
-public class LayoutNode {
+public final class LayoutNode {
// static (class) variables
- private static int lockedNodes = 0;
static final double EPSILON = 0.0000001D;
// instance variables
@@ -66,12 +65,6 @@
private ArrayList<LayoutNode> neighbors = null;
/**
- * Empty constructor
- */
- public LayoutNode() {
- }
-
- /**
* The main constructor for a LayoutNode.
*
* @param nodeView The View<CyNode> of this node
@@ -197,7 +190,6 @@
*/
public void lock() {
this.isLocked = true;
- lockedNodes += 1;
}
/**
@@ -207,7 +199,6 @@
*/
public void unLock() {
this.isLocked = false;
- lockedNodes -= 1;
}
/**
@@ -407,16 +398,4 @@
return ret;
}
-
- /**
- * Returns the number of locked nodes. This is a static that is
incremented whenever
- * lock() is called and decremented whenever unlock() is called. It is
useful for some
- * algorithms that only want to get the number of unlocked nodes for
the purposes of their
- * layout loops.
- *
- * @return the number of unlocked nodes.
- */
- public static int lockedNodeCount() {
- return lockedNodes;
- }
}
Modified:
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/LayoutPartition.java
===================================================================
---
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/LayoutPartition.java
2011-04-29 22:33:35 UTC (rev 24860)
+++
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/LayoutPartition.java
2011-04-29 22:43:31 UTC (rev 24861)
@@ -65,12 +65,10 @@
* @author <a href="mailto:[email protected]";>Scooter Morris</a>
* @version 0.9
*/
-public class LayoutPartition {
+public final class LayoutPartition {
private ArrayList<LayoutNode> nodeList;
private ArrayList<LayoutEdge> edgeList;
- private static HashMap<CyNode, LayoutNode> nodeToLayoutNode = null;
- private static Map<Integer,Integer> nodesSeenMap = null;
- private static Map<Integer,Integer> edgesSeenMap = null;
+ private HashMap<CyNode, LayoutNode> nodeToLayoutNode;
private int nodeIndex = 0;
private int partitionNumber = 0;
private EdgeWeighter edgeWeighter = null;
@@ -110,10 +108,8 @@
public LayoutPartition(int nodeCount, int edgeCount) {
nodeList = new ArrayList<LayoutNode>(nodeCount);
edgeList = new ArrayList<LayoutEdge>(edgeCount);
+ nodeToLayoutNode = new HashMap<CyNode,LayoutNode>(nodeCount);
partitionNumber = 1;
-
- if (nodeToLayoutNode == null)
- nodeToLayoutNode = new
HashMap<CyNode,LayoutNode>(nodeCount);
}
/**
@@ -125,9 +121,9 @@
* @param nodeSet the nodes to be considered
* @param edgeWeighter the weighter to use for edge weighting
*/
- public LayoutPartition(CyNetwork network, CyNetworkView networkView,
Collection<CyNode>nodeSet,
+ public LayoutPartition(CyNetworkView networkView,
Collection<CyNode>nodeSet,
EdgeWeighter edgeWeighter) {
- initialize(network,networkView,nodeSet,edgeWeighter);
+ initialize(networkView,nodeSet,edgeWeighter);
}
@@ -140,30 +136,28 @@
* @param selectedOnly if true, only include selected nodes in the
partition
* @param edgeWeighter the weighter to use for edge weighting
*/
- public LayoutPartition(CyNetwork network, CyNetworkView networkView,
boolean selectedOnly,
+ public LayoutPartition(CyNetworkView networkView, boolean selectedOnly,
EdgeWeighter edgeWeighter) {
if (selectedOnly) {
-
initialize(network,networkView,CyTableUtil.getNodesInState(network,"selected",true),edgeWeighter);
+
initialize(networkView,CyTableUtil.getNodesInState(networkView.getModel(),"selected",true),edgeWeighter);
} else {
-
initialize(network,networkView,network.getNodeList(),edgeWeighter);
+
initialize(networkView,networkView.getModel().getNodeList(),edgeWeighter);
}
}
- protected void initialize(CyNetwork network, CyNetworkView networkView,
Collection<CyNode>nodeSet,
+ private void initialize(CyNetworkView networkView,
Collection<CyNode>nodeSet,
EdgeWeighter edgeWeighter) {
this.edgeWeighter = edgeWeighter;
// Initialize
- nodeList = new ArrayList<LayoutNode>(network.getNodeCount());
- edgeList = new ArrayList<LayoutEdge>(network.getEdgeCount());
+ nodeList = new
ArrayList<LayoutNode>(networkView.getModel().getNodeCount());
+ edgeList = new
ArrayList<LayoutEdge>(networkView.getModel().getEdgeCount());
+ nodeToLayoutNode = new
HashMap<CyNode,LayoutNode>(networkView.getModel().getNodeCount());
- if (nodeToLayoutNode == null)
- nodeToLayoutNode = new
HashMap<CyNode,LayoutNode>(network.getNodeCount());
-
// Now, walk the iterators and fill in the values
- nodeListInitialize(network, networkView, nodeSet);
- edgeListInitialize(network, networkView);
+ nodeListInitialize(networkView, nodeSet);
+ edgeListInitialize(networkView);
trimToSize();
partitionNumber = 1;
}
@@ -196,8 +190,6 @@
} else {
updateMinMax(nv.getVisualProperty(MinimalVisualLexicon.NODE_X_LOCATION),
nv.getVisualProperty(MinimalVisualLexicon.NODE_Y_LOCATION));
- // this.width += Math.sqrt(nv.getWidth());
- // this.height += Math.sqrt(nv.getHeight());
this.width +=
nv.getVisualProperty(MinimalVisualLexicon.NODE_WIDTH);
this.height +=
nv.getVisualProperty(MinimalVisualLexicon.NODE_HEIGHT);
}
@@ -283,8 +275,8 @@
if (nodeToLayoutNode.containsKey(source) &&
nodeToLayoutNode.containsKey(target)) {
// Add the connecting nodes
- lEdge.addNodes((LayoutNode)
nodeToLayoutNode.get(source),
- (LayoutNode)
nodeToLayoutNode.get(target));
+ lEdge.addNodes(nodeToLayoutNode.get(source),
+ nodeToLayoutNode.get(target));
}
}
}
@@ -514,13 +506,13 @@
/**
* Private routines
*/
- private void nodeListInitialize(CyNetwork network, CyNetworkView
networkView,
+ private void nodeListInitialize(CyNetworkView networkView,
Collection<CyNode> nodeSet) {
int nodeIndex = 0;
- this.nodeList = new
ArrayList<LayoutNode>(network.getNodeCount());
+ this.nodeList = new
ArrayList<LayoutNode>(networkView.getModel().getNodeCount());
for (View<CyNode>nv: networkView.getNodeViews()){
- CyNode node = (CyNode) nv.getModel();
+ CyNode node = nv.getModel();
if (!nodeSet.contains(node)) {
addNode(nv, true);
@@ -530,20 +522,20 @@
}
}
- private void edgeListInitialize(CyNetwork network, CyNetworkView
networkView) {
+ private void edgeListInitialize(CyNetworkView networkView) {
for (View<CyEdge>ev: networkView.getEdgeViews()){
CyEdge edge = ev.getModel();
// Make sure we clean up after any previous layouts
//ev.clearBends(); // FIXME: this will mean some
cleanup in VisualProperty, right?
- CyNode source = (CyNode) edge.getSource();
- CyNode target = (CyNode) edge.getTarget();
+ CyNode source = edge.getSource();
+ CyNode target = edge.getTarget();
if (source == target)
continue;
- LayoutNode v1 = (LayoutNode)
nodeToLayoutNode.get(source);
- LayoutNode v2 = (LayoutNode)
nodeToLayoutNode.get(target);
+ LayoutNode v1 = nodeToLayoutNode.get(source);
+ LayoutNode v2 = nodeToLayoutNode.get(target);
// Do we care about this edge?
if (v1.isLocked() && v2.isLocked())
@@ -556,9 +548,9 @@
/**
* Space saving convenience function to trim the internal arrays to fit
the
* contained data. Useful to call this after a partition has been
created
- * and filled. This is used by the static method
LayoutPartition.partition
+ * and filled. This is used by the static method
PartitionUtil.partition()
*/
- private void trimToSize() {
+ void trimToSize() {
nodeList.trimToSize();
edgeList.trimToSize();
}
@@ -579,169 +571,4 @@
// System.out.println("Updating "+newEdge);
}
-
- // Static routines
-
- /**
- * Partition the graph -- this builds the LayoutEdge and LayoutNode
- * arrays as a byproduct. The algorithm for this was taken from
- * algorithms/graphPartition/SGraphPartition.java.
- *
- * @param network the GraphPerspective containing the graph
- * @param networkView the CyNetworkView representing the graph
- * @param selectedOnly only consider selected nodes
- * @param edgeWeighter the weighter to use for edge weighting
- * @return a List of LayoutPartitions
- */
- public static List<LayoutPartition> partition(CyNetwork network,
CyNetworkView networkView,
- boolean selectedOnly, EdgeWeighter
edgeWeighter) {
-
- if (selectedOnly) {
- return partition(network,networkView,
CyTableUtil.getNodesInState(network,"selected",true),edgeWeighter);
- }
-
- return
partition(network,networkView,network.getNodeList(),edgeWeighter);
-
- }
-
- /**
- * Partition the graph -- this builds the LayoutEdge and LayoutNode
- * arrays as a byproduct. The algorithm for this was taken from
- * algorithms/graphPartition/SGraphPartition.java.
- *
- * @param network the GraphPerspective containing the graph
- * @param networkView the CyNetworkView representing the graph
- * @param nodeSet the set of nodes to consider
- * @param edgeWeighter the weighter to use for edge weighting
- * @return a List of LayoutPartitions
- */
- public static List<LayoutPartition> partition(CyNetwork network,
CyNetworkView networkView,
- Collection<CyNode> nodeSet, EdgeWeighter
edgeWeighter) {
- ArrayList<LayoutPartition> partitions = new
ArrayList<LayoutPartition>();
-
- nodesSeenMap = new HashMap<Integer,Integer>();
- edgesSeenMap = new HashMap<Integer,Integer>();
-
- Map<Integer,View<CyNode>> nodesToViews = new
HashMap<Integer,View<CyNode>>();
- nodeToLayoutNode = new
HashMap<CyNode,LayoutNode>(network.getNodeCount());
-
- // Initialize the maps
- for (View<CyNode> nv: networkView.getNodeViews()){
- int node = nv.getModel().getIndex();
- nodesSeenMap.put(node, m_NODE_HAS_NOT_BEEN_SEEN);
- nodesToViews.put(node, nv);
- }
-
- for (CyEdge edge: network.getEdgeList()) {
- int edgeIndex = edge.getIndex();
- edgesSeenMap.put(edgeIndex, m_NODE_HAS_NOT_BEEN_SEEN);
- }
-
- // OK, now traverse the graph
- for (CyNode node: nodeSet) {
- int nodeIndex = node.getIndex();
-
- // Have we seen this already?
- if (nodesSeenMap.get(nodeIndex) == m_NODE_HAS_BEEN_SEEN)
- continue;
-
- // Nope, first time
- LayoutPartition part = new
LayoutPartition(network.getNodeCount(),
-
network.getEdgeCount());
- // Set the edge weighter
- part.setEdgeWeighter(edgeWeighter);
-
- nodesSeenMap.put(nodeIndex, m_NODE_HAS_BEEN_SEEN);
-
- // Traverse through all connected nodes
- traverse(network, networkView, nodesToViews, node,
part);
-
- // Done -- finalize the parition
- part.trimToSize();
-
- // Finally, now that we're sure we've touched all of our
- // nodes. Fix up our edgeLayout list to have all of our
- // layoutNodes
- part.fixEdges();
-
- partitions.add(part);
- }
-
- // Now sort the partitions based on the partition's node count
- LayoutPartition[] a = new LayoutPartition[1];
- LayoutPartition[] parts = partitions.toArray(a);
- Arrays.sort(parts,
- new Comparator<LayoutPartition>() {
- public int compare(LayoutPartition p1,
LayoutPartition p2) {
- return (p2.size() - p1.size());
- }
-
- public boolean equals(LayoutPartition obj) {
- return false;
- }
- });
-
- return Arrays.asList(parts);
- }
-
- /**
- * This method traverses nodes connected to the specified node.
- * @param network The GraphPerspective we are laying out
- * @param networkView The CyNetworkView we are laying out
- * @param nodesToViews A map that maps between nodes and views
- * @param node The node to search for connected nodes.
- * @param partition The partition that we're laying out
- */
- private static void traverse(CyNetwork network, CyNetworkView
networkView,
- Map<Integer,View<CyNode>> nodesToViews,
CyNode node,
- LayoutPartition partition) {
- int nodeIndex = node.getIndex();
-
- // Get the View<CyNode>
- View<CyNode> nv = nodesToViews.get(nodeIndex);
-
- // Add this node to the partition
- partition.addNode(nv, false);
-
- // Iterate through each connected edge
- for (CyEdge incidentEdge: network.getAdjacentEdgeList(node,
CyEdge.Type.ANY)){
-
- int edgeIndex = incidentEdge.getIndex();
-
- // Have we already seen this edge?
- if (edgesSeenMap.get(edgeIndex) ==
m_NODE_HAS_BEEN_SEEN) {
- // Yes, continue since it means we *must* have
seen both sides
- continue;
- }
-
- edgesSeenMap.put(edgeIndex, m_NODE_HAS_BEEN_SEEN);
-
- // Make sure we clean up after any previous layouts
- //View<CyEdge> ev =
networkView.getEdgeView(incidentEdge);
- //ev.clearBends(); FIXME: punted
-
- // Add the edge to the partition
- partition.addEdge(incidentEdge);
-
- // Determine the node's index that is on the other side
of the edge
- CyNode otherNode;
-
- if (incidentEdge.getSource() == node) {
- otherNode = incidentEdge.getTarget();
- } else {
- otherNode = incidentEdge.getSource();
- }
-
- int incidentNodeIndex = otherNode.getIndex();
-
- // Have we seen the connecting node yet?
- if (nodesSeenMap.get(incidentNodeIndex) ==
m_NODE_HAS_NOT_BEEN_SEEN) {
- // Mark it as having been seen
- nodesSeenMap.put(incidentNodeIndex,
m_NODE_HAS_BEEN_SEEN);
-
- // Traverse through this one
- traverse(network, networkView, nodesToViews,
otherNode, partition);
- }
- }
- }
}
Modified:
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/LayoutTask.java
===================================================================
---
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/LayoutTask.java
2011-04-29 22:33:35 UTC (rev 24860)
+++
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/LayoutTask.java
2011-04-29 22:43:31 UTC (rev 24861)
@@ -20,18 +20,16 @@
public abstract class LayoutTask extends AbstractTask {
- protected static final Logger logger =
LoggerFactory.getLogger(LayoutTask.class);
-
+ private static final Logger logger =
LoggerFactory.getLogger(LayoutTask.class);
protected static final String LAYOUT_ALGORITHM = "layoutAlgorithm";
protected final CyNetworkView networkView;
- private final String name;
protected final boolean selectedOnly;
protected final Set<View<CyNode>> staticNodes;
- protected boolean cancelled = false;
+ private final String name;
- public LayoutTask(final CyNetworkView networkView, final String name,
final boolean selectedOnly,
+ public LayoutTask(final CyNetworkView networkView, final String name,
boolean selectedOnly,
final Set<View<CyNode>> staticNodes)
{
super();
@@ -71,45 +69,10 @@
logger.debug("Layout finished: " +
(System.currentTimeMillis()-start) + " msec.");
}
- /**
- * Lock these nodes (i.e. prevent them from moving).
- *
- * @param nodes An array of View<CyNode>'s to lock
- */
- public void lockNodes(View<CyNode>[] nodes) {
- for (int i = 0; i < nodes.length; ++i) {
- staticNodes.add(nodes[i]);
- }
- }
- /**
- * Lock this node (i.e. prevent it from moving).
- *
- * @param v A View<CyNode> to lock
- */
- public void lockNode(View<CyNode> v) {
- staticNodes.add(v);
- }
-
- /**
- * Unlock this node
- *
- * @param v A View<CyNode> to unlock
- */
- public void unlockNode(View<CyNode> v) {
- staticNodes.remove(v);
- }
-
protected boolean isLocked(View<CyNode> v) {
- return (staticNodes.contains(v));
+ return ((staticNodes != null) && (staticNodes.contains(v)));
}
- /**
- * Unlock all nodes
- */
- public void unlockAllNodes() {
- staticNodes.clear();
- }
-
protected abstract void doLayout(final TaskMonitor taskMonitor, final
CyNetwork network);
-}
\ No newline at end of file
+}
Added:
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
(rev 0)
+++
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/PartitionUtil.java
2011-04-29 22:43:31 UTC (rev 24861)
@@ -0,0 +1,229 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2006 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package org.cytoscape.view.layout;
+
+import org.cytoscape.model.CyTableUtil;
+import org.cytoscape.model.CyEdge;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNode;
+import org.cytoscape.view.model.View;
+import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.view.presentation.property.MinimalVisualLexicon;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Collection;
+import java.util.Comparator;
+import java.util.Date;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.ListIterator;
+import java.util.Map;
+import java.util.Random;
+
+import java.awt.Dimension;
+import org.cytoscape.work.TaskMonitor;
+
+
+/**
+ * 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 {
+
+ private static final int m_NODE_HAS_NOT_BEEN_SEEN = 0;
+ private static final int m_NODE_HAS_BEEN_SEEN = 1;
+
+ private PartitionUtil() {};
+
+
+ /**
+ * Partition the graph -- this builds the LayoutEdge and LayoutNode
+ * arrays as a byproduct. The algorithm for this was taken from
+ * algorithms/graphPartition/SGraphPartition.java.
+ *
+ * @param network the GraphPerspective containing the graph
+ * @param networkView the CyNetworkView representing the graph
+ * @param selectedOnly only consider selected nodes
+ * @param edgeWeighter the weighter to use for edge weighting
+ * @return a List of LayoutPartitions
+ */
+ public static List<LayoutPartition> partition(CyNetworkView networkView,
+ boolean selectedOnly, EdgeWeighter
edgeWeighter) {
+
+ if (selectedOnly)
+ return partition(networkView,
CyTableUtil.getNodesInState(networkView.getModel(),"selected",true),edgeWeighter);
+ else
+ return
partition(networkView,networkView.getModel().getNodeList(),edgeWeighter);
+ }
+
+ /**
+ * Partition the graph -- this builds the LayoutEdge and LayoutNode
+ * arrays as a byproduct. The algorithm for this was taken from
+ * algorithms/graphPartition/SGraphPartition.java.
+ *
+ * @param network the GraphPerspective containing the graph
+ * @param networkView the CyNetworkView representing the graph
+ * @param nodeSet the set of nodes to consider
+ * @param edgeWeighter the weighter to use for edge weighting
+ * @return a List of LayoutPartitions
+ */
+ public static List<LayoutPartition> partition(CyNetworkView networkView,
+ Collection<CyNode> nodeSet, EdgeWeighter
edgeWeighter) {
+ List<LayoutPartition> partitions = new
ArrayList<LayoutPartition>();
+
+ final CyNetwork network = networkView.getModel();
+
+ Map<Integer,Integer> nodesSeenMap = new
HashMap<Integer,Integer>();
+ Map<Integer,Integer> edgesSeenMap = new
HashMap<Integer,Integer>();
+ Map<Integer,View<CyNode>> nodesToViews = new
HashMap<Integer,View<CyNode>>();
+
+ // Initialize the maps
+ for (View<CyNode> nv: networkView.getNodeViews()){
+ int node = nv.getModel().getIndex();
+ nodesSeenMap.put(node, m_NODE_HAS_NOT_BEEN_SEEN);
+ nodesToViews.put(node, nv);
+ }
+
+ for (CyEdge edge: network.getEdgeList()) {
+ int edgeIndex = edge.getIndex();
+ edgesSeenMap.put(edgeIndex, m_NODE_HAS_NOT_BEEN_SEEN);
+ }
+
+ // OK, now traverse the graph
+ for (CyNode node: nodeSet) {
+ int nodeIndex = node.getIndex();
+
+ // Have we seen this already?
+ if (nodesSeenMap.get(nodeIndex) == m_NODE_HAS_BEEN_SEEN)
+ continue;
+
+ // Nope, first time
+ LayoutPartition part = new
LayoutPartition(network.getNodeCount(),
+
network.getEdgeCount());
+ // Set the edge weighter
+ part.setEdgeWeighter(edgeWeighter);
+
+ nodesSeenMap.put(nodeIndex, m_NODE_HAS_BEEN_SEEN);
+
+ // Traverse through all connected nodes
+ traverse(network, networkView, nodesToViews, node,
part, nodesSeenMap, edgesSeenMap);
+
+ // Done -- finalize the parition
+ part.trimToSize();
+
+ // Finally, now that we're sure we've touched all of our
+ // nodes. Fix up our edgeLayout list to have all of our
+ // layoutNodes
+ part.fixEdges();
+
+ partitions.add(part);
+ }
+
+ // Now sort the partitions based on the partition's node count
+ Collections.sort(partitions,
+ new Comparator<LayoutPartition>() {
+ public int compare(LayoutPartition p1,
LayoutPartition p2) {
+ return (p2.size() - p1.size());
+ }
+
+ public boolean equals(LayoutPartition obj) {
+ return false;
+ }
+ });
+
+ return partitions;
+ }
+
+ /**
+ * This method traverses nodes connected to the specified node.
+ * @param network The GraphPerspective we are laying out
+ * @param networkView The CyNetworkView we are laying out
+ * @param nodesToViews A map that maps between nodes and views
+ * @param node The node to search for connected nodes.
+ * @param partition The partition that we're laying out
+ * @param nodesSeenMap A map of nodes already visited.
+ * @param edgesSeenMap A map of edges already visited.
+ */
+ private static void traverse(CyNetwork network, CyNetworkView
networkView,
+ Map<Integer,View<CyNode>> nodesToViews,
CyNode node,
+ LayoutPartition partition,
Map<Integer,Integer> nodesSeenMap,
+
Map<Integer,Integer> edgesSeenMap ) {
+ int nodeIndex = node.getIndex();
+
+ // Get the View<CyNode>
+ View<CyNode> nv = nodesToViews.get(nodeIndex);
+
+ // Add this node to the partition
+ partition.addNode(nv, false);
+
+ // Iterate through each connected edge
+ for (CyEdge incidentEdge: network.getAdjacentEdgeList(node,
CyEdge.Type.ANY)){
+
+ int edgeIndex = incidentEdge.getIndex();
+
+ // Have we already seen this edge?
+ if (edgesSeenMap.get(edgeIndex) ==
m_NODE_HAS_BEEN_SEEN) {
+ // Yes, continue since it means we *must* have
seen both sides
+ continue;
+ }
+
+ edgesSeenMap.put(edgeIndex, m_NODE_HAS_BEEN_SEEN);
+
+ // Add the edge to the partition
+ partition.addEdge(incidentEdge);
+
+ // Determine the node's index that is on the other side
of the edge
+ CyNode otherNode;
+
+ if (incidentEdge.getSource() == node) {
+ otherNode = incidentEdge.getTarget();
+ } else {
+ otherNode = incidentEdge.getSource();
+ }
+
+ int incidentNodeIndex = otherNode.getIndex();
+
+ // Have we seen the connecting node yet?
+ if (nodesSeenMap.get(incidentNodeIndex) ==
m_NODE_HAS_NOT_BEEN_SEEN) {
+ // Mark it as having been seen
+ nodesSeenMap.put(incidentNodeIndex,
m_NODE_HAS_BEEN_SEEN);
+
+ // Traverse through this one
+ traverse(network, networkView, nodesToViews,
otherNode, partition, nodesSeenMap, edgesSeenMap);
+ }
+ }
+ }
+}
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 22:33:35 UTC (rev 24860)
+++
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/internal/algorithms/GridNodeLayout.java
2011-04-29 22:43:31 UTC (rev 24861)
@@ -63,7 +63,7 @@
* Creates a new GridNodeLayout object.
*/
public GridNodeLayout(UndoSupport un) {
- super(un);
+ super(un,CyLayouts.DEFAULT_LAYOUT_NAME,"Grid Layout");
}
public boolean tunablesAreValid(final Appendable errMsg) {
@@ -88,24 +88,6 @@
}
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String getName() {
- return CyLayouts.DEFAULT_LAYOUT_NAME;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String toString() {
- return "Grid Layout";
- }
-
- /**
* We do support selected only
*
* @return true
--
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