Author: scooter
Date: 2010-08-17 15:23:39 -0700 (Tue, 17 Aug 2010)
New Revision: 21417
Modified:
cytoscape/trunk/application/src/main/java/cytoscape/groups/CyGroup.java
cytoscape/trunk/application/src/main/java/cytoscape/groups/CyGroupImpl.java
cytoscape/trunk/application/src/main/java/cytoscape/groups/CyGroupManager.java
Log:
First cut at storing groups internally as a GraphPerspective. This
will be used significantly with the refactored metanode plugin.
Modified:
cytoscape/trunk/application/src/main/java/cytoscape/groups/CyGroup.java
===================================================================
--- cytoscape/trunk/application/src/main/java/cytoscape/groups/CyGroup.java
2010-08-17 22:19:22 UTC (rev 21416)
+++ cytoscape/trunk/application/src/main/java/cytoscape/groups/CyGroup.java
2010-08-17 22:23:39 UTC (rev 21417)
@@ -126,6 +126,13 @@
public CyNetwork getNetwork();
/**
+ * Get the graph (network) that represents this network
+ *
+ * @return graph perspective (in the form of a CyNetwork) for this
network
+ */
+ public CyNetwork getGraphPerspective();
+
+ /**
* Set the network for this group
*
* @param network the network for this group or "null" if this is a
global group
Modified:
cytoscape/trunk/application/src/main/java/cytoscape/groups/CyGroupImpl.java
===================================================================
--- cytoscape/trunk/application/src/main/java/cytoscape/groups/CyGroupImpl.java
2010-08-17 22:19:22 UTC (rev 21416)
+++ cytoscape/trunk/application/src/main/java/cytoscape/groups/CyGroupImpl.java
2010-08-17 22:23:39 UTC (rev 21417)
@@ -43,7 +43,11 @@
import cytoscape.CyEdge;
import cytoscape.data.CyAttributes;
+import cytoscape.giny.CytoscapeRootGraph;
+import giny.model.Edge;
+import giny.model.GraphPerspective;
+import giny.model.Node;
import giny.model.RootGraph;
import java.util.ArrayList;
@@ -65,27 +69,17 @@
// Instance data
/**
- * The members of this group, indexed by the Node.
+ * A map storing the list of edges for a node at the time it was
+ * added to the group
*/
- private HashMap<CyNode, CyNode> nodeMap;
+ private HashMap<CyNode,List<CyEdge>> nodeToEdgeMap;
/**
- * The edges in this group that only involve members of this group
- */
- private HashMap<CyEdge, CyEdge> innerEdgeMap;
-
- /**
* The edges in this group that involve members outside of this group
*/
private HashMap<CyEdge, CyEdge> outerEdgeMap;
/**
- * A map storing the list of edges for a node at the time it was
- * added to the group
- */
- private HashMap<CyNode,List<CyEdge>> nodeToEdgeMap;
-
- /**
* This is the network that this group is part of. If this
* is null, it's a global group.
*/
@@ -118,28 +112,92 @@
*/
private String viewer = null;
+ /**
+ * the internal graph that represents this network
+ */
+ private CyNetwork myGraph = null;
+
// Public methods
/**
* Empty constructor
*/
protected CyGroupImpl() {
- this.nodeMap = new HashMap();
- this.nodeToEdgeMap = new HashMap();
- this.innerEdgeMap = new HashMap();
- this.outerEdgeMap = new HashMap();
+ this.nodeToEdgeMap = new HashMap<CyNode, List<CyEdge>>();
+ this.outerEdgeMap = new HashMap<CyEdge,CyEdge>();
this.network = null;
}
/**
* Constructor to create an empty group.
*
+ * @param groupNode the CyNode to use for this group
+ * @param nodeList the initial set of nodes for this group
+ * @param internalEdges the initial set of internal edges for this group
+ * @param externalEdges the initial set of external edges for this group
+ * @param network the network this group is part of
+ *
+ */
+ protected CyGroupImpl(CyNode groupNode, List<CyNode> nodeList,
List<CyEdge> internalEdges,
+ List<CyEdge> externalEdges, CyNetwork network) {
+
+ // System.out.println("Creating group "+groupNode);
+
+ this.nodeToEdgeMap = new HashMap<CyNode, List<CyEdge>>();
+ this.outerEdgeMap = new HashMap<CyEdge,CyEdge>();
+ this.network = network;
+
+ this.groupNode = groupNode;
+ this.groupName = this.groupNode.getIdentifier();
+
+ if (nodeList == null && internalEdges == null && externalEdges
== null)
+ return;
+
+ // System.out.println(" Group "+groupNode+" has
"+nodeList.size()+" nodes");
+
+ CyNetwork thisNetwork = network;
+ if (network == null)
+ thisNetwork = Cytoscape.getCurrentNetwork();
+
+ // If we aren't provided with any inner or outer edges, we need
to get them
+ if (internalEdges == null) {
+ // Get our list of internal edges
+ internalEdges = (List<CyEdge>)
thisNetwork.getConnectingEdges(nodeList);
+ }
+
+ // At this point, we've got a list of nodes and a list of
edges. We
+ // could now create a CyNetwork that contains the internal
components
+ // of this group.
+ CytoscapeRootGraph rootGraph = Cytoscape.getRootGraph();
+ myGraph = rootGraph.createNetwork(nodeList.toArray(new
Node[0]), internalEdges.toArray(new Edge[0]));
+
+ // Create our node and edge map
+ for (CyNode node: nodeList) {
+ List<CyEdge> adjacentEdges =
(List<CyEdge>)thisNetwork.getAdjacentEdgesList(node, true, true, true);
+ nodeToEdgeMap.put(node, adjacentEdges);
+ // If we don't have external edges, add them now
+ if (externalEdges == null) {
+ for (CyEdge edge: adjacentEdges) {
+ if (!myGraph.containsEdge(edge))
+ outerEdgeMap.put(edge, edge);
+ }
+ }
+ }
+
+ // If we were provided with an external edge list, create our
map now.
+ if (externalEdges != null) {
+ for (CyEdge edge: externalEdges)
+ outerEdgeMap.put(edge, edge);
+ }
+ }
+
+ /**
+ * Constructor to create an empty group
+ *
* @param groupName the identifier to use for this group -- should be
unique!
*/
protected CyGroupImpl(String groupName) {
- this();
- this.groupNode = Cytoscape.getCyNode(groupName, true);
- this.groupName = groupName;
+ this(Cytoscape.getCyNode(groupName, true), null, null, null,
null);
}
/**
@@ -148,9 +206,7 @@
* @param groupNode the CyNode to use for this group
*/
protected CyGroupImpl(CyNode groupNode) {
- this();
- this.groupNode = groupNode;
- this.groupName = this.groupNode.getIdentifier();
+ this(groupNode, null, null, null, null);
}
/**
@@ -161,11 +217,7 @@
* @param nodeList the initial set of nodes for this group
*/
protected CyGroupImpl(CyNode groupNode, List<CyNode> nodeList) {
- this(groupNode); // Create all of the necessary structures
-
- for (CyNode node: nodeList) {
- this.addNodeToGroup ( node );
- }
+ this(groupNode, nodeList, null, null, null);
}
/**
@@ -175,10 +227,7 @@
* @param nodeList the initial set of nodes for this group
*/
protected CyGroupImpl(String groupName, List<CyNode> nodeList) {
- this(groupName); // Create all of the necessary structures
-
- for(CyNode node: nodeList)
- this.addNodeToGroup (node);
+ this(Cytoscape.getCyNode(groupName, true), nodeList, null,
null, null);
}
/**
@@ -201,9 +250,7 @@
* @return list of nodes in the group
*/
public List<CyNode> getNodes() {
- Collection<CyNode> v = nodeMap.values();
-
- return new ArrayList<CyNode>(v);
+ return (List<CyNode>)myGraph.nodesList();
}
/**
@@ -221,9 +268,7 @@
* @return node iterator
*/
public Iterator<CyNode> getNodeIterator() {
- Collection<CyNode> v = nodeMap.values();
-
- return v.iterator();
+ return (Iterator<CyNode>)myGraph.nodesIterator();
}
/**
@@ -232,9 +277,7 @@
* @return list of edges in the group
*/
public List<CyEdge> getInnerEdges() {
- Collection<CyEdge> v = innerEdgeMap.values();
-
- return new ArrayList<CyEdge>(v);
+ return (List<CyEdge>)myGraph.edgesList();
}
/**
@@ -265,7 +308,7 @@
* @param edge the CyEdge to add to the innter edge map
*/
public void addInnerEdge(CyEdge edge) {
- innerEdgeMap.put(edge, edge);
+ myGraph.addEdge(edge);
}
/**
@@ -310,13 +353,23 @@
* @return true if node is a member of the group
*/
public boolean contains(CyNode node) {
- if (nodeMap.containsKey(node))
+ if (myGraph.containsNode(node))
return true;
return false;
}
/**
+ * Return a CyNetwork that represents
+ * the internal components of this group
+ *
+ * @return the CyNetwork
+ */
+ public CyNetwork getGraphPerspective() {
+ return myGraph;
+ }
+
+ /**
* Set the state of the group. Setting the state of a group has
* two byproducts. First, the attribute "__groupState" is set to
* the state value to allow persistance across saves and restores.
@@ -410,10 +463,24 @@
* @param node the node to add
*/
public void addNode ( CyNode node ) {
+ addNode(node, true);
+ }
+
+ /**
+ * Add a new node to this group
+ *
+ * @param node the node to add
+ */
+ public void addNode ( CyNode node, boolean addEdges ) {
// First see if this node is already in this group
- if (nodeToEdgeMap.containsKey(node))
+ if (myGraph.containsNode(node))
return;
+ myGraph.addNode(node);
+
+ if (!addEdges)
+ return;
+
// We need to go throught our outerEdgeMap first to see if this
// node has outer edges and proactively move them to inner
edges.
// this needs to be done here because some viewers might have
@@ -427,7 +494,7 @@
}
for (CyEdge edge: eMove) {
outerEdgeMap.remove(edge);
- innerEdgeMap.put(edge,edge);
+ myGraph.addEdge(edge);
}
// Note the cute little trick we play -- making sure these
@@ -466,8 +533,6 @@
* @param node the node to add
*/
private void addNodeToGroup ( CyNode node ) {
- // Put this node in our map
- nodeMap.put(node, node);
CyNetwork groupNetwork = this.network;
if (groupNetwork == null)
@@ -482,13 +547,10 @@
}
// Add all of the edges
- int [] edgeArray =
groupNetwork.getAdjacentEdgeIndicesArray(node.getRootGraphIndex(),true,true,true);
- if (edgeArray == null)
- edgeArray = new int[]{};
- for (int edgeIndex = 0; edgeIndex < edgeArray.length;
edgeIndex++) {
- CyEdge edge =
(CyEdge)groupNetwork.getEdge(edgeArray[edgeIndex]);
+ List<CyEdge> adjacentEdges =
(List<CyEdge>)groupNetwork.getAdjacentEdgesList(node, true, true, true);
+ for (CyEdge edge: adjacentEdges) {
// Not sure if this is faster or slower than going
through the entire loop
- if (edgeList.contains(edge))
+ if (myGraph.containsEdge(edge))
continue;
edgeList.add(edge);
@@ -503,10 +565,10 @@
if (outerEdgeMap.containsKey(edge)) {
outerEdgeMap.remove(edge);
- innerEdgeMap.put(edge,edge);
- } else if (nodeMap.containsKey(target) &&
nodeMap.containsKey(source)) {
- innerEdgeMap.put(edge,edge);
- } else if (nodeMap.containsKey(target) ||
nodeMap.containsKey(source)) {
+ myGraph.addEdge(edge);
+ } else if (myGraph.containsNode(target) &&
myGraph.containsNode(source)) {
+ myGraph.addEdge(edge);
+ } else if (myGraph.containsNode(target) ||
myGraph.containsNode(source)) {
outerEdgeMap.put(edge,edge);
}
}
@@ -523,16 +585,10 @@
* @param node the node to remove
*/
private void removeNodeFromGroup ( CyNode node ) {
- // Remove the node from our map
- nodeMap.remove(node);
-
- RootGraph rg = node.getRootGraph();
-
// Get the list of edges
List <CyEdge>edgeArray = nodeToEdgeMap.get(node);
for (CyEdge edge: edgeArray) {
- if (innerEdgeMap.containsKey(edge)) {
- innerEdgeMap.remove(edge);
+ if (myGraph.containsEdge(edge)) {
outerEdgeMap.put(edge,edge);
} else if (outerEdgeMap.containsKey(edge)) {
outerEdgeMap.remove(edge);
@@ -540,6 +596,9 @@
}
nodeToEdgeMap.remove(node);
+ // Remove the node from our map
+ myGraph.hideNode(node);
+
// Tell the node about it (if necessary)
if (node.inGroup(this))
node.removeFromGroup(this);
Modified:
cytoscape/trunk/application/src/main/java/cytoscape/groups/CyGroupManager.java
===================================================================
---
cytoscape/trunk/application/src/main/java/cytoscape/groups/CyGroupManager.java
2010-08-17 22:19:22 UTC (rev 21416)
+++
cytoscape/trunk/application/src/main/java/cytoscape/groups/CyGroupManager.java
2010-08-17 22:23:39 UTC (rev 21417)
@@ -43,6 +43,7 @@
import java.util.List;
import java.util.Map;
+import cytoscape.CyEdge;
import cytoscape.CyNetwork;
import cytoscape.CyNode;
import cytoscape.Cytoscape;
@@ -196,6 +197,38 @@
}
/**
+ * Create a new group by specifying all components. Use this to get a
new group.
+ * This constructor allows the caller to provide all of the components
required
+ * to create a group. This is the most efficient of all of the
constructors in
+ * that no additional processing is done to find internal and external
edges,
+ * etc. If innerEdgeList and outerEdgeList are both null, the
underlying implementation
+ * will find all internal and external edges.
+ *
+ * @param groupName the identifier to use for this group -- should be
unique!
+ * @param nodeList the initial set of nodes for this group
+ * @param innerEdgeList the initial set of internal edges for this group
+ * @param outerEdgeList the initial set of external edges for this group
+ * @param viewer the name of the viewer to manage this group
+ * @param network the network that this group is in
+ * @return the newly created group
+ */
+ public static CyGroup createGroup(String groupName, List<CyNode>
nodeList,
+ List<CyEdge> innerEdgeList,
List<CyEdge> outerEdgeList,
+ String viewer, CyNetwork network) {
+ // Do we already have a group by this name?
+ if (findGroup(groupName) != null) return null;
+ // Create a node for the group
+ CyNode groupNode = Cytoscape.getCyNode(groupName, true);
+ // Create the group itself
+ CyGroup group = new CyGroupImpl(groupNode, nodeList,
innerEdgeList, outerEdgeList, network);
+ groupMap.put(group.getGroupNode(), group);
+ notifyListeners(group,
CyGroupChangeListener.ChangeType.GROUP_CREATED);
+ if (viewer != null)
+ setGroupViewer(group, viewer, null, true);
+ return group;
+ }
+
+ /**
* Create a new, empty group. Use this to get a new group. In
particular,
* this form should be used by internal routines (as opposed to view
* implementations) as this form will cause the viewer to be notified of
@@ -230,7 +263,8 @@
* @param viewer the name of the viewer to manage this group
* @param network the network that this group is in
*/
- public static CyGroup createGroup(String groupName, List<CyNode>
nodeList, String viewer, CyNetwork network) {
+ public static CyGroup createGroup(String groupName, List<CyNode>
nodeList, String viewer,
+ CyNetwork network) {
// Do we already have a group by this name?
if (findGroup(groupName) != null) return null;
// Create the group
@@ -254,7 +288,8 @@
* @param viewer the name of the viewer to manage this group
* @param network the network that this group is in
*/
- public static CyGroup createGroup(CyNode groupNode, List<CyNode>
nodeList, String viewer, CyNetwork network) {
+ public static CyGroup createGroup(CyNode groupNode, List<CyNode>
nodeList, String viewer,
+ CyNetwork network) {
// Do we already have a group by this name?
if (findGroup(groupNode.getIdentifier()) != null) return null;
// Create the group
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