Author: chinmoy
Date: 2009-08-07 02:25:23 -0700 (Fri, 07 Aug 2009)
New Revision: 17735
Modified:
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/CommonFunctions.java
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/CircularCladogram.java
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/RadialCladogram.java
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/RectangularCladogram.java
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/SlantedCladogram.java
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/phylograms/CircularPhylogram.java
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/phylograms/RadialPhylogram.java
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/phylograms/RectangularPhylogram.java
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/phylograms/SlantedPhylogram.java
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/visualstyle/DepthwiseSize.java
Log:
Cleanup
Modified:
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/CommonFunctions.java
===================================================================
---
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/CommonFunctions.java
2009-08-07 06:21:26 UTC (rev 17734)
+++
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/CommonFunctions.java
2009-08-07 09:25:23 UTC (rev 17735)
@@ -14,6 +14,37 @@
public class CommonFunctions {
+
+ public boolean hasLeaf(CyNetwork network)
+ {
+ // Get all nodes
+ List<Node> nodesList = network.nodesList();
+ Iterator <Node> nodesListIterator = nodesList.iterator();
+ while(nodesListIterator.hasNext())
+ {
+ Node node = nodesListIterator.next();
+ if(network.getOutDegree(node)==0)
+ return true;
+
+ }
+ return false;
+ }
+
+ public boolean isTree(CyNetwork network)
+ {
+ // Get all nodes
+ List<Node> nodesList = network.nodesList();
+ Iterator <Node> nodesListIterator = nodesList.iterator();
+ while(nodesListIterator.hasNext())
+ {
+ Node node = nodesListIterator.next();
+
if(network.getInDegree(node)==0||network.getInDegree(node)==1)
+ continue;
+ else
+ return false;
+ }
+ return true;
+ }
/**
* getTreeRoot(network)
* Finds the root of the tree and returns it
@@ -286,11 +317,16 @@
{
int [] incomingEdges =
network.getAdjacentEdgeIndicesArray(node.getRootGraphIndex(), false, true,
false);
- int depth= getDepth(network,
network.getEdge(incomingEdges[0]).getSource());
-
-
+ int max = 0;
+ for (int i = 0; i < incomingEdges.length; i++)
+ {
+ int depth = getLevel(network,
network.getEdge(incomingEdges[i]).getSource());
+ if(depth > max)
+ max = depth;
- return depth+1;
+ }
+
+ return max+1;
}
}
/**
Modified:
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/CircularCladogram.java
===================================================================
---
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/CircularCladogram.java
2009-08-07 06:21:26 UTC (rev 17734)
+++
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/CircularCladogram.java
2009-08-07 09:25:23 UTC (rev 17735)
@@ -15,22 +15,22 @@
import giny.model.Node;
public class CircularCladogram extends AbstractLayout{
-
+
static double BASE_RADIUS = 100.0;
-
+
private LayoutProperties layoutProperties;
-
+
CommonFunctions commonFunctions = new CommonFunctions();
-
+
private int numLeavesVisited = 0; //
-
+
public CircularCladogram()
{
super();
layoutProperties = new LayoutProperties(getName());
initialize_properties();
}
-
+
protected void initialize_properties()
{
layoutProperties.initializeProperties();
@@ -44,7 +44,7 @@
public void updateSettings() {
updateSettings(false);
}
-
+
/**
* DOCUMENT ME!
*
@@ -100,67 +100,72 @@
BASE_RADIUS += radius;
construct();
}
-
+
public void construct() {
taskMonitor.setStatus("Initializing");
initialize();
-
- // Find the root of the tree
- Node root = commonFunctions.getTreeRoot(network);
+ // Verify that tree is indeed a tree
- // Remove bends
+
if(commonFunctions.hasLeaf(network)&&commonFunctions.isTree(network))
+ {
+ // Find the root of the tree
+ Node root = commonFunctions.getTreeRoot(network);
- List<Edge> allEdges = network.edgesList();
- Iterator<Edge> edgesIterator = allEdges.iterator();
+ // Remove bends
- while(edgesIterator.hasNext())
- {
+ List<Edge> allEdges = network.edgesList();
+ Iterator<Edge> edgesIterator = allEdges.iterator();
- Edge edge = edgesIterator.next();
- networkView.getEdgeView(edge).clearBends();
- }
- numLeavesVisited = 0;
+ while(edgesIterator.hasNext())
+ {
- // Obtain post order traversal of nodes starting from the root
- List<Node> postOrderNodes =
commonFunctions.postOrderTraverse(network, root);
+ Edge edge = edgesIterator.next();
+ networkView.getEdgeView(edge).clearBends();
+ }
+ numLeavesVisited = 0;
- // Position each node
- Iterator<Node> it = postOrderNodes.iterator();
- while(it.hasNext())
- {
- Node node = it.next();
-
-
- // If leaf position it accordingly
-
if(network.getAdjacentEdgeIndicesArray(node.getRootGraphIndex(), false, false,
true).length == 0)
- positionLeaf(node);
- else
- positionInternalNode(node);
-
-
-
- }
-
- // Bend each edge to make it look circular
+ // Obtain post order traversal of nodes starting from
the root
+ List<Node> postOrderNodes =
commonFunctions.postOrderTraverse(network, root);
- allEdges = network.edgesList();
- edgesIterator = allEdges.iterator();
+ // Position each node
+ Iterator<Node> it = postOrderNodes.iterator();
+ while(it.hasNext())
+ {
+ Node node = it.next();
- while(edgesIterator.hasNext())
- {
- Edge edge = edgesIterator.next();
- networkView.getEdgeView(edge).clearBends();
- commonFunctions.addCircularBends(network, networkView,
edge);
+ // If leaf position it accordingly
+
if(network.getAdjacentEdgeIndicesArray(node.getRootGraphIndex(), false, false,
true).length == 0)
+ positionLeaf(node);
+ else
+ positionInternalNode(node);
+
+
+
+ }
+
+ // Bend each edge to make it look circular
+
+ allEdges = network.edgesList();
+ edgesIterator = allEdges.iterator();
+
+ while(edgesIterator.hasNext())
+ {
+
+ Edge edge = edgesIterator.next();
+ networkView.getEdgeView(edge).clearBends();
+ commonFunctions.addCircularBends(network,
networkView, edge);
+ }
+
}
+ else
+ System.out.println("The "+getName()+" layout can only
be applied to trees.");
-
-
}
-
-
+
+
/**
* positionLeaf(Node)
* Positions the leaves
@@ -179,9 +184,9 @@
networkView.getNodeView(node).setXPosition(nodeX,true);
networkView.getNodeView(node).setYPosition(nodeY, true);
-
+
}
-
+
/**
* positionInternalNode(Node)
* Positions the internal nodes
@@ -225,7 +230,7 @@
double nodeX = radius * Math.cos(meanAngle);
double nodeY = radius * Math.sin(meanAngle);
-
+
// Position
networkView.getNodeView(node).setXPosition(nodeX,true);
networkView.getNodeView(node).setYPosition(nodeY, true);
@@ -233,6 +238,6 @@
}
-
+
}
Modified:
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/RadialCladogram.java
===================================================================
---
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/RadialCladogram.java
2009-08-07 06:21:26 UTC (rev 17734)
+++
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/RadialCladogram.java
2009-08-07 09:25:23 UTC (rev 17735)
@@ -104,6 +104,10 @@
public void construct() {
taskMonitor.setStatus("Initializing");
initialize();
+
+
if(commonFunctions.hasLeaf(network)&&commonFunctions.isTree(network))
+ {
+
// Remove bends
List<Edge> allEdges = network.edgesList();
@@ -139,8 +143,10 @@
}
-
}
+ else
+ System.out.println("The "+getName()+" layout can only be
applied to trees.");
+ }
/**
Modified:
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/RectangularCladogram.java
===================================================================
---
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/RectangularCladogram.java
2009-08-07 06:21:26 UTC (rev 17734)
+++
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/RectangularCladogram.java
2009-08-07 09:25:23 UTC (rev 17735)
@@ -104,7 +104,9 @@
taskMonitor.setStatus("Initializing");
initialize();
-
+
if(commonFunctions.hasLeaf(network)&&commonFunctions.isTree(network))
+ {
+
// Find the root of the tree
Node root = commonFunctions.getTreeRoot(network);
// Remove bends
@@ -151,6 +153,9 @@
networkView.getEdgeView(edge).clearBends();
commonFunctions.addRectangularBends(network,
networkView, edge);
}
+ }
+ else
+ System.out.println("The "+getName()+" layout can only
be applied to trees.");
Modified:
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/SlantedCladogram.java
===================================================================
---
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/SlantedCladogram.java
2009-08-07 06:21:26 UTC (rev 17734)
+++
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/SlantedCladogram.java
2009-08-07 09:25:23 UTC (rev 17735)
@@ -105,7 +105,8 @@
taskMonitor.setStatus("Initializing");
initialize();
-
+
if(commonFunctions.hasLeaf(network)&&commonFunctions.isTree(network))
+ {
// Find the root of the tree
Node root = commonFunctions.getTreeRoot(network);
// Remove bends
@@ -139,8 +140,11 @@
}
-
}
+ else
+ System.out.println("The "+getName()+" layout can only be
applied to trees.");
+
+ }
/**
Modified:
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/phylograms/CircularPhylogram.java
===================================================================
---
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/phylograms/CircularPhylogram.java
2009-08-07 06:21:26 UTC (rev 17734)
+++
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/phylograms/CircularPhylogram.java
2009-08-07 09:25:23 UTC (rev 17735)
@@ -115,6 +115,9 @@
// Intialize the common functions
commonFunctions = new CommonFunctions();
+
+
if(commonFunctions.hasLeaf(network)&&commonFunctions.isTree(network))
+ {
// Remove bends
List<Edge> allEdges = network.edgesList();
@@ -174,6 +177,9 @@
commonFunctions.addCircularBends(network, networkView,
edge);
}
+ }
+ else
+ System.out.println("The "+getName()+" layout can only
be applied to trees.");
Modified:
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/phylograms/RadialPhylogram.java
===================================================================
---
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/phylograms/RadialPhylogram.java
2009-08-07 06:21:26 UTC (rev 17734)
+++
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/phylograms/RadialPhylogram.java
2009-08-07 09:25:23 UTC (rev 17735)
@@ -115,7 +115,8 @@
// Intialize the common functions
commonFunctions = new CommonFunctions();
-
+
if(commonFunctions.hasLeaf(network)&&commonFunctions.isTree(network))
+ {
// Remove bends
List<Edge> allEdges = network.edgesList();
@@ -162,6 +163,9 @@
}
+ }
+ else
+ System.out.println("The "+getName()+" layout can only be
applied to trees.");
}
Modified:
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/phylograms/RectangularPhylogram.java
===================================================================
---
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/phylograms/RectangularPhylogram.java
2009-08-07 06:21:26 UTC (rev 17734)
+++
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/phylograms/RectangularPhylogram.java
2009-08-07 09:25:23 UTC (rev 17735)
@@ -115,6 +115,9 @@
// Intialize the common functions
commonFunctions = new CommonFunctions();
+
+
if(commonFunctions.hasLeaf(network)&&commonFunctions.isTree(network))
+ {
// Remove bends
List<Edge> allEdges = network.edgesList();
@@ -175,6 +178,9 @@
commonFunctions.addRectangularBends(network,
networkView, edge);
}
+ }
+ else
+ System.out.println("The "+getName()+" layout can only be
applied to trees.");
Modified:
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/phylograms/SlantedPhylogram.java
===================================================================
---
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/phylograms/SlantedPhylogram.java
2009-08-07 06:21:26 UTC (rev 17734)
+++
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/phylograms/SlantedPhylogram.java
2009-08-07 09:25:23 UTC (rev 17735)
@@ -117,6 +117,9 @@
// Intialize the common functions
commonFunctions = new CommonFunctions();
+
+
if(commonFunctions.hasLeaf(network)&&commonFunctions.isTree(network))
+ {
// Remove bends
List<Edge> allEdges = network.edgesList();
@@ -162,8 +165,11 @@
positionNodeX(node);
}
-
+ }
+ else
+ System.out.println("The "+getName()+" layout can only
be applied to trees.");
+
}
Modified:
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/visualstyle/DepthwiseSize.java
===================================================================
---
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/visualstyle/DepthwiseSize.java
2009-08-07 06:21:26 UTC (rev 17734)
+++
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/visualstyle/DepthwiseSize.java
2009-08-07 09:25:23 UTC (rev 17735)
@@ -116,9 +116,24 @@
{
Edge edge =
network.getEdge(edgeIndicesArray[i]);
edgeAttributes.setAttribute(edge.getIdentifier(),"Depth", depth);
+
}
}
+ List<Edge> edgeList = network.edgesList();
+ Iterator<Edge> edgeListIterator = edgeList.iterator();
+
+ while(edgeListIterator.hasNext())
+ {
+ Edge edge = edgeListIterator.next();
+ if(edge.getSource().getRootGraphIndex() ==
edge.getTarget().getRootGraphIndex())
+ {
+ int depth =
nodeAttributes.getIntegerAttribute(edge.getSource().getIdentifier(), "Depth");
+
edgeAttributes.setAttribute(edge.getIdentifier(),"Depth",depth);
+ }
+ }
+
+
nodeAttributes.setUserVisible("Depth", false);
edgeAttributes.setUserVisible("Depth", false);
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