Author: chinmoy
Date: 2009-07-24 13:00:37 -0700 (Fri, 24 Jul 2009)
New Revision: 17556
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
Log:
Fixed arc drawing in circular layout algorithms
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
2009-07-24 19:20:14 UTC (rev 17555)
+++
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/CommonFunctions.java
2009-07-24 20:00:37 UTC (rev 17556)
@@ -293,6 +293,12 @@
return numLeaves;
}
+
+ /**
+ * Calculates the optimum factor by which edges must be scaled to
obtain an optimum view
+ * @param network - the network from which the scaling factor is to be
calculated
+ * @return - the factor to be multiplied to the branchLengths to obtain
the optimum view
+ */
public double getScalingFactor(CyNetwork network)
{
@@ -324,6 +330,9 @@
/**
* Adds the bends to make the edges look rectangular
+ * * @param network - the network on which the bends are to be added
+ * @param networkView - the networkView on which bends are to be added
+ * @param edge - the edge onto which bends are to be added
*/
public void addRectangularBends(CyNetwork network, CyNetworkView
networkView, Edge edge)
{
@@ -352,6 +361,9 @@
/**
* Adds the bends to make the edges look circular
+ * @param network - the network on which the bends are to be added
+ * @param networkView - the networkView on which bends are to be added
+ * @param edge - the edge onto which bends are to be added
*/
public void addCircularBends(CyNetwork network, CyNetworkView
networkView, Edge edge)
{
@@ -382,37 +394,52 @@
Point2D handlePoint = new
Point2D.Double(radius*Math.cos(angle),radius*Math.sin(angle));
Point2D sourcePoint = new
Point2D.Double(sourceX, sourceY);
circularBend.addHandle(handlePoint);
-
+
// Algorithm to draw arcs:
+ // Find the length of the chord from the source
to the first handle in the bend
+ // Find the length of the segment that would
produce an arc of the desired handleInterval
+ // Divide the length of the chord and the
subSegment to calculate how many subSegments are required
+ // Number of subSegments on chord = number of
handles to produce the arc from the bend
-// double distance =
handlePoint.distance(sourcePoint);
-// double handleInterval = 18.0;
-// int iterations = 5;
-//
-// if(compareAngles(angle,sourceAngle)==0)
-//
-// {
-// for(int i = 0;i<iterations; i
++)
-// {
-// angle =
angle+(Math.PI/handleInterval);
-//
circularBend.addHandle(new
Point2D.Double(radius*Math.cos(angle),radius*Math.sin(angle)));
-//
-// }
-// }
-// else
if(compareAngles(angle,sourceAngle)==1)
-// {
-// for(int i =0; i<iterations; i++)
-// {
-// angle =
angle-(Math.PI/handleInterval);
-//
circularBend.addHandle(new
Point2D.Double(radius*Math.cos(angle),radius*Math.sin(angle)));
-//
-// }
-// }
+ double chordLength =
handlePoint.distance(sourcePoint);
+ double handleInterval = Math.PI/18.0;
+ double subSegmentLength =
2*radius*Math.sin(handleInterval/2.0);
+
+ int iterations =
(int)(chordLength/subSegmentLength);
+
+ if(compareAngles(angle,sourceAngle)==0)
+
+ {
+ for(int i = 0;i<iterations; i
++)
+ {
+ angle =
angle+(handleInterval);
+
circularBend.addHandle(new
Point2D.Double(radius*Math.cos(angle),radius*Math.sin(angle)));
+
+ }
+ }
+ else
if(compareAngles(angle,sourceAngle)==1)
+ {
+ for(int i =0; i<iterations; i++)
+ {
+ angle =
angle-(handleInterval);
+
circularBend.addHandle(new
Point2D.Double(radius*Math.cos(angle),radius*Math.sin(angle)));
+
+ }
+ }
+
}
}
+ /**
+ * Important for the functioning of addCircularBends
+ * Given the angle of the initial handle in the bend(arc) and the angle
of the source node
+ * calculates which one is smaller
+ * @param angle1 - the angle of the initial handle
+ * @param angle2 - the angle of the source node
+ * @return 1 if angle1 is smaller, 0 if angle2 is smaller, 2 if error
+ */
private int compareAngles(double angle1, double angle2)
{
int result = 2;
@@ -425,11 +452,11 @@
}
else if(angle1>=0 && angle2<0)
{
- result = 1;
+ result = 0;
}
else if(angle1<0 && angle2>=0)
{
- result = 0;
+ result = 1;
}
return result;
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
2009-07-24 19:20:14 UTC (rev 17555)
+++
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/CircularCladogram.java
2009-07-24 20:00:37 UTC (rev 17556)
@@ -115,8 +115,7 @@
{
Node node = it.next();
- System.out.println(node.getIdentifier()+":
"+Math.atan2(networkView.getNodeView(node).getYPosition(),
networkView.getNodeView(node).getXPosition()));
-
+
// If leaf position it accordingly
if(network.getAdjacentEdgeIndicesArray(node.getRootGraphIndex(), false, false,
true).length == 0)
positionLeaf(node);
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