Author: scooter
Date: 2009-08-11 10:33:45 -0700 (Tue, 11 Aug 2009)
New Revision: 17770
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/GLay/GLayCluster.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/Histogram.java
Log:
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/GLay/GLayCluster.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/GLay/GLayCluster.java
2009-08-11 16:38:11 UTC (rev 17769)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/GLay/GLayCluster.java
2009-08-11 17:33:45 UTC (rev 17770)
@@ -69,7 +69,7 @@
}
public String getShortName() {return "GLay";};
- public String getName() {return "GLay (community) cluster";};
+ public String getName() {return "Community cluster (GLay)";};
public JPanel getSettingsPanel() {
// Everytime we ask for the panel, we want to update our
attributes
@@ -143,7 +143,7 @@
CyNetwork network = Cytoscape.getCurrentNetwork();
// Sanity check all of our settings
if (debug)
- logger.debug("Performing GLay clustering");
+ logger.debug("Performing community clustering (GLay)");
String clusterAttrName = network.getIdentifier()+"_cluster";
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/Histogram.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/Histogram.java
2009-08-11 16:38:11 UTC (rev 17769)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/Histogram.java
2009-08-11 17:33:45 UTC (rev 17770)
@@ -12,9 +12,12 @@
import java.awt.Color;
import java.awt.Dimension;
import java.awt.Graphics;
+import java.awt.Graphics2D;
import java.awt.event.*;
import java.awt.Font;
import java.awt.FontMetrics;
+import java.awt.RenderingHints;
+import java.awt.RenderingHints.Key;
import java.awt.font.TextAttribute;
import java.text.AttributedString;
import java.text.AttributedCharacterIterator;
@@ -74,7 +77,7 @@
fontSize = 5+ (int)(this.getPreferredSize().getWidth()/(NBINS));
if(fontSize>18)
fontSize=18;
- adjSizeFont = new Font("Helvetica", Font.PLAIN, fontSize);
+ adjSizeFont = new Font("Sans", Font.PLAIN, fontSize);
// System.out.println("fontSize = "+fontSize);
}
@@ -88,13 +91,19 @@
public void paint(Graphics g) {
super.paint(g);
+ Graphics2D g2 = (Graphics2D) g;
+ g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_ON);
+ g2.setRenderingHint(RenderingHints.KEY_RENDERING,
+ RenderingHints.VALUE_RENDER_QUALITY);
+
fontSize = 3 +(int)(this.getPreferredSize().getWidth()/(NBINS));
if(fontSize>18)
fontSize=18;
- adjSizeFont = new Font("Helvetica", Font.PLAIN, fontSize);
- System.out.println("fontSize = "+fontSize);
- drawGraph(g);
+ adjSizeFont = new Font("Sans", Font.PLAIN, fontSize);
+ // System.out.println("fontSize = "+fontSize);
+ drawGraph(g2);
if(boolShowLine)
mouseLine(mouseX, g);
}
@@ -181,15 +190,17 @@
private void createHistogram(double[] inputData){
calculateXScale();
+
+ // System.out.println("Creating histogram: low = "+low);
// Bin the data
for(double dataItr : inputData){
for(int nI=0; nI < NBINS; nI++){
- if(dataItr==minValue){
+ if(dataItr==low){
histoArray[0]+=1;
break;
}
- if(dataItr>minValue+xInterval*nI &&
dataItr<=minValue+xInterval*(nI+1) ){
+ if(dataItr>low+xInterval*nI &&
dataItr<=low+xInterval*(nI+1) ){
histoArray[nI]+=1;
break;
}
@@ -206,8 +217,6 @@
maxValue = Math.max(maxValue, graphData[i]);
}
- System.out.println("range = "+minValue+" - "+maxValue);
-
// Calculate our X scale
double range = maxValue - minValue;
double oomRange = Math.log10(range); //order of magnitude
@@ -246,7 +255,7 @@
histoMaxUp = 10;
}
- private void drawGraph(Graphics g){
+ private void drawGraph(Graphics2D g){
Dimension dim = getPreferredSize();
int height = dim.height-100;
int width = dim.width;
@@ -256,7 +265,7 @@
drawData(g, height, width);
}
- private void drawAxes(Graphics g, int height, int width) {
+ private void drawAxes(Graphics2D g, int height, int width) {
int xIncrement = (width-125)/NBINS;
int maxX = xIncrement*NBINS+XSTART;
@@ -282,14 +291,14 @@
}
g.setColor(Color.black);
- for(int nI=0; nI<=NBINS; nI++){
+ for(int nI=0; nI<NBINS; nI++){
if(nI%10==0){
g.drawLine(XSTART+xIncrement*nI,height,XSTART+xIncrement*nI,height+10);
}
}
}
- private void drawLabels(Graphics g, int height, int width) {
+ private void drawLabels(Graphics2D g, int height, int width) {
g.setColor(Color.black);
g.setFont(adjSizeFont);
FontMetrics metrics = g.getFontMetrics();
@@ -306,7 +315,7 @@
// Now draw the X labels
int xIncrement = (width-125)/NBINS;
- for(int nI=0; nI<=NBINS; nI++){
+ for(int nI=0; nI<NBINS; nI++){
double value = low+(xInterval*nI);
String str = form.format(value);
int offset = XSTART+metrics.stringWidth(str)/2 - 50;
@@ -323,26 +332,26 @@
// TODO: Change this method to use height and width. You may need to
scale the
// the font also.
- private void drawData(Graphics g, int height, int width){
+ private void drawData(Graphics2D g, int height, int width){
int nBlueChange = 100;
double yIncrement = (height-50)/(double)(histoMaxUp);
//System.out.println("yIncrement = "+yIncrement);
int xIncrement = (width-125)/NBINS;
double xValue = low;
- int histoIndex = 0;
- for(int nI=0; nI<=NBINS; nI++){
- if (xValue >= minValue) {
+ for(int nI=0; nI<NBINS; nI++){
+ double barHeight = histoArray[nI]*yIncrement;
+
+ if (barHeight > 0) {
g.setColor(new Color(0,0,nBlueChange));
- g.fillRect(XSTART+xIncrement*nI,
(int)(height-(histoArray[histoIndex]*yIncrement)), xIncrement,
(int)(histoArray[histoIndex]*yIncrement));
+ g.fillRect(XSTART+xIncrement*nI,
(int)(height-barHeight), xIncrement, (int)barHeight);
g.setColor(Color.black);
- g.drawRect(XSTART+xIncrement*nI,
(int)(height-(histoArray[histoIndex]*yIncrement)), xIncrement,
(int)(histoArray[histoIndex]*yIncrement));
- histoIndex++;
+ g.drawRect(XSTART+xIncrement*nI,
(int)(height-barHeight), xIncrement, (int)barHeight);
+ }
- nBlueChange+=15;
- if(nBlueChange >= 250)
- nBlueChange = 100;
- }
+ nBlueChange+=15;
+ if(nBlueChange >= 250)
+ nBlueChange = 100;
xValue += xInterval;
}
}
@@ -364,6 +373,7 @@
AttributedString str;
if (Integer.parseInt(exponent) == 0) {
str = new AttributedString(returnString+suffix);
+ str.addAttribute(TextAttribute.FONT, adjSizeFont, 0,
returnString.length());
} else {
returnString += "x10";
int superOffset = returnString.length();
@@ -371,10 +381,10 @@
int superEnd = returnString.length();
str = new AttributedString(returnString+suffix);
+ str.addAttribute(TextAttribute.FONT, adjSizeFont, 0,
returnString.length());
str.addAttribute(TextAttribute.SUPERSCRIPT,
TextAttribute.SUPERSCRIPT_SUPER, superOffset, superEnd);
}
- str.addAttribute(TextAttribute.FONT, adjSizeFont, 0,
returnString.length());
return str.getIterator();
}
}
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