Author: scooter
Date: 2009-08-11 15:23:21 -0700 (Tue, 11 Aug 2009)
New Revision: 17774
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/MCL/MCLCluster.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/Histogram.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/HistogramDialog.java
Log:
Fixed MCL to use newNetwork visualizer and further fixes to the Histogram code.
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/MCL/MCLCluster.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/MCL/MCLCluster.java
2009-08-11 20:29:03 UTC (rev 17773)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/MCL/MCLCluster.java
2009-08-11 22:23:21 UTC (rev 17774)
@@ -69,7 +69,6 @@
int rNumber = 8;
double clusteringThresh = 1e-15;
boolean takeNegLOG = false;
- boolean createNewNetwork = false;
boolean createMetaNodes = false;
boolean selectedOnly = false;
boolean adjustLoops = true;
@@ -195,13 +194,9 @@
clusterProperties.add(new Tunable("options_panel2",
"Results options",
- Tunable.GROUP, new
Integer(2)));
+ Tunable.GROUP, new
Integer(1)));
// Whether or not to create a new network from the results
- clusterProperties.add(new Tunable("createNewNetwork","Create a
new network with independent clusters",
- Tunable.BOOLEAN, new
Boolean(false)));
-
- // Whether or not to create a new network from the results
clusterProperties.add(new Tunable("createMetaNodes","Create
meta nodes for clusters",
Tunable.BOOLEAN, new
Boolean(false)));
@@ -242,10 +237,6 @@
if ((t != null) && (t.valueChanged() || force))
createMetaNodes = ((Boolean)
t.getValue()).booleanValue();
- t = clusterProperties.get("createNewNetwork");
- if ((t != null) && (t.valueChanged() || force))
- createNewNetwork = ((Boolean)
t.getValue()).booleanValue();
-
t = clusterProperties.get("selectedOnly");
if ((t != null) && (t.valueChanged() || force))
selectedOnly = ((Boolean) t.getValue()).booleanValue();
@@ -298,8 +289,9 @@
if (takeNegLOG) {
if (dataArray[index] == 0)
dataArray[index] = 500; // Arbitrarily
small value (1X10^-500)
- } else
+ else
dataArray[index] =
-Math.log10(dataArray[index]);
+ }
index++;
}
int nbins = 100;
@@ -443,7 +435,10 @@
// Set up the appropriate attributes
CyAttributes netAttr = Cytoscape.getNetworkAttributes();
-
netAttr.setAttribute(Cytoscape.getCurrentNetwork().getIdentifier(),
ClusterMaker.CLUSTER_TYPE_ATTRIBUTE, "mcl");
+
netAttr.setAttribute(Cytoscape.getCurrentNetwork().getIdentifier(),
+ ClusterMaker.CLUSTER_TYPE_ATTRIBUTE,
"mcl");
+
netAttr.setAttribute(Cytoscape.getCurrentNetwork().getIdentifier(),
+ ClusterMaker.CLUSTER_ATTRIBUTE,
clusterAttrName);
// Tell any listeners that we're done
pcs.firePropertyChange(ClusterAlgorithm.CLUSTER_COMPUTED, null,
this);
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/Histogram.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/Histogram.java
2009-08-11 20:29:03 UTC (rev 17773)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/Histogram.java
2009-08-11 22:23:21 UTC (rev 17774)
@@ -56,29 +56,37 @@
private int mouseX;
private boolean boolShowLine = false;
private List<HistoChangeListener> listeners = null;
- private Font adjSizeFont;
- private int fontSize;
private double xInterval;
+ private double xIncrement;
+ private int height;
+ private int width;
+
+ private int yTicks = 10;
+ private int xTicks = 10;
+
+ private static final String FONT_FAMILY = "SansSerif";
+
+ private Font adjFont;
+
DecimalFormat form = new DecimalFormat("0.0E0"); //rounds values for
drawString
Histogram(double[] inputData, int nBins) {
super();
NBINS = nBins;
- setPreferredSize(new Dimension(1000,400));
+ height = 400;
+ width = 1000;
+ setPreferredSize(new Dimension(width,height));
histoArray = new int[NBINS];
this.graphData = inputData;
listeners = new ArrayList();
+ adjFont = new Font(FONT_FAMILY, Font.PLAIN, 14);
+
createHistogram(graphData);
addMouseMotionListener(this);
addMouseListener(this);
- fontSize = 5+ (int)(this.getPreferredSize().getWidth()/(NBINS));
- if(fontSize>18)
- fontSize=18;
- adjSizeFont = new Font("Sans", Font.PLAIN, fontSize);
- // System.out.println("fontSize = "+fontSize);
}
public void updateData(double[] graphData) {
@@ -89,20 +97,23 @@
createHistogram(graphData);
}
- public void paint(Graphics g) {
- super.paint(g);
+ public void paintComponent(Graphics g) {
+ super.paintComponent(g);
+ Dimension dim = getSize();
+ if (dim.width == 0 || dim.height == 0) {
+ dim = getPreferredSize();
+ }
+
+ width = dim.width;
+ height = dim.height;
+ xIncrement = (double)(width-200)/(double)NBINS;
+
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("Sans", Font.PLAIN, fontSize);
- // System.out.println("fontSize = "+fontSize);
drawGraph(g2);
if(boolShowLine)
mouseLine(mouseX, g);
@@ -110,36 +121,33 @@
public void mouseMoved(MouseEvent e) {}
public void mouseDragged(MouseEvent e) {
- Dimension dim = getPreferredSize();
- int width = dim.width;
- int xIncrement = (width-125)/NBINS;
- int histoMousePos = (e.getX()-XSTART)/xIncrement;
+ int histoMousePos =
(int)(((double)(e.getX()-XSTART))/xIncrement);
+ repaint(mouseX-1, YEND, 2, height-YEND);
+ repaint(mouseX-50, YEND-30, 150, 30);
if(e.getX()>XSTART && boolShowLine){
mouseX = e.getX();
- repaint();
+ repaint(mouseX-1, YEND, 2, height-YEND);
+ repaint(mouseX-50, YEND-30, 150, 30);
}
}
public void mouseClicked(MouseEvent e){}
public void mouseEntered(MouseEvent e){}
public void mouseExited(MouseEvent e){}
public void mousePressed(MouseEvent e){
- Dimension dim = getPreferredSize();
- int width = dim.width;
- int xIncrement = (width-125)/NBINS;
- int histoMousePos = (e.getX()-XSTART)/xIncrement;
+ int histoMousePos =
(int)(((double)(e.getX()-XSTART))/xIncrement);
+ repaint(mouseX-1, YEND, 2, height-YEND);
+ repaint(mouseX-50, YEND-30, 150, 30);
if(e.getX()>XSTART && boolShowLine){
mouseX = e.getX();
- repaint();
+ repaint(mouseX-1, YEND, 2, height-YEND);
+ repaint(mouseX-50, YEND-30, 150, 30);
}
}
public void mouseReleased(MouseEvent e){
- Dimension dim = getPreferredSize();
- int width = dim.width;
- int xIncrement = (width-125)/NBINS;
- int histoMousePos = (e.getX()-XSTART)/xIncrement;
+ int histoMousePos =
(int)(((double)(e.getX()-XSTART))/xIncrement);
if(e.getX()>XSTART &&
e.getX()<(XSTART+xIncrement*histoArray.length) && boolShowLine){
double binValue = minValue+(xInterval*histoMousePos);
// System.out.println("histoArray["+histoMousePos+"] =
"+ histoArray[histoMousePos]+", "+form.format((binValue)));
@@ -173,18 +181,14 @@
private void mouseLine(int mX, Graphics g){
- Dimension dim = getPreferredSize();
- int height = dim.height-100;
- int width = dim.width;
- int xIncrement = (width-125)/NBINS;
- int histoMousePos = (mX-XSTART)/xIncrement;
+ int histoMousePos = (int)((double)(mX-XSTART)/xIncrement);
if(histoMousePos >= histoArray.length)
histoMousePos = histoArray.length-1;
g.setColor(Color.red);
g.drawLine(mX, YEND, mX, height);
g.setColor(Color.black);
- g.setFont(adjSizeFont);
+ g.setFont(adjFont);
g.drawString(toSciNotation(form.format((minValue+(xInterval*histoMousePos))).toString(),"
("+histoArray[histoMousePos]+" values)"),mX-50,YEND-5);
}
@@ -222,12 +226,10 @@
double oomRange = Math.log10(range); //order of magnitude
// System.out.println("oomRange = "+oomRange);
oomRange = oomRange + (.5*oomRange/Math.abs(oomRange)); //
Increase our oom by .5
- // System.out.println("oomRange = "+oomRange);
oomRange = (int)(oomRange); //make it an integer
double high = (Math.rint((maxValue/Math.pow(10, oomRange))+.5))
* (Math.pow(10, oomRange)); // This is our initial high value
- // System.out.println("high = "+high);
if (maxValue <= high/2)
high = high/2; // A little fine-tuning
@@ -237,7 +239,6 @@
low = low/2;
xInterval = (high - low) / NBINS;
-
}
private void calculateYScale() {
@@ -256,20 +257,31 @@
}
private void drawGraph(Graphics2D g){
- Dimension dim = getPreferredSize();
+ Dimension dim = getSize();
+ if (dim.height == 0 || dim.width == 0) {
+ dim = getPreferredSize();
+ }
int height = dim.height-100;
int width = dim.width;
+ // Since we allow scaling in the X dimension, we want to
+ // check to see if we should increase the number of
+ // ticks on the X axis
+ if (NBINS > 1000)
+ xTicks = 20;
+ if (NBINS > 5000)
+ xTicks = 50;
+ if (NBINS > 10000)
+ xTicks = 100;
+
drawAxes(g, height, width);
drawLabels(g, height, width);
drawData(g, height, width);
}
private void drawAxes(Graphics2D g, int height, int width) {
+ int maxX = (int)(xIncrement*NBINS+XSTART);
- int xIncrement = (width-125)/NBINS;
- int maxX = xIncrement*NBINS+XSTART;
-
// Draw the Y axis
g.setColor(Color.black);
g.drawLine(XSTART,YEND,XSTART,height);
@@ -280,11 +292,11 @@
// Draw the Y incremental lines
double yIncrement = (height-YEND)/(double)histoMaxUp;
for(int nI=1;nI<=histoMaxUp;nI++){
- if(((double)nI%((double)histoMaxUp/10.0)) == 0.0){
+ if(((double)nI%((double)histoMaxUp/yTicks)) == 0.0){
g.setColor(Color.red);
g.drawLine(XSTART-5,(int)(height-(yIncrement*nI)),maxX,(int)(height-(yIncrement*nI)));
}
- else if(((double)nI%((double)histoMaxUp/20.0)) == 0.0){
+ else if(((double)nI%((double)histoMaxUp/(yTicks*2))) ==
0.0){
g.setColor(Color.gray);
g.drawLine(XSTART,(int)(height-(yIncrement*nI)),maxX,(int)(height-(yIncrement*nI)));
}
@@ -292,15 +304,18 @@
g.setColor(Color.black);
for(int nI=0; nI<NBINS; nI++){
- if(nI%10==0){
-
g.drawLine(XSTART+xIncrement*nI,height,XSTART+xIncrement*nI,height+10);
+ int x = XSTART + (int)(xIncrement * nI);
+ if(nI%(NBINS/xTicks)==0){
+ g.drawLine(x,height,x,height+10);
+ } else if (nI%(NBINS/(xTicks*5)) == 0) {
+ g.drawLine(x,height,x,height+5);
}
}
}
private void drawLabels(Graphics2D g, int height, int width) {
g.setColor(Color.black);
- g.setFont(adjSizeFont);
+ g.setFont(adjFont);
FontMetrics metrics = g.getFontMetrics();
// Draw the Y labels
@@ -309,23 +324,21 @@
String str = ""+nI;
int offset = 90-metrics.stringWidth(str);
- if(nI%(histoMaxUp/10)==0)
+ if(nI%(histoMaxUp/yTicks)==0)
g.drawString(str, offset,
height-(int)(yIncrement*nI)+5);
}
// 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;
if (value == 0 || (value > 1 && value < 10))
offset += 20;
- if(nI%20==0)
- g.drawString(toSciNotation(str,
""),offset+xIncrement*nI,height+25);
- if(nI%20==10)
- g.drawString(toSciNotation(str,
""),offset+xIncrement*nI,height+30);
+ int x = (int)(xIncrement*nI)+offset;
+ if(nI%(NBINS/xTicks)==0)
+ g.drawString(toSciNotation(str,
""),x,height+25);
}
}
@@ -334,19 +347,25 @@
// the font also.
private void drawData(Graphics2D g, int height, int width){
int nBlueChange = 100;
+ int barWidth = 0;
+
double yIncrement = (height-50)/(double)(histoMaxUp);
//System.out.println("yIncrement = "+yIncrement);
- int xIncrement = (width-125)/NBINS;
double xValue = low;
+
+ if (xIncrement < 1)
+ barWidth = 1;
+ else
+ barWidth = (int) xIncrement;
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-barHeight), xIncrement, (int)barHeight);
+ g.fillRect(XSTART+(int)(xIncrement*nI),
(int)(height-barHeight), barWidth, (int)barHeight);
g.setColor(Color.black);
- g.drawRect(XSTART+xIncrement*nI,
(int)(height-barHeight), xIncrement, (int)barHeight);
+ g.drawRect(XSTART+(int)(xIncrement*nI),
(int)(height-barHeight), barWidth, (int)barHeight);
}
nBlueChange+=15;
@@ -371,9 +390,9 @@
}
AttributedString str;
- if (Integer.parseInt(exponent) == 0) {
+ if (exponent.length() == 0 || Integer.parseInt(exponent) == 0) {
str = new AttributedString(returnString+suffix);
- str.addAttribute(TextAttribute.FONT, adjSizeFont, 0,
returnString.length());
+ str.addAttribute(TextAttribute.FONT, adjFont);
} else {
returnString += "x10";
int superOffset = returnString.length();
@@ -381,7 +400,8 @@
int superEnd = returnString.length();
str = new AttributedString(returnString+suffix);
- str.addAttribute(TextAttribute.FONT, adjSizeFont, 0,
returnString.length());
+ str.addAttribute(TextAttribute.FAMILY, FONT_FAMILY);
+ str.addAttribute(TextAttribute.SIZE, new Float(14));
str.addAttribute(TextAttribute.SUPERSCRIPT,
TextAttribute.SUPERSCRIPT_SUPER, superOffset, superEnd);
}
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/HistogramDialog.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/HistogramDialog.java
2009-08-11 20:29:03 UTC (rev 17773)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/HistogramDialog.java
2009-08-11 22:23:21 UTC (rev 17774)
@@ -172,8 +172,8 @@
scrollPanel = new
ScrollPane(ScrollPane.SCROLLBARS_AS_NEEDED);
scrollPanel.addComponentListener(this);
scrollPanel.add(histo);
- scrollPanel.setPreferredSize(new Dimension(dim.width,
height));
- histo.setPreferredSize(new Dimension(histoWidth,
height));
+ scrollPanel.setPreferredSize(new Dimension(dim.width,
histoDim.height));
+ histo.setPreferredSize(new Dimension(histoWidth,
histoDim.height));
mainPanel.add(scrollPanel);
} else {
histo.setPreferredSize(new Dimension(dim.width,
dim.height));
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