Author: ghannum
Date: 2010-09-02 15:06:45 -0700 (Thu, 02 Sep 2010)
New Revision: 21674
Added:
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/utilities/NumberFormatter.java
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/ModFinder/HCSearch2.java
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/ui/SearchPropertyPanel.java
Log:
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/ModFinder/HCSearch2.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/ModFinder/HCSearch2.java
2010-09-02 22:05:00 UTC (rev 21673)
+++
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/ModFinder/HCSearch2.java
2010-09-02 22:06:45 UTC (rev 21674)
@@ -19,6 +19,7 @@
import org.idekerlab.PanGIAPlugin.networks.linkedNetworks.TypedLinkNode;
import org.idekerlab.PanGIAPlugin.networks.linkedNetworks.TypedLinkNodeModule;
import org.idekerlab.PanGIAPlugin.utilities.MemoryReporter;
+import org.idekerlab.PanGIAPlugin.utilities.NumberFormatter;
import org.idekerlab.PanGIAPlugin.utilities.ThreadPriorityFactory;
import cytoscape.task.Task;
@@ -396,9 +397,9 @@
csizes.add(m.value().size());
}
- builder.append("Best cluster score: " + cscores.max(false) +
"\n");
- builder.append("Worst cluster score: " + cscores.min(false) +
"\n");
- builder.append("Largest cluster size: " + csizes.max(false) +
"\n");
+ builder.append("Best cluster score: " +
NumberFormatter.formatNumber(cscores.max(false),3) + "\n");
+ builder.append("Worst cluster score: " +
NumberFormatter.formatNumber(cscores.min(false),3) + "\n");
+ builder.append("Largest cluster size: " +
(int)csizes.max(false) + "\n");
DoubleVector escores = new DoubleVector(results.numEdges());
for (TypedLinkEdge<TypedLinkNodeModule<String, BFEdge>, BFEdge>
ed : results
@@ -408,7 +409,7 @@
escores.add(score);
}
- builder.append("Best edge score: " + escores.max(false) + "\n");
+ builder.append("Best edge score: " +
NumberFormatter.formatNumber(escores.max(false),3) + "\n");
// csizes.plothist(30);
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/ui/SearchPropertyPanel.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/ui/SearchPropertyPanel.java
2010-09-02 22:05:00 UTC (rev 21673)
+++
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/ui/SearchPropertyPanel.java
2010-09-02 22:06:45 UTC (rev 21674)
@@ -41,9 +41,10 @@
private static final double DEF_ALPHA = 1.6;
private static final double DEF_ALPHA_MUL = 0.0;
+ private static final double DEF_COMPLEX_REWARD = 0;
private static final String DEF_DEGREE = "2";
private static final double DEF_CUTOFF = 20.0;
- private static final double DEF_PVALUE_THRESHOLD = 80;
+ private static final double DEF_PVALUE_THRESHOLD = 90;
private static final int DEF_NUMBER_OF_SAMPLES = 1000;
private static final String DEFAULT_ATTRIBUTE = "none";
@@ -95,11 +96,11 @@
updateFilteringOptions(null);
// Set defaults
- this.alphaTextField.setText(Double.toString(DEF_ALPHA));
-
this.alphaMultiplierTextField.setText(Double.toString(DEF_ALPHA_MUL));
+ //this.alphaTextField.setText(Double.toString(DEF_ALPHA));
+
//this.alphaMultiplierTextField.setText(Double.toString(DEF_ALPHA_MUL));
+
this.complexRewardTextField.setText(Double.toString(DEF_COMPLEX_REWARD));
this.degreeTextField.setText(DEF_DEGREE);
-
this.pValueThresholdTextField.setText(Double.toString(DEF_PVALUE_THRESHOLD));
-
this.numberOfSamplesTextField.setText(Integer.toString(DEF_NUMBER_OF_SAMPLES));
+
this.edgeFilterTextField.setText(Double.toString(DEF_PVALUE_THRESHOLD));
Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(Cytoscape.ATTRIBUTES_CHANGED,
this);
}
@@ -344,19 +345,30 @@
pnlParameter = new javax.swing.JPanel();
scorePanel = new javax.swing.JPanel();
+
+ /*
alphaLabel = new javax.swing.JLabel();
alphaMultiplierLabel = new javax.swing.JLabel();
- degreeLabel = new javax.swing.JLabel();
alphaTextField = new javax.swing.JTextField();
alphaMultiplierTextField = new javax.swing.JTextField();
+ */
+
+ degreeLabel = new javax.swing.JLabel();
degreeTextField = new javax.swing.JTextField();
+
+ complexRewardLabel = new JLabel();
+ complexRewardSlider = new JSlider();
+ complexRewardSliderLabels = new JLabel();
+ complexRewardTextField = new JTextField();
+
lbPlaceHolder1 = new javax.swing.JLabel();
+
edgeFilteringPanel = new javax.swing.JPanel();
pValueThresholdLabel = new javax.swing.JLabel();
- pValueThresholdTextField = new javax.swing.JTextField();
+ edgeFilterTextField = new javax.swing.JTextField();
+ edgeFilterSlider = new JSlider();
+ edgeFilterSliderLabels = new JLabel();
lbPlaceHolder2 = new javax.swing.JLabel();
- lbNumberOfSamples = new javax.swing.JLabel();
- numberOfSamplesTextField = new javax.swing.JTextField();
lbPlaceHolder3 = new javax.swing.JLabel();
trainingCheckBoxPhysical = new JCheckBox();
trainingCheckBoxGenetic = new JCheckBox();
@@ -390,33 +402,94 @@
scorePanel.setBorder(javax.swing.BorderFactory.createTitledBorder("Search
Parameters"));
scorePanel.setToolTipText("Specify parameters relating to the search
procedure.");
+ complexRewardLabel.setText("Module size:");
+ complexRewardLabel.setToolTipText("Module size parameters AB. (Module
reward = AB * size ^ |AB|)");
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(0, 5,3, 20);
+ gridBagConstraints.gridx = 1;
+ gridBagConstraints.gridy = 1;
+ scorePanel.add(complexRewardLabel, gridBagConstraints);
+
+ complexRewardSliderLabels.setText("Smaller Larger");
+
complexRewardSliderLabels.setToolTipText(complexRewardLabel.getToolTipText());
+
complexRewardSliderLabels.setFont(edgeFilterSliderLabels.getFont().deriveFont(10.0f));
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHEAST;
+ gridBagConstraints.insets = new java.awt.Insets(0, 5,3, 10);
+ gridBagConstraints.gridx = 1;
+ gridBagConstraints.gridy = 1;
+ scorePanel.add(complexRewardSliderLabels, gridBagConstraints);
+
+
complexRewardSlider.setToolTipText(complexRewardLabel.getToolTipText());
+ complexRewardSlider.setPreferredSize(new java.awt.Dimension(100, 25));
+ complexRewardSlider.setExtent(0);
+ complexRewardSlider.setMinimum(0);
+ complexRewardSlider.setMaximum(600);
+ complexRewardSlider.setValue(300);
+ complexRewardSlider.setMajorTickSpacing(100);
+ complexRewardSlider.setMinorTickSpacing(100);
+ complexRewardSlider.setPaintLabels(false);
+ complexRewardSlider.setPaintTicks(false);
+ complexRewardSlider.setPaintTrack(true);
+ complexRewardSlider.setEnabled(true);
+ complexRewardSlider.addChangeListener(new
javax.swing.event.ChangeListener() {
+ public void stateChanged(javax.swing.event.ChangeEvent evt) {
+ complexRewardSliderMoved(evt);
+ }
+ });
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.insets = new java.awt.Insets(10, 20, 10, 10);
+ gridBagConstraints.gridx = 1;
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.EAST;
+ scorePanel.add(complexRewardSlider, gridBagConstraints);
+
+ complexRewardTextField.setPreferredSize(new java.awt.Dimension(50,
25));
+ complexRewardTextField.addKeyListener(textFieldKeyListener);
+
complexRewardTextField.setToolTipText(complexRewardSlider.getToolTipText());
+ complexRewardTextField.addKeyListener(new java.awt.event.KeyListener(){
+ public void keyPressed(java.awt.event.KeyEvent evt){
+ }
+ public void keyTyped(java.awt.event.KeyEvent evt){
+
+ }
+ public void keyReleased(java.awt.event.KeyEvent evt){
+ complexRewardTextChanged(evt);
+ }
+ });
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 2;
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(0, 0, 3, 0);
+ scorePanel.add(complexRewardTextField, gridBagConstraints);
+
+ /*
alphaLabel.setText("Alpha (Exponent):");
alphaLabel.setToolTipText("The exponent for rewarding module size.
(reward = multiplier * moduleSize^exponent)");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.anchor = java.awt.GridBagConstraints.EAST;
gridBagConstraints.insets = new java.awt.Insets(0, 5,3, 0);
+ gridBagConstraints.gridx = 1;
+ gridBagConstraints.gridy = 2;
scorePanel.add(alphaLabel, gridBagConstraints);
alphaMultiplierLabel.setText("Beta (Multiplier):");
alphaMultiplierLabel.setToolTipText("The multiplier for rewarding
module size. (reward = multiplier * moduleSize^exponent)");
gridBagConstraints = new java.awt.GridBagConstraints();
- gridBagConstraints.gridy = 1;
+ gridBagConstraints.gridx = 1;
+ gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.EAST;
gridBagConstraints.insets = new java.awt.Insets(0, 0, 3, 0);
scorePanel.add(alphaMultiplierLabel, gridBagConstraints);
- degreeLabel.setText("Network filter degree (optional):");
- degreeLabel.setToolTipText("Remove nodes in the physical network which
are distant from any node in the genetic network. The maximum distance allowed
is the filter degree. (ex. 1 means the physical node, or any of its neighbors,
must be present in the genetic network)");
- gridBagConstraints = new java.awt.GridBagConstraints();
- gridBagConstraints.gridy = 2;
- gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
- gridBagConstraints.insets = new java.awt.Insets(0, 0, 3, 0);
- scorePanel.add(degreeLabel, gridBagConstraints);
-
alphaTextField.setPreferredSize(new java.awt.Dimension(50, 25));
alphaTextField.addKeyListener(textFieldKeyListener);
alphaTextField.setToolTipText(alphaLabel.getToolTipText());
gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 2;
+ gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
gridBagConstraints.insets = new java.awt.Insets(0, 0, 3, 0);
scorePanel.add(alphaTextField, gridBagConstraints);
@@ -425,15 +498,27 @@
alphaMultiplierTextField.addKeyListener(textFieldKeyListener);
alphaMultiplierTextField.setToolTipText(alphaMultiplierLabel.getToolTipText());
gridBagConstraints = new java.awt.GridBagConstraints();
- gridBagConstraints.gridy = 1;
+ gridBagConstraints.gridx = 2;
+ gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
gridBagConstraints.insets = new java.awt.Insets(0, 0, 3, 0);
scorePanel.add(alphaMultiplierTextField, gridBagConstraints);
-
+ */
+
+ degreeLabel.setText("Network filter degree (optional):");
+ degreeLabel.setToolTipText("Remove nodes in the physical network which
are distant from any node in the genetic network. The maximum distance allowed
is the filter degree. (ex. 1 means the physical node, or any of its neighbors,
must be present in the genetic network)");
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 1;
+ gridBagConstraints.gridy = 2;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(0, 0, 3, 0);
+ scorePanel.add(degreeLabel, gridBagConstraints);
+
degreeTextField.setPreferredSize(new java.awt.Dimension(50, 25));
degreeTextField.addKeyListener(textFieldKeyListener);
degreeTextField.setToolTipText(degreeLabel.getToolTipText());
gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 2;
gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
gridBagConstraints.insets = new java.awt.Insets(0, 0, 3, 0);
@@ -441,6 +526,7 @@
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.gridx=2;
gridBagConstraints.weightx = 1.0;
scorePanel.add(lbPlaceHolder1, gridBagConstraints);
@@ -453,46 +539,79 @@
//EdgeFilteringPanel
edgeFilteringPanel.setLayout(new java.awt.GridBagLayout());
edgeFilteringPanel.setToolTipText("Specify options for filtering
PanGIA results.");
-
edgeFilteringPanel.setBorder(javax.swing.BorderFactory.createTitledBorder("Edge
Filtering"));
+
edgeFilteringPanel.setBorder(javax.swing.BorderFactory.createTitledBorder("Edge
Reporting"));
+ /*
pValueThresholdLabel.setText("Percentile Threshold:");
pValueThresholdLabel.setToolTipText("The percentile above which edges
should be included in the results.");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
gridBagConstraints.insets = new java.awt.Insets(3, 0, 3, 0);
edgeFilteringPanel.add(pValueThresholdLabel, gridBagConstraints);
-
- pValueThresholdTextField.setToolTipText("The percentile above which
edges should be included in the results.");
- pValueThresholdTextField.addKeyListener(textFieldKeyListener);
+ */
+
+ edgeFilterSliderLabels.setText("More Less");
+ edgeFilterSliderLabels.setToolTipText("Strength of the edge filter. (0
returns all edges)");
+
edgeFilterSliderLabels.setFont(edgeFilterSliderLabels.getFont().deriveFont(12.0f));
+ edgeFilterSliderLabels.setEnabled(false);
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 1;
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTH;
gridBagConstraints.insets = new java.awt.Insets(3, 0, 3, 0);
- pValueThresholdTextField.setPreferredSize(new java.awt.Dimension(50,
25));
+ edgeFilteringPanel.add(edgeFilterSliderLabels, gridBagConstraints);
+
+ edgeFilterSlider.setToolTipText("Strength of the edge filter. (0
returns all edges)");
+ edgeFilterSlider.setPreferredSize(new java.awt.Dimension(200, 25));
+ edgeFilterSlider.setExtent(0);
+ edgeFilterSlider.setMinimum(0);
+ edgeFilterSlider.setMaximum(100);
+ edgeFilterSlider.setValue(90);
+ edgeFilterSlider.setMajorTickSpacing(10);
+ edgeFilterSlider.setMinorTickSpacing(5);
+ edgeFilterSlider.setPaintLabels(false);
+ edgeFilterSlider.setPaintTicks(true);
+ edgeFilterSlider.setPaintTrack(true);
+ edgeFilterSlider.setEnabled(false);
+ edgeFilterSlider.addChangeListener(new
javax.swing.event.ChangeListener() {
+ public void stateChanged(javax.swing.event.ChangeEvent evt) {
+ edgeFilterSliderMoved(evt);
+ }
+ });
gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.insets = new java.awt.Insets(20, 5, 5, 10);
+ gridBagConstraints.gridx = 1;
+ gridBagConstraints.gridy = 1;
gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
- edgeFilteringPanel.add(pValueThresholdTextField, gridBagConstraints);
-
+ edgeFilteringPanel.add(edgeFilterSlider, gridBagConstraints);
+
+ edgeFilterTextField.setToolTipText("Strength of the edge filter. (0
returns all edges)");
+ edgeFilterTextField.addKeyListener(new java.awt.event.KeyListener(){
+ public void keyPressed(java.awt.event.KeyEvent evt){
+ }
+ public void keyTyped(java.awt.event.KeyEvent evt){
+
+ }
+ public void keyReleased(java.awt.event.KeyEvent evt){
+ edgeFilterTextChanged(evt);
+ }
+ });
+ edgeFilterTextField.setPreferredSize(new java.awt.Dimension(50, 25));
gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.insets = new java.awt.Insets(5, 10, 5, 0);
+ gridBagConstraints.gridx = 2;
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ edgeFilteringPanel.add(edgeFilterTextField, gridBagConstraints);
+
+ gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.gridx = 2;
+ gridBagConstraints.gridy = 1;
edgeFilteringPanel.add(lbPlaceHolder2, gridBagConstraints);
- lbNumberOfSamples.setText("Number of samples:");
- lbNumberOfSamples.setToolTipText("The number of random samples to be
used in estimating edge score percentiles.");
gridBagConstraints = new java.awt.GridBagConstraints();
- gridBagConstraints.gridy = 1;
- gridBagConstraints.anchor = java.awt.GridBagConstraints.EAST;
- gridBagConstraints.insets = new java.awt.Insets(3, 0, 3, 0);
- edgeFilteringPanel.add(lbNumberOfSamples, gridBagConstraints);
-
- numberOfSamplesTextField.setText("10000");
- numberOfSamplesTextField.setToolTipText("The number of random samples
to be used in estimating edge score percentiles.");
- numberOfSamplesTextField.addKeyListener(textFieldKeyListener);
- numberOfSamplesTextField.setPreferredSize(new java.awt.Dimension(70,
25));
- gridBagConstraints = new java.awt.GridBagConstraints();
- gridBagConstraints.gridy = 1;
- gridBagConstraints.insets = new java.awt.Insets(3, 0, 3, 0);
- edgeFilteringPanel.add(numberOfSamplesTextField, gridBagConstraints);
-
- gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridy = 3;
gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
gridBagConstraints.weightx = 1.0;
@@ -504,112 +623,107 @@
trainingPanel.setBorder(javax.swing.BorderFactory.createTitledBorder("Annotation"));
trainingPanel.setToolTipText("Specify options for module training and
annotation.");
- trainingLabel.setText("Annotation training:");
- trainingLabel.setToolTipText("Train the edge attribute scores against
a reference annotation.");
+ lbComplexFile.setText("Annotation attribute:");
+ lbComplexFile.setToolTipText("Select the node attribute which provides
annotation information.");
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
gridBagConstraints.gridy = 1;
gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
+ gridBagConstraints.insets = new java.awt.Insets(3, 0, 3, 0);
+ trainingPanel.add(lbComplexFile, gridBagConstraints);
+
+
annotationAttribComboBox.setToolTipText(lbComplexFile.getToolTipText());
+ annotationAttribComboBox.addActionListener(new
java.awt.event.ActionListener() {
+ public void actionPerformed(java.awt.event.ActionEvent evt) {
+ trainingComboBoxActionPerformed(evt);
+ }
+ });
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 2;
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.insets = new java.awt.Insets(3, 0, 3, 5);
+ trainingPanel.add(annotationAttribComboBox, gridBagConstraints);
+
+ trainingLabel.setText("Train PanGIA:");
+ trainingLabel.setToolTipText("Train the edge attribute scores against
a reference annotation.");
+ trainingLabel.setEnabled(false);
+ gridBagConstraints = new java.awt.GridBagConstraints();
+ gridBagConstraints.gridx = 1;
+ gridBagConstraints.gridy = 2;
+ gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
gridBagConstraints.insets = new java.awt.Insets(0, 0, 3, 0);
trainingPanel.add(trainingLabel, gridBagConstraints);
trainingCheckBoxPhysical.setSelected(false);
trainingCheckBoxPhysical.setToolTipText(trainingLabel.getToolTipText());
+ trainingCheckBoxPhysical.setEnabled(false);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
- gridBagConstraints.gridy = 1;
+ gridBagConstraints.gridy = 2;
gridBagConstraints.weightx = 1.0;
gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
gridBagConstraints.insets = new java.awt.Insets(0, 0, 3, 0);
- trainingCheckBoxPhysical.addActionListener(new
java.awt.event.ActionListener() {
- public void actionPerformed(java.awt.event.ActionEvent evt) {
- trainingCheckBoxActionPerformed(evt);
- }
- });
trainingPanel.add(trainingCheckBoxPhysical, gridBagConstraints);
trainingLabelPhysical.setText("Physical");
trainingLabelPhysical.setToolTipText("Train the edge attribute scores
against a reference annotation.");
+ trainingLabelPhysical.setEnabled(false);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
- gridBagConstraints.gridy = 1;
+ gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
gridBagConstraints.insets = new java.awt.Insets(0, 20, 3, 0);
trainingPanel.add(trainingLabelPhysical, gridBagConstraints);
trainingCheckBoxGenetic.setSelected(false);
trainingCheckBoxGenetic.setToolTipText(trainingLabel.getToolTipText());
+ trainingCheckBoxGenetic.setEnabled(false);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
- gridBagConstraints.gridy = 1;
+ gridBagConstraints.gridy = 2;
gridBagConstraints.weightx = 1.0;
gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
gridBagConstraints.insets = new java.awt.Insets(0, 90, 3, 0);
- trainingCheckBoxGenetic.addActionListener(new
java.awt.event.ActionListener() {
- public void actionPerformed(java.awt.event.ActionEvent evt) {
- trainingCheckBoxActionPerformed(evt);
- }
- });
trainingPanel.add(trainingCheckBoxGenetic, gridBagConstraints);
trainingLabelGenetic.setText("Genetic");
trainingLabelGenetic.setToolTipText("Train the edge attribute scores
against a reference annotation.");
+ trainingLabelGenetic.setEnabled(false);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
- gridBagConstraints.gridy = 1;
+ gridBagConstraints.gridy = 2;
gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
gridBagConstraints.insets = new java.awt.Insets(0, 110, 3, 0);
trainingPanel.add(trainingLabelGenetic, gridBagConstraints);
- annotationLabel.setText("Annotation labeling:");
+ annotationLabel.setText("Label modules:");
annotationLabel.setToolTipText("Label the modules using a reference
annotation.");
+ annotationLabel.setEnabled(false);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 1;
- gridBagConstraints.gridy = 2;
+ gridBagConstraints.gridy = 3;
gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
gridBagConstraints.insets = new java.awt.Insets(0, 0, 3, 0);
trainingPanel.add(annotationLabel, gridBagConstraints);
annotationCheckBox.setSelected(false);
annotationCheckBox.setToolTipText(annotationLabel.getToolTipText());
+ annotationCheckBox.setEnabled(false);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 2;
- gridBagConstraints.gridy = 2;
+ gridBagConstraints.gridy = 3;
gridBagConstraints.weightx = 1.0;
gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
gridBagConstraints.insets = new java.awt.Insets(0, 0, 3, 0);
-
annotationCheckBox.addActionListener(new
java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
annotationCheckBoxActionPerformed(evt);
}
});
-
trainingPanel.add(annotationCheckBox, gridBagConstraints);
-
-
- lbComplexFile.setText("Annotation attribute:");
- lbComplexFile.setToolTipText("Select the node attribute which provides
annotation information.");
- lbComplexFile.setEnabled(false);
- gridBagConstraints = new java.awt.GridBagConstraints();
- gridBagConstraints.gridx = 1;
- gridBagConstraints.gridy = 3;
- gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST;
- gridBagConstraints.insets = new java.awt.Insets(3, 0, 3, 0);
- trainingPanel.add(lbComplexFile, gridBagConstraints);
-
- annotationAttribComboBox.setEnabled(false);
-
annotationAttribComboBox.setToolTipText(lbComplexFile.getToolTipText());
- gridBagConstraints = new java.awt.GridBagConstraints();
- gridBagConstraints.gridx = 2;
- gridBagConstraints.gridy = 3;
- gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL;
- gridBagConstraints.weightx = 1.0;
- gridBagConstraints.insets = new java.awt.Insets(3, 0, 3, 5);
- trainingPanel.add(annotationAttribComboBox, gridBagConstraints);
-
-
annotationThresholdLabel.setText("Labeling Threshold:");
annotationThresholdLabel.setToolTipText("Choose a threshold based on
the Jaccard overlap score for annotating modules.");
annotationThresholdLabel.setEnabled(false);
@@ -734,6 +848,52 @@
updateSearchButtonState();
}
+ private void edgeFilterSliderMoved(javax.swing.event.ChangeEvent evt)
+ {
+ if (!edgeFilterSliderEventLock)
+ {
+
edgeFilterTextField.setText(String.valueOf(edgeFilterSlider.getValue()));
+ updateSearchButtonState();
+ }
+ }
+
+ private void complexRewardSliderMoved(javax.swing.event.ChangeEvent evt)
+ {
+ if (!complexRewardSliderEventLock)
+ {
+
complexRewardTextField.setText(String.valueOf(complexRewardSlider.getValue()/601.0*6.0-3.0).substring(0,
4));
+ updateSearchButtonState();
+ }
+ }
+
+ private void edgeFilterTextChanged(java.awt.event.KeyEvent evt)
+ {
+ try
+ {
+ double val =
Double.valueOf(edgeFilterTextField.getText());
+ edgeFilterSliderEventLock = true;
+ edgeFilterSlider.setValue((int)Math.round(val));
+ edgeFilterSliderEventLock = false;
+
//edgeFilterTextField.setText(String.valueOf((int)Math.round(val)));
+ } catch (Exception e){}
+
+ updateSearchButtonState();
+ }
+
+ private void complexRewardTextChanged(java.awt.event.KeyEvent evt)
+ {
+ try
+ {
+ double val =
Double.valueOf(complexRewardTextField.getText());
+ complexRewardSliderEventLock = true;
+
complexRewardSlider.setValue((int)Math.round((val+3.0)*(601/6)));
+ complexRewardSliderEventLock = false;
+ //complexRewardTextField.setText(String.valueOf(val));
+ } catch (Exception e){}
+
+ updateSearchButtonState();
+ }
+
private void
reportPathButtionActionPerformed(java.awt.event.ActionEvent evt) {
JFileChooser reportFileChooser = new JFileChooser(".");
@@ -763,30 +923,62 @@
}
- private void trainingCheckBoxActionPerformed(java.awt.event.ActionEvent
evt)
+ private void trainingComboBoxActionPerformed(java.awt.event.ActionEvent
evt)
{
annotationCheckBoxActionPerformed(evt);
}
private void
annotationCheckBoxActionPerformed(java.awt.event.ActionEvent evt)
{
- boolean needAttrib = trainingCheckBoxPhysical.isSelected() ||
trainingCheckBoxGenetic.isSelected() || annotationCheckBox.isSelected();
+ boolean attribChosen =
annotationAttribComboBox.getSelectedIndex()>=0;
- annotationAttribComboBox.setEnabled(needAttrib);
- lbComplexFile.setEnabled(needAttrib);
+ if (attribChosen)
+ {
+ trainingLabel.setEnabled(true);
+ trainingCheckBoxPhysical.setEnabled(true);
+ trainingLabelPhysical.setEnabled(true);
+ trainingCheckBoxGenetic.setEnabled(true);
+ trainingLabelGenetic.setEnabled(true);
+ annotationLabel.setEnabled(true);
+ annotationCheckBox.setEnabled(true);
+
+ if (annotationCheckBox.isEnabled())
+ {
+
annotationThresholdTextField.setEnabled(annotationCheckBox.isSelected());
+
annotationThresholdLabel.setEnabled(annotationCheckBox.isSelected());
+ }
+ }else
+ {
+ trainingLabel.setEnabled(false);
+ trainingCheckBoxPhysical.setEnabled(false);
+ trainingLabelPhysical.setEnabled(false);
+ trainingCheckBoxGenetic.setEnabled(false);
+ trainingLabelGenetic.setEnabled(false);
+ annotationThresholdTextField.setEnabled(false);
+ annotationThresholdLabel.setEnabled(false);
+ annotationLabel.setEnabled(false);
+ annotationCheckBox.setEnabled(false);
+ }
-
annotationThresholdTextField.setEnabled(annotationCheckBox.isSelected());
-
annotationThresholdLabel.setEnabled(annotationCheckBox.isSelected());
-
updateSearchButtonState();
}
// Variables declaration - do not modify
private javax.swing.JButton aboutButton;
+
+ /*
private javax.swing.JLabel alphaLabel;
private javax.swing.JLabel alphaMultiplierLabel;
private javax.swing.JTextField alphaMultiplierTextField;
private javax.swing.JTextField alphaTextField;
+ */
+
+ private JLabel complexRewardLabel;
+ private boolean complexRewardSliderEventLock = false;
+ private JSlider complexRewardSlider;
+ private JLabel complexRewardSliderLabels;
+ private JTextField complexRewardTextField;
+
private javax.swing.JPanel buttonPanel;
private javax.swing.JButton closeButton;
private javax.swing.JLabel degreeLabel;
@@ -795,13 +987,11 @@
private javax.swing.JPanel edgeFilteringPanel;
private javax.swing.JComboBox geneticEdgeAttribComboBox;
private javax.swing.JLabel geneticEdgeLabel;
- private javax.swing.JLabel lbNumberOfSamples;
private javax.swing.JLabel lbPlaceHolder1;
private javax.swing.JLabel lbPlaceHolder2;
private javax.swing.JLabel lbPlaceHolder3;
- private javax.swing.JTextField numberOfSamplesTextField;
private javax.swing.JLabel pValueThresholdLabel;
- private javax.swing.JTextField pValueThresholdTextField;
+ private javax.swing.JTextField edgeFilterTextField;
private javax.swing.JComboBox physicalEdgeAttribComboBox;
private javax.swing.JLabel physicalEdgeLabel;
private javax.swing.JPanel scorePanel;
@@ -836,6 +1026,10 @@
private String reportPath="";
private JTextArea parameterErrorTextArea;
+
+ private JLabel edgeFilterSliderLabels;
+ private boolean edgeFilterSliderEventLock = false;
+ private JSlider edgeFilterSlider;
// End of variables declaration
@@ -942,22 +1136,24 @@
parameters.setPhysicalScalingMethod((String)phyScalingMethodComboBox.getSelectedItem());
parameters.setGeneticScalingMethod((String)genScalingMethodComboBox.getSelectedItem());
-
parameters.setAlpha(Double.parseDouble(alphaTextField.getText()));
+
//parameters.setAlpha(Double.parseDouble(alphaTextField.getText()));
+
//parameters.setAlphaMultiplier(Double.parseDouble(alphaMultiplierTextField.getText()));
+
parameters.setAlpha(Math.abs(Double.parseDouble(complexRewardTextField.getText())));
+
parameters.setAlphaMultiplier(Double.parseDouble(complexRewardTextField.getText()));
-
parameters.setAlphaMultiplier(Double.parseDouble(alphaMultiplierTextField.getText()));
-
final String degree = degreeTextField.getText();
if (degree.length() > 0)
parameters.setPhysicalNetworkFilterDegree(Integer.parseInt(degree));
else parameters.setPhysicalNetworkFilterDegree(-1);
- if (pValueThresholdTextField.isEnabled())
+ if (edgeFilterTextField.isEnabled())
{
- final double pValueThreshold =
Double.parseDouble(pValueThresholdTextField.getText());
+ final double pValueThreshold =
Double.parseDouble(edgeFilterTextField.getText());
parameters.setPValueThreshold(pValueThreshold);
}else parameters.setPValueThreshold(Double.NaN);
- final int numberOfSamples =
Integer.parseInt(numberOfSamplesTextField.getText());
- parameters.setNumberOfSamples(numberOfSamples);
+ //final int numberOfSamples =
Integer.parseInt(numberOfSamplesTextField.getText());
+ //parameters.setNumberOfSamples(numberOfSamples);
+ parameters.setNumberOfSamples(1000);
parameters.setAnnotationThreshold(Double.valueOf(annotationThresholdTextField.getText()));
parameters.setComplexAnnotation(annotationCheckBox.isSelected());
@@ -997,16 +1193,20 @@
if (geneticAttrName==null ||
geneticAttrName.equals(DEFAULT_ATTRIBUTE))
{
- lbNumberOfSamples.setEnabled(false);
- numberOfSamplesTextField.setEnabled(false);
+ //lbNumberOfSamples.setEnabled(false);
+ //numberOfSamplesTextField.setEnabled(false);
+ edgeFilterSliderLabels.setEnabled(false);
+ edgeFilterSlider.setEnabled(false);
pValueThresholdLabel.setEnabled(false);
- pValueThresholdTextField.setEnabled(false);
+ edgeFilterTextField.setEnabled(false);
}else
{
- lbNumberOfSamples.setEnabled(true);
- numberOfSamplesTextField.setEnabled(true);
+ edgeFilterSliderLabels.setEnabled(true);
+ edgeFilterSlider.setEnabled(true);
+ //lbNumberOfSamples.setEnabled(true);
+ //numberOfSamplesTextField.setEnabled(true);
pValueThresholdLabel.setEnabled(true);
- pValueThresholdTextField.setEnabled(true);
+ edgeFilterTextField.setEnabled(true);
}
}
@@ -1079,6 +1279,7 @@
//TextField validity
+ /*
try{Double.parseDouble(alphaTextField.getText());}
catch (NumberFormatException e)
{
@@ -1093,8 +1294,25 @@
searchButton.setEnabled(false);
parameterErrorTextArea.setText("Please choose a valid
value for Beta.");
return;
+ }*/
+
+
+ try{Double.parseDouble(complexRewardTextField.getText());}
+ catch (NumberFormatException e)
+ {
+ searchButton.setEnabled(false);
+ parameterErrorTextArea.setText("Please choose a valid
value for module size.");
+ return;
}
+ if (Double.parseDouble(complexRewardTextField.getText())<-3 ||
Double.parseDouble(complexRewardTextField.getText())>3)
+ {
+ searchButton.setEnabled(false);
+ parameterErrorTextArea.setText("Please set module size
in the range [-3,3].");
+ return;
+ }
+
+
if (degreeTextField.getText().length()>0)
{
try
@@ -1118,7 +1336,7 @@
try
{
- double p =
Double.parseDouble(pValueThresholdTextField.getText());
+ double p =
Double.parseDouble(edgeFilterTextField.getText());
if (p<0 || p>100)
{
searchButton.setEnabled(false);
@@ -1134,6 +1352,7 @@
return;
}
+ /*
try
{
int n =
Integer.parseInt(numberOfSamplesTextField.getText());
@@ -1150,7 +1369,7 @@
searchButton.setEnabled(false);
parameterErrorTextArea.setText("Please choose a valid
value for number of samples.");
return;
- }
+ }*/
if (annotationCheckBox.isSelected())
Added:
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/utilities/NumberFormatter.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/utilities/NumberFormatter.java
(rev 0)
+++
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/utilities/NumberFormatter.java
2010-09-02 22:06:45 UTC (rev 21674)
@@ -0,0 +1,12 @@
+package org.idekerlab.PanGIAPlugin.utilities;
+
+import java.text.NumberFormat;
+
+public class NumberFormatter
+{
+ public static String formatNumber(Number n, int decimals)
+ {
+ String ns = NumberFormat.getInstance().format(n);
+ return ns.substring(0,Math.min(ns.length()-1,
ns.indexOf(".")+decimals+1));
+ }
+}
--
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