Author: kono
Date: 2010-01-12 10:47:44 -0800 (Tue, 12 Jan 2010)
New Revision: 18873
Removed:
csplugins/trunk/ucsd/ruschein/DenovoPGNetworkAlignment/src/org/cytoscape/DenovoPGNetworkAlignmentPlugin/SearchPanel.java
Modified:
csplugins/trunk/ucsd/ruschein/DenovoPGNetworkAlignment/src/org/cytoscape/DenovoPGNetworkAlignmentPlugin/SearchTask.java
csplugins/trunk/ucsd/ruschein/DenovoPGNetworkAlignment/src/org/cytoscape/DenovoPGNetworkAlignmentPlugin/ui/SearchPropertyPanel.java
Log:
Search runs from GUI.
Deleted:
csplugins/trunk/ucsd/ruschein/DenovoPGNetworkAlignment/src/org/cytoscape/DenovoPGNetworkAlignmentPlugin/SearchPanel.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/DenovoPGNetworkAlignment/src/org/cytoscape/DenovoPGNetworkAlignmentPlugin/SearchPanel.java
2010-01-12 18:05:28 UTC (rev 18872)
+++
csplugins/trunk/ucsd/ruschein/DenovoPGNetworkAlignment/src/org/cytoscape/DenovoPGNetworkAlignmentPlugin/SearchPanel.java
2010-01-12 18:47:44 UTC (rev 18873)
@@ -1,560 +0,0 @@
-package org.cytoscape.DenovoPGNetworkAlignmentPlugin;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-import java.beans.PropertyChangeSupport;
-import java.beans.PropertyChangeListener;
-import java.beans.PropertyChangeEvent;
-import java.util.*;
-import java.io.File;
-import cytoscape.Cytoscape;
-import cytoscape.CyNetwork;
-import cytoscape.util.FileUtil;
-import cytoscape.view.cytopanels.CytoPanel;
-
-public class SearchPanel extends JPanel
-{
- JTextField classFileField;
- File classFile = null;
- JTextField expressionMatrixFileField;
- File expressionMatrixFile = null;
- JComboBox networkComboBox;
- JComboBox scoreModelComboBox;
- JSpinner numOfTrialsSpinner;
- JSpinner st1Spinner;
- JSpinner st2Spinner;
- JSpinner st3Spinner;
- JSpinner st3TrialsSpinner;
- JSpinner maxNodeDegreeSpinner;
- JSpinner minImprovementSpinner;
- JSpinner maxModuleSizeSpinner;
- JSpinner maxRadiusSpinner;
- JButton searchButton;
-
- public SearchPanel()
- {
- setLayout(new GridBagLayout());
-
- JLabel classFileLabel = new JLabel("Class file:");
- classFileField = new JTextField("None chosen");
- classFileField.setEditable(false);
- JButton classFileButton = new JButton("Choose...");
- classFileButton.addActionListener(new ChooseClassFileAction());
- JLabel expressionMatrixFileLabel = new JLabel("Expression
matrix file:");
- expressionMatrixFileField = new JTextField("None chosen");
- expressionMatrixFileField.setEditable(false);
- JButton expressionMatrixFileButton = new JButton("Choose...");
- expressionMatrixFileButton.addActionListener(new
ChooseExpressionMatrixFileAction());
- JLabel networkLabel = new JLabel("Network:");
- networkComboBox = new JComboBox();
- loadNetworks();
- {
- JPanel filePanel = new JPanel(new GridBagLayout());
- GridBagConstraints c = new GridBagConstraints();
- c.anchor = GridBagConstraints.FIRST_LINE_START;
- c.insets = new Insets(5,5,5,5);
-
- c.gridx = 0; c.gridy = 0;
- c.gridwidth = 1; c.gridheight = 1;
- c.fill = GridBagConstraints.NONE;
- c.weightx = 0.0; c.weighty = 0.0;
- filePanel.add(classFileLabel, c);
-
- c.gridx = 1; c.gridy = 0;
- c.gridwidth = 1; c.gridheight = 1;
- c.fill = GridBagConstraints.HORIZONTAL;
- c.weightx = 1.0; c.weighty = 0.0;
- filePanel.add(classFileField, c);
-
- c.gridx = 2; c.gridy = 0;
- c.gridwidth = 1; c.gridheight = 1;
- c.fill = GridBagConstraints.NONE;
- c.weightx = 0.0; c.weighty = 0.0;
- filePanel.add(classFileButton, c);
-
- c.gridx = 0; c.gridy = 1;
- c.gridwidth = 1; c.gridheight = 1;
- c.fill = GridBagConstraints.NONE;
- c.weightx = 0.0; c.weighty = 0.0;
- filePanel.add(expressionMatrixFileLabel, c);
-
- c.gridx = 1; c.gridy = 1;
- c.gridwidth = 1; c.gridheight = 1;
- c.fill = GridBagConstraints.HORIZONTAL;
- c.weightx = 1.0; c.weighty = 0.0;
- filePanel.add(expressionMatrixFileField, c);
-
- c.gridx = 2; c.gridy = 1;
- c.gridwidth = 1; c.gridheight = 1;
- c.fill = GridBagConstraints.NONE;
- c.weightx = 0.0; c.weighty = 0.0;
- filePanel.add(expressionMatrixFileButton, c);
-
- c.gridx = 0; c.gridy = 2;
- c.gridwidth = 1; c.gridheight = 1;
- c.fill = GridBagConstraints.NONE;
- c.weightx = 0.0; c.weighty = 0.0;
- filePanel.add(networkLabel, c);
-
- c.gridx = 1; c.gridy = 2;
- c.gridwidth = 2; c.gridheight = 1;
- c.fill = GridBagConstraints.HORIZONTAL;
- c.weightx = 1.0; c.weighty = 0.0;
- filePanel.add(networkComboBox, c);
-
- c.gridx = 0; c.gridy = 0;
- c.gridwidth = 1; c.gridheight = 1;
- c.fill = GridBagConstraints.HORIZONTAL;
- c.weightx = 1.0; c.weighty = 0.0;
- add(filePanel, c);
- }
-
- JSeparator separator0 = new JSeparator();
- {
- GridBagConstraints c = new GridBagConstraints();
- c.insets = new Insets(5,5,5,5);
- c.gridx = 0; c.gridy = 1;
- c.gridwidth = 1; c.gridheight = 1;
- c.fill = GridBagConstraints.HORIZONTAL;
- c.weightx = 1.0; c.weighty = 0.0;
- add(separator0, c);
- }
-
- JLabel scoreModelLabel = new JLabel("Score model:");
- String[] scoreModelOptions = {"Mutual Information", "T Test"};
- scoreModelComboBox = new JComboBox(scoreModelOptions);
- {
- JPanel scoreModelPanel = new JPanel(new
FlowLayout(FlowLayout.LEFT));
- scoreModelPanel.add(scoreModelLabel);
- scoreModelPanel.add(scoreModelComboBox);
-
- GridBagConstraints c = new GridBagConstraints();
- c.insets = new Insets(5,5,5,5);
- c.gridx = 0; c.gridy = 2;
- c.gridwidth = 1; c.gridheight = 1;
- c.fill = GridBagConstraints.HORIZONTAL;
- c.weightx = 1.0; c.weighty = 0.0;
- add(scoreModelPanel, c);
- }
-
- JLabel numOfTrialsLabel = new JLabel("Number of random
trials:");
- numOfTrialsSpinner = newIntSpinner(100);
- {
- JPanel numOfTrialsPanel = new JPanel(new
FlowLayout(FlowLayout.LEFT));
- numOfTrialsPanel.add(numOfTrialsLabel);
- numOfTrialsPanel.add(numOfTrialsSpinner);
-
- GridBagConstraints c = new GridBagConstraints();
- c.insets = new Insets(5,5,5,5);
- c.gridx = 0; c.gridy = 3;
- c.gridwidth = 1; c.gridheight = 1;
- c.fill = GridBagConstraints.HORIZONTAL;
- c.weightx = 1.0; c.weighty = 0.0;
- add(numOfTrialsPanel, c);
- }
-
- JLabel st1Label = new JLabel("ST1 P-value cutoff:");
- st1Spinner = newDoubleSpinner(0.05);
- JLabel st2Label = new JLabel("ST2 P-value cutoff:");
- st2Spinner = newDoubleSpinner(0.05);
- JLabel st3Label = new JLabel("ST3 P-value cutoff:");
- st3Spinner = newDoubleSpinner(0.00005);
- JLabel st3TrialsLabel = new JLabel("Number of ST3 trials:");
- st3TrialsSpinner = newIntSpinner(20000);
- {
- JPanel testsPanel = new JPanel(new GridBagLayout());
-
testsPanel.setBorder(BorderFactory.createTitledBorder("Statistical Tests"));
-
- {
- JPanel st1Panel = new JPanel(new
FlowLayout(FlowLayout.LEFT));
- st1Panel.add(st1Label);
- st1Panel.add(st1Spinner);
-
- GridBagConstraints c = new GridBagConstraints();
- c.insets = new Insets(5,5,5,5);
- c.gridwidth = 1; c.gridheight = 1;
- c.gridx = 0; c.gridy = 0;
- c.fill = GridBagConstraints.HORIZONTAL;
- c.weightx = 1.0; c.weighty = 0.0;
-
- testsPanel.add(st1Panel, c);
- }
-
- {
- JPanel st2Panel = new JPanel(new
FlowLayout(FlowLayout.LEFT));
- st2Panel.add(st2Label);
- st2Panel.add(st2Spinner);
-
- GridBagConstraints c = new GridBagConstraints();
- c.insets = new Insets(5,5,5,5);
- c.gridwidth = 1; c.gridheight = 1;
- c.gridx = 0; c.gridy = 1;
- c.fill = GridBagConstraints.HORIZONTAL;
- c.weightx = 1.0; c.weighty = 0.0;
-
- testsPanel.add(st2Panel, c);
- }
-
- {
- JPanel st3Panel = new JPanel(new
FlowLayout(FlowLayout.LEFT));
- st3Panel.add(st3Label);
- st3Panel.add(st3Spinner);
-
- GridBagConstraints c = new GridBagConstraints();
- c.insets = new Insets(5,5,5,5);
- c.gridwidth = 1; c.gridheight = 1;
- c.gridx = 0; c.gridy = 2;
- c.fill = GridBagConstraints.HORIZONTAL;
- c.weightx = 1.0; c.weighty = 0.0;
-
- testsPanel.add(st3Panel, c);
- }
-
- {
- JPanel st3TrialsPanel = new JPanel(new
FlowLayout(FlowLayout.LEFT));
- st3TrialsPanel.add(st3TrialsLabel);
- st3TrialsPanel.add(st3TrialsSpinner);
-
- GridBagConstraints c = new GridBagConstraints();
- c.insets = new Insets(5,5,5,5);
- c.gridwidth = 1; c.gridheight = 1;
- c.gridx = 0; c.gridy = 3;
- c.fill = GridBagConstraints.HORIZONTAL;
- c.weightx = 1.0; c.weighty = 0.0;
-
- testsPanel.add(st3TrialsPanel, c);
- }
-
- GridBagConstraints c = new GridBagConstraints();
- c.anchor = GridBagConstraints.FIRST_LINE_START;
- c.insets = new Insets(5,5,5,5);
- c.gridwidth = 1; c.gridheight = 1;
- c.gridx = 0; c.gridy = 4;
- c.fill = GridBagConstraints.HORIZONTAL;
- c.weightx = 1.0; c.weighty = 0.0;
- add(testsPanel, c);
- }
-
- JLabel maxNodeDegreeLabel = new JLabel("Max node degree:");
- maxNodeDegreeSpinner = newIntSpinner(200);
- JLabel minImprovementLabel = new JLabel("Min improvement:");
- minImprovementSpinner = newDoubleSpinner(0.05, 0.0);
- JLabel maxModuleSizeLabel = new JLabel("Max module size:");
- maxModuleSizeSpinner = newIntSpinner(20);
- JLabel maxRadiusLabel = new JLabel("Max radius:");
- maxRadiusSpinner = newIntSpinner(0,2);
- JLabel infLabel = new JLabel("(set radius to 0 for infinite
radius)");
- {
- JPanel searchPanel = new JPanel(new GridBagLayout());
-
searchPanel.setBorder(BorderFactory.createTitledBorder("Search"));
-
- {
- JPanel maxNodeDegreePanel = new JPanel(new
FlowLayout(FlowLayout.LEFT));
- maxNodeDegreePanel.add(maxNodeDegreeLabel);
- maxNodeDegreePanel.add(maxNodeDegreeSpinner);
-
- GridBagConstraints c = new GridBagConstraints();
- c.insets = new Insets(5,5,5,5);
- c.gridwidth = 1; c.gridheight = 1;
- c.gridx = 0; c.gridy = 0;
- c.fill = GridBagConstraints.HORIZONTAL;
- c.weightx = 1.0; c.weighty = 0.0;
-
- searchPanel.add(maxNodeDegreePanel, c);
- }
-
- {
- JPanel minImprovementPanel = new JPanel(new
FlowLayout(FlowLayout.LEFT));
- minImprovementPanel.add(minImprovementLabel);
- minImprovementPanel.add(minImprovementSpinner);
-
- GridBagConstraints c = new GridBagConstraints();
- c.insets = new Insets(5,5,5,5);
- c.gridwidth = 1; c.gridheight = 1;
- c.gridx = 0; c.gridy = 1;
- c.fill = GridBagConstraints.HORIZONTAL;
- c.weightx = 1.0; c.weighty = 0.0;
-
- searchPanel.add(minImprovementPanel, c);
- }
-
- {
- JPanel maxModuleSizePanel = new JPanel(new
FlowLayout(FlowLayout.LEFT));
- maxModuleSizePanel.add(maxModuleSizeLabel);
- maxModuleSizePanel.add(maxModuleSizeSpinner);
-
- GridBagConstraints c = new GridBagConstraints();
- c.insets = new Insets(5,5,5,5);
- c.gridwidth = 1; c.gridheight = 1;
- c.gridx = 0; c.gridy = 2;
- c.fill = GridBagConstraints.HORIZONTAL;
- c.weightx = 1.0; c.weighty = 0.0;
-
- searchPanel.add(maxModuleSizePanel, c);
- }
-
- {
- JPanel maxRadiusPanel = new JPanel(new
FlowLayout(FlowLayout.LEFT));
- maxRadiusPanel.add(maxRadiusLabel);
- maxRadiusPanel.add(maxRadiusSpinner);
- maxRadiusPanel.add(infLabel);
-
- GridBagConstraints c = new GridBagConstraints();
- c.insets = new Insets(5,5,5,5);
- c.gridwidth = 1; c.gridheight = 1;
- c.gridx = 0; c.gridy = 3;
- c.fill = GridBagConstraints.HORIZONTAL;
- c.weightx = 1.0; c.weighty = 0.0;
- searchPanel.add(maxRadiusPanel, c);
-
- }
-
- GridBagConstraints c = new GridBagConstraints();
- c.anchor = GridBagConstraints.FIRST_LINE_START;
- c.insets = new Insets(5,5,5,5);
- c.gridwidth = 1; c.gridheight = 1;
- c.gridx = 0; c.gridy = 5;
- c.fill = GridBagConstraints.HORIZONTAL;
- c.weightx = 1.0; c.weighty = 0.0;
- add(searchPanel, c);
- }
-
- searchButton = new JButton("Search");
- updateSearchButton();
- JButton closeButton = new JButton("Close");
- closeButton.addActionListener(new CloseAction());
- {
- JPanel buttonsPanel = new JPanel(new
FlowLayout(FlowLayout.RIGHT));
- buttonsPanel.add(closeButton);
- buttonsPanel.add(searchButton);
-
- GridBagConstraints c = new GridBagConstraints();
- c.insets = new Insets(5,5,5,5);
- c.anchor = GridBagConstraints.LAST_LINE_END;
- c.gridwidth = 1; c.gridheight = 1;
- c.gridx = 0; c.gridy = 6;
- c.fill = GridBagConstraints.NONE;
- c.weightx = 1.0; c.weighty = 1.0;
- add(buttonsPanel, c);
- }
-
- NetworkChangeListener networkChangeListener = new
NetworkChangeListener();
-
Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(Cytoscape.NETWORK_CREATED,
networkChangeListener);
-
Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(Cytoscape.NETWORK_DESTROYED,
networkChangeListener);
- }
-
- private JSpinner newDoubleSpinner(double defaultValue)
- {
- return newDoubleSpinner(defaultValue, Double.MIN_VALUE);
- }
-
- private JSpinner newDoubleSpinner(double defaultValue, double minValue)
- {
- return newNumberSpinner(new SpinnerNumberModel(defaultValue,
minValue, 1.0, 0.01));
- }
-
- private JSpinner newIntSpinner(int defaultValue)
- {
- return newIntSpinner(1, defaultValue);
- }
-
- private JSpinner newIntSpinner(int minValue, int defaultValue)
- {
- return newNumberSpinner(new SpinnerNumberModel(defaultValue,
minValue, Integer.MAX_VALUE, 1));
- }
-
- private JSpinner newNumberSpinner(SpinnerNumberModel numberModel)
- {
- JSpinner spinner = new JSpinner();
- spinner.setModel(numberModel);
- new JSpinner.NumberEditor(spinner);
- ((JSpinner.DefaultEditor)
spinner.getEditor()).getTextField().setColumns(5);
- ((JSpinner.NumberEditor)
spinner.getEditor()).getFormat().setMaximumFractionDigits(9);
- return spinner;
- }
-
- class Network
- {
- public CyNetwork network;
-
- public Network(CyNetwork network)
- {
- this.network = network;
- }
-
- public String toString()
- {
- return network.getTitle();
- }
-
- public boolean equals(final Network other)
- {
- if (other == null) return false;
- return this.network.equals(other.network);
- }
- }
-
- private void loadNetworks()
- {
- Network selectedNetwork = null;
- Object selectedItem = networkComboBox.getSelectedItem();
- if (selectedItem != null && selectedItem instanceof Network)
- selectedNetwork = (Network) selectedItem;
-
- networkComboBox.removeAllItems();
- Iterator networks = Cytoscape.getNetworkSet().iterator();
- int selectedIndex = -1;
- while (networks.hasNext())
- {
- Network newNetwork = new Network((CyNetwork)
networks.next());
- networkComboBox.addItem(newNetwork);
- if (newNetwork.equals(selectedNetwork))
- selectedIndex = networkComboBox.getItemCount()
- 1;
- }
- if (networkComboBox.getItemCount() == 0)
- {
- networkComboBox.addItem("No networks are available");
- networkComboBox.setEnabled(false);
- }
- else
- {
- networkComboBox.setEnabled(true);
- if (selectedIndex != -1)
- networkComboBox.setSelectedIndex(selectedIndex);
- }
- }
-
- private void updateSearchButton()
- {
- searchButton.setEnabled(false);
- if (classFile == null)
- searchButton.setToolTipText("A class file must be
selected before searching.");
- else if (expressionMatrixFile == null)
- searchButton.setToolTipText("An expression matrix file
must be selected before searching.");
- else if (networkComboBox.getItemCount() == 0)
- searchButton.setToolTipText("There must be at least one
network available before searching.");
- else
- {
- searchButton.setEnabled(true);
- searchButton.setToolTipText(null);
- }
- }
-
- class ChooseClassFileAction implements ActionListener
- {
- public void actionPerformed(ActionEvent e)
- {
- File file = FileUtil.getFile("DenovoPGNetworkAlignment:
Open class file", FileUtil.LOAD);
- if (file != null)
- {
- classFile = file;
- classFileField.setText(classFile.getPath());
- }
- updateSearchButton();
- }
- }
-
- class ChooseExpressionMatrixFileAction implements ActionListener
- {
- public void actionPerformed(ActionEvent e)
- {
- File file = FileUtil.getFile("DenovoPGNetworkAlignment:
Open expression matrix file", FileUtil.LOAD);
- if (file != null)
- {
- expressionMatrixFile = file;
-
expressionMatrixFileField.setText(expressionMatrixFile.getPath());
- }
- updateSearchButton();
- }
- }
-
- class CloseAction implements ActionListener
- {
- public void actionPerformed(ActionEvent e)
- {
- CytoPanel cytoPanel =
Cytoscape.getDesktop().getCytoPanel(SwingConstants.WEST);
- cytoPanel.remove(SearchPanel.this);
- }
- }
-
- class NetworkChangeListener implements PropertyChangeListener
- {
- public void propertyChange(PropertyChangeEvent event)
- {
- loadNetworks();
- updateSearchButton();
- }
- }
-
- public void addSearchActionListener(ActionListener l)
- {
- searchButton.addActionListener(l);
- }
-
- public File getClassFile()
- {
- return classFile;
- }
-
- public File getExpressionMatrixFile()
- {
- return expressionMatrixFile;
- }
-
- public CyNetwork getNetwork()
- {
- return ((Network) networkComboBox.getSelectedItem()).network;
- }
-
- public String getScoreModel()
- {
- return (String) scoreModelComboBox.getSelectedItem();
- }
-
- public int getNumOfTrials()
- {
- return ((Number) numOfTrialsSpinner.getValue()).intValue();
- }
-
- public double getST1Cutoff()
- {
- return ((Number) st1Spinner.getValue()).doubleValue();
- }
-
- public double getST2Cutoff()
- {
- return ((Number) st2Spinner.getValue()).doubleValue();
- }
-
- public double getST3Cutoff()
- {
- return ((Number) st3Spinner.getValue()).doubleValue();
- }
-
- public int getNumOfST3Trials()
- {
- return ((Number) st3TrialsSpinner.getValue()).intValue();
- }
-
- public int getMaxNodeDegree()
- {
- return ((Number) maxNodeDegreeSpinner.getValue()).intValue();
- }
-
- public double getMinImprovement()
- {
- return ((Number)
minImprovementSpinner.getValue()).doubleValue();
- }
-
- public int getMaxModuleSize()
- {
- return ((Number) maxModuleSizeSpinner.getValue()).intValue();
- }
-
- public int getMaxRadius()
- {
- int maxRadius = ((Number)
maxRadiusSpinner.getValue()).intValue();
- return (maxRadius == 0 ? Integer.MAX_VALUE : maxRadius);
- }
-}
Modified:
csplugins/trunk/ucsd/ruschein/DenovoPGNetworkAlignment/src/org/cytoscape/DenovoPGNetworkAlignmentPlugin/SearchTask.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/DenovoPGNetworkAlignment/src/org/cytoscape/DenovoPGNetworkAlignmentPlugin/SearchTask.java
2010-01-12 18:05:28 UTC (rev 18872)
+++
csplugins/trunk/ucsd/ruschein/DenovoPGNetworkAlignment/src/org/cytoscape/DenovoPGNetworkAlignmentPlugin/SearchTask.java
2010-01-12 18:47:44 UTC (rev 18873)
@@ -1,46 +1,45 @@
package org.cytoscape.DenovoPGNetworkAlignmentPlugin;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.swing.SwingConstants;
-
-import cytoscape.Cytoscape;
+import networks.denovoPGNetworkAlignment.BFEdge;
+import networks.denovoPGNetworkAlignment.HCScoringFunction;
+import networks.denovoPGNetworkAlignment.HCSearch2;
+import networks.denovoPGNetworkAlignment.SouravScore;
+import networks.linkedNetworks.TypedLinkNetwork;
+import networks.linkedNetworks.TypedLinkNodeModule;
import cytoscape.task.Task;
import cytoscape.task.TaskMonitor;
-import cytoscape.view.cytopanels.CytoPanel;
-import cytoscape.view.cytopanels.CytoPanelState;
public class SearchTask implements Task {
private TaskMonitor taskMonitor = null;
boolean needsToHalt = false;
static int numOfRuns = 1;
-
+
private SearchParameters parameters;
+ private HCScoringFunction hcScoringFunction;
+
public SearchTask(final SearchParameters parameters) {
this.parameters = parameters;
}
public void run() {
setPercentCompleted(0);
- setStatus("Searching...");
+ setStatus("Searching complexes...");
+ final ConvertCyNetworkToSFNetworks converter = new
ConvertCyNetworkToSFNetworks(
+ parameters.getNetwork(),
parameters.getPhysicalEdgeAttrName(),
+ parameters.getGeneticEdgeAttrName());
+ hcScoringFunction = new
SouravScore(converter.getPhysicalNetwork(),
+ converter.getGeneticNetwork(), (float)
parameters.getAlpha(),
+ (float) parameters.getAlphaMultiplier());
+ hcScoringFunction.Initialize(converter.getPhysicalNetwork(),
converter
+ .getGeneticNetwork());
+ final TypedLinkNetwork<TypedLinkNodeModule<String, BFEdge>,
BFEdge> results = HCSearch2
+ .search(converter.getPhysicalNetwork(),
converter.getGeneticNetwork(), hcScoringFunction);
+ setStatus("Search finished!");
+ setPercentCompleted(100);
- //
- // Stage 1.C: Read network file
- //
-
- List<Result> results = new ArrayList<Result>();
- ResultsPanel resultsPanel = new ResultsPanel(null, results);
- resultsPanel.setVisible(true);
- CytoPanel cytoPanel = Cytoscape.getDesktop().getCytoPanel(
- SwingConstants.EAST);
- cytoPanel.add("DenovoPGNetworkAlignment Results " +
(numOfRuns++),
- resultsPanel);
-
cytoPanel.setSelectedIndex(cytoPanel.indexOfComponent(resultsPanel));
- cytoPanel.setState(CytoPanelState.DOCK);
}
public void halt() {
Modified:
csplugins/trunk/ucsd/ruschein/DenovoPGNetworkAlignment/src/org/cytoscape/DenovoPGNetworkAlignmentPlugin/ui/SearchPropertyPanel.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/DenovoPGNetworkAlignment/src/org/cytoscape/DenovoPGNetworkAlignmentPlugin/ui/SearchPropertyPanel.java
2010-01-12 18:05:28 UTC (rev 18872)
+++
csplugins/trunk/ucsd/ruschein/DenovoPGNetworkAlignment/src/org/cytoscape/DenovoPGNetworkAlignmentPlugin/ui/SearchPropertyPanel.java
2010-01-12 18:47:44 UTC (rev 18873)
@@ -1,7 +1,6 @@
package org.cytoscape.DenovoPGNetworkAlignmentPlugin.ui;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
+import java.awt.Dimension;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
import java.util.Arrays;
@@ -43,6 +42,7 @@
/** Creates new form SearchPropertyPanel */
public SearchPropertyPanel() {
initComponents();
+ this.setMinimumSize(new Dimension(370, 450));
Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(this);
Cytoscape.getEdgeAttributes().getMultiHashMapDefinition()
@@ -469,12 +469,12 @@
// Run search algorithm
JTaskConfig jTaskConfig = new JTaskConfig();
- jTaskConfig.displayCancelButton(true);
- jTaskConfig.displayCloseButton(false);
+ jTaskConfig.displayCancelButton(false);
+ jTaskConfig.displayCloseButton(true);
jTaskConfig.displayStatus(true);
jTaskConfig.displayTimeElapsed(true);
jTaskConfig.displayTimeRemaining(false);
- jTaskConfig.setAutoDispose(true);
+ jTaskConfig.setAutoDispose(false);
jTaskConfig.setModal(true);
jTaskConfig.setOwner(Cytoscape.getDesktop());
TaskManager.executeTask(new SearchTask(parameters),
jTaskConfig);
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