Author: kono
Date: 2010-02-16 18:35:39 -0800 (Tue, 16 Feb 2010)
New Revision: 19345
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules3/src/csplugins/jActiveModules/ActiveModulesUI.java
csplugins/trunk/ucsd/pwang/jActiveModules3/src/csplugins/jActiveModules/dialogs/ActivePathsParameterPanel.java
Log:
Fixed lots of layout code. Also, NetworkSelectorPalen had been added to select
target network.
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules3/src/csplugins/jActiveModules/ActiveModulesUI.java
===================================================================
---
csplugins/trunk/ucsd/pwang/jActiveModules3/src/csplugins/jActiveModules/ActiveModulesUI.java
2010-02-17 00:22:50 UTC (rev 19344)
+++
csplugins/trunk/ucsd/pwang/jActiveModules3/src/csplugins/jActiveModules/ActiveModulesUI.java
2010-02-17 02:35:39 UTC (rev 19345)
@@ -11,6 +11,7 @@
import javax.swing.AbstractAction;
import javax.swing.JMenuItem;
import javax.swing.JOptionPane;
+import javax.swing.JPanel;
import javax.swing.SwingConstants;
import csplugins.jActiveModules.data.ActivePathFinderParameters;
@@ -33,12 +34,16 @@
protected ActivePathFinderParameters apfParams;
protected ThreadExceptionHandler xHandler;
+ private ActivePathsParameterPanel mainPanel;
+
public ActiveModulesUI() {
System.out.println("Starting jActiveModules plugin!\n");
final JMenuItem menuItem = new JMenuItem("jActiveModules...");
- menuItem.addActionListener(new SetParametersAction());
-
Cytoscape.getDesktop().getCyMenus().getMenuBar().getMenu("Plugins.Module
Finders...").add(menuItem);
+ menuItem.addActionListener(new SetParametersAction());
+
+ Cytoscape.getDesktop().getCyMenus().getMenuBar().
+ getMenu("Plugins.Module Finders...").add(menuItem);
/* initialize variables */
apfParams = new ActivePathFinderParameters(CytoscapeInit
@@ -57,9 +62,9 @@
if (evt.getPropertyName() == Cytoscape.CYTOSCAPE_INITIALIZED
&& apfParams.getRun()) {
if (apfParams.getRandomizeExpression()) {
-
startRandomizeAndRun(Cytoscape.getCurrentNetwork());
+
startRandomizeAndRun(mainPanel.getTargetNetwork());
} else {
- activePaths = new
ActivePaths(Cytoscape.getCurrentNetwork(),
+ activePaths = new
ActivePaths(mainPanel.getTargetNetwork(),
apfParams, this);
Thread t = new Thread(activePaths);
t.start();
@@ -72,7 +77,8 @@
* jActiveModules, wiht a gui interface
*/
protected class SetParametersAction extends AbstractAction {
- private ActivePathsParameterPanel paramsDialog = null;
+
+ private static final long serialVersionUID =
-7836213413255212288L;
public SetParametersAction() {
super("jActiveModules");
@@ -83,25 +89,24 @@
JOptionPane
.showMessageDialog(
Cytoscape.getDesktop(),
- "JActiveModules
cannot start because it cannot find\n" +
- "any p-value
attributes! JActiveModules requires at\n" +
- "least one node
attribute with values ranging between\n" +
- "0 and 1 of
type 'float' (i.e. decimal or real number).\n" +
- "Please load an
appropriate attribute and try again.",
+ "JActiveModules
cannot start because it cannot find\n"
+
+ "any p-value attributes! JActiveModules requires at\n"
+
+ "least one node attribute with values ranging between\n"
+
+ "0 and 1 of type 'float' (i.e. decimal or real number).\n"
+
+ "Please load an appropriate attribute and try again.",
"jActiveModules", JOptionPane.ERROR_MESSAGE);
return;
}
final CytoPanel cytoPanel =
Cytoscape.getDesktop().getCytoPanel(
SwingConstants.WEST);
- if (paramsDialog == null) {
- paramsDialog = new ActivePathsParameterPanel(
- apfParams,
ActiveModulesUI.this);
- paramsDialog.setVisible(true);
+ if (mainPanel == null) {
+ mainPanel = new
ActivePathsParameterPanel(apfParams,
+ ActiveModulesUI.this);
}
- int index = cytoPanel.indexOfComponent(paramsDialog);
+ int index = cytoPanel.indexOfComponent(mainPanel);
if (index < 0) {
- cytoPanel.add("jActiveModules", paramsDialog);
- index =
cytoPanel.indexOfComponent(paramsDialog);
+ cytoPanel.add("jActiveModules", mainPanel);
+ index = cytoPanel.indexOfComponent(mainPanel);
}
cytoPanel.setSelectedIndex(index);
cytoPanel.setState(CytoPanelState.DOCK);
@@ -132,7 +137,7 @@
}
public void actionPerformed(ActionEvent ae) {
- startFindActivePaths(Cytoscape.getCurrentNetwork());
+ startFindActivePaths(mainPanel.getTargetNetwork());
}
}
@@ -161,7 +166,7 @@
}
public void actionPerformed(ActionEvent e) {
- activePaths = new
ActivePaths(Cytoscape.getCurrentNetwork(),
+ activePaths = new
ActivePaths(mainPanel.getTargetNetwork(),
apfParams, ActiveModulesUI.this);
activePaths.scoreActivePath();
}
@@ -181,7 +186,7 @@
}
public void actionPerformed(ActionEvent e) {
- startRandomizeAndRun(Cytoscape.getCurrentNetwork());
+ startRandomizeAndRun(mainPanel.getTargetNetwork());
}
}
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules3/src/csplugins/jActiveModules/dialogs/ActivePathsParameterPanel.java
===================================================================
---
csplugins/trunk/ucsd/pwang/jActiveModules3/src/csplugins/jActiveModules/dialogs/ActivePathsParameterPanel.java
2010-02-17 00:22:50 UTC (rev 19344)
+++
csplugins/trunk/ucsd/pwang/jActiveModules3/src/csplugins/jActiveModules/dialogs/ActivePathsParameterPanel.java
2010-02-17 02:35:39 UTC (rev 19345)
@@ -5,14 +5,14 @@
// $Author: rmkelley $
//-----------------------------------------------------------------------------
package csplugins.jActiveModules.dialogs;
+
//-----------------------------------------------------------------------------
import java.awt.BorderLayout;
import java.awt.CardLayout;
import java.awt.Color;
-import java.awt.Component;
+import java.awt.Container;
import java.awt.Dimension;
import java.awt.FlowLayout;
-import java.awt.Frame;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.awt.GridLayout;
@@ -26,8 +26,8 @@
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.io.IOException;
+import java.util.ArrayList;
import java.util.List;
-import java.util.Vector;
import javax.swing.AbstractAction;
import javax.swing.BorderFactory;
@@ -52,18 +52,19 @@
import csplugins.jActiveModules.ActiveModulesUI;
import csplugins.jActiveModules.data.ActivePathFinderParameters;
+import cytoscape.CyNetwork;
import cytoscape.Cytoscape;
+import cytoscape.util.swing.NetworkSelectorPanel;
import cytoscape.view.cytopanels.CytoPanel;
+public class ActivePathsParameterPanel extends JPanel {
-public class ActivePathsParameterPanel extends JPanel {
-
private static final long serialVersionUID = -6759180275710507653L;
JTextField readout;
ActivePathFinderParameters apfParams;
-
+
static String NONRANDOM = "Non-Random Starting Graph";
static String ANNEAL = "Anneal";
static String SEARCH = "Search";
@@ -79,9 +80,9 @@
JTextField intervalNum;
JLabel intervalLabel;
- JPanel overlapPanel;
- JTextField overlapNum;
- JLabel overlapLabel;
+ JPanel overlapPanel;
+ JTextField overlapNum;
+ JLabel overlapLabel;
JPanel pathPanel;
JTextField pathNum;
@@ -92,7 +93,6 @@
JLabel iterLabel;
JPanel annealExtPanel;
- JPanel generalExtPanel;
JPanel hfcPanel;
JCheckBox quenchCheck;
JCheckBox edgesCheck;
@@ -125,130 +125,160 @@
JPanel searchContentPanel;
JPanel currentContentPanel;
- JPanel attrSelectPanel;
JPanel optionsPanel;
- JList exprAttrsList;
- JButton findModulesButton;
- ActiveModulesUI parentUI;
+ private JList exprAttrsList;
+
+ // Button Panel for command buttons.
+ private JButton findModulesButton;
+
+ private ActiveModulesUI pluginMainClass;
JDialog helpDialog;
+
+ private NetworkSelectorPanel networkPanel;
+
//
-----------------------------------------------------------------------------
public ActivePathsParameterPanel(
ActivePathFinderParameters incomingApfParams,
ActiveModulesUI parentUI) {
+
+ // Set global parameters
+ this.setLayout(new BorderLayout());
+ this.setMinimumSize(new Dimension(320, 420));
+ this.setPreferredSize(new Dimension(320, 420));
+
// uses copy constructor so that changes aren't committed if you
// dismiss.
apfParams = incomingApfParams;
- this.parentUI = parentUI;
+ this.pluginMainClass = parentUI;
- if ( apfParams == null )
- System.out.println("WTF");
+ if (apfParams == null)
+ throw new IllegalStateException(
+ "Parametr object is null. Could not
initialize jActiveModules plugin.");
+
+ final JPanel mainPanel = new JPanel(new BorderLayout());
+ mainPanel.setPreferredSize(new Dimension(200, 600));
- JPanel childPanel = new JPanel(new GridBagLayout());
-
readout = new JTextField(new String("seed: "
+ apfParams.getRandomSeed()));
RandomSeedTextListener readoutListener = new
RandomSeedTextListener();
readout.addFocusListener(readoutListener);
- createExtsController();
+ final Container extController = createExtsControllerPanel();
+ createSearchContentPanel();
createAnnealContentPanel();
- createSearchContentPanel();
- createAnnealSearchController();
+
+ createAnnealSearchControlPanel();
createHelpDialog();
+
+ this.add(createTopPanel(), BorderLayout.PAGE_START);
- GridBagConstraints c = new GridBagConstraints();
+ final JPanel subOptionsPanel = new JPanel(new BorderLayout());
+ subOptionsPanel.add(extController, BorderLayout.PAGE_START);
+ subOptionsPanel.add(annealSearchControlPanel,
BorderLayout.CENTER);
+
+ optionsPanel = new JPanel(new CardLayout());
+ optionsPanel.add(new JPanel(), "INACTIVE");
+ optionsPanel.add(subOptionsPanel, "ACTIVE");
+ mainPanel.add(optionsPanel, BorderLayout.CENTER);
- createAttrSelectionPanel();
- c.fill = GridBagConstraints.BOTH;
- c.gridx = 0; c.gridy = 0;
- c.weightx = 1.0; c.weighty = 1.0;
- childPanel.add(attrSelectPanel,c);
+ this.add(createButtonPanel(), BorderLayout.PAGE_END);
- JPanel subOptionsPanel = new JPanel(new GridBagLayout());
- c.fill = GridBagConstraints.HORIZONTAL;
- c.gridx = 0; c.gridy = 0;
- c.weightx = 1.0; c.weighty = 0.0;
- subOptionsPanel.add(generalExtPanel,c);
+ updateOptionsPanel();
- c.gridx = 0; c.gridy = 1;
- subOptionsPanel.add(annealSearchControlPanel,c);
+ final JScrollPane scrollPane = new JScrollPane(mainPanel);
+ this.add(scrollPane, BorderLayout.CENTER);
- optionsPanel = new JPanel(new CardLayout());
- optionsPanel.add(new JPanel(), "INACTIVE");
- optionsPanel.add(subOptionsPanel, "ACTIVE");
- childPanel.add(optionsPanel,c);
+ }
+
+ private Container createTopPanel() {
+ final JPanel topPanel = new JPanel();
+ topPanel.setLayout(new BorderLayout());
+
+ // target network selector
+ networkPanel = new NetworkSelectorPanel();
+
networkPanel.setBorder(BorderFactory.createTitledBorder("Analysis Target"));
+ topPanel.add(networkPanel, BorderLayout.PAGE_START);
+ topPanel.add(createAttrSelectionPanel(), BorderLayout.CENTER);
+ return topPanel;
+ }
+
+ public CyNetwork getTargetNetwork() {
+ return this.networkPanel.getSelectedNetwork();
+ }
- // /////////////////////////////////////////
- JPanel buttonPanel = new JPanel();
+ /**
+ * Setup button panel components.
+ *
+ */
+ private Container createButtonPanel() {
+ final JPanel buttonPanel = new JPanel();
+ buttonPanel.setBorder(BorderFactory.createEtchedBorder());
+ final JButton helpButton = new JButton(new AbstractAction("?") {
- JButton helpButton = new JButton(new AbstractAction("?")
- {
- public void actionPerformed(ActionEvent e)
- {
+ private static final long serialVersionUID =
-5964319275031340146L;
+
+ public void actionPerformed(ActionEvent e) {
helpDialog.setVisible(true);
}
});
+
buttonPanel.add(helpButton, BorderLayout.EAST);
findModulesButton = new JButton(new FindModulesAction());
buttonPanel.add(findModulesButton, BorderLayout.EAST);
- JButton dismissButton = new JButton("Close");
+
+ final JButton dismissButton = new JButton("Close");
dismissButton.addActionListener(new DismissAction());
buttonPanel.add(dismissButton, BorderLayout.WEST);
- c.gridx = 0; c.gridy = 2;
- childPanel.add(buttonPanel,c);
+ return buttonPanel;
+ }
- updateOptionsPanel();
+
+ private Container createAttrSelectionPanel() {
+ final JPanel attrSelectPanel = new JPanel();
+ attrSelectPanel.setPreferredSize(new Dimension(200, 150));
+ attrSelectPanel.setLayout(new BorderLayout());
- JScrollPane scrollPane = new JScrollPane(childPanel);
- setLayout(new GridLayout(1,1));
- add(scrollPane);
-
- } // PopupDialog ctor
-
- private void createAttrSelectionPanel() {
- attrSelectPanel = new JPanel();
- attrSelectPanel.setLayout(new GridLayout(1,1));
- attrSelectPanel.setAlignmentX(Component.CENTER_ALIGNMENT);
-
- Border border = BorderFactory.createLineBorder(Color.black);
- Border titledBorder = BorderFactory.createTitledBorder(border,
+ final Border border =
BorderFactory.createLineBorder(Color.black);
+ final Border titledBorder =
BorderFactory.createTitledBorder(border,
"Expression Attributes For Analysis",
TitledBorder.CENTER,
TitledBorder.DEFAULT_POSITION);
attrSelectPanel.setBorder(titledBorder);
-
- List<String> selectedNames =
apfParams.getExpressionAttributes();
- Vector<String> allNames = new
Vector<String>(apfParams.getPossibleExpressionAttributes());
- exprAttrsList = new JList(allNames);
-
exprAttrsList.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
+
+ final List<String> selectedNames =
apfParams.getExpressionAttributes();
+ final List<String> allNames = new ArrayList<String>(apfParams
+ .getPossibleExpressionAttributes());
+ exprAttrsList = new JList(allNames.toArray());
+ exprAttrsList
+
.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
exprAttrsList.setLayoutOrientation(JList.VERTICAL);
- exprAttrsList.setVisibleRowCount(3);
- exprAttrsList.addMouseListener(new
ExprAttrsListListener(exprAttrsList, apfParams));
- for ( String name : selectedNames ) {
+ //exprAttrsList.setVisibleRowCount(3);
+ exprAttrsList.addMouseListener(new
ExprAttrsListListener(exprAttrsList,
+ apfParams));
+ for (String name : selectedNames) {
int index = allNames.indexOf(name);
- if ( index != -1 )
+ if (index != -1)
exprAttrsList.addSelectionInterval(index,
index);
}
-
- JScrollPane scrollPane = new JScrollPane(exprAttrsList);
- attrSelectPanel.add(scrollPane);
+ final JScrollPane scrollPane = new JScrollPane(exprAttrsList);
+ scrollPane.setViewportView(exprAttrsList);
+ attrSelectPanel.add(scrollPane, BorderLayout.CENTER);
+
+ return attrSelectPanel;
}
- protected void updateOptionsPanel()
- {
- if (exprAttrsList == null || optionsPanel == null ||
findModulesButton == null)
+ protected void updateOptionsPanel() {
+ if (exprAttrsList == null || optionsPanel == null
+ || findModulesButton == null)
return;
boolean showOptions = exprAttrsList.getSelectedIndices().length
!= 0;
CardLayout cl = (CardLayout) optionsPanel.getLayout();
- if (showOptions)
- {
+ if (showOptions) {
cl.show(optionsPanel, "ACTIVE");
findModulesButton.setEnabled(true);
- }
- else
- {
+ } else {
cl.show(optionsPanel, "INACTIVE");
findModulesButton.setEnabled(false);
}
@@ -256,7 +286,8 @@
private void createAnnealContentPanel() {
annealContentPanel = new JPanel();
- annealContentPanel.setLayout(new BoxLayout(annealContentPanel,
BoxLayout.PAGE_AXIS));
+ annealContentPanel.setLayout(new BoxLayout(annealContentPanel,
+ BoxLayout.PAGE_AXIS));
GridBagConstraints c = new GridBagConstraints();
createIterationsController();
@@ -280,7 +311,7 @@
private void createSearchContentPanel() {
searchContentPanel = new JPanel();
- searchContentPanel.setMinimumSize(new Dimension(300, 400));
+ searchContentPanel.setMinimumSize(new Dimension(200, 200));
GridBagLayout gridbag = new GridBagLayout();
GridBagConstraints c = new GridBagConstraints();
searchContentPanel.setLayout(gridbag);
@@ -299,15 +330,15 @@
gridbag.setConstraints(searchPanel, c);
searchContentPanel.add(searchPanel);
- Border border = BorderFactory.createLineBorder(Color.black);
- Border titledBorder = BorderFactory.createTitledBorder(border,
+ final Border border =
BorderFactory.createLineBorder(Color.black);
+ final Border titledBorder =
BorderFactory.createTitledBorder(border,
"Searching Parameters", TitledBorder.CENTER,
TitledBorder.DEFAULT_POSITION);
searchContentPanel.setBorder(titledBorder);
}
//
-----------------------------------------------------------------------------
- private void createExtsController() {
+ private Container createExtsControllerPanel() {
annealExtPanel = new JPanel();
createHubfindingController();
@@ -319,32 +350,25 @@
quenchCheck.addItemListener(qcListener);
JPanel quenchPanel = new JPanel(new
FlowLayout(FlowLayout.LEFT));
quenchPanel.add(quenchCheck);
-
+
JLabel annealingExtLabel = new JLabel("Annealing Extensions:");
GroupLayout layout = new GroupLayout(annealExtPanel);
annealExtPanel.setLayout(layout);
- layout.setHorizontalGroup(
- layout.createParallelGroup()
- .add(annealingExtLabel)
- .add(quenchPanel)
- .add(hfcPanel)
- );
- layout.setVerticalGroup(
- layout.createSequentialGroup()
- .add(annealingExtLabel)
- .add(quenchPanel)
- .add(hfcPanel)
- );
+ layout.setHorizontalGroup(layout.createParallelGroup().add(
+
annealingExtLabel).add(quenchPanel).add(hfcPanel));
+ layout.setVerticalGroup(layout.createSequentialGroup().add(
+
annealingExtLabel).add(quenchPanel).add(hfcPanel));
// -------------------------------------------------------------
- generalExtPanel = new JPanel();
+ final JPanel generalExtPanel = new JPanel();
+ generalExtPanel.setPreferredSize(new Dimension(300, 150));
layout = new GroupLayout(generalExtPanel);
generalExtPanel.setLayout(layout);
- Border generalBorder =
BorderFactory.createLineBorder(Color.black);
- Border generalTitledBorder = BorderFactory.createTitledBorder(
+ final Border generalBorder =
BorderFactory.createLineBorder(Color.black);
+ final Border generalTitledBorder =
BorderFactory.createTitledBorder(
generalBorder, "General Parameters",
TitledBorder.CENTER,
TitledBorder.DEFAULT_POSITION);
generalExtPanel.setBorder(generalTitledBorder);
@@ -353,28 +377,19 @@
createPathsController();
createOverlapController();
- layout.setHorizontalGroup(
- layout.createParallelGroup()
- .add(pathPanel)
- .add(overlapPanel)
- .add(mcBox)
- .add(regionalBox)
- );
+
layout.setHorizontalGroup(layout.createParallelGroup().add(pathPanel)
+ .add(overlapPanel).add(mcBox).add(regionalBox));
- layout.setVerticalGroup(
- layout.createSequentialGroup()
- .add(pathPanel)
- .add(overlapPanel)
- .add(mcBox)
- .add(regionalBox)
- );
+
layout.setVerticalGroup(layout.createSequentialGroup().add(pathPanel)
+ .add(overlapPanel).add(mcBox).add(regionalBox));
- return;
-
+ return generalExtPanel;
}
- private void createAnnealSearchController() {
+ private void createAnnealSearchControlPanel() {
annealSearchControlPanel = new JPanel();
+ annealSearchControlPanel.setMinimumSize(new Dimension(300,
400));
+ annealSearchControlPanel.setPreferredSize(new Dimension(300,
400));
annealSearchContentPanel = new JPanel(new CardLayout());
GroupLayout layout = new GroupLayout(annealSearchControlPanel);
annealSearchControlPanel.setLayout(layout);
@@ -388,18 +403,12 @@
annealSearchGroup.add(searchButton);
buttonsPanel.add(annealButton);
buttonsPanel.add(searchButton);
-
- layout.setHorizontalGroup(
- layout.createParallelGroup()
- .add(buttonsPanel)
- .add(annealSearchContentPanel)
- );
- layout.setVerticalGroup(
- layout.createSequentialGroup()
- .add(buttonsPanel)
- .add(annealSearchContentPanel)
- );
+ layout.setHorizontalGroup(layout.createParallelGroup()
+
.add(buttonsPanel).add(annealSearchContentPanel));
+
+ layout.setVerticalGroup(layout.createSequentialGroup()
+
.add(buttonsPanel).add(annealSearchContentPanel));
Border ascBorder = BorderFactory.createLineBorder(Color.black);
Border ascTitledBorder =
BorderFactory.createTitledBorder(ascBorder,
"Strategy", TitledBorder.CENTER,
TitledBorder.DEFAULT_POSITION);
@@ -409,7 +418,6 @@
annealButton.addActionListener(switchListener);
searchButton.addActionListener(switchListener);
- CardLayout cl = (CardLayout)
annealSearchContentPanel.getLayout();
annealSearchContentPanel.add(searchContentPanel, SEARCH);
annealSearchContentPanel.add(annealContentPanel, ANNEAL);
if (apfParams.getGreedySearch()) {
@@ -424,8 +432,7 @@
annealSearchControlPanel.add(annealSearchContentPanel);
}
- private void switchAnnealSearchContentPanel(String name)
- {
+ private void switchAnnealSearchContentPanel(String name) {
CardLayout cl = (CardLayout)
annealSearchContentPanel.getLayout();
cl.show(annealSearchContentPanel, name);
}
@@ -519,13 +526,13 @@
.getSearchDepth()), 2);
searchFromNodesBox = new JCheckBox("Search from selected
nodes?",
apfParams.getSearchFromNodes());
- JPanel searchFromNodesPanel = new JPanel(new
FlowLayout(FlowLayout.LEFT));
- searchFromNodesPanel.add(searchFromNodesBox);
+ final JPanel searchFromNodesPanel = new JPanel(new
BorderLayout());
+ searchFromNodesPanel.add(searchFromNodesBox,
BorderLayout.LINE_START);
- JPanel searchDepthPanel = new JPanel(new
FlowLayout(FlowLayout.LEFT));
- searchDepthPanel.add(new JLabel("Search depth: "));
- searchDepthPanel.add(searchDepth);
-
+ final JPanel searchDepthPanel = new JPanel(new BorderLayout());
+ searchDepthPanel.add(new JLabel("Search depth: "),
BorderLayout.LINE_START);
+ searchDepthPanel.add(searchDepth, BorderLayout.CENTER);
+
maxBox = new JCheckBox("Max depth from start nodes:", apfParams
.getEnableMaxDepth());
maxDepth = new
JTextField(Integer.toString(apfParams.getMaxDepth()), 2);
@@ -534,28 +541,17 @@
maxBox.addItemListener(mListener);
maxDepth.addFocusListener(mListener);
- JPanel maxDepthPanel = new JPanel(new
FlowLayout(FlowLayout.LEFT));
- maxDepthPanel.add(maxBox);
- maxDepthPanel.add(maxDepth);
+ final JPanel maxDepthPanel = new JPanel(new BorderLayout());
+ maxDepthPanel.add(maxBox, BorderLayout.LINE_START);
+ maxDepthPanel.add(maxDepth, BorderLayout.CENTER);
searchDepth.addFocusListener(listener);
searchFromNodesBox.addItemListener(new SFNListener());
- layout.setHorizontalGroup(
- layout.createParallelGroup()
- .add(searchDepthPanel)
- .add(searchFromNodesPanel)
- .add(maxDepthPanel)
- );
+ layout.setHorizontalGroup(layout.createParallelGroup().add(
+
searchDepthPanel).add(searchFromNodesPanel).add(maxDepthPanel));
- layout.setVerticalGroup(
- layout.createSequentialGroup()
- .add(searchDepthPanel)
- .add(searchFromNodesPanel)
- .add(maxDepthPanel)
- );
-
- return;
-
+ layout.setVerticalGroup(layout.createSequentialGroup().add(
+
searchDepthPanel).add(searchFromNodesPanel).add(maxDepthPanel));
} // createSearchController
//
-----------------------------------------------------------------------------
@@ -584,21 +580,17 @@
pathLabel = new JLabel("Number of Modules (1-1000): ");
pathNum = new
JTextField(Integer.toString(apfParams.getNumberOfPaths()));
- java.awt.FontMetrics fontMetrics =
pathNum.getFontMetrics(pathNum.getFont());
- pathNum.setMaximumSize(new Dimension(
fontMetrics.charWidth('m') * 7, fontMetrics.getHeight() ));
+ java.awt.FontMetrics fontMetrics =
pathNum.getFontMetrics(pathNum
+ .getFont());
+ pathNum.setMaximumSize(new Dimension(fontMetrics.charWidth('m')
* 7,
+ fontMetrics.getHeight()));
pathNum.addFocusListener(new PathListener());
- layout.setHorizontalGroup(
- layout.createSequentialGroup()
- .add(pathLabel)
- .add(pathNum)
- );
+
layout.setHorizontalGroup(layout.createSequentialGroup().add(pathLabel)
+ .add(pathNum));
- layout.setVerticalGroup(
- layout.createParallelGroup()
- .add(pathLabel)
- .add(pathNum)
- );
+
layout.setVerticalGroup(layout.createParallelGroup().add(pathLabel)
+ .add(pathNum));
} // createPathsController
private void createOverlapController() {
@@ -607,24 +599,21 @@
overlapPanel.setLayout(layout);
overlapLabel = new JLabel("Overlap Threshold: ");
- overlapNum = new
JTextField(Double.toString(apfParams.getOverlapThreshold()));
- java.awt.FontMetrics fontMetrics =
overlapNum.getFontMetrics(pathNum.getFont());
- overlapNum.setMaximumSize(new Dimension(
fontMetrics.charWidth('m') * 7, fontMetrics.getHeight() ));
+ overlapNum = new JTextField(Double.toString(apfParams
+ .getOverlapThreshold()));
+ java.awt.FontMetrics fontMetrics =
overlapNum.getFontMetrics(pathNum
+ .getFont());
+ overlapNum.setMaximumSize(new
Dimension(fontMetrics.charWidth('m') * 7,
+ fontMetrics.getHeight()));
overlapNum.addFocusListener(new OverlapListener());
- layout.setHorizontalGroup(
- layout.createSequentialGroup()
- .add(overlapLabel)
- .add(overlapNum)
- );
+ layout.setHorizontalGroup(layout.createSequentialGroup().add(
+ overlapLabel).add(overlapNum));
- layout.setVerticalGroup(
- layout.createParallelGroup()
- .add(overlapLabel)
- .add(overlapNum)
- );
+
layout.setVerticalGroup(layout.createParallelGroup().add(overlapLabel)
+ .add(overlapNum));
} // createPathsController
-
+
//
-----------------------------------------------------------------------------
class TempController {
@@ -642,13 +631,15 @@
tempLabelStart = new JLabel("Start Temp (0.0001 -
100)");
tempLabelEnd = new JLabel("End Temp (0.0001 - Start)");
- //tStartPanel.setLayout(new GridLayout(0, 1));
- tStartPanel.setLayout(new
java.awt.FlowLayout(java.awt.FlowLayout.LEFT));
+ // tStartPanel.setLayout(new GridLayout(0, 1));
+ tStartPanel.setLayout(new java.awt.FlowLayout(
+ java.awt.FlowLayout.LEFT));
tStartPanel.add(tempLabelStart);
tStartPanel.add(startNum);
- //tEndPanel.setLayout(new GridLayout(0, 1));
- tEndPanel.setLayout(new
java.awt.FlowLayout(java.awt.FlowLayout.LEFT));
+ // tEndPanel.setLayout(new GridLayout(0, 1));
+ tEndPanel.setLayout(new java.awt.FlowLayout(
+ java.awt.FlowLayout.LEFT));
tEndPanel.add(tempLabelEnd);
tEndPanel.add(endNum);
@@ -691,21 +682,17 @@
regionalBox.addItemListener(new RSListener());
} // createRegionalScoringController
-
- private void createHelpDialog()
- {
+ private void createHelpDialog() {
helpDialog = new JDialog(Cytoscape.getDesktop(),
"jActiveModules Help");
helpDialog.setDefaultCloseOperation(JDialog.HIDE_ON_CLOSE);
- try
- {
- JEditorPane helpPane = new
JEditorPane(parentUI.getClass().getResource("/help.html"));
+ try {
+ JEditorPane helpPane = new
JEditorPane(pluginMainClass.getClass()
+ .getResource("/help.html"));
helpPane.setEditable(false);
JScrollPane scrollPane = new JScrollPane(helpPane);
helpDialog.setContentPane(scrollPane);
helpDialog.setPreferredSize(new Dimension(750, 400));
- }
- catch (IOException e)
- {
+ } catch (IOException e) {
JLabel label = new JLabel("Could not find help.html.");
helpDialog.setContentPane(label);
}
@@ -731,9 +718,11 @@
public void focusGained(FocusEvent e) {
validate();
}
+
public void focusLost(FocusEvent e) {
validate();
}
+
public void actionPerformed(ActionEvent e) {
String setting = e.getActionCommand();
if (setting.equals(ANNEAL)) {
@@ -744,6 +733,7 @@
switchToSearch();
}
}
+
private void switchToAnneal() {
if (currentContentPanel != annealContentPanel) {
currentContentPanel = annealContentPanel;
@@ -751,6 +741,7 @@
apfParams.setGreedySearch(false);
}
}
+
private void switchToSearch() {
if (currentContentPanel != searchContentPanel) {
currentContentPanel = searchContentPanel;
@@ -758,10 +749,11 @@
apfParams.setGreedySearch(true);
}
}
+
private void validate() {
if (searchButton.isSelected()) {
String st = searchDepth.getText();
- //String st2 = st.replaceAll("[^0-9]", ""); //
ditch all
+ // String st2 = st.replaceAll("[^0-9]", ""); //
ditch all
// non-numeric
if (st.length() > 0) {
try {
@@ -797,6 +789,7 @@
// System.out.println("gained");
validate();
}
+
public void focusLost(FocusEvent e) {
// System.out.println("lost");
validate();
@@ -830,16 +823,19 @@
apfParams.setMCboolean(mcBox.isSelected());
}
}
+
class RSListener implements ItemListener {
public void itemStateChanged(ItemEvent e) {
apfParams.setRegionalBoolean(regionalBox.isSelected());
}
}
+
class SFNListener implements ItemListener {
public void itemStateChanged(ItemEvent e) {
apfParams.setSearchFromNodes(searchFromNodesBox.isSelected());
}
}
+
class QuenchCheckListener implements ItemListener {
public void itemStateChanged(ItemEvent e) {
JCheckBox jcb = (JCheckBox) e.getItem();
@@ -852,10 +848,12 @@
// System.out.println("gained");
validate();
}
+
public void focusLost(FocusEvent e) {
// System.out.println("lost");
validate();
}
+
public void itemStateChanged(ItemEvent e) {
hubNum.setEnabled(hubBox.isSelected());
validate();
@@ -907,10 +905,12 @@
// System.out.println("gained");
validate();
}
+
public void focusLost(FocusEvent e) {
// System.out.println("lost");
validate();
}
+
public void itemStateChanged(ItemEvent e) {
hubAdjustmentNum.setEnabled(hubAdjustmentBox.isSelected());
validate();
@@ -958,19 +958,22 @@
// System.out.println("gained");
validate();
}
+
public void focusLost(FocusEvent e) {
// System.out.println("lost");
validate();
}
+
public void itemStateChanged(ItemEvent e) {
maxDepth.setEnabled(maxBox.isSelected());
apfParams.setEnableMaxDepth(maxBox.isSelected());
validate();
}
+
private void validate() {
if (maxBox.isSelected()) {
String st = maxDepth.getText();
- //String st2 = st.replaceAll("[^0-9]", ""); //
ditch all
+ // String st2 = st.replaceAll("[^0-9]", ""); //
ditch all
// non-numeric
if (st.length() > 0) {
try {
@@ -1010,6 +1013,7 @@
// System.out.println("gained");
validate();
}
+
public void focusLost(FocusEvent e) {
// System.out.println("lost");
validate();
@@ -1058,6 +1062,7 @@
// System.out.println("gained");
validate();
}
+
public void focusLost(FocusEvent e) {
// System.out.println("lost");
validate();
@@ -1065,28 +1070,30 @@
private void validate() {
String pt = overlapNum.getText();
- try{
- double overlap = Double.parseDouble(pt);
- if(overlap < 0.0){
- overlap = 0.0;
- }
- if(overlap > 1.0){
- overlap = 1.0;
- }
- overlapNum.setText((new
Double(overlap)).toString());
- apfParams.setOverlapThreshold(overlap);
+ try {
+ double overlap = Double.parseDouble(pt);
+ if (overlap < 0.0) {
+ overlap = 0.0;
+ }
+ if (overlap > 1.0) {
+ overlap = 1.0;
+ }
+ overlapNum.setText((new
Double(overlap)).toString());
+ apfParams.setOverlapThreshold(overlap);
} catch (NumberFormatException nfe) {
- overlapNum.setText("0.8");
- apfParams.setOverlapThreshold(0.8);
+ overlapNum.setText("0.8");
+ apfParams.setOverlapThreshold(0.8);
}
}
} // PathListener
+
class PathListener implements FocusListener {
public void focusGained(FocusEvent e) {
// System.out.println("gained");
validate();
}
+
public void focusLost(FocusEvent e) {
// System.out.println("lost");
validate();
@@ -1135,6 +1142,7 @@
// System.out.println("gained");
validate();
}
+
public void focusLost(FocusEvent e) {
// System.out.println("lost");
validate();
@@ -1213,6 +1221,7 @@
// System.out.println("gained");
validate();
}
+
public void focusLost(FocusEvent e) {
// System.out.println("lost");
validate();
@@ -1265,7 +1274,8 @@
public void actionPerformed(ActionEvent e) {
// listener.cancelActivePathsFinding ();
- CytoPanel cytoPanel =
Cytoscape.getDesktop().getCytoPanel(SwingConstants.WEST);
+ CytoPanel cytoPanel =
Cytoscape.getDesktop().getCytoPanel(
+ SwingConstants.WEST);
cytoPanel.remove(ActivePathsParameterPanel.this);
}
@@ -1278,34 +1288,33 @@
}
public void actionPerformed(ActionEvent e) {
-
parentUI.startFindActivePaths(Cytoscape.getCurrentNetwork());
+
pluginMainClass.startFindActivePaths(networkPanel.getSelectedNetwork());
}
}
-
- class GenericListener extends FocusAdapter implements ActionListener{
- public void focusLost(FocusEvent fe){
- this.actionPerformed(new ActionEvent(this,0,""));
+
+ class GenericListener extends FocusAdapter implements ActionListener {
+ public void focusLost(FocusEvent fe) {
+ this.actionPerformed(new ActionEvent(this, 0, ""));
}
- public void actionPerformed(ActionEvent ae){
- //do nothing
+
+ public void actionPerformed(ActionEvent ae) {
+ // do nothing
}
-
+
}
- class ExprAttrsListListener extends MouseAdapter
- {
+ class ExprAttrsListListener extends MouseAdapter {
private JList parentList;
private ActivePathFinderParameters apfParams;
- public ExprAttrsListListener(JList parentList,
ActivePathFinderParameters apfParams)
- {
+ public ExprAttrsListListener(JList parentList,
+ ActivePathFinderParameters apfParams) {
this.parentList = parentList;
this.apfParams = apfParams;
}
- public void mouseClicked(MouseEvent e)
- {
+ public void mouseClicked(MouseEvent e) {
String selectedString =
parentList.getSelectedValue().toString();
if
(apfParams.getExpressionAttributes().contains(selectedString))
apfParams.removeExpressionAttribute(selectedString);
@@ -1313,10 +1322,10 @@
apfParams.addExpressionAttribute(selectedString);
int[] indices = new
int[apfParams.getExpressionAttributes().size()];
- int count = 0;
- for (String exprAttr :
apfParams.getExpressionAttributes())
- {
- int i =
apfParams.getPossibleExpressionAttributes().indexOf(exprAttr);
+ int count = 0;
+ for (String exprAttr :
apfParams.getExpressionAttributes()) {
+ int i =
apfParams.getPossibleExpressionAttributes().indexOf(
+ exprAttr);
if (i != -1)
indices[count++] = i;
}
@@ -1328,7 +1337,7 @@
}
private boolean isSignificanceValue(String name) {
- return true;
+ return true;
}
//
-----------------------------------------------------------------------------
--
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