Author: kono
Date: 2009-07-24 15:45:28 -0700 (Fri, 24 Jul 2009)
New Revision: 17561
Modified:
csplugins/trunk/ucsd/kono/ShortestPath2/build.xml
csplugins/trunk/ucsd/kono/ShortestPath2/resources/plugin.props
csplugins/trunk/ucsd/kono/ShortestPath2/src/org/cytoscape/analysis/shortestpath/ShortestPath.java
csplugins/trunk/ucsd/kono/ShortestPath2/src/org/cytoscape/analysis/shortestpath/ShortestPathPlugin.java
csplugins/trunk/ucsd/kono/ShortestPath2/src/org/cytoscape/analysis/shortestpath/internal/ShortestPathDialog.java
Log:
Table format had been modified.
Modified: csplugins/trunk/ucsd/kono/ShortestPath2/build.xml
===================================================================
--- csplugins/trunk/ucsd/kono/ShortestPath2/build.xml 2009-07-24 21:42:32 UTC
(rev 17560)
+++ csplugins/trunk/ucsd/kono/ShortestPath2/build.xml 2009-07-24 22:45:28 UTC
(rev 17561)
@@ -1,15 +1,14 @@
<?xml version = "1.0"?>
-<project name="shortestPathPlugin2" default="all" basedir=".">
+<project name="ShortestPathPlugin2" default="all" basedir=".">
<property name="src" location="src" />
<property name="build" location="build" />
<property name="build.compiler" value="modern" />
<!-- path to Cytoscape under development (CVS) -->
<property name="cylib" location="../cytoscape" />
- <property name="lib" location="lib" />
<property name="jar" location="jar" />
<property name="doc" location="doc" />
- <property name="projectName" value="shortestPathPlugin2" />
+ <property name="projectName" value="ShortestPathPlugin2" />
<property name="cytoscape.plugin" value="${lib}/plugins" />
@@ -17,9 +16,6 @@
<fileset dir="${cylib}">
<include name="**/*.jar" />
</fileset>
- <fileset dir="${lib}">
- <include name="**/*.jar" />
- </fileset>
</path>
<target name="prepare" depends="clean">
@@ -40,20 +36,14 @@
</target>
<target name="jar" depends="compile" description="makes a jar for
Cytoscape under development">
- <mkdir dir="${jar}" />
- <unzip dest="${build}">
- <fileset dir="${lib}" includes="*" />
- </unzip>
- <copy todir="build/org/cytoscape/view/ui/networkpanel"
file="resources/plugin.props" />
- <mkdir dir="build/org/cytoscape/view/ui/networkpanel/images"/>
- <copy todir="build/org/cytoscape/view/ui/networkpanel/images">
- <fileset dir="images"/>
- </copy>
- <jar jarfile="${jar}/${projectName}.jar">
- <manifest>
- <attribute name="Cytoscape-Plugin"
value="org.cytoscape.view.ui.networkpanel.NetworkBrowserPlugin" />
- </manifest>
+
+ <copy todir="build/org/cytoscape/analysis/shortestpath"
file="resources/plugin.props" />
+
+ <jar jarfile="build/${projectName}.jar">
<fileset dir="${build}" />
+ <manifest>
+ <attribute name="Cytoscape-Plugin"
value="org.cytoscape.analysis.shortestpath.ShortestPathPlugin" />
+ </manifest>
</jar>
</target>
@@ -71,7 +61,7 @@
<!-- Target to Run JavaDoc -->
<target name="doc" description="Runs JavaDoc.">
- <javadoc packagenames="cytoscape.groups.results.*"
sourcepath="src" source="1.5" destdir="doc" classpathref="classpath_release">
+ <javadoc packagenames="org.cytoscape.analysis.shortestpath.*"
sourcepath="src" source="1.5" destdir="doc" classpathref="classpath_release">
<link href="http://java.sun.com/j2se/1.5.0/docs/api/"; />
<link href="http://csbi.sourceforge.net/API/"; />
<link
href="http://chianti.ucsd.edu/Cyto-2_4_1/javadoc/"; />
Modified: csplugins/trunk/ucsd/kono/ShortestPath2/resources/plugin.props
===================================================================
--- csplugins/trunk/ucsd/kono/ShortestPath2/resources/plugin.props
2009-07-24 21:42:32 UTC (rev 17560)
+++ csplugins/trunk/ucsd/kono/ShortestPath2/resources/plugin.props
2009-07-24 22:45:28 UTC (rev 17561)
@@ -6,20 +6,20 @@
# -- The following properties are REQUIRED -- #
# The plugin name that will be displayed to users
-pluginName=networkBrowser
+pluginName=ShortestPath2
# Description used to give users information about the plugin such as what it
does.
# Html tags are encouraged for formatting purposes.
-pluginDescription=Displays a list of groups created in a results panel.
+pluginDescription=Shortest Path plugin modified by Kei Ono
# Plugin version number, this must be two numbers separated by a decimlal.
Ex. 0.2, 14.03
-pluginVersion=1.0
+pluginVersion=2.0
# Compatible Cytoscape version
cytoscapeVersion=2.6
# Category, use one of the categories listed on the website or create your own
-pluginCategory=Other
+pluginCategory=Analysis
# -- The following properties are OPTIONAL -- #
@@ -31,4 +31,4 @@
pluginAuthorsIntsitutions=Keiichiro Ono:UCSD
# Date this plugin/plugin version was released
-releaseDate=July 1, 2009
+releaseDate=July 20, 2009
Modified:
csplugins/trunk/ucsd/kono/ShortestPath2/src/org/cytoscape/analysis/shortestpath/ShortestPath.java
===================================================================
---
csplugins/trunk/ucsd/kono/ShortestPath2/src/org/cytoscape/analysis/shortestpath/ShortestPath.java
2009-07-24 21:42:32 UTC (rev 17560)
+++
csplugins/trunk/ucsd/kono/ShortestPath2/src/org/cytoscape/analysis/shortestpath/ShortestPath.java
2009-07-24 22:45:28 UTC (rev 17561)
@@ -1,27 +1,36 @@
package org.cytoscape.analysis.shortestpath;
+import giny.model.Node;
+import java.io.BufferedWriter;
+import java.io.FileOutputStream;
+import java.io.OutputStreamWriter;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Random;
+import java.util.Set;
-import java.util.*;
-
import javax.swing.JOptionPane;
+import cytoscape.CyEdge;
import cytoscape.CyNetwork;
import cytoscape.CyNode;
-import cytoscape.CyEdge;
import cytoscape.Cytoscape;
-import cytoscape.data.*;
-//import cytoscape.data.Semantics;
+import cytoscape.data.CyAttributes;
import cytoscape.giny.CytoscapeRootGraph;
import cytoscape.view.CyNetworkView;
/**
*
- * Class to calculate the shortest path between 2 nodes in the network
+ * Class to calculate the shortest path between 2 nodes in the network
* considering the network as a directed or undirected graph.
*
* @author mrsva
- *
+ *
*/
public class ShortestPath {
@@ -30,7 +39,7 @@
private CytoscapeRootGraph root;
private CyAttributes NodeAttributes;
private CyAttributes EdgeAttributes;
- //private boolean debug = true;
+ // private boolean debug = true;
private boolean undirected;
private boolean incoming;
private boolean outcoming;
@@ -41,31 +50,34 @@
/**
* Get the selected nodes and calculate the shortest path
- * @param directed use this parameter to indicate if the network is
directed
+ *
+ * @param directed
+ * use this parameter to indicate if the network is directed
*/
- public void calculate(boolean directed,String attribute) {
+ public List<Node> calculate(boolean directed, String attribute) {
network = Cytoscape.getCurrentNetwork();
view = Cytoscape.getCurrentNetworkView();
NodeAttributes = Cytoscape.getNodeAttributes();
EdgeAttributes = Cytoscape.getEdgeAttributes();
root = Cytoscape.getRootGraph();
selectedAttribute = attribute;
-
- if(!selectedAttribute.equals("Hop Distance"))
- {
+
+ if (!selectedAttribute.equals("Hop Distance")) {
byte type = EdgeAttributes.getType(selectedAttribute);
-
- if(type == EdgeAttributes.TYPE_INTEGER)
+
+ if (type == EdgeAttributes.TYPE_INTEGER)
attributeIsInt = true;
- else if(type == EdgeAttributes.TYPE_FLOATING)
+ else if (type == EdgeAttributes.TYPE_FLOATING)
attributeIsDouble = true;
else {
-
JOptionPane.showMessageDialog(view.getComponent(),
- "The Attribute selected is no longer availible.
Please update the attribute list");
- return;
+ JOptionPane
+ .showMessageDialog(
+
view.getComponent(),
+ "The Attribute
selected is no longer availible. Please update the attribute list");
+ return null;
}
}
-
+
if (directed) {
setDirected();
} else {
@@ -73,39 +85,42 @@
}
int[] selNodes = view.getSelectedNodeIndices();
if (selNodes.length != 2) {
- JOptionPane.showMessageDialog(view.getComponent(),
- "You should select 2 nodes to get the
shortest path between them");
+ JOptionPane
+ .showMessageDialog(view.getComponent(),
+ "You should select 2
nodes to get the shortest path between them");
}
int result = 0;
int node1 = selNodes[1];
int node2 = selNodes[0];
- CyNode n1 = (CyNode)network.getNode(node1);
- CyNode n2 = (CyNode)network.getNode(node2);
-
+ CyNode n1 = (CyNode) network.getNode(node1);
+ CyNode n2 = (CyNode) network.getNode(node2);
+
if (directed) {
- result =
JOptionPane.showConfirmDialog(view.getComponent(),"Source node = " +
- n1.getIdentifier() +
- "\nTarget node = " +
- n2.getIdentifier() +
- "\n \n Do you want to switch them
around?");
-
+ result =
JOptionPane.showConfirmDialog(view.getComponent(),
+ "Source node = " + n1.getIdentifier() +
"\nTarget node = "
+ + n2.getIdentifier()
+ + "\n \n Do you want to
switch them around?");
+
if (result == 0) {
int tmp = node1;
node1 = node2;
node2 = tmp;
-
+
}
}
- if (result == 2) return;
- List shortestPath = getShortestPath(node1,node2);
-
- if (shortestPath == null){
+ if (result == 2)
+ return null;
+
+ List<Node> shortestPath = getShortestPath(node1, node2);
+
+ if (shortestPath == null) {
JOptionPane.showMessageDialog(view.getComponent(),
"There is no path between the selected
nodes");
- }
- else {
+ } else {
network.setSelectedNodeState(shortestPath, true);
+
}
+ return shortestPath;
}
/**
@@ -143,114 +158,219 @@
/**
* Calculates the shortest path between node1 and node2
*
- * The algorithm is based on the code from dijkstra() function from
NetworkX:
+ * The algorithm is based on the code from dijkstra() function from
+ * NetworkX:
*
*
http://networkx.sourceforge.net/Reference/NX.paths-module.html#dijkstra
*
* but I didn't used the weight to calculate the distance. To do this,
just
* change the line:
*
- * <pre>int vwLength = tmp.intValue() + 1;</pre>
+ * <pre>
+ * int vwLength = tmp.intValue() + 1;
+ * </pre>
*
* in the source code to:
*
- * <pre>int vwLength = tmp.intValue() + getWeight();</pre>
+ * <pre>
+ * int vwLength = tmp.intValue() + getWeight();
+ * </pre>
*
- * and implement the method <pre>getWeight()</pre>.
+ * and implement the method
*
+ * <pre>
+ * getWeight()
+ * </pre>
+ *
+ * .
+ *
* NetworkX website: http://networkx.sourceforge.net/
*
- * @param node1 source node
- * @param node2 target node
- * @return list of nodes in the path between node1 and node2. If there
is no path, returns null
+ * @param node1
+ * source node
+ * @param node2
+ * target node
+ * @return list of nodes in the path between node1 and node2. If there
is no
+ * path, returns null
*/
- public List getShortestPath(int node1, int node2) {
+ public List<Node> getShortestPath(int node1, int node2) {
boolean foundContradictory = false;
- if (node1 == node2) return null;
- int nnodes = root.getNodeCount();
- CyNode cynode1 = (CyNode) network.getNode(node1);
- CyNode cynode2 = (CyNode) network.getNode(node2);
- HashMap dist = new HashMap();
- HashMap paths = new HashMap();
- List tmpList = new ArrayList();
+ if (node1 == node2)
+ return null;
+
+ selectedAttribute = "Hop Distance";
+ setUndirected();
+ network = Cytoscape.getCurrentNetwork();
+ view = Cytoscape.getCurrentNetworkView();
+ NodeAttributes = Cytoscape.getNodeAttributes();
+ EdgeAttributes = Cytoscape.getEdgeAttributes();
+ root = Cytoscape.getRootGraph();
+ Node cynode1 = network.getNode(node1);
+ Node cynode2 = network.getNode(node2);
+
+ final Map<Node, Double> dist = new HashMap<Node, Double>();
+ final Map<Node, List<Node>> paths = new HashMap<Node,
List<Node>>();
+
+ List<Node> tmpList = new ArrayList<Node>();
+
tmpList.add(cynode1);
paths.put(cynode1, tmpList);
- Hashtable seen = new Hashtable();
- seen.put(cynode1, new Double(0));
- List fringe = new ArrayList();
+ Hashtable<Node, Double> seen = new Hashtable<Node, Double>();
+ seen.put(cynode1, 0.0);
+ List<Node> fringe = new ArrayList<Node>();
fringe.add(cynode1);
+
+ Node v;
while (!fringe.isEmpty()) {
- CyNode v = (CyNode) fringe.get(0);
+ v = fringe.get(0);
int nv = root.getIndex(v);
int vnv = network.getIndex(v);
fringe.remove(0);
dist.put(v, seen.get(v));
- if (nv == node2) break;
- int[] adjEdges =
network.getAdjacentEdgeIndicesArray(vnv,undirected,incoming,outcoming);
+ if (nv == node2)
+ break;
+
+ int[] adjEdges =
network.getAdjacentEdgeIndicesArray(vnv,
+ undirected, incoming, outcoming);
int[] adjNodes = new int[adjEdges.length];
for (int i = 0; i < adjNodes.length; i++) {
int node =
network.getEdgeSourceIndex(adjEdges[i]);
- if (node == nv)
+ if (node == nv)
node =
network.getEdgeTargetIndex(adjEdges[i]);
adjNodes[i] = node;
}
- if ((adjEdges.length == 0) && (paths.size() == 1))
return null;
+ if ((adjEdges.length == 0) && (paths.size() == 1))
+ return null;
for (int n = 0; n < adjNodes.length; n++) {
int nw = adjNodes[n];
CyNode w = (CyNode) network.getNode(nw);
Double tmp = (Double) dist.get(v);
- CyEdge edge =
(CyEdge)network.getEdge(adjEdges[n]);
+ CyEdge edge = (CyEdge)
network.getEdge(adjEdges[n]);
double vwLength = tmp.doubleValue() +
getWeight(edge);
if (dist.containsKey(w)) {
- Double tmp2 = (Double)dist.get(w);
- if (vwLength < tmp2.doubleValue()){
+ Double tmp2 = (Double) dist.get(w);
+ if (vwLength < tmp2.doubleValue()) {
if (!foundContradictory) {
System.err.println("Contraditory paths found");
- foundContradictory=true;
+ foundContradictory =
true;
}
}
+ } else {
+ Double tmp3 = (Double) seen.get(w);
+ if ((!seen.containsKey(w))
+ || (vwLength <
tmp3.doubleValue())) {
+ seen.put(w, new
Double(vwLength));
+ fringe.add(w);
+ List tmpList2 = new ArrayList();
+ tmpList2.add(w);
+ List tmpList3 = (List)
paths.get(v);
+ List tmpList4 = new ArrayList();
+ tmpList4.addAll(tmpList3);
+ tmpList4.addAll(tmpList2);
+ paths.put(w, tmpList4);
+ }
}
- else {
- Double tmp3 = (Double)
seen.get(w);
- if ((!seen.containsKey(w)) ||
(vwLength < tmp3.doubleValue())) {
- seen.put(w, new
Double(vwLength));
- fringe.add(w);
- List tmpList2 = new
ArrayList();
- tmpList2.add(w);
- List tmpList3 =
(List)paths.get(v);
- List tmpList4 = new
ArrayList();
-
tmpList4.addAll(tmpList3);
-
tmpList4.addAll(tmpList2);
- paths.put(w, tmpList4);
- }
- }
}
}
- List path = (List) paths.get(cynode2);
- double pathDist = ((Double)dist.get(cynode2)).doubleValue();
+
+ List<Node> path = paths.get(cynode2);
+
+ Double pathDist = dist.get(cynode2);
+
if (attributeIsNegLog && pathDist != 0.0) {
- pathDist = Math.pow(10,-pathDist);
+ pathDist = Math.pow(10, -pathDist);
}
- JOptionPane.showMessageDialog(view.getComponent(),
- "Length of Path is " + pathDist);
+ // JOptionPane.showMessageDialog(view.getComponent(),
+ // "Length of Path is "
+ // + pathDist);
return path;
}
-
- private double getWeight(CyEdge edge) {
-
- if(selectedAttribute.equals("Hop Distance"))
+ private double getWeight(CyEdge edge) {
+
+ if (selectedAttribute.equals("Hop Distance"))
return 1;
-
- else if(attributeIsInt)
- return
EdgeAttributes.getIntegerAttribute(edge.getIdentifier(),selectedAttribute).doubleValue();
+
+ else if (attributeIsInt)
+ return
EdgeAttributes.getIntegerAttribute(edge.getIdentifier(),
+ selectedAttribute).doubleValue();
else {
- double attr =
EdgeAttributes.getDoubleAttribute(edge.getIdentifier(),selectedAttribute).doubleValue();
+ double attr = EdgeAttributes.getDoubleAttribute(
+ edge.getIdentifier(),
selectedAttribute).doubleValue();
if (attributeIsNegLog) {
attr = -Math.log10(attr);
}
- return attr;
+ return attr;
}
}
+
+ public void searchAll() {
+ CyNetwork net = Cytoscape.getCurrentNetwork();
+ Random rnd = new Random(System.currentTimeMillis());
+ List<Node> nodes = net.nodesList();
+
+ final Set<String> pairs = new HashSet<String>();
+
+ try {
+ FileOutputStream fos = new FileOutputStream("path_"
+ + net.getTitle() + ".txt");
+ OutputStreamWriter osw = new OutputStreamWriter(fos);
+ BufferedWriter bw = new BufferedWriter(osw);
+ StringBuilder builder = new StringBuilder();
+
+
+ Node node2;
+ Node node1;
+ int index = 0;
+ String pairName;
+ String pairNameR;
+
+ builder.append("Index\tPath\tPath Length\n");
+ while(index < 1000) {
+ node1 = nodes.get(rnd.nextInt(nodes.size()));
+ node2 = nodes.get(rnd.nextInt(nodes.size()));
+
if(node1.getIdentifier().equals(node2.getIdentifier()))
+ continue;
+
+ pairName = node1.getIdentifier() + ":" +
node2.getIdentifier();
+ pairNameR = node2.getIdentifier() + ":" +
node1.getIdentifier();
+ if(pairs.contains(pairName) ||
pairs.contains(pairNameR))
+ continue;
+ pairs.add(pairName);
+ pairs.add(pairNameR);
+
+ builder.append("Pair " + (index+1) + ":\t");
+ builder.append(node1.getIdentifier() + " to "
+ + node2.getIdentifier() + "\t");
+
+ List<Node> path =
getShortestPath(node1.getRootGraphIndex(),
+ node2.getRootGraphIndex());
+
+
+ if (path != null) {
+ builder.append(path.size() + "\t");
+
+ for (Node n2 : path) {
+
builder.append(n2.getIdentifier() + "\t");
+ }
+ builder.append("\n");
+ } else {
+ builder.append("0\t");
+ builder.append("No Path!!\n");
+ }
+ index++;
+
+ }
+ bw.write(builder.toString());
+
+ bw.close();
+ osw.close();
+ fos.close();
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ System.out.println("Path search done!!");
+ }
}
-
Modified:
csplugins/trunk/ucsd/kono/ShortestPath2/src/org/cytoscape/analysis/shortestpath/ShortestPathPlugin.java
===================================================================
---
csplugins/trunk/ucsd/kono/ShortestPath2/src/org/cytoscape/analysis/shortestpath/ShortestPathPlugin.java
2009-07-24 21:42:32 UTC (rev 17560)
+++
csplugins/trunk/ucsd/kono/ShortestPath2/src/org/cytoscape/analysis/shortestpath/ShortestPathPlugin.java
2009-07-24 22:45:28 UTC (rev 17561)
@@ -10,15 +10,13 @@
import javax.swing.JMenu;
import javax.swing.JMenuItem;
import javax.swing.SwingUtilities;
-import javax.swing.JOptionPane;
import org.cytoscape.analysis.shortestpath.internal.ShortestPathDialog;
import cytoscape.Cytoscape;
import cytoscape.data.CyAttributes;
-import cytoscape.view.CyNetworkView;
+import cytoscape.plugin.CytoscapePlugin;
import cytoscape.view.CytoscapeDesktop;
-import cytoscape.plugin.CytoscapePlugin;
/**
* Plugin for Cytoscape to find the shortest path between 2 nodes in a network.
@@ -56,6 +54,11 @@
// Now add our default
addMenuItem(menu, "Hop Distance");
+
+ JMenuItem item = new JMenuItem("Search All");
+ SearchAllMenuActionListener va = new
SearchAllMenuActionListener();
+ item.addActionListener(va);
+ menu.add(item);
//Finds all attributes that are integers or doubles, and adds
them to list
for(int i = 0; i < attributeNames.length; i++)
@@ -97,7 +100,22 @@
});
}
}
+
+ private class SearchAllMenuActionListener extends AbstractAction {
+ public SearchAllMenuActionListener () {
+ }
+
+ public void actionPerformed(ActionEvent ev) {
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ ShortestPath alg = new ShortestPath();
+ alg.searchAll();
+ }
+ });
+ }
+ }
+
public void propertyChange(PropertyChangeEvent evt) {
if ( evt.getPropertyName() == CytoscapeDesktop.NETWORK_VIEW_CREATED ){
// Recreate the menu
Modified:
csplugins/trunk/ucsd/kono/ShortestPath2/src/org/cytoscape/analysis/shortestpath/internal/ShortestPathDialog.java
===================================================================
---
csplugins/trunk/ucsd/kono/ShortestPath2/src/org/cytoscape/analysis/shortestpath/internal/ShortestPathDialog.java
2009-07-24 21:42:32 UTC (rev 17560)
+++
csplugins/trunk/ucsd/kono/ShortestPath2/src/org/cytoscape/analysis/shortestpath/internal/ShortestPathDialog.java
2009-07-24 22:45:28 UTC (rev 17561)
@@ -1,88 +1,91 @@
package org.cytoscape.analysis.shortestpath.internal;
-
-
+import java.awt.Frame;
+import java.awt.GridLayout;
import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
-import javax.swing.*;
-import javax.swing.WindowConstants.*;
-import javax.swing.border.*;
+import javax.swing.BorderFactory;
+import javax.swing.BoxLayout;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JDialog;
+import javax.swing.JPanel;
+import javax.swing.border.CompoundBorder;
+import javax.swing.border.EmptyBorder;
+import javax.swing.border.EtchedBorder;
import org.cytoscape.analysis.shortestpath.ShortestPath;
-import java.awt.Frame;
-import java.awt.GridLayout;
-import java.awt.event.*;
-
import cytoscape.Cytoscape;
import cytoscape.data.CyAttributes;
-import cytoscape.view.CyNetworkView;
-import cytoscape.plugin.CytoscapePlugin;
/**
* Plugin for Cytoscape to find the shortest path between 2 nodes in a network.
* It is possible to find the shortest path in directed and undirected networks
*
* @author mrsva
- *
+ *
*/
public class ShortestPathDialog extends JDialog implements ActionListener {
String selectedAttribute = null;
JCheckBox dirButton;
JCheckBox logButton;
- public ShortestPathDialog (Frame parent, String attribute) {
+ public ShortestPathDialog(Frame parent, String attribute) {
super(parent, false);
this.selectedAttribute = attribute;
setDefaultCloseOperation(DISPOSE_ON_CLOSE);
- setTitle("Find Shorted Path using "+selectedAttribute);
+ setTitle("Find Shorted Path using " + selectedAttribute);
JPanel dataPanel = new JPanel();
BoxLayout layout = new BoxLayout(dataPanel,
BoxLayout.PAGE_AXIS);
- dataPanel.setLayout(layout);
+ dataPanel.setLayout(layout);
- JPanel checkBoxes = new JPanel(new GridLayout(2,1));
+ JPanel checkBoxes = new JPanel(new GridLayout(2, 1));
// Set up our radio buttons (Directed vs Undirected)
dirButton = new JCheckBox("Calculate path assuming directed
edges");
dirButton.setSelected(false);
checkBoxes.add(dirButton);
- logButton = new JCheckBox("Weights are expectation values (will
use negative log)");
+ logButton = new JCheckBox(
+ "Weights are expectation values (will use
negative log)");
{
logButton.setSelected(false);
checkBoxes.add(logButton);
// Is the negative log option available?
CyAttributes EdgeAttributes =
Cytoscape.getEdgeAttributes();
byte type = EdgeAttributes.getType(selectedAttribute);
- if(type == EdgeAttributes.TYPE_INTEGER) {
+ if (type == EdgeAttributes.TYPE_INTEGER) {
// No
logButton.setEnabled(false);
}
}
checkBoxes.add(logButton);
- checkBoxes.setBorder(new CompoundBorder(
- BorderFactory.createEtchedBorder(EtchedBorder.LOWERED),
- new EmptyBorder(10,10,10,10)));
+ checkBoxes.setBorder(new CompoundBorder(BorderFactory
+ .createEtchedBorder(EtchedBorder.LOWERED), new
EmptyBorder(10,
+ 10, 10, 10)));
dataPanel.add(checkBoxes);
- // Create the button box
- JPanel buttonBox = new JPanel();
- JButton doneButton = new JButton("Done");
- doneButton.setActionCommand("done");
- doneButton.addActionListener(this);
+ // Create the button box
+ JPanel buttonBox = new JPanel();
+ JButton doneButton = new JButton("Done");
+ doneButton.setActionCommand("done");
+ doneButton.addActionListener(this);
- JButton findButton = new JButton("Find Shortest Path");
- findButton.setActionCommand("find");
- findButton.addActionListener(this);
- buttonBox.add(doneButton);
- buttonBox.add(findButton);
-
buttonBox.setBorder(BorderFactory.createEtchedBorder(EtchedBorder.LOWERED));
+ JButton findButton = new JButton("Find Shortest Path");
+ findButton.setActionCommand("find");
+ findButton.addActionListener(this);
+ buttonBox.add(doneButton);
+ buttonBox.add(findButton);
+ buttonBox.setBorder(BorderFactory
+ .createEtchedBorder(EtchedBorder.LOWERED));
- dataPanel.add(buttonBox);
- setContentPane(dataPanel);
+ dataPanel.add(buttonBox);
+ setContentPane(dataPanel);
}
-
+
public void actionPerformed(ActionEvent e) {
if ("done".equals(e.getActionCommand())) {
setVisible(false);
@@ -94,9 +97,9 @@
sp.setNegativeLog(false);
}
if (dirButton.isSelected()) {
- sp.calculate(true,selectedAttribute);
+ sp.calculate(true, selectedAttribute);
} else {
- sp.calculate(false,selectedAttribute);
+ sp.calculate(false, selectedAttribute);
}
}
}
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