Author: laylaoesper
Date: 2010-08-05 08:46:13 -0700 (Thu, 05 Aug 2010)
New Revision: 21215
Modified:
csplugins/trunk/soc/layla/SemanticSummary/jars/SemanticSummary.jar
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/AddDelimiterDialog.java
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/CloudDisplayPanel.java
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/CloudListMouseListener.java
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/CloudListSelectionHandler.java
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/CloudParameters.java
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/CloudWordInfo.java
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/CreateCloudAction.java
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/CreateCloudNetworkAction.java
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/DeleteCloudAction.java
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/EditCloudNameDialog.java
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/ModifiedClusterFlowLayout.java
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/ModifiedFlowLayout.java
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SemanticSummaryClusterBuilder.java
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SemanticSummaryInputPanel.java
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SemanticSummaryPluginAction.java
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SliderBarPanel.java
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/UpdateCloudAction.java
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/WordFilter.java
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/WordPair.java
Log:
Clean up of some of the code.
Modified: csplugins/trunk/soc/layla/SemanticSummary/jars/SemanticSummary.jar
===================================================================
(Binary files differ)
Modified:
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/AddDelimiterDialog.java
===================================================================
---
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/AddDelimiterDialog.java
2010-08-05 14:36:13 UTC (rev 21214)
+++
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/AddDelimiterDialog.java
2010-08-05 15:46:13 UTC (rev 21215)
@@ -45,6 +45,9 @@
public class AddDelimiterDialog extends JDialog implements ActionListener
{
+
+ private static final long serialVersionUID = -2295450101951048637L;
+
//VARIABLES
private String newName = "";
Modified:
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/CloudDisplayPanel.java
===================================================================
---
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/CloudDisplayPanel.java
2010-08-05 14:36:13 UTC (rev 21214)
+++
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/CloudDisplayPanel.java
2010-08-05 15:46:13 UTC (rev 21215)
@@ -24,22 +24,14 @@
import java.awt.BorderLayout;
import java.awt.Color;
-import java.awt.Component;
-import java.awt.Container;
-import java.awt.Dimension;
-import java.awt.FlowLayout;
-import java.awt.Font;
-import java.awt.Insets;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.Iterator;
-import java.util.SortedMap;
import java.util.SortedSet;
import java.util.TreeSet;
import javax.swing.BorderFactory;
-import javax.swing.BoxLayout;
import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
@@ -57,6 +49,8 @@
public class CloudDisplayPanel extends JPanel
{
+
+ private static final long serialVersionUID = 5996569544692738989L;
//VARIABLES
JPanel tagCloudFlowPanel;//add JLabels here for words
@@ -77,7 +71,6 @@
}
//METHODS
- //TODO
/**
* Initialized a blank tag cloud JPanel object.
Modified:
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/CloudListMouseListener.java
===================================================================
---
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/CloudListMouseListener.java
2010-08-05 14:36:13 UTC (rev 21214)
+++
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/CloudListMouseListener.java
2010-08-05 15:46:13 UTC (rev 21215)
@@ -32,8 +32,6 @@
import javax.swing.JList;
import javax.swing.JOptionPane;
import javax.swing.JPopupMenu;
-import javax.swing.ListSelectionModel;
-import javax.swing.SwingUtilities;
import cytoscape.Cytoscape;
import cytoscape.util.CytoscapeAction;
@@ -78,7 +76,6 @@
}
- //TODO
private void rightClickList(MouseEvent e)
{
//RightClickMenu menu = new RightClickPopUpMenu();
@@ -109,6 +106,9 @@
public class ChangeCloudNameAction extends CytoscapeAction
{
+
+ private static final long serialVersionUID =
3741354852598317680L;
+
//CONSTRUCTOR
public ChangeCloudNameAction()
{
Modified:
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/CloudListSelectionHandler.java
===================================================================
---
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/CloudListSelectionHandler.java
2010-08-05 14:36:13 UTC (rev 21214)
+++
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/CloudListSelectionHandler.java
2010-08-05 15:46:13 UTC (rev 21215)
@@ -22,10 +22,7 @@
package cytoscape.csplugins.semanticsummary;
-import giny.view.NodeView;
-
import java.util.HashSet;
-import java.util.Iterator;
import java.util.List;
import java.util.Set;
Modified:
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/CloudParameters.java
===================================================================
---
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/CloudParameters.java
2010-08-05 14:36:13 UTC (rev 21214)
+++
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/CloudParameters.java
2010-08-05 15:46:13 UTC (rev 21215)
@@ -23,13 +23,10 @@
package cytoscape.csplugins.semanticsummary;
import java.awt.Component;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.io.PrintWriter;
+
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
-import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Set;
@@ -52,12 +49,11 @@
*
*/
-public class CloudParameters implements Comparable
+public class CloudParameters implements Comparable<CloudParameters>
{
//VARIABLES
private String cloudName;
- //private String attributeName;
private ArrayList<String> attributeNames;
private String displayStyle;
@@ -131,7 +127,6 @@
this.cloudWords = new ArrayList<CloudWordInfo>();
this.netWeightFactor = this.getDefaultNetWeight();
- //this.attributeName = this.getDefaultAttName();
this.clusterCutoff = this.getDefaultClusterCutoff();
this.maxWords = this.getDefaultMaxWords();
this.displayStyle = this.getDefaultDisplayStyle();
@@ -164,7 +159,6 @@
}
this.cloudName = props.get("CloudName");
- //this.attributeName = props.get("AttributeName");
this.displayStyle = props.get("DisplayStyle");
this.selectedNumNodes = new
Integer(props.get("SelectedNumNodes"));
this.networkNumNodes = new
Integer(props.get("NetworkNumNodes"));
@@ -364,7 +358,6 @@
*/
public void updateSelectedCounts()
{
-
//do nothing if selected hasn't changed initialized
if (selInitialized)
return;
@@ -609,7 +602,6 @@
//Iterate through to calculate ratios
Iterator<String> pairIter = words.iterator();
- boolean pairInitialized = false;
while (pairIter.hasNext())
{
String curWord = (String)pairIter.next();
@@ -717,34 +709,9 @@
Double yIntercept = maxFont - (slope*zeroedMaxWeight);
//maxRatio maps to maxFont
//Round up to nearest Integer
- //Double temp = Math.ceil((slope*newRatio) + yIntercept);
long temp = Math.round((slope*newRatio) + yIntercept);
-
- //Integer fontSize = temp.intValue();
Integer fontSize = Math.round(temp);
- /*
- //Original
- //Map the interval minRatio to maxRatio to the new interval
- //minFont to maxFont using a linear transformation
- Integer maxFont = networkParams.getMaxFont();
- Integer minFont = networkParams.getMinFont();
-
- //Check if maxRatio and minRatio are the same
- if (maxRatio.equals(minRatio))
- return (minFont + (maxFont - minFont)/2);
-
- Double slope = (maxFont - minFont)/(maxRatio - minRatio);
- Double yIntercept = maxFont - (slope*maxRatio); //maxRatio maps
to maxFont
-
- //Round up to nearest Integer
- //Double temp = Math.ceil((slope*ratio) + yIntercept);
- long temp = Math.round((slope*ratio) + yIntercept);
-
- //Integer fontSize = temp.intValue();
- Integer fontSize = Math.round(temp);
- */
-
return fontSize;
}
@@ -767,7 +734,6 @@
//Attribute
- //Object attribute =
inputPanel.getCMBAttributes().getSelectedItem();
Object[] attributes =
inputPanel.getAttributeList().getSelectedValues();
ArrayList<String> attributeList = new ArrayList<String>();
@@ -778,23 +744,8 @@
if (curAttribute instanceof String)
{
attributeList.add((String) curAttribute);
- //setAttributeName((String) attribute);
}
- /*
- else
- {
- //setAttributeName(defaultAttName);
-
//inputPanel.getCMBAttributes().setSelectedItem(attributeName);
-
- ArrayList<String> attributeList = new
ArrayList<String>();
- attributeList.add(defaultAttName);
- this.setAttributeNames(attributeList);
-
//inputPanel.getCMBAttributes().setSelectedItem(defaultAttName);
-
inputPanel.getAttributeList().setSelectedIndex(0);
- String message = "You must select a valid
String attribute or use the node ID.";
-
JOptionPane.showMessageDialog(Cytoscape.getDesktop(), message, "Parameter out
of bounds", JOptionPane.WARNING_MESSAGE);
- }
- */
+
this.setAttributeNames(attributeList);
}
@@ -853,7 +804,6 @@
StringBuffer paramVariables = new StringBuffer();
paramVariables.append("CloudName\t" + cloudName + "\n");
- //paramVariables.append("AttributeName\t" + attributeName +
"\n");
paramVariables.append("DisplayStyle\t" + displayStyle + "\n");
//List of Nodes as a comma delimited list
@@ -1074,71 +1024,6 @@
/**
- * This method takes in the ID of a node and returns the string that is
associated
- * with that node and the current attribute of this CloudParameters.
- * @param CyNode - node we are interested in
- * @return String - value stored in the current attribute for the given
node.
- */
- /*
- private String getNodeAttributeVal(CyNode curNode)
- {
- //Retrieve value based on attribute
- String nodeValue = "";
-
- //if we should use the ID
- if (this.attributeName.equals("nodeID"))
- {
- nodeValue = curNode.toString();
- }
-
- //Use a different attribute
- else
- {
- CyAttributes cyNodeAttrs =
Cytoscape.getNodeAttributes();
-
- if (cyNodeAttrs.getType(attributeName)==
CyAttributes.TYPE_STRING)
- {
- nodeValue =
cyNodeAttrs.getStringAttribute(curNode.getIdentifier(), attributeName);
- }
-
- else if (cyNodeAttrs.getType(attributeName) ==
CyAttributes.TYPE_SIMPLE_LIST)
- {
- List attribute =
cyNodeAttrs.getListAttribute(curNode.getIdentifier(), attributeName);
-
- if (attribute == null)
- return null;
-
- else
- {
- for (Iterator iter =
attribute.iterator(); iter.hasNext();)
- {
- Object curObj = iter.next();
- if (curObj instanceof String)
- {
- //Turn list into space
separated string
- String curObjString =
(String)curObj;
- nodeValue = nodeValue +
curObjString + " ";
- }//
- }
- }
- }
- else
- {
- //Don't currently handle non string attributes
- //This code should currently never be accessed
- Component desktop = Cytoscape.getDesktop();
-
- JOptionPane.showMessageDialog(desktop,
- "Current implementation does not handle
non-String attributes.");
- return null;
- }//end else
- }//end else
-
- return nodeValue;
- }//end method
- */
-
- /**
* This method takes in a string from a node and processes it to lower
case, removes
* punctuation and separates the words into a non repeated list.
* @param String from a node that we are processing.
@@ -1183,18 +1068,11 @@
* @param CloudParameters object to compare this object to
* @return
*/
- public int compareTo(Object o)
- {
- if (o instanceof CloudParameters)
- {
- CloudParameters compare = (CloudParameters)o;
-
- Integer thisCount = this.getCloudNum();
- Integer compareCount = compare.getCloudNum();
- return thisCount.compareTo(compareCount);
- }
- else
- return 0;
+ public int compareTo(CloudParameters compare)
+ {
+ Integer thisCount = this.getCloudNum();
+ Integer compareCount = compare.getCloudNum();
+ return thisCount.compareTo(compareCount);
}
/**
@@ -1221,27 +1099,6 @@
cloudName = name;
}
- /*
- public String getAttributeName()
- {
- return attributeName;
- }
-
- public void setAttributeName(String name)
- {
- //Set flags if it is changing
- if (!attributeName.equals(name))
- {
- countInitialized = false;
- selInitialized = false;
- ratiosInitialized = false;
- }
-
- attributeName = name;
-
- }
- */
-
public ArrayList<String> getAttributeNames()
{
return attributeNames;
@@ -1528,12 +1385,7 @@
public void setClusterCutoff(Double val)
{
- //Rest flags if it changes
- if (!clusterCutoff.equals(val))
- //TODO - SOMETHING HERE
- ;
clusterCutoff = val;
-
}
public Integer getMaxWords()
Modified:
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/CloudWordInfo.java
===================================================================
---
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/CloudWordInfo.java
2010-08-05 14:36:13 UTC (rev 21214)
+++
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/CloudWordInfo.java
2010-08-05 15:46:13 UTC (rev 21215)
@@ -24,7 +24,6 @@
import java.awt.Color;
import java.awt.Font;
-import java.awt.FontMetrics;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.util.ArrayList;
@@ -32,7 +31,6 @@
import java.util.Iterator;
import java.util.List;
-import javax.swing.BorderFactory;
import javax.swing.JLabel;
import cytoscape.CyNetwork;
@@ -194,15 +192,12 @@
CyNetwork network =
Cytoscape.getCurrentNetwork();
CyNetworkView view =
Cytoscape.getCurrentNetworkView();
if (view.getNetwork().equals(network))
- //if
(!Cytoscape.getCurrentNetworkView().equals(Cytoscape.getNullNetworkView()))
{
- //CyNetwork network =
Cytoscape.getCurrentNetwork();
network.unselectAllNodes();
network.unselectAllEdges();
network.setSelectedNodeState(nodes,
true);
//Redraw the graph with selected nodes
- //CyNetworkView view =
Cytoscape.getCurrentNetworkView();
view.redrawGraph(false, true);
//Bring panels to the front
@@ -215,12 +210,10 @@
public void mouseEntered(MouseEvent me)
{
JLabel clickedLabel = (JLabel)me.getComponent();
- String word = clickedLabel.getText();
CyNetwork network =
Cytoscape.getCurrentNetwork();
CyNetworkView view =
Cytoscape.getCurrentNetworkView();
if (view.getNetwork().equals(network))
- //if
(!Cytoscape.getCurrentNetworkView().equals(Cytoscape.getNullNetworkView()))
{
clickedLabel.setForeground(new
Color(0,200,255));
clickedLabel.repaint();
@@ -231,7 +224,6 @@
public void mouseExited(MouseEvent me)
{
JLabel clickedLabel = (JLabel)me.getComponent();
- String word = clickedLabel.getText();
if
(!Cytoscape.getCurrentNetworkView().equals(Cytoscape.getNullNetworkView()))
{
Modified:
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/CreateCloudAction.java
===================================================================
---
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/CreateCloudAction.java
2010-08-05 14:36:13 UTC (rev 21214)
+++
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/CreateCloudAction.java
2010-08-05 15:46:13 UTC (rev 21215)
@@ -47,9 +47,11 @@
public class CreateCloudAction extends CytoscapeAction
{
//VARIABLES
+ private static final long serialVersionUID = 1103296239269358444L;
//CONSTRUCTORS
+
/**
* CreateCloudAction constructor.
*/
@@ -77,7 +79,6 @@
CyNetworkView view = Cytoscape.getCurrentNetworkView();
//Unable to proceed if either of these is null
- //TODO - This never happens since network and view will be
special
//empty CyNetwork(View)
if (network == null || view == null)
{return;}
Modified:
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/CreateCloudNetworkAction.java
===================================================================
---
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/CreateCloudNetworkAction.java
2010-08-05 14:36:13 UTC (rev 21214)
+++
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/CreateCloudNetworkAction.java
2010-08-05 15:46:13 UTC (rev 21215)
@@ -50,6 +50,8 @@
public class CreateCloudNetworkAction extends CytoscapeAction
{
+ private static final long serialVersionUID = 2683655996962050569L;
+
//VARIABLES
public static String WORD_VAL = "Word_Prob";
public static String CO_VAL = "CO_Prob";
@@ -154,10 +156,6 @@
//Create view
view.applyLayout(CyLayouts.getLayout("force-directed"));
-
- //make sure that network is registered so that Quickfind works
-
Cytoscape.firePropertyChange(cytoscape.view.CytoscapeDesktop.NETWORK_VIEW_CREATED,
network, view);
-
}
}
Modified:
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/DeleteCloudAction.java
===================================================================
---
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/DeleteCloudAction.java
2010-08-05 14:36:13 UTC (rev 21214)
+++
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/DeleteCloudAction.java
2010-08-05 15:46:13 UTC (rev 21215)
@@ -24,19 +24,11 @@
import java.awt.Component;
import java.awt.event.ActionEvent;
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Set;
import javax.swing.JOptionPane;
-import cytoscape.CyNetwork;
-import cytoscape.CyNode;
import cytoscape.Cytoscape;
import cytoscape.util.CytoscapeAction;
-import cytoscape.view.CyNetworkView;
/**
* This is the action associated with deleting a Semantic Summary Tag Cloud
@@ -49,8 +41,10 @@
{
//VARIABLES
- //CONSTRUCTORS
+ private static final long serialVersionUID = -321557784440369508L;
+ //CONSTRUCTORS
+
/**
* DeleteCloudAction constructor.
*/
Modified:
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/EditCloudNameDialog.java
===================================================================
---
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/EditCloudNameDialog.java
2010-08-05 14:36:13 UTC (rev 21214)
+++
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/EditCloudNameDialog.java
2010-08-05 15:46:13 UTC (rev 21215)
@@ -45,6 +45,8 @@
public class EditCloudNameDialog extends JDialog implements ActionListener
{
+ private static final long serialVersionUID = 6753430486708487015L;
+
//VARIABLES
private String newName = "";
Modified:
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/ModifiedClusterFlowLayout.java
===================================================================
---
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/ModifiedClusterFlowLayout.java
2010-08-05 14:36:13 UTC (rev 21214)
+++
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/ModifiedClusterFlowLayout.java
2010-08-05 15:46:13 UTC (rev 21215)
@@ -35,8 +35,12 @@
* @author Babu Kalakrishnan
* @author Layla Oesper
*/
-public class ModifiedClusterFlowLayout extends FlowLayout {
- public ModifiedClusterFlowLayout() {
+public class ModifiedClusterFlowLayout extends FlowLayout
+{
+ private static final long serialVersionUID = 6950793266604882517L;
+
+
+ public ModifiedClusterFlowLayout() {
super();
}
Modified:
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/ModifiedFlowLayout.java
===================================================================
---
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/ModifiedFlowLayout.java
2010-08-05 14:36:13 UTC (rev 21214)
+++
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/ModifiedFlowLayout.java
2010-08-05 15:46:13 UTC (rev 21215)
@@ -31,8 +31,11 @@
* @author Babu Kalakrishnan
*/
-public class ModifiedFlowLayout extends FlowLayout {
- public ModifiedFlowLayout() {
+public class ModifiedFlowLayout extends FlowLayout
+{
+ private static final long serialVersionUID = 3306786779359311470L;
+
+ public ModifiedFlowLayout() {
super();
}
Modified:
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SemanticSummaryClusterBuilder.java
===================================================================
---
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SemanticSummaryClusterBuilder.java
2010-08-05 14:36:13 UTC (rev 21214)
+++
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SemanticSummaryClusterBuilder.java
2010-08-05 15:46:13 UTC (rev 21215)
@@ -24,11 +24,6 @@
import java.awt.Color;
import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Set;
/**
* The SemanticSummaryClusterBuilder class contains the methods and
@@ -45,7 +40,6 @@
private CloudParameters params;
private ClusterPriorityQueue queue;
private WordClusters clusters;
- private Double cutoff;
private ArrayList<CloudWordInfo> cloudWords;
boolean initialized;
private final static Integer NUMCOLORS = 7;
@@ -60,7 +54,6 @@
params = new CloudParameters();
queue = new ClusterPriorityQueue();
clusters = new WordClusters();
- cutoff = 0.0;
cloudWords = new ArrayList<CloudWordInfo>();
initialized = false;
@@ -90,8 +83,6 @@
if (!initialized)
return;
- cutoff = cutoffVal;
-
boolean isDone = false; //flag for when we pass the cutoff value
while (!isDone && !queue.isEmpty())
Modified:
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SemanticSummaryInputPanel.java
===================================================================
---
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SemanticSummaryInputPanel.java
2010-08-05 14:36:13 UTC (rev 21214)
+++
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SemanticSummaryInputPanel.java
2010-08-05 15:46:13 UTC (rev 21215)
@@ -58,20 +58,16 @@
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JPopupMenu;
-import javax.swing.JRadioButton;
import javax.swing.JScrollPane;
import javax.swing.JTextArea;
import javax.swing.JTextField;
-import javax.swing.ListModel;
import javax.swing.ListSelectionModel;
import javax.swing.ScrollPaneConstants;
import javax.swing.event.ChangeListener;
import javax.swing.event.ListSelectionEvent;
import javax.swing.event.ListSelectionListener;
-import javax.swing.event.PopupMenuEvent;
-import javax.swing.event.PopupMenuListener;
-import javax.swing.text.MaskFormatter;
+
import cytoscape.Cytoscape;
import cytoscape.data.CyAttributes;
import cytoscape.util.swing.CheckBoxJList;
@@ -90,9 +86,10 @@
{
//VARIABLES
+ private static final long serialVersionUID = 2453517387682663100L;
- DecimalFormat decFormat; //used in formatted text fields with decimals
- NumberFormat intFormat; //used in formatted text fields with integers
+ private DecimalFormat decFormat; //used in formatted text fields with
decimals
+ private NumberFormat intFormat; //used in formatted text fields with
integers
//Text Fields
Modified:
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SemanticSummaryPluginAction.java
===================================================================
---
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SemanticSummaryPluginAction.java
2010-08-05 14:36:13 UTC (rev 21214)
+++
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SemanticSummaryPluginAction.java
2010-08-05 15:46:13 UTC (rev 21215)
@@ -24,10 +24,8 @@
import java.awt.event.ActionEvent;
-import javax.swing.JList;
import javax.swing.SwingConstants;
-import cytoscape.CyNetwork;
import cytoscape.Cytoscape;
import cytoscape.util.CytoscapeAction;
import cytoscape.view.CytoscapeDesktop;
@@ -48,8 +46,8 @@
public class SemanticSummaryPluginAction extends CytoscapeAction
{
//VARIABLES
+ private static final long serialVersionUID = -5407980202304156167L;
-
//CONSTRUCTORS
/**
Modified:
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SliderBarPanel.java
===================================================================
---
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SliderBarPanel.java
2010-08-05 14:36:13 UTC (rev 21214)
+++
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SliderBarPanel.java
2010-08-05 15:46:13 UTC (rev 21215)
@@ -22,18 +22,11 @@
package cytoscape.csplugins.semanticsummary;
-import cytoscape.CyNetwork;
-import cytoscape.Cytoscape;
-import cytoscape.data.CyAttributes;
-
import javax.swing.*;
-import javax.swing.event.ChangeListener;
-import javax.swing.event.ChangeEvent;
-import java.util.Iterator;
+
import java.util.Hashtable;
import java.awt.*;
-import giny.model.Node;
import prefuse.data.query.NumberRangeModel;
Modified:
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/UpdateCloudAction.java
===================================================================
---
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/UpdateCloudAction.java
2010-08-05 14:36:13 UTC (rev 21214)
+++
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/UpdateCloudAction.java
2010-08-05 15:46:13 UTC (rev 21215)
@@ -49,10 +49,12 @@
public class UpdateCloudAction extends CytoscapeAction
{
-//VARIABLES
+ //VARIABLES
+ private static final long serialVersionUID = -814444939886393362L;
//CONSTRUCTORS
+
/**
* DeleteCloudAction constructor.
*/
Modified:
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/WordFilter.java
===================================================================
---
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/WordFilter.java
2010-08-05 14:36:13 UTC (rev 21214)
+++
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/WordFilter.java
2010-08-05 15:46:13 UTC (rev 21215)
@@ -21,23 +21,20 @@
*/
package cytoscape.csplugins.semanticsummary;
-import cytoscape.Cytoscape;
+
import cytoscape.data.readers.TextFileReader;
import cytoscape.data.readers.TextJarReader;
-import java.io.BufferedReader;
import java.io.File;
-import java.io.InputStream;
-import java.io.InputStreamReader;
+
import java.net.URISyntaxException;
import java.net.URL;
-import java.util.ArrayList;
+
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.StringTokenizer;
-import javax.swing.JOptionPane;
/**
Modified:
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/WordPair.java
===================================================================
---
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/WordPair.java
2010-08-05 14:36:13 UTC (rev 21214)
+++
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/WordPair.java
2010-08-05 15:46:13 UTC (rev 21215)
@@ -29,7 +29,7 @@
* @version 1.0
*/
-public class WordPair implements Comparable
+public class WordPair implements Comparable<WordPair>
{
//VARIABLES
private String firstWord;
@@ -79,14 +79,8 @@
probability = doubleNumerator/doubleDenom;
}
- public int compareTo(Object o)
+ public int compareTo(WordPair second)
{
- WordPair second;
- if (o instanceof WordPair)
- second = (WordPair)o;
- else
- return 0;
-
Double firstProb = this.probability;
Double secondProb = second.probability;
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