Author: laylaoesper
Date: 2010-07-27 10:19:35 -0700 (Tue, 27 Jul 2010)
New Revision: 21032
Added:
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/AddDelimiterDialog.java
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/WordDelimiters.java
Modified:
csplugins/trunk/soc/layla/SemanticSummary/jars/SemanticSummary.jar
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/CloudParameters.java
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SemanticSummaryInputPanel.java
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SemanticSummaryParameters.java
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SemanticSummaryPlugin.java
Log:
Adding the functionality to add/remove delimiters from use with the WordCloud.
Modified: csplugins/trunk/soc/layla/SemanticSummary/jars/SemanticSummary.jar
===================================================================
(Binary files differ)
Added:
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/AddDelimiterDialog.java
===================================================================
---
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/AddDelimiterDialog.java
(rev 0)
+++
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/AddDelimiterDialog.java
2010-07-27 17:19:35 UTC (rev 21032)
@@ -0,0 +1,154 @@
+/*
+ File: EditCloudNameDialog.java
+
+ Copyright 2010 - The Cytoscape Consortium (www.cytoscape.org)
+
+ Code written by: Layla Oesper
+ Authors: Layla Oesper, Ruth Isserlin, Daniele Merico
+
+ This library is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this project. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package cytoscape.csplugins.semanticsummary;
+
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.Insets;
+
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+
+/**
+ * This class handles all the dialog box associated with defining your own
delimiter.
+ * @author Layla Oesper
+ * @version 1.0
+ */
+
+public class AddDelimiterDialog extends JDialog implements ActionListener
+{
+ //VARIABLES
+ private String newName = "";
+
+ private JButton btnCancel;
+ private JButton btnOK;
+ private JLabel jLabel1;
+ private JPanel jPanel1;
+ private JTextField tfDelimiter;
+
+
+ //CONSTRUCTOR
+ /**
+ * Creates a new AddDelimiterDialog object
+ * @param parent - parent component to display this in
+ * @param modal - whether this is a modal display
+ */
+ public AddDelimiterDialog(Component parent, boolean modal)
+ {
+ super((JFrame) parent, modal);
+ initComponents();
+
+ setSize(new java.awt.Dimension(300, 170));
+ }
+
+ //METHODS
+ /**
+ * Initializes all components for this dialog.
+ */
+ private void initComponents() {
+ GridBagConstraints gridBagConstraints;
+
+ jLabel1 = new JLabel();
+ tfDelimiter = new JTextField();
+ jPanel1 = new JPanel();
+ btnOK = new JButton();
+ btnCancel = new JButton();
+
+ btnOK.addActionListener(this);
+ btnCancel.addActionListener(this);
+
+ getContentPane().setLayout(new GridBagLayout());
+
+
setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
+ setTitle("Add Word Tokenization Delimiter");
+ jLabel1.setText("Please enter the new delimiter:");
+ gridBagConstraints = new GridBagConstraints();
+ gridBagConstraints.anchor = GridBagConstraints.WEST;
+ gridBagConstraints.insets = new Insets(15, 10, 0, 0);
+ getContentPane().add(jLabel1, gridBagConstraints);
+
+ gridBagConstraints = new GridBagConstraints();
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.fill = GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.insets = new Insets(10, 10, 10, 10);
+ getContentPane().add(tfDelimiter, gridBagConstraints);
+
+ btnOK.setText("OK");
+ btnOK.setPreferredSize(new Dimension(65, 23));
+ btnCancel.setPreferredSize(new Dimension(65, 23));
+
+ jPanel1.add(btnOK);
+
+ btnCancel.setText("Cancel");
+ jPanel1.add(btnCancel);
+
+ gridBagConstraints = new GridBagConstraints();
+ gridBagConstraints.gridy = 2;
+ gridBagConstraints.insets = new Insets(10, 0, 10, 0);
+ getContentPane().add(jPanel1, gridBagConstraints);
+
+ pack();
+ }
+
+ /**
+ * Called when an action is performed on this dialog.
+ * @param ActionEvent
+ */
+ public void actionPerformed(ActionEvent e)
+ {
+ Object _actionObject = e.getSource();
+
+ // handle button events
+ if(_actionObject instanceof JButton)
+ {
+ JButton _btn = (JButton) _actionObject;
+
+ if (_btn == btnOK)
+ {
+ newName = tfDelimiter.getText();
+ this.dispose();
+ } else if (_btn == btnCancel)
+ {
+ this.dispose();
+ }
+ }
+ }
+
+ /**
+ * Returns the new Cloud Name.
+ */
+ public String getNewDelimiter()
+ {
+ return newName;
+ }
+}
+
Modified:
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/CloudParameters.java
===================================================================
---
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/CloudParameters.java
2010-07-26 23:39:22 UTC (rev 21031)
+++
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/CloudParameters.java
2010-07-27 17:19:35 UTC (rev 21032)
@@ -88,7 +88,9 @@
//String Delimeters
private static final String NODEDELIMITER = "CloudParamNodeDelimiter";
private static final String WORDDELIMITER = "CloudParamWordDelimiter";
+ private static final char controlChar = '\u001F';
+
//Default Values for User Input
private Double defaultNetWeight = 0.5;
private String defaultAttName = "nodeID";
@@ -894,12 +896,23 @@
nodeValue = nodeValue.toLowerCase();
//replace all punctuation with white spaces except ' and -
- nodeValue = nodeValue.replaceAll("[[\\p{Punct}] && [^'-]]", "
");
+ //nodeValue = nodeValue.replaceAll("[[\\p{Punct}] && [^'-]]", "
");
+ String controlString = Character.toString(controlChar);
+
+ //Remove all standard delimiters and replace with controlChar
+ WordDelimiters delims = this.getNetworkParams().getDelimiter();
+ nodeValue =
nodeValue.replaceAll(delims.getRegex(),controlString);
+ //Remove all user stated delimiters and replace with controlChar
+ for (Iterator<String> iter = delims.getUserDelims().iterator();
iter.hasNext();)
+ {
+ String userDelim = iter.next();
+ nodeValue = nodeValue.replaceAll(userDelim,
controlString);
+ }
+
//Separate into non repeating set of words
List<String> wordSet = new ArrayList<String>();
- //Set<String> wordSet = new HashSet<String>();
- StringTokenizer token = new StringTokenizer(nodeValue);
+ StringTokenizer token = new StringTokenizer(nodeValue,
controlString);
while (token.hasMoreTokens())
{
String a = token.nextToken();
Modified:
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SemanticSummaryInputPanel.java
===================================================================
---
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SemanticSummaryInputPanel.java
2010-07-26 23:39:22 UTC (rev 21031)
+++
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SemanticSummaryInputPanel.java
2010-07-27 17:19:35 UTC (rev 21032)
@@ -23,6 +23,7 @@
package cytoscape.csplugins.semanticsummary;
import java.awt.BorderLayout;
+import java.awt.Component;
import java.awt.Dimension;
import java.awt.FlowLayout;
import java.awt.GridBagConstraints;
@@ -92,6 +93,8 @@
private JComboBox cmbAttributes;
private JComboBox cmbRemoval;
private JComboBox cmbStyle;
+ private JComboBox cmbDelimiterRemoval;
+ private JComboBox cmbDelimiterAddition;
//JLabels
private JLabel networkLabel;
@@ -104,6 +107,8 @@
//Buttons
private JButton removeWordButton;
private JButton addWordButton;
+ private JButton addDelimiterButton;
+ private JButton removeDelimiterButton;
//Checkbox
private JCheckBox numExclusion;
@@ -113,6 +118,11 @@
private static final String flaggedSeparator = "--Flagged Words--";
private static final String stopSeparator = "--Stop Words--";
+ //String COnstants for Separators in delimiter combo boxes
+ private static final String commonDelimiters = "--Common Delimiters--";
+ private static final String userAddDelimiters = "--User Defined--";
+ private static final String selectMe = "Select to add your own";
+
private static final int DEF_ROW_HEIGHT = 20;
@@ -242,6 +252,12 @@
networkPanel.add(exclusionList);
+ //Delimiter/Tokenization Panel
+ CollapsiblePanel tokenizationPanel = createTokenizationPanel();
+ tokenizationPanel.setCollapsed(true);
+
+ networkPanel.add(tokenizationPanel);
+
//Add to collapsible panel
collapsiblePanel2.getContentPane().add(networkPanel,
BorderLayout.NORTH);
@@ -519,6 +535,121 @@
}
/**
+ * Creates a CollapsiblePanel that holds the word tokenization
information.
+ * @return CollapsiblePanel - word tokenization panel interface.
+ */
+ private CollapsiblePanel createTokenizationPanel()
+ {
+ CollapsiblePanel collapsiblePanel = new CollapsiblePanel("Word
Tokenization");
+
+ JPanel panel = new JPanel();
+ panel.setLayout(new GridLayout(0,1));
+
+ //Add Delimiter
+ JLabel addDelimiterLabel = new JLabel("Add Delimiter");
+
+ //Delimiter Addition Combo Box
+ WidestStringComboBoxModel wscbm = new
WidestStringComboBoxModel();
+ cmbDelimiterAddition = new JComboBox(wscbm);
+ cmbDelimiterAddition.addPopupMenuListener(new
WidestStringComboBoxPopupMenuListener());
+ cmbDelimiterAddition.setEditable(false);
+ Dimension d = cmbDelimiterAddition.getPreferredSize();
+ cmbDelimiterAddition.setPreferredSize(new Dimension(15, d.height));
+ cmbDelimiterAddition.addItemListener(this);
+
+ StringBuffer buf = new StringBuffer();
+ buf.append("<html>" + "Allows for specification of an
additional delimiter to be used when tokenizing nodes" + "<br>");
+ buf.append("<b>Acceptable Values:</b> Values entered must have
proper escape character if necessary" + "</html>");
+ cmbDelimiterAddition.setToolTipText(buf.toString());
+
+ addDelimiterButton = new JButton();
+ addDelimiterButton.setText("Add");
+ addDelimiterButton.setEnabled(false);
+ addDelimiterButton.addActionListener(this);
+
+ //Word panel
+ JPanel wordPanel = new JPanel();
+ wordPanel.setLayout(new GridBagLayout());
+
+ GridBagConstraints gridBagConstraints = new
GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.anchor = GridBagConstraints.WEST;
+ gridBagConstraints.insets = new Insets(5,0,0,0);
+ wordPanel.add(addDelimiterLabel, gridBagConstraints);
+
+ gridBagConstraints = new GridBagConstraints();
+ gridBagConstraints.gridx = 1;
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.fill = GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.insets = new Insets(5,10,0,10);
+ wordPanel.add(cmbDelimiterAddition, gridBagConstraints);
+
+ //Button stuff
+ gridBagConstraints = new GridBagConstraints();
+ gridBagConstraints.gridx = 2;
+ gridBagConstraints.gridy = 0;
+ gridBagConstraints.anchor = GridBagConstraints.EAST;
+ gridBagConstraints.insets = new Insets(5,0,0,0);
+ wordPanel.add(addDelimiterButton, gridBagConstraints);
+
+
+ // Word Removal Label
+ JLabel removeDelimiterLabel = new JLabel("Remove Delimiter");
+
+ //Word Removal Combo Box
+ wscbm = new WidestStringComboBoxModel();
+ cmbDelimiterRemoval = new JComboBox(wscbm);
+ cmbDelimiterRemoval.addPopupMenuListener(new
WidestStringComboBoxPopupMenuListener());
+ cmbDelimiterRemoval.setEditable(false);
+ d = cmbDelimiterRemoval.getPreferredSize();
+ cmbDelimiterRemoval.setPreferredSize(new Dimension(15, d.height));
+ cmbDelimiterRemoval.addItemListener(this);
+ cmbDelimiterRemoval.setToolTipText("Allows for selection of a
delimiter to remove from the list used when tokenizing");
+
+ //Word Removal Button
+ removeDelimiterButton = new JButton();
+ removeDelimiterButton.setText("Remove");
+ removeDelimiterButton.setEnabled(false);
+ removeDelimiterButton.addActionListener(this);
+
+ gridBagConstraints = new GridBagConstraints();
+ gridBagConstraints.gridx = 0;
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.anchor = GridBagConstraints.WEST;
+ gridBagConstraints.insets = new Insets(5,0,0,0);
+ wordPanel.add(removeDelimiterLabel, gridBagConstraints);
+
+ gridBagConstraints = new GridBagConstraints();
+ gridBagConstraints.gridx = 1;
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.fill = GridBagConstraints.HORIZONTAL;
+ gridBagConstraints.weightx = 1.0;
+ gridBagConstraints.insets = new Insets(5, 10, 0, 10);
+ wordPanel.add(cmbDelimiterRemoval, gridBagConstraints);
+
+ //Button stuff
+ gridBagConstraints = new GridBagConstraints();
+ gridBagConstraints.gridx = 2;
+ gridBagConstraints.gridy = 1;
+ gridBagConstraints.anchor = GridBagConstraints.EAST;
+ gridBagConstraints.insets = new java.awt.Insets(5, 0, 0, 0);
+ wordPanel.add(removeDelimiterButton, gridBagConstraints);
+
+ updateDelimiterCMBs();
+
+ //Add components to main panel
+ panel.add(wordPanel);
+
+ //Add to collapsible panel
+ collapsiblePanel.getContentPane().add(panel,
BorderLayout.NORTH);
+
+ return collapsiblePanel;
+ }
+
+
+ /**
* Creates a CollapsiblePanel that holds the Cloud Layout information.
* @return CollapsiblePanel - cloud Layout panel interface.
*/
@@ -668,7 +799,6 @@
}
SemanticSummaryManager.getInstance().setCurCloud(params);
- //this.refreshRemovalCMB();
this.refreshNetworkSettings();
}
@@ -713,6 +843,80 @@
}
/**
+ * Update the delimiter combo boxes.
+ */
+ private void updateDelimiterCMBs()
+ {
+ // Add Box
+ DefaultComboBoxModel cmb;
+ cmb = ((DefaultComboBoxModel)cmbDelimiterAddition.getModel());
+ cmb.removeAllElements();
+
+ SemanticSummaryParameters networkParams =
SemanticSummaryManager.getInstance().getCurNetwork();
+ WordDelimiters curDelimiters = networkParams.getDelimiter();
+
+ //Check if we are dealing with the Null
SemanticSummaryParameters
+ Boolean isNull = false;
+ if
(networkParams.equals(SemanticSummaryManager.getInstance().getNullSemanticSummary()))
+ isNull = true;
+
+ //Common Delimiters
+ cmb.addElement(commonDelimiters);
+
+ if (!isNull)
+ {
+ //Add alphabetically order list of delimiters
+ for(Iterator<String> iter =
curDelimiters.getDelimsToAdd().iterator(); iter.hasNext();)
+ {
+ String curDelim = iter.next();
+ cmb.addElement(curDelim);
+ }
+ }
+
+ //User to add
+ cmb.addElement(userAddDelimiters);
+
+ if (!isNull)
+ {
+ cmb.addElement(selectMe);
+ }
+
+ cmbDelimiterAddition.repaint();
+
+ //Remove Box
+ cmb = ((DefaultComboBoxModel)cmbDelimiterRemoval.getModel());
+ cmb.removeAllElements();
+
+ //Common Delimiters
+ cmb.addElement(commonDelimiters);
+
+ if (!isNull)
+ {
+ //Add alphabetically order list of delimiters
+ for(Iterator<String> iter =
curDelimiters.getDelimsInUse().iterator(); iter.hasNext();)
+ {
+ String curDelim = iter.next();
+ cmb.addElement(curDelim);
+ }
+ }
+
+ //User to add
+ cmb.addElement(userAddDelimiters);
+
+ if (!isNull)
+ {
+ //Add alphabetically order list of delimiters
+ for(Iterator<String> iter =
curDelimiters.getUserDelims().iterator(); iter.hasNext();)
+ {
+ String curDelim = iter.next();
+ cmb.addElement(curDelim);
+ }
+ }
+
+ cmbDelimiterRemoval.repaint();
+ }
+
+ /**
* Update the remove word list in the remove combobox.
*/
private void updateCMBRemoval()
@@ -818,6 +1022,7 @@
{
this.refreshRemovalCMB();
this.updateNumExclusionBox();
+ this.updateDelimiterCMBs();
}
@@ -957,6 +1162,35 @@
removeWordButton.setEnabled(true);
}//end if not null
}//end if cmbRemoval
+
+ if (cmb == cmbDelimiterRemoval)
+ {
+ Object selectObject =
cmbDelimiterRemoval.getSelectedItem();
+ if (selectObject != null)
+ {
+ String selectItem =
selectObject.toString();
+ if
(selectItem.equalsIgnoreCase(commonDelimiters) ||
+
selectItem.equalsIgnoreCase(userAddDelimiters))
+
removeDelimiterButton.setEnabled(false);
+ else
+
removeDelimiterButton.setEnabled(true);
+ }//end if not null
+ }//end if cmbDelimiterRemoval
+
+ if (cmb == cmbDelimiterAddition)
+ {
+ Object selectObject =
cmbDelimiterAddition.getSelectedItem();
+ if (selectObject != null)
+ {
+ String selectItem =
selectObject.toString();
+ if
(selectItem.equalsIgnoreCase(commonDelimiters) ||
+
selectItem.equalsIgnoreCase(userAddDelimiters))
+
addDelimiterButton.setEnabled(false);
+ else
+
addDelimiterButton.setEnabled(true);
+ }//end if not null
+ }//end if cmbDelimiterRemoval
+
}//end if combo box
}
@@ -1030,7 +1264,72 @@
JOptionPane.showMessageDialog(Cytoscape.getDesktop(), message, "Parameter out
of bounds", JOptionPane.WARNING_MESSAGE);
}
}
+
+ if (_btn == removeDelimiterButton)
+ {
+ //Get Selected word
+ Object selectObject =
cmbDelimiterRemoval.getSelectedItem();
+ if (selectObject != null)
+ {
+ String selectItem =
selectObject.toString();
+ if
(!selectItem.equalsIgnoreCase(commonDelimiters) ||
+
!selectItem.equalsIgnoreCase(userAddDelimiters))
+ {
+ SemanticSummaryParameters
networkParams = SemanticSummaryManager.getInstance().getCurNetwork();
+ WordDelimiters curDelimiters =
networkParams.getDelimiter();
+
+ //Remove from delimiters
+
curDelimiters.removeDelimiter(selectItem);
+
+ //Reset flags
+ networkParams.networkChanged();
+
+ //Refresh word removal list
+ this.updateDelimiterCMBs();
+ }//end if appropriate selection
+ }//end if not null selected
+ }//end remove delimiter button
+
+ if (_btn == addDelimiterButton)
+ {
+ //Get Selected word
+ Object selectObject =
cmbDelimiterAddition.getSelectedItem();
+ if (selectObject != null)
+ {
+ String selectItem =
selectObject.toString();
+ if
(!selectItem.equalsIgnoreCase(commonDelimiters) ||
+
!selectItem.equalsIgnoreCase(userAddDelimiters))
+ {
+ //Dialog if user add
+ if (selectItem.equals(selectMe))
+ {
+ Component parent =
Cytoscape.getDesktop();
+ AddDelimiterDialog
dialog = new AddDelimiterDialog(parent, true);
+
dialog.setLocationRelativeTo(parent);
+ dialog.setVisible(true);
+
+ selectItem =
dialog.getNewDelimiter();
+ }
+
+ if (!selectItem.equals(""))
+ {
+
SemanticSummaryParameters networkParams =
SemanticSummaryManager.getInstance().getCurNetwork();
+ WordDelimiters
curDelimiters = networkParams.getDelimiter();
+
+ //Add to delimiters
+
curDelimiters.addDelimToUse(selectItem);
+
+ //Reset flags
+
networkParams.networkChanged();
+
+ //Refresh word removal
list
+
this.updateDelimiterCMBs();
+ }
+ }//end if appropriate selection
+ }//end if not null selected
+ }//end remove delimiter button
}//end button
+
else if (_actionObject instanceof JCheckBox)
{
JCheckBox _box = (JCheckBox)_actionObject;
@@ -1123,7 +1422,27 @@
numExclusion = box;
}
+ public JComboBox getCMBDelimiterRemoval()
+ {
+ return cmbDelimiterRemoval;
+ }
+ public JComboBox getCMBDelimiterAddition()
+ {
+ return cmbDelimiterAddition;
+ }
+
+ public JButton getAddDelimiterButton()
+ {
+ return addDelimiterButton;
+ }
+
+ public JButton getRemoveDelimiterButton()
+ {
+ return removeDelimiterButton;
+ }
+
+
/**
* Private Class to ensure that text fields are being set properly
*/
Modified:
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SemanticSummaryParameters.java
===================================================================
---
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SemanticSummaryParameters.java
2010-07-26 23:39:22 UTC (rev 21031)
+++
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SemanticSummaryParameters.java
2010-07-27 17:19:35 UTC (rev 21032)
@@ -63,6 +63,7 @@
//Filter stuff
private WordFilter filter;
+ private WordDelimiters delimiters;
//CONSTRUCTORS
@@ -74,6 +75,7 @@
this.clouds = new HashMap<String,CloudParameters>();
this.nodeList = new ArrayList<String>();
this.filter = new WordFilter();
+ this.delimiters = new WordDelimiters();
}
/**
@@ -378,4 +380,14 @@
filter = aFilter;
}
+ public WordDelimiters getDelimiter()
+ {
+ return delimiters;
+ }
+
+ public void setDelimiter(WordDelimiters aDelimiter)
+ {
+ delimiters = aDelimiter;
+ }
+
}
Modified:
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SemanticSummaryPlugin.java
===================================================================
---
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SemanticSummaryPlugin.java
2010-07-26 23:39:22 UTC (rev 21031)
+++
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/SemanticSummaryPlugin.java
2010-07-27 17:19:35 UTC (rev 21032)
@@ -163,6 +163,12 @@
filterWriter.close();
pFileList.add(current_filter);
+ File current_delimiter = new File(tmpDir,
netNameSep + networkName + netNameSep + ".DELIMITER.txt");
+ BufferedWriter delimiterWriter = new
BufferedWriter(new FileWriter(current_delimiter));
+
delimiterWriter.write(params.getDelimiter().toString());
+ delimiterWriter.close();
+ pFileList.add(current_delimiter);
+
//Loop on Clouds
if (!params.getClouds().isEmpty())
{
@@ -345,6 +351,25 @@
WordFilter curFilter = new
WordFilter(fullText);
networkParams.setFilter(curFilter);
}
+
+ if
(prop_file.getName().contains(".DELIMITER.txt"))
+ {
+ TextFileReader reader = new
TextFileReader(prop_file.getAbsolutePath());
+ reader.read();
+ String fullText = reader.getText();
+
+ //Get the networkID from the props file
+ String[] fullname =
prop_file.getName().split(netNameSep);
+ String net_name = fullname[1];
+
+ //Get the Network Parameters
+ SemanticSummaryParameters networkParams
=
+
SemanticSummaryManager.getInstance().getCyNetworkList().get(net_name);
+
+ //Recreate the Delimiter and set
pointer in cloud
+ WordDelimiters curDelimiter = new
WordDelimiters(fullText);
+
networkParams.setDelimiter(curDelimiter);
+ }
}//end loop through all props files
@@ -355,7 +380,8 @@
if (prop_file.getName().contains(".CLOUDS.txt")
||
prop_file.getName().contains(".props") ||
-
prop_file.getName().contains(".FILTER.txt"))
+
prop_file.getName().contains(".FILTER.txt") ||
+
prop_file.getName().contains(".DELIMITER.txt"))
continue;
TextFileReader reader = new
TextFileReader(prop_file.getAbsolutePath());
Added:
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/WordDelimiters.java
===================================================================
---
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/WordDelimiters.java
(rev 0)
+++
csplugins/trunk/soc/layla/SemanticSummary/src/cytoscape/csplugins/semanticsummary/WordDelimiters.java
2010-07-27 17:19:35 UTC (rev 21032)
@@ -0,0 +1,350 @@
+/*
+ File: WordDelimiters.java
+
+ Copyright 2010 - The Cytoscape Consortium (www.cytoscape.org)
+
+ Code written by: Layla Oesper
+ Authors: Layla Oesper, Ruth Isserlin, Daniele Merico
+
+ This library is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this project. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package cytoscape.csplugins.semanticsummary;
+
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.TreeSet;
+
+/**
+ * This class defines the WordDelimiters class. This class is used to
determine
+ * if a delimiter in question should be used to tokenize text.
+ *
+ * @author Layla Oesper
+ * @version 1.0
+ */
+
+public class WordDelimiters
+{
+
+ //VARIABLES
+
+ private TreeSet<String> delimsInUse= new TreeSet<String>();
+ private TreeSet<String> delimsToAdd= new TreeSet<String>();
+ private TreeSet<String> userDelims= new TreeSet<String>();
+
+ private HashMap<String, String> regexTranslation = new HashMap<String,
String>();
+
+ //String Delimeters
+ private static final String DELIMITER = "SAVEDELIMITER";
+ private static final String FIRSTDELIMITER = "NewLineEquivalent";
+ private static final String SECONDDELIMITER = "TabbedEquivalent";
+
+ //CONSTRUCTORS
+
+ /**
+ * Creates the default WordDelimiters object.
+ */
+ public WordDelimiters()
+ {
+ delimsInUse.add("tab");
+ delimsInUse.add("space");
+ delimsInUse.add("newline");
+ delimsInUse.add("carriage return");
+ delimsInUse.add("form feed");
+ delimsInUse.add("!");
+ delimsInUse.add("\"");
+ delimsInUse.add("#");
+ delimsInUse.add("$");
+ delimsInUse.add("%");
+ delimsInUse.add("&");
+ delimsInUse.add("(");
+ delimsInUse.add(")");
+ delimsInUse.add("*");
+ delimsInUse.add("+");
+ delimsInUse.add(",");
+ delimsInUse.add(".");
+ delimsInUse.add("/");
+ delimsInUse.add(":");
+ delimsInUse.add(";");
+ delimsInUse.add("<");
+ delimsInUse.add("=");
+ delimsInUse.add(">");
+ delimsInUse.add("?");
+ delimsInUse.add("@");
+ delimsInUse.add("[");
+ delimsInUse.add("\\");
+ delimsInUse.add("]");
+ delimsInUse.add("^");
+ delimsInUse.add("_");
+ delimsInUse.add("`");
+ delimsInUse.add("{");
+ delimsInUse.add("|");
+ delimsInUse.add("}");
+ delimsInUse.add("~");
+
+ delimsToAdd.add("-");
+ delimsToAdd.add("'");
+
+ regexTranslation.put("tab", "\\t");
+ regexTranslation.put("space", " ");
+ regexTranslation.put("newline", "\\n");
+ regexTranslation.put("carriage return", "\\r");
+ regexTranslation.put("form feed", "\\f");
+ regexTranslation.put("!","!");
+ regexTranslation.put("\"", "\" ");
+ regexTranslation.put("#", "#");
+ regexTranslation.put("$", "$");
+ regexTranslation.put("%", "%");
+ regexTranslation.put("&", "&");
+ regexTranslation.put("(", "(");
+ regexTranslation.put(")", ")");
+ regexTranslation.put("*", "*");
+ regexTranslation.put("+", "+");
+ regexTranslation.put(",", ",");
+ regexTranslation.put(".", ".");
+ regexTranslation.put("/", "/");
+ regexTranslation.put(":", ":");
+ regexTranslation.put(";", ";");
+ regexTranslation.put("<", "<");
+ regexTranslation.put("=", "=");
+ regexTranslation.put(">", ">");
+ regexTranslation.put("?", "?");
+ regexTranslation.put("@", "@");
+ regexTranslation.put("[", "\\[");
+ regexTranslation.put("\\", "\\\\");
+ regexTranslation.put("]", "\\]");
+ regexTranslation.put("^", "\\^");
+ regexTranslation.put("_", "_");
+ regexTranslation.put("`", "`");
+ regexTranslation.put("{", "{");
+ regexTranslation.put("|", "|");
+ regexTranslation.put("}", "}");
+ regexTranslation.put("~", "~");
+ regexTranslation.put("-", "\\-");
+ regexTranslation.put("'", "'");
+ }
+
+
+ /**
+ * Constructor to create WordDelimiters from a cytoscape property file
+ * while restoring a session. Property file is created when the
session is saved.
+ * @param propFile - the contents of the property file as a String
+ */
+ public WordDelimiters(String propFile)
+ {
+ //Initialize to be backwards compatible
+ this();
+
+ //Create a hashmap to contain all the values in the rpt file
+ HashMap<String, String> props = new HashMap<String,String>();
+
+ String[] lines = propFile.split(FIRSTDELIMITER);
+
+ for (int i = 0; i < lines.length; i++)
+ {
+ String line = lines[i];
+ String[] tokens = line.split(SECONDDELIMITER);
+ //there should be two values in each line
+ if(tokens.length == 2)
+ props.put(tokens[0],tokens[1]);
+ }
+
+ //Check if this is new version, clear out initialization
+ if ((props.get("DelimsInUse") != null) ||
(props.get("DelimsToAdd") != null))
+ {
+ delimsInUse = new TreeSet<String>();
+ delimsToAdd = new TreeSet<String>();
+ }
+
+ //Rebuild inUse List
+ String value = props.get("DelimsInUse");
+ if (value != null)
+ {
+ String[] delims = value.split(DELIMITER);
+ for (int i = 0; i < delims.length; i++)
+ {
+ String curDelim = delims[i];
+ delimsInUse.add(curDelim);
+ }
+ }
+
+ //Rebuild toAdd List
+ value = props.get("DelimsToAdd");
+ if (value != null)
+ {
+ String[] delims = value.split(DELIMITER);
+ for (int i = 0; i < delims.length; i++)
+ {
+ String curDelim = delims[i];
+ delimsToAdd.add(curDelim);
+ }
+ }
+
+
+ //Rebuild added List
+ value = props.get("AddedDelims");
+ if (value != null)
+ {
+ String[] delims = value.split(DELIMITER);
+ for (int i = 0; i < delims.length; i++)
+ {
+ String curDelim = delims[i];
+ userDelims.add(curDelim);
+ }
+ }
+ }
+
+
+ /**
+ * Creates a String representation of all words currently in this
+ * WordDelimiters used for saving sessions.
+ *
+ * @return String - list of words in this WordDelimiter used for
restoring.
+ */
+
+ public String toString()
+ {
+ StringBuffer delimVariables = new StringBuffer();
+
+ //List of inUse words as a delimited list
+ StringBuffer output = new StringBuffer();
+ if (delimsInUse.size()> 0)
+ {
+ for (Iterator<String> iter = delimsInUse.iterator();
iter.hasNext();)
+ {
+ String curDelim = iter.next();
+ output.append(curDelim + DELIMITER);
+ }
+ delimVariables.append("DelimsInUse" + SECONDDELIMITER +
output.toString() + FIRSTDELIMITER);
+ }
+
+ //List of toAdd words as a delimeted list
+ output = new StringBuffer();
+ if (delimsToAdd.size()> 0)
+ {
+ for (Iterator<String> iter = delimsToAdd.iterator();
iter.hasNext();)
+ {
+ String curWord = iter.next();
+ output.append(curWord + DELIMITER);
+ }
+ delimVariables.append("DelimsToAdd" + SECONDDELIMITER +
output.toString() + FIRSTDELIMITER);
+ }
+
+ //List of added delimiters as a delimeted list
+ output = new StringBuffer();
+ if (userDelims.size()>0)
+ {
+ for (Iterator<String> iter = userDelims.iterator();
iter.hasNext();)
+ {
+ String curWord = iter.next();
+ output.append(curWord + DELIMITER);
+ }
+ delimVariables.append("AddedDelims" + SECONDDELIMITER +
output.toString() + FIRSTDELIMITER);
+ }
+
+ return delimVariables.toString();
+ }
+
+ /**
+ * Returns a String regular expression for all the delimiters currently
in use.
+ * @return String regex of all delimiters
+ */
+ public String getRegex()
+ {
+ String reg = "";
+
+ for (Iterator<String> iter = delimsInUse.iterator();
iter.hasNext();)
+ {
+ String curDelim = iter.next();
+ String addDelim = this.translateToRegex(curDelim);
+
+ reg = reg + addDelim;
+ }//end for loop
+
+ String regEx = "[" + reg + "]";
+
+ return regEx;
+ }
+
+ /**
+ * Adds the specified delimiter into use if it is not currently in use.
+ */
+ public void addDelimToUse(String delim)
+ {
+ //If it is one of the defined delims
+ if (delimsToAdd.contains(delim))
+ {
+ delimsToAdd.remove(delim);
+ delimsInUse.add(delim);
+ }
+ //Add to user list
+ else
+ {
+ if (!userDelims.contains(delim))
+ userDelims.add(delim);
+ }
+ }
+
+ /**
+ * Removes the specified delimiter from use if it is currently in use.
+ */
+ public void removeDelimiter(String delim)
+ {
+ //First check user delims
+ if (userDelims.contains(delim))
+ {
+ userDelims.remove(delim);
+ }
+ else if (delimsInUse.contains(delim))
+ {
+ delimsInUse.remove(delim);
+ delimsToAdd.add(delim);
+ }
+ }
+
+ /**
+ * Retrieves the regex translation of the given string or null if the
string is bad
+ */
+ public String translateToRegex(String val)
+ {
+ if (regexTranslation.containsKey(val))
+ return regexTranslation.get(val);
+ else
+ return null;
+ }
+
+
+ //Getters and Setters
+
+ public TreeSet<String> getDelimsInUse()
+ {
+ return delimsInUse;
+ }
+
+ public TreeSet<String> getDelimsToAdd()
+ {
+ return delimsToAdd;
+ }
+
+ public TreeSet<String> getUserDelims()
+ {
+ return userDelims;
+ }
+
+ public HashMap<String,String> getRegExTranslation()
+ {
+ return regexTranslation;
+ }
+
+}
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