obo-svn-commit — sends mail for all commits to svn repository

[Obo-svn-commit] SF.net SVN: obo: [678] phenote/trunk

[<nl...@us...>]

Revision: 678
          http://svn.sourceforge.net/obo/?rev=678&view=rev
Author:   nlw
Date:     2007-06-20 14:57:51 -0700 (Wed, 20 Jun 2007)

Log Message:
-----------
move icons/images to new common dir

Modified Paths:
--------------
    phenote/trunk/build.xml

Added Paths:
-----------
    phenote/trunk/images/
    phenote/trunk/images/OK.GIF
    phenote/trunk/images/arrow.small.left.gif
    phenote/trunk/images/arrow.small.right.gif
    phenote/trunk/images/phenote_logo.jpg

Removed Paths:
-------------
    phenote/trunk/OK.GIF
    phenote/trunk/arrow.small.left.gif
    phenote/trunk/arrow.small.right.gif

Deleted: phenote/trunk/OK.GIF
===================================================================
(Binary files differ)

Deleted: phenote/trunk/arrow.small.left.gif
===================================================================
(Binary files differ)

Deleted: phenote/trunk/arrow.small.right.gif
===================================================================
(Binary files differ)

Modified: phenote/trunk/build.xml
===================================================================
--- phenote/trunk/build.xml	2007-06-20 21:13:58 UTC (rev 677)
+++ phenote/trunk/build.xml	2007-06-20 21:57:51 UTC (rev 678)
@@ -30,6 +30,8 @@
     <property name="jarfile" value="jars/phenote.jar"/>
     <property name="obo" value="obo-files"/>
     <property name="conf" value="conf"/>
+    <property name="images" value="images"/>
+
     <!-- override this from command line with  -DCONF-FILE=initial-zfin.cfg -->
     <property name="CONF_FILE" value="initial-flybase.cfg"/>
 

Copied: phenote/trunk/images/OK.GIF (from rev 677, phenote/trunk/OK.GIF)
===================================================================
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Copied: phenote/trunk/images/arrow.small.left.gif (from rev 677, phenote/trunk/arrow.small.left.gif)
===================================================================
(Binary files differ)

Copied: phenote/trunk/images/arrow.small.right.gif (from rev 677, phenote/trunk/arrow.small.right.gif)
===================================================================
(Binary files differ)

Copied: phenote/trunk/images/phenote_logo.jpg (from rev 677, phenote/trunk/src/java/phenote/images/phenote_logo.jpg)
===================================================================
(Binary files differ)


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[Obo-svn-commit] SF.net SVN: obo: [677] phenote/trunk/src/java/phenote

[<nl...@us...>]

Revision: 677
          http://svn.sourceforge.net/obo/?rev=677&view=rev
Author:   nlw
Date:     2007-06-20 14:13:58 -0700 (Wed, 20 Jun 2007)

Log Message:
-----------
*Indications for OBSOLETE terms added in title area.

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/gui/TermInfo.java
    phenote/trunk/src/java/phenote/util/HtmlUtil.java

Modified: phenote/trunk/src/java/phenote/gui/TermInfo.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/TermInfo.java	2007-06-20 20:45:16 UTC (rev 676)
+++ phenote/trunk/src/java/phenote/gui/TermInfo.java	2007-06-20 21:13:58 UTC (rev 677)
@@ -56,6 +56,7 @@
   private UseTermListener useTermListener;
   private JPanel termInfoPanel;
   private JPanel naviPanel;
+  private JButton useTermButton;
   private JEditorPane termField;
   private static int TERM_INFO_DEFAULT_WIDTH=350;
   private static int TERM_INFO_DEFAULT_HEIGHT=400;
@@ -95,7 +96,7 @@
     termInfoPanel.add(scrollPane,BorderLayout.CENTER);
     //Layout doesn't look good right now.  Will fix
     ImageIcon ok = new ImageIcon("OK.GIF");
-    JButton useTermButton = new JButton(ok);
+    useTermButton = new JButton(ok);
 //    JButton useTermButton = new JButton("Use Term");
     useTermButton.addActionListener(new UseTermActionListener());
     useTermButton.setPreferredSize(new Dimension(BUTTON_HEIGHT, BUTTON_HEIGHT));
@@ -204,9 +205,10 @@
     currentOboClass = oboClass;
 
     String html = HtmlUtil.termInfo(oboClass);
-
+    String term = HtmlUtil.termName(oboClass);
     textArea.setText(html);
-    termField.setText("<b>"+oboClass.getName()+"</b>");
+    termField.setText(term);
+    useTermButton.setEnabled(!oboClass.isObsolete());
     // scroll to top (by default does bottom)
     textArea.setCaretPosition(0);
   }

Modified: phenote/trunk/src/java/phenote/util/HtmlUtil.java
===================================================================
--- phenote/trunk/src/java/phenote/util/HtmlUtil.java	2007-06-20 20:45:16 UTC (rev 676)
+++ phenote/trunk/src/java/phenote/util/HtmlUtil.java	2007-06-20 21:13:58 UTC (rev 677)
@@ -71,6 +71,14 @@
 		return sb.toString();
 	}
 
+	public static String termName(OBOClass oboClass) {
+		StringBuffer sb = new StringBuffer();
+		if (oboClass.isObsolete()) {
+			sb.append(bold(colorFont(bold("(OBSOLETE) "), "red")));
+		}
+		sb.append(bold(oboClass.getName()));
+		return sb.toString();
+	}
 	//Nicole's attempt at making the Term Info box look a little better   
 	//I'm puting all the information into an html table.  rhs are each single table cells
 	//but are separated by line breaks.  
@@ -83,7 +91,6 @@
 		sb.append("<table>");
 		sb.append(makeRow(makeLeftCol(bold("ONTOLOGY"))+makeRightCol(oboClass.getNamespace().toString())));
 		if (oboClass.isObsolete()) {
-			//sb.append(makeRow(makeLeftCol(bold("TERM"))+makeRightCol(bold(oboClass.getName())+colorFont(bold("   (OBSOLETE)"), "red"))));
 			sb.append(makeObsLinks(oboClass));
 		}
 		else {


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[Obo-svn-commit] SF.net SVN: obo: [676] phenote/trunk

[<nl...@us...>]

Revision: 676
          http://svn.sourceforge.net/obo/?rev=676&view=rev
Author:   nlw
Date:     2007-06-20 13:45:16 -0700 (Wed, 20 Jun 2007)

Log Message:
-----------
*edits to the navi icons

Modified Paths:
--------------
    phenote/trunk/arrow.small.left.gif
    phenote/trunk/arrow.small.right.gif

Added Paths:
-----------
    phenote/trunk/OK.GIF

Added: phenote/trunk/OK.GIF
===================================================================
(Binary files differ)


Property changes on: phenote/trunk/OK.GIF
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Modified: phenote/trunk/arrow.small.left.gif
===================================================================
(Binary files differ)

Modified: phenote/trunk/arrow.small.right.gif
===================================================================
(Binary files differ)


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[Obo-svn-commit] SF.net SVN: obo: [675] phenote/trunk/src/java/phenote

[<nl...@us...>]

Revision: 675
          http://svn.sourceforge.net/obo/?rev=675&view=rev
Author:   nlw
Date:     2007-06-20 13:44:30 -0700 (Wed, 20 Jun 2007)

Log Message:
-----------
*moved around navi icons; changed to JEditorPane to utilize html commands (bold); 
*changed use term button to be a checkmark, moved up to navi bar

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/gui/TermInfo.java
    phenote/trunk/src/java/phenote/main/Phenote.java
    phenote/trunk/src/java/phenote/util/HtmlUtil.java

Modified: phenote/trunk/src/java/phenote/gui/TermInfo.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/TermInfo.java	2007-06-20 19:00:28 UTC (rev 674)
+++ phenote/trunk/src/java/phenote/gui/TermInfo.java	2007-06-20 20:44:30 UTC (rev 675)
@@ -56,7 +56,7 @@
   private UseTermListener useTermListener;
   private JPanel termInfoPanel;
   private JPanel naviPanel;
-  private JTextField termField;
+  private JEditorPane termField;
   private static int TERM_INFO_DEFAULT_WIDTH=350;
   private static int TERM_INFO_DEFAULT_HEIGHT=400;
   private static int BUTTON_HEIGHT = 30;
@@ -70,7 +70,7 @@
   public JComponent getComponent() {
     termInfoPanel = new JPanel(new BorderLayout(0,0)); // hgap,vgap
     termInfoPanel.setPreferredSize(new Dimension(TERM_INFO_DEFAULT_WIDTH,TERM_INFO_DEFAULT_HEIGHT));
-    termInfoPanel.setMinimumSize(new Dimension(200,150));
+    termInfoPanel.setMinimumSize(new Dimension(200,200));
     //termInfoPanel.setMaximumSize(new Dimension(380,400));
     if (DO_HTML) {
     	JEditorPane editorPane = new JEditorPane(); 
@@ -94,10 +94,13 @@
     termInfoPanel.setBorder(BorderFactory.createTitledBorder("Term Info"));
     termInfoPanel.add(scrollPane,BorderLayout.CENTER);
     //Layout doesn't look good right now.  Will fix
-    JButton useTermButton = new JButton("Use Term");
+    ImageIcon ok = new ImageIcon("OK.GIF");
+    JButton useTermButton = new JButton(ok);
+//    JButton useTermButton = new JButton("Use Term");
     useTermButton.addActionListener(new UseTermActionListener());
-    useTermButton.setPreferredSize(new Dimension(TERM_INFO_DEFAULT_WIDTH, 30));
-    useTermButton.setMinimumSize(new Dimension(TERM_INFO_DEFAULT_WIDTH, 30));
+    useTermButton.setPreferredSize(new Dimension(BUTTON_HEIGHT, BUTTON_HEIGHT));
+    useTermButton.setMinimumSize(new Dimension(BUTTON_HEIGHT, BUTTON_HEIGHT));
+    useTermButton.setToolTipText("Use Term");
     ImageIcon back = new ImageIcon("arrow.small.left.gif");
     JButton backButton = new JButton(back);
     backButton.setToolTipText("Go back a term");
@@ -111,9 +114,9 @@
     forwardButton.setMinimumSize(new Dimension(BUTTON_HEIGHT, BUTTON_HEIGHT));
     forwardButton.setMaximumSize(new Dimension(BUTTON_HEIGHT, BUTTON_HEIGHT));
     JPanel naviButtons = new JPanel();
-    naviButtons.setMinimumSize(new Dimension((2*BUTTON_HEIGHT), BUTTON_HEIGHT));
-    naviButtons.setPreferredSize(new Dimension((2*BUTTON_HEIGHT), BUTTON_HEIGHT));
-    naviButtons.setMaximumSize(new Dimension((2*BUTTON_HEIGHT), BUTTON_HEIGHT));
+    naviButtons.setMinimumSize(new Dimension((3*BUTTON_HEIGHT), BUTTON_HEIGHT));
+    naviButtons.setPreferredSize(new Dimension((3*BUTTON_HEIGHT), BUTTON_HEIGHT));
+    naviButtons.setMaximumSize(new Dimension((3*BUTTON_HEIGHT), BUTTON_HEIGHT));
     naviButtons.setLayout(new BorderLayout(0,0));
     naviPanel = new JPanel();
     naviPanel.setLayout(new BorderLayout(0,0));
@@ -124,15 +127,17 @@
     backButton.addActionListener(new BackNaviActionListener());
 //    bottomPanel.add(backButton, BorderLayout.WEST);
 //    bottomPanel.add(forwardButton, BorderLayout.CENTER);
-    bottomPanel.add(useTermButton);
-    termInfoPanel.add(bottomPanel,BorderLayout.SOUTH);
-    termField = new JTextField();
+    naviPanel.add(useTermButton);
+    //termInfoPanel.add(bottomPanel,BorderLayout.SOUTH);
+    termField =  new JEditorPane();
+    termField.setContentType("text/html");
     termField.setText("(no term selected)");
-    termField.setPreferredSize(new Dimension(TERM_INFO_DEFAULT_WIDTH,20));
+    termField.setPreferredSize(new Dimension(TERM_INFO_DEFAULT_WIDTH,BUTTON_HEIGHT));
     termField.setEditable(false);  
-    naviButtons.add(backButton, BorderLayout.WEST);
+    naviButtons.add(useTermButton, BorderLayout.WEST);
+    naviButtons.add(backButton, BorderLayout.CENTER);
     naviButtons.add(forwardButton, BorderLayout.EAST);
-    naviPanel.add(naviButtons, BorderLayout.WEST);
+    naviPanel.add(naviButtons, BorderLayout.EAST);
     naviPanel.add(termField, BorderLayout.CENTER);
     termInfoPanel.add(naviPanel, BorderLayout.NORTH);
     return termInfoPanel;
@@ -201,7 +206,7 @@
     String html = HtmlUtil.termInfo(oboClass);
 
     textArea.setText(html);
-    termField.setText(oboClass.getName());
+    termField.setText("<b>"+oboClass.getName()+"</b>");
     // scroll to top (by default does bottom)
     textArea.setCaretPosition(0);
   }

Modified: phenote/trunk/src/java/phenote/main/Phenote.java
===================================================================
--- phenote/trunk/src/java/phenote/main/Phenote.java	2007-06-20 19:00:28 UTC (rev 674)
+++ phenote/trunk/src/java/phenote/main/Phenote.java	2007-06-20 20:44:30 UTC (rev 675)
@@ -206,11 +206,10 @@
     	  n = JOptionPane.showConfirmDialog(null, m, "Phenote Exit",
     			  JOptionPane.YES_NO_OPTION);
     	  if (n==JOptionPane.YES_OPTION) {
+    	  	//  now quit
     	  	System.exit(0);
     	  } else { return; }
-      
-    	} //now quit
-        System.exit(0);
+     	} 
     }
   }
 

Modified: phenote/trunk/src/java/phenote/util/HtmlUtil.java
===================================================================
--- phenote/trunk/src/java/phenote/util/HtmlUtil.java	2007-06-20 19:00:28 UTC (rev 674)
+++ phenote/trunk/src/java/phenote/util/HtmlUtil.java	2007-06-20 20:44:30 UTC (rev 675)
@@ -83,11 +83,11 @@
 		sb.append("<table>");
 		sb.append(makeRow(makeLeftCol(bold("ONTOLOGY"))+makeRightCol(oboClass.getNamespace().toString())));
 		if (oboClass.isObsolete()) {
-			sb.append(makeRow(makeLeftCol(bold("TERM"))+makeRightCol(bold(oboClass.getName())+colorFont(bold("   (OBSOLETE)"), "red"))));
+			//sb.append(makeRow(makeLeftCol(bold("TERM"))+makeRightCol(bold(oboClass.getName())+colorFont(bold("   (OBSOLETE)"), "red"))));
 			sb.append(makeObsLinks(oboClass));
 		}
 		else {
-			sb.append(makeRow(makeLeftCol(bold("TERM"))+makeRightCol(bold(oboClass.getName()))));
+			//sb.append(makeRow(makeLeftCol(bold("TERM"))+makeRightCol(bold(oboClass.getName()))));
 		}
 
 		sb.append(makeRow(makeLeftCol(bold("ID"))+makeRightCol(oboClass.getID())));


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[Obo-svn-commit] SF.net SVN: obo: [674] phenote/trunk

[<nl...@us...>]

Revision: 674
          http://svn.sourceforge.net/obo/?rev=674&view=rev
Author:   nlw
Date:     2007-06-20 12:00:28 -0700 (Wed, 20 Jun 2007)

Log Message:
-----------
*arrow icons for navi control

Added Paths:
-----------
    phenote/trunk/arrow.small.left.gif
    phenote/trunk/arrow.small.right.gif

Added: phenote/trunk/arrow.small.left.gif
===================================================================
(Binary files differ)


Property changes on: phenote/trunk/arrow.small.left.gif
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Added: phenote/trunk/arrow.small.right.gif
===================================================================
(Binary files differ)


Property changes on: phenote/trunk/arrow.small.right.gif
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream


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[Obo-svn-commit] SF.net SVN: obo: [673] phenote/trunk/src/java/phenote

[<nl...@us...>]

Revision: 673
          http://svn.sourceforge.net/obo/?rev=673&view=rev
Author:   nlw
Date:     2007-06-20 11:56:47 -0700 (Wed, 20 Jun 2007)

Log Message:
-----------
*added exit behaviour to main window closing
*removed printlns from charactertablepanel

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/gui/CharacterTablePanel.java
    phenote/trunk/src/java/phenote/gui/TermInfo.java
    phenote/trunk/src/java/phenote/main/Phenote.java

Modified: phenote/trunk/src/java/phenote/gui/CharacterTablePanel.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/CharacterTablePanel.java	2007-06-20 18:39:18 UTC (rev 672)
+++ phenote/trunk/src/java/phenote/gui/CharacterTablePanel.java	2007-06-20 18:56:47 UTC (rev 673)
@@ -173,9 +173,9 @@
       charJTable.getTableHeader().setResizingColumn(column);
       column.setWidth(width);
       totalWidth+=width;
-     	System.out.println("Set column "+characterTableModel.getColumnName(i)+" width = "+width);  	
+     	//System.out.println("Set column "+characterTableModel.getColumnName(i)+" width = "+width);  	
     }
-    System.out.println("Total width = "+totalWidth);
+    //System.out.println("Total width = "+totalWidth);
     tableWidth=totalWidth;
   }
   
@@ -467,7 +467,7 @@
   				//only flag modified if changed from original settings
   				Config.inst().setFieldColwidth(colIndex, w);
   				Config.inst().setConfigModified(true);
-  				System.out.println("column "+colIndex+" "+e.getPropertyName()+" changed: "+ e.getOldValue()+" --> "+w);
+//  				System.out.println("column "+colIndex+" "+e.getPropertyName()+" changed: "+ e.getOldValue()+" --> "+w);
   			}
   		}
   	}	

Modified: phenote/trunk/src/java/phenote/gui/TermInfo.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/TermInfo.java	2007-06-20 18:39:18 UTC (rev 672)
+++ phenote/trunk/src/java/phenote/gui/TermInfo.java	2007-06-20 18:56:47 UTC (rev 673)
@@ -98,13 +98,13 @@
     useTermButton.addActionListener(new UseTermActionListener());
     useTermButton.setPreferredSize(new Dimension(TERM_INFO_DEFAULT_WIDTH, 30));
     useTermButton.setMinimumSize(new Dimension(TERM_INFO_DEFAULT_WIDTH, 30));
-    ImageIcon back = new ImageIcon("/Users/Nicole/Desktop/arrow.small.left.gif");
+    ImageIcon back = new ImageIcon("arrow.small.left.gif");
     JButton backButton = new JButton(back);
     backButton.setToolTipText("Go back a term");
     backButton.setPreferredSize(new Dimension(BUTTON_HEIGHT, BUTTON_HEIGHT));
     backButton.setMinimumSize(new Dimension(BUTTON_HEIGHT, BUTTON_HEIGHT));
     backButton.setMaximumSize(new Dimension(BUTTON_HEIGHT, BUTTON_HEIGHT));
-    ImageIcon forward = new ImageIcon("/Users/Nicole/Desktop/arrow.small.right.gif");
+    ImageIcon forward = new ImageIcon("arrow.small.right.gif");
     JButton forwardButton = new JButton(forward);
     forwardButton.setToolTipText("Go forward a term");
     forwardButton.setPreferredSize(new Dimension(BUTTON_HEIGHT, BUTTON_HEIGHT));

Modified: phenote/trunk/src/java/phenote/main/Phenote.java
===================================================================
--- phenote/trunk/src/java/phenote/main/Phenote.java	2007-06-20 18:39:18 UTC (rev 672)
+++ phenote/trunk/src/java/phenote/main/Phenote.java	2007-06-20 18:56:47 UTC (rev 673)
@@ -183,7 +183,33 @@
       whole servlet down */
   private class WindowExit extends WindowAdapter {
     public void windowClosing(WindowEvent e) {
-      if (standalone)
+    	String m="";
+    	int n;
+      if (standalone) {
+    		if (Config.inst().isConfigModified()) {
+    			m="Your Default Settings have been modified.  Do you wish to save them?";
+    			n = JOptionPane.showConfirmDialog(null,m,"Configuration Alert", JOptionPane.YES_NO_OPTION);
+    			if (n==JOptionPane.YES_OPTION) { 
+    				Config.inst().setAutocompleteSettings();
+    				//write out configuration!
+    		    Config.inst().saveModifiedConfig();
+    		    m="";
+    			}
+    			else { 
+    				m="Your changes have not been saved.\n";
+    			}
+    		}
+//    		else {
+//    			System.out.println("your settings have not changed");
+//    		}
+    	  m += "Are you sure you want to quit?";
+    	  n = JOptionPane.showConfirmDialog(null, m, "Phenote Exit",
+    			  JOptionPane.YES_NO_OPTION);
+    	  if (n==JOptionPane.YES_OPTION) {
+    	  	System.exit(0);
+    	  } else { return; }
+      
+    	} //now quit
         System.exit(0);
     }
   }


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[Obo-svn-commit] SF.net SVN: obo: [672] phenote/trunk/src/java/phenote/gui/TermInfo.java

[<nl...@us...>]

Revision: 672
          http://svn.sourceforge.net/obo/?rev=672&view=rev
Author:   nlw
Date:     2007-06-20 11:39:18 -0700 (Wed, 20 Jun 2007)

Log Message:
-----------
*Term Info now keeps track of worn paths, and user can navigate forward/backward in their worn paths with icons.
*Also included a separate text field that displays the term name...  want to get feedback

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/gui/TermInfo.java

Modified: phenote/trunk/src/java/phenote/gui/TermInfo.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/TermInfo.java	2007-06-20 18:19:52 UTC (rev 671)
+++ phenote/trunk/src/java/phenote/gui/TermInfo.java	2007-06-20 18:39:18 UTC (rev 672)
@@ -2,7 +2,9 @@
 
 import java.net.URL;
 import java.util.Iterator;
+import java.awt.List;
 import java.awt.BorderLayout;
+import java.awt.FlowLayout;
 import java.awt.Color;
 import java.awt.Dimension;
 import java.awt.event.ActionEvent;
@@ -15,7 +17,9 @@
 import javax.swing.JPanel;
 import javax.swing.JScrollPane;
 import javax.swing.JTextArea;
+import javax.swing.JTextField;
 import javax.swing.text.JTextComponent;
+import javax.swing.ImageIcon;
 import javax.swing.event.HyperlinkEvent;
 import javax.swing.event.HyperlinkListener;
 import javax.swing.event.ListSelectionEvent;
@@ -51,6 +55,13 @@
   private OBOClass currentOboClass;
   private UseTermListener useTermListener;
   private JPanel termInfoPanel;
+  private JPanel naviPanel;
+  private JTextField termField;
+  private static int TERM_INFO_DEFAULT_WIDTH=350;
+  private static int TERM_INFO_DEFAULT_HEIGHT=400;
+  private static int BUTTON_HEIGHT = 30;
+  private List termInfoNaviHistory = new List();
+  private int naviIndex=-1;
   
   public TermInfo() { //TermPanel termPanel) {
     SelectionManager.inst().addTermSelectionListener(new InfoTermSelectionListener());
@@ -58,11 +69,11 @@
 
   public JComponent getComponent() {
     termInfoPanel = new JPanel(new BorderLayout(0,0)); // hgap,vgap
-    termInfoPanel.setPreferredSize(new Dimension(350,200));
+    termInfoPanel.setPreferredSize(new Dimension(TERM_INFO_DEFAULT_WIDTH,TERM_INFO_DEFAULT_HEIGHT));
     termInfoPanel.setMinimumSize(new Dimension(200,150));
     //termInfoPanel.setMaximumSize(new Dimension(380,400));
     if (DO_HTML) {
-      JEditorPane editorPane = new JEditorPane(); 
+    	JEditorPane editorPane = new JEditorPane(); 
       editorPane.setContentType("text/html"); // sets up HTMLEditorKit
       termHyperlinkListener = new TermHyperlinkListener();
       editorPane.addHyperlinkListener(termHyperlinkListener);
@@ -82,11 +93,48 @@
     //scrollPane.setBorder(BorderFactory.createTitledBorder("Term Info"));
     termInfoPanel.setBorder(BorderFactory.createTitledBorder("Term Info"));
     termInfoPanel.add(scrollPane,BorderLayout.CENTER);
-
+    //Layout doesn't look good right now.  Will fix
     JButton useTermButton = new JButton("Use Term");
     useTermButton.addActionListener(new UseTermActionListener());
-    termInfoPanel.add(useTermButton,BorderLayout.SOUTH);
-
+    useTermButton.setPreferredSize(new Dimension(TERM_INFO_DEFAULT_WIDTH, 30));
+    useTermButton.setMinimumSize(new Dimension(TERM_INFO_DEFAULT_WIDTH, 30));
+    ImageIcon back = new ImageIcon("/Users/Nicole/Desktop/arrow.small.left.gif");
+    JButton backButton = new JButton(back);
+    backButton.setToolTipText("Go back a term");
+    backButton.setPreferredSize(new Dimension(BUTTON_HEIGHT, BUTTON_HEIGHT));
+    backButton.setMinimumSize(new Dimension(BUTTON_HEIGHT, BUTTON_HEIGHT));
+    backButton.setMaximumSize(new Dimension(BUTTON_HEIGHT, BUTTON_HEIGHT));
+    ImageIcon forward = new ImageIcon("/Users/Nicole/Desktop/arrow.small.right.gif");
+    JButton forwardButton = new JButton(forward);
+    forwardButton.setToolTipText("Go forward a term");
+    forwardButton.setPreferredSize(new Dimension(BUTTON_HEIGHT, BUTTON_HEIGHT));
+    forwardButton.setMinimumSize(new Dimension(BUTTON_HEIGHT, BUTTON_HEIGHT));
+    forwardButton.setMaximumSize(new Dimension(BUTTON_HEIGHT, BUTTON_HEIGHT));
+    JPanel naviButtons = new JPanel();
+    naviButtons.setMinimumSize(new Dimension((2*BUTTON_HEIGHT), BUTTON_HEIGHT));
+    naviButtons.setPreferredSize(new Dimension((2*BUTTON_HEIGHT), BUTTON_HEIGHT));
+    naviButtons.setMaximumSize(new Dimension((2*BUTTON_HEIGHT), BUTTON_HEIGHT));
+    naviButtons.setLayout(new BorderLayout(0,0));
+    naviPanel = new JPanel();
+    naviPanel.setLayout(new BorderLayout(0,0));
+    JPanel bottomPanel = new JPanel();
+    bottomPanel.setBackground(Color.lightGray);
+    bottomPanel.setLayout(new BorderLayout(0,0));
+    forwardButton.addActionListener(new ForwardNaviActionListener());
+    backButton.addActionListener(new BackNaviActionListener());
+//    bottomPanel.add(backButton, BorderLayout.WEST);
+//    bottomPanel.add(forwardButton, BorderLayout.CENTER);
+    bottomPanel.add(useTermButton);
+    termInfoPanel.add(bottomPanel,BorderLayout.SOUTH);
+    termField = new JTextField();
+    termField.setText("(no term selected)");
+    termField.setPreferredSize(new Dimension(TERM_INFO_DEFAULT_WIDTH,20));
+    termField.setEditable(false);  
+    naviButtons.add(backButton, BorderLayout.WEST);
+    naviButtons.add(forwardButton, BorderLayout.EAST);
+    naviPanel.add(naviButtons, BorderLayout.WEST);
+    naviPanel.add(termField, BorderLayout.CENTER);
+    termInfoPanel.add(naviPanel, BorderLayout.NORTH);
     return termInfoPanel;
   }
   
@@ -108,9 +156,42 @@
       if (useTermListener == null) return;
       if (currentOboClass == null) return; // shouldnt happen
       useTermListener.useTerm(new UseTermEvent(TermInfo.this,currentOboClass));
+
     }
   }
-
+  
+  private class BackNaviActionListener implements ActionListener {
+    public void actionPerformed(ActionEvent e) {
+    	String id="";
+    	if (naviIndex>0) {
+    		naviIndex--;
+    		id = getTermFromNaviHistory(naviIndex);
+    		try {
+    			OBOClass term = OntologyManager.inst().getOboClass(id); // ex
+    			setTextFromOboClass(term);
+    			// send out term selection (non mouse over) for DAG view
+    			SelectionManager.inst().selectTerm(TermInfo.this, term, true);
+    		}
+    		catch (TermNotFoundException ex) { return; }
+    	}
+    }
+  }
+  private class ForwardNaviActionListener implements ActionListener {
+    public void actionPerformed(ActionEvent e) {
+  	int tot = termInfoNaviHistory.getItemCount();
+    	if (naviIndex<(tot-1)) {
+    		naviIndex++;
+    		String id = getTermFromNaviHistory(naviIndex);
+    		try {
+    			OBOClass term = OntologyManager.inst().getOboClass(id); // ex
+    			setTextFromOboClass(term);
+    			// send out term selection (non mouse over) for DAG view
+    			SelectionManager.inst().selectTerm(TermInfo.this, term, true);
+    		}
+    		catch (TermNotFoundException ex) { return; }
+    	}
+    }
+  }
   // for TestPhenote
   String getText() { return textArea.getText(); }
 
@@ -120,6 +201,7 @@
     String html = HtmlUtil.termInfo(oboClass);
 
     textArea.setText(html);
+    termField.setText(oboClass.getName());
     // scroll to top (by default does bottom)
     textArea.setCaretPosition(0);
   }
@@ -129,7 +211,12 @@
   private class InfoTermSelectionListener implements TermSelectionListener {
     public boolean termSelected(TermSelectionEvent e) {
     	
-      if (!e.isMouseOverEvent() ) return false;
+      if (!e.isMouseOverEvent() ) {
+      	//add the item to the navi history if selected from list only
+      	String id=e.getOboClass().getID();
+        addTermToNaviHistory(id);
+      	return false;
+      }
       setTextFromOboClass(e.getOboClass());
       // This sets who now listens to use term button clicks (only 1 listener)
       setUseTermListener(e.getUseTermListener());
@@ -147,7 +234,27 @@
     termHyperlinkListener.hyperlinkUpdate(e);
   }
 
+  private void addTermToNaviHistory(String link) {
+  	int tot = termInfoNaviHistory.getItemCount();
+  	if ((tot-1)>naviIndex) { //we're in the middle of the navi
+  		if (naviIndex>=0) { //we're not at the beginning
+  		//remove all the items between end and here
+  			for (int i=(tot-1); i>naviIndex; i--) {
+  				termInfoNaviHistory.remove(i);
+  			}
+  		}
+  	}
+		termInfoNaviHistory.add(link);
+		naviIndex++;  //we should be at the end of the history
+//  	System.out.println("tot="+tot+"; naviIndex="+naviIndex);
+  }
 
+  private String getTermFromNaviHistory(int position) {
+  	if (termInfoNaviHistory.getItemCount() >= 1)
+  		return termInfoNaviHistory.getItem(position);
+  	else 
+  		return "";
+  }
   /** inner class TermHyperlink Listener, listens for clicks on term & external
       hyper links and brings up the term or brings up the external web page */
   private class TermHyperlinkListener implements HyperlinkListener {
@@ -197,6 +304,7 @@
       try {
         OBOClass term = OntologyManager.inst().getOboClass(id); // ex
         setTextFromOboClass(term);
+        addTermToNaviHistory(id);
         // send out term selection (non mouse over) for DAG view
         SelectionManager.inst().selectTerm(TermInfo.this, term, true);
       }


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[Obo-svn-commit] SF.net SVN: obo: [671] phenote/trunk/conf/birn2.cfg

[<nl...@us...>]

Revision: 671
          http://svn.sourceforge.net/obo/?rev=671&view=rev
Author:   nlw
Date:     2007-06-20 11:19:52 -0700 (Wed, 20 Jun 2007)

Log Message:
-----------
changed GO to GO-edit file

Modified Paths:
--------------
    phenote/trunk/conf/birn2.cfg

Modified: phenote/trunk/conf/birn2.cfg
===================================================================
--- phenote/trunk/conf/birn2.cfg	2007-06-20 18:17:38 UTC (rev 670)
+++ phenote/trunk/conf/birn2.cfg	2007-06-20 18:19:52 UTC (rev 671)
@@ -30,7 +30,7 @@
     <ns:ontology name="FMA" file="fma_obo.obo"/>
     <ns:ontology name="Mouse" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/mouse/adult_mouse_anatomy.obo"/>
     <ns:ontology name="GO"
-       file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene_ontology.obo"/>
+       file="ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology_edit.obo"/>
     <ns:ontology name="CL"
         file="http://www.berkeleybop.org/ontologies/obo-all/cell/cell.obo" />
     <ns:ontology name="CHEBI"
@@ -48,7 +48,7 @@
     <ns:ontology name="FMA" file="fma_obo.obo"/>
     <ns:ontology name="Mouse" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/mouse/adult_mouse_anatomy.obo"/>
     <ns:ontology name="GO"
-     file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene_ontology.obo"/>
+     file="ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology_edit.obo"/>
     <ns:ontology name="CL"
         file="http://www.berkeleybop.org/ontologies/obo-all/cell/cell.obo" />
     <ns:ontology name="CHEBI"
@@ -67,5 +67,7 @@
   <!--set to 0 if you want to bypass the check; time in seconds-->
   <ns:update-timer timer="10"/>
 
+  <!-- ******************** REVISION HISTORY *********************** --> 
+  <!-- 06.20.2007 - added link to GO-edit file -->
 
 </ns:phenote-configuration>


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[Obo-svn-commit] SF.net SVN: obo: [670] phenote/trunk/conf/birn2.cfg

[<nl...@us...>]

Revision: 670
          http://svn.sourceforge.net/obo/?rev=670&view=rev
Author:   nlw
Date:     2007-06-20 11:17:38 -0700 (Wed, 20 Jun 2007)

Log Message:
-----------
other changes to birn2

Modified Paths:
--------------
    phenote/trunk/conf/birn2.cfg

Modified: phenote/trunk/conf/birn2.cfg
===================================================================
--- phenote/trunk/conf/birn2.cfg	2007-06-19 22:01:24 UTC (rev 669)
+++ phenote/trunk/conf/birn2.cfg	2007-06-20 18:17:38 UTC (rev 670)
@@ -26,7 +26,7 @@
   <ns:field name="Entity" syntax-abbrev="E" enable="true">
      <ns:ontology name="Relationship" is-postcomp-rel="true"
       file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo"/>
-    <!--ns:ontology name="SAO" file="SAO.obo"/-->
+    <ns:ontology name="SAO" file="SAO.obo"/>
     <ns:ontology name="FMA" file="fma_obo.obo"/>
     <ns:ontology name="Mouse" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/mouse/adult_mouse_anatomy.obo"/>
     <ns:ontology name="GO"


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[Obo-svn-commit] SF.net SVN: obo: [669] phenote/trunk/conf/birn2.cfg

[<nl...@us...>]

Revision: 669
          http://svn.sourceforge.net/obo/?rev=669&view=rev
Author:   nlw
Date:     2007-06-19 15:01:24 -0700 (Tue, 19 Jun 2007)

Log Message:
-----------
adding ns to log file

Modified Paths:
--------------
    phenote/trunk/conf/birn2.cfg

Modified: phenote/trunk/conf/birn2.cfg
===================================================================
--- phenote/trunk/conf/birn2.cfg	2007-06-19 22:00:42 UTC (rev 668)
+++ phenote/trunk/conf/birn2.cfg	2007-06-19 22:01:24 UTC (rev 669)
@@ -3,12 +3,12 @@
 		       name="BIRN Test Config 2" 
 		       author="Nicole Washington"
 		       description="A test for finding a config for BIRN so I can test annotate from their spreadsheet.  It includes their converted brain subcellular anatomy ontology (SAO).">
-  <log config-file="conf/log4j-standalone.xml"/>
+  <ns:log config-file="conf/log4j-standalone.xml"/>
 
   <!-- wipeout always means that the master will always wipeout the local copy
     in this mode modifying the local is useless -->
-  <ns:master-to-local-config mode="WIPEOUT" when="ALWAYS" 
-     overriding-master-url="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/phenote/trunk/conf/birn2.cfg" />
+  <!--ns:master-to-local-config mode="WIPEOUT" when="ALWAYS" 
+     overriding-master-url="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/phenote/trunk/conf/birn2.cfg" /-->
 
   <!-- ********************* FILE ADAPTERS ************************** -->
   <!-- be sure to include at least one enabled file adapter -->                                      
@@ -26,7 +26,7 @@
   <ns:field name="Entity" syntax-abbrev="E" enable="true">
      <ns:ontology name="Relationship" is-postcomp-rel="true"
       file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo"/>
-    <ns:ontology name="SAO" file="SAO.obo"/>
+    <!--ns:ontology name="SAO" file="SAO.obo"/-->
     <ns:ontology name="FMA" file="fma_obo.obo"/>
     <ns:ontology name="Mouse" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/mouse/adult_mouse_anatomy.obo"/>
     <ns:ontology name="GO"
@@ -44,7 +44,7 @@
   <ns:field name="Add'l Entity" syntax-abbrev="E2" enable="true">
      <ns:ontology name="Relationship" is-postcomp-rel="true"
       file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo"/>
-    <ns:ontology name="SAO" file="SAO.obo"/>
+    <!--ns:ontology name="SAO" file="SAO.obo"/-->
     <ns:ontology name="FMA" file="fma_obo.obo"/>
     <ns:ontology name="Mouse" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/mouse/adult_mouse_anatomy.obo"/>
     <ns:ontology name="GO"


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[Obo-svn-commit] SF.net SVN: obo: [668] phenote/trunk/src/java/phenote

[<nl...@us...>]

Revision: 668
          http://svn.sourceforge.net/obo/?rev=668&view=rev
Author:   nlw
Date:     2007-06-19 15:00:42 -0700 (Tue, 19 Jun 2007)

Log Message:
-----------
*Table column widths are saved per session (if using File->Exit)
*Table is horiz scrollable now.  (TODO:  make configurable to fit to screen width)

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/config/Config.java
    phenote/trunk/src/java/phenote/config/FieldConfig.java
    phenote/trunk/src/java/phenote/gui/CharacterTableModel.java
    phenote/trunk/src/java/phenote/gui/CharacterTablePanel.java
    phenote/trunk/src/java/phenote/gui/TableRightClickMenu.java

Modified: phenote/trunk/src/java/phenote/config/Config.java
===================================================================
--- phenote/trunk/src/java/phenote/config/Config.java	2007-06-19 21:45:36 UTC (rev 667)
+++ phenote/trunk/src/java/phenote/config/Config.java	2007-06-19 22:00:42 UTC (rev 668)
@@ -664,6 +664,14 @@
   public String getFieldLabel(int index) {
     return getEnbldFieldCfg(index).getLabel();
   }
+  
+  public int getFieldColwidth(int index) {
+  	return getEnbldFieldCfg(index).getColwidth();
+  }
+  
+  public void setFieldColwidth(int index, int width) {
+  	getEnbldFieldCfg(index).setColwidth(width);
+  }
 
 //   public CharFieldEnum getCharFieldEnum(int index) {
 //     return getFieldConfig(index).getCharFieldEnum();

Modified: phenote/trunk/src/java/phenote/config/FieldConfig.java
===================================================================
--- phenote/trunk/src/java/phenote/config/FieldConfig.java	2007-06-19 21:45:36 UTC (rev 667)
+++ phenote/trunk/src/java/phenote/config/FieldConfig.java	2007-06-19 22:00:42 UTC (rev 668)
@@ -87,6 +87,18 @@
 
   //public String getLabel() { return label; }
   public String getDesc() { return desc; }
+  
+  public int getColwidth() { 
+  	//if 0 then uninitialized;
+  	//if -1 indicates not to display
+   	return fieldBean.getColwidth(); 
+  }
+  
+  public void setColwidth(int w) {
+  	fieldBean.setColwidth(w);
+  	return;
+  }
+  
   // boolean hasLabel(String label) { return label.equals(this.label); } 
   boolean hasDesc(String desc) { return desc.equals(this.desc); }
 

Modified: phenote/trunk/src/java/phenote/gui/CharacterTableModel.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/CharacterTableModel.java	2007-06-19 21:45:36 UTC (rev 667)
+++ phenote/trunk/src/java/phenote/gui/CharacterTableModel.java	2007-06-19 22:00:42 UTC (rev 668)
@@ -61,6 +61,10 @@
   public String getColumnName(int col) {
     return cfg().getFieldLabel(col);
   }
+  
+  public int getColwidth(int col) {
+  	return cfg().getFieldColwidth(col);
+  }
 
   public int getColumnCount() {
     return cfg().getEnbldFieldsNum();
@@ -158,7 +162,8 @@
       CharField cf = OntologyManager.inst().getCharField(col);
       if (!chr.hasValue(cf))
         return null;
-      return chr.getValue(cf).getName();
+      return chr.getValue(cf);
+      //      return chr.getValue(cf).getName();
     } 
     catch (Exception e) {
       log().error("column "+col+" not configured properly in "+

Modified: phenote/trunk/src/java/phenote/gui/CharacterTablePanel.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/CharacterTablePanel.java	2007-06-19 21:45:36 UTC (rev 667)
+++ phenote/trunk/src/java/phenote/gui/CharacterTablePanel.java	2007-06-19 22:00:42 UTC (rev 668)
@@ -2,6 +2,7 @@
 
 import java.util.ArrayList;
 import java.util.List;
+import java.lang.Integer;
 
 import java.awt.Dimension;
 //import java.awt.GridLayout;
@@ -14,6 +15,9 @@
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 
+import java.beans.PropertyChangeListener;
+import java.beans.PropertyChangeEvent;
+
 import javax.swing.Box;
 import javax.swing.JButton;
 import javax.swing.JPanel;
@@ -23,6 +27,10 @@
 import javax.swing.JPopupMenu;
 import javax.swing.JOptionPane;
 import javax.swing.JMenuItem;
+import javax.swing.table.TableColumn;
+import javax.swing.table.TableColumnModel;
+import javax.swing.event.TableColumnModelEvent;
+import javax.swing.event.TableColumnModelListener;
 import javax.swing.ListSelectionModel;
 import javax.swing.event.ChangeEvent;
 import javax.swing.event.ChangeListener;
@@ -33,6 +41,8 @@
 
 import phenote.datamodel.CharacterI;
 import phenote.datamodel.CharacterListI;
+import phenote.datamodel.CharField;
+import phenote.datamodel.CharFieldValue;
 import phenote.edit.CharChangeEvent;
 import phenote.edit.CharChangeListener;
 import phenote.edit.EditManager;
@@ -51,7 +61,11 @@
 
   private CharacterTableModel characterTableModel = new CharacterTableModel();
   private JTable charJTable = new JTable(characterTableModel);
-
+  private static int DEFAULT_COLWIDTH=150; //default column width for table
+  private static int INIT_TABLE_WIDTH=1400;
+  private static int INIT_TABLE_HEIGHT=500;
+  private static int DEFAULT_VIEW_WIDTH=500;
+  private static int DEFAULT_VIEW_HEIGHT=600;
   //private FieldPanel fieldPanel;
   //private JButton newButton;
   private JButton copyButton;
@@ -60,9 +74,12 @@
   private JButton commitButton;
   private JButton graphWindow;
   private JScrollBar verticalScrollBar;
+  private JScrollBar horizontalScrollBar;
   private boolean scrollToNewLastRowOnRepaint = false;
   private boolean ignoreSelectionChange = false;
   private Point currentMousePoint = new Point(0,0);
+  private int tableWidth=INIT_TABLE_WIDTH;
+  private int tableHeight=INIT_TABLE_HEIGHT;
   
   //private int selectedRow;
   // get from file menu?
@@ -81,7 +98,8 @@
     //setLayout(new GridLayout(2,1)); // row,col
     setLayout(new GridBagLayout());
     //setPreferredSize(new Dimension(1800,800));
-    setPreferredSize(new Dimension(1400,500));
+    setColumns();
+    setPreferredSize(new Dimension(tableWidth, tableHeight));
     //setMinimumSize(new Dimension(1400,630)); // 630   
 
     //charJTable.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
@@ -95,8 +113,11 @@
     verticalScrollBar = tableScroll.getVerticalScrollBar();//needed for scroll to new
     // wierd - changes to scrollbar seem to happen on own thread?
     verticalScrollBar.getModel().addChangeListener(new ScrollChangeListener());
+    horizontalScrollBar = tableScroll.getHorizontalScrollBar();
+    if (tableWidth>DEFAULT_VIEW_WIDTH)
+    	charJTable.setAutoResizeMode(JTable.AUTO_RESIZE_OFF);
     // width config? 150 * # of cols? set column width? column width config?
-    charJTable.setPreferredScrollableViewportSize(new Dimension(500, 600));//150
+    charJTable.setPreferredScrollableViewportSize(new Dimension(DEFAULT_VIEW_WIDTH, DEFAULT_VIEW_HEIGHT));//150
 
     GridBagConstraints gbc = GridBagUtil.makeFillingConstraint(0,0);
 
@@ -106,7 +127,7 @@
     charJTable.addMouseListener(popupListener);
 
     add(tableScroll,gbc);
-
+    
     // add in buttons
     JPanel buttonPanel = new JPanel();
     //buttonPanel.setBorder(new javax.swing.border.LineBorder(java.awt.Color.BLUE));
@@ -135,6 +156,29 @@
     getCharListManager().addCharListChangeListener(new TableCharListChangeListener());
   }
 
+  private void setColumns() {
+  	//this method sets the column widths according to those in the configuration
+  	//default width=30
+  	//will determine the total table width according to dimensions in config
+  	int columnCount = characterTableModel.getColumnCount();
+  	int totalWidth = 0;
+    for (int i = 0; i < columnCount; i++) {
+      TableColumn column = charJTable.getColumnModel().getColumn(i);
+      //get the field width from the model
+      int width = characterTableModel.getColwidth(i);
+      if (width==0) //-1 is no display
+      	{width=DEFAULT_COLWIDTH;}
+      column.setPreferredWidth(width);
+      column.addPropertyChangeListener(new ColwidthChangeListener());
+      charJTable.getTableHeader().setResizingColumn(column);
+      column.setWidth(width);
+      totalWidth+=width;
+     	System.out.println("Set column "+characterTableModel.getColumnName(i)+" width = "+width);  	
+    }
+    System.out.println("Total width = "+totalWidth);
+    tableWidth=totalWidth;
+  }
+  
   private String getCommitButtonString() {
     if (Config.inst().hasQueryableDataAdapter())
       return Config.inst().getQueryableDataAdapter().getCommitButtonLabel();
@@ -169,6 +213,11 @@
   	} else return s.toString();
   }
   
+  public CharFieldValue getCellCharField(int row, int col) {
+  	CharFieldValue cfv = (CharFieldValue) charJTable.getValueAt(row,col);
+  	return cfv;
+  }
+  
   /** row number is zero based for tables */
   private void selectRow(int row) {
     if (charJTable == null) return;
@@ -403,8 +452,28 @@
       scrollToNewLastRowOnRepaint = false;
     }
   }
+  
+  private class ColwidthChangeListener implements PropertyChangeListener {
+  	public void propertyChange(PropertyChangeEvent e)
+  	{
+  		//listens for changes to the column widths, makes changes to config,
+  		//and flags that there's been changes (so that they'll be saved)
+  		if (e.getPropertyName().equals("width")) {
+  			TableColumn col = (TableColumn)e.getSource();
+  			int colIndex = col.getModelIndex();
+  			Integer newWidth = (Integer)e.getNewValue();
+  			int w = newWidth.intValue();
+  			if (w!=(Config.inst().getFieldColwidth(colIndex))) {
+  				//only flag modified if changed from original settings
+  				Config.inst().setFieldColwidth(colIndex, w);
+  				Config.inst().setConfigModified(true);
+  				System.out.println("column "+colIndex+" "+e.getPropertyName()+" changed: "+ e.getOldValue()+" --> "+w);
+  			}
+  		}
+  	}	
+  }
+  
 
-
   private class TableSorter extends MouseAdapter {
     public void mouseClicked(MouseEvent e) {
       if (e.getClickCount() != 1) return; // ?

Modified: phenote/trunk/src/java/phenote/gui/TableRightClickMenu.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/TableRightClickMenu.java	2007-06-19 21:45:36 UTC (rev 667)
+++ phenote/trunk/src/java/phenote/gui/TableRightClickMenu.java	2007-06-19 22:00:42 UTC (rev 668)
@@ -26,6 +26,8 @@
 import phenote.gui.CharacterTablePanel;
 import phenote.gui.CharacterTableModel;
 import phenote.main.Phenote;
+import phenote.datamodel.CharField;
+import phenote.datamodel.CharFieldValue;
 
 
 
@@ -42,11 +44,17 @@
 //		Create the popup menu.
 		JMenuItem menuItem;
 		menuItem = new JMenuItem();
-		menuItem.setText("Copy");
+		menuItem.setText("Copy as Text");
 		menuItem.setMnemonic(KeyEvent.VK_C);
-		menuItem.addActionListener(new CopyActionListener());
+		menuItem.addActionListener(new CopyTextActionListener());
 		add(menuItem);
 		menuItem = new JMenuItem();
+		menuItem.setText("Copy Term");
+		menuItem.setMnemonic(KeyEvent.VK_C);
+		menuItem.setEnabled(true);
+		menuItem.addActionListener(new CopyCharActionListener());
+		add(menuItem);
+		menuItem = new JMenuItem();
 //		menuItem.addActionListener(new CutActionListener());
 		menuItem.setText("Cut");
 		menuItem.setEnabled(false);
@@ -60,7 +68,7 @@
 		add(menuItem);
 	}
 
-	private class CopyActionListener implements ActionListener {
+	private class CopyTextActionListener implements ActionListener {
 		public void actionPerformed(ActionEvent e) {
 			CharacterTablePanel table = Phenote.getPhenote().getCharacterTablePanel();
 			Point coord = table.getTableCoord();
@@ -75,6 +83,24 @@
 		}
 	}
 
+	private class CopyCharActionListener implements ActionListener {
+		public void actionPerformed(ActionEvent e) {
+			CharacterTablePanel table = Phenote.getPhenote().getCharacterTablePanel();
+			Point coord = table.getTableCoord();
+			int row = (int) coord.getX();
+			int col = (int) coord.getY();
+			CharFieldValue cfv = table.getCellCharField(row,col);
+			String s="";
+			if (cfv!=null)
+				s = cfv.getName();
+			System.out.println("copied ("+row+","+col+") "+s);
+			Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+			//System.out.println("system clipboard="+c.getContents(null));
+			StringSelection stringSelection = new StringSelection( s );
+			c.setContents( stringSelection , null);
+		}
+	}
+
 	private class PasteActionListener implements ActionListener {
 		public void actionPerformed(ActionEvent e) {
 


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[Obo-svn-commit] SF.net SVN: obo: [667] phenote/trunk/conf

[<nl...@us...>]

Revision: 667
          http://svn.sourceforge.net/obo/?rev=667&view=rev
Author:   nlw
Date:     2007-06-19 14:45:36 -0700 (Tue, 19 Jun 2007)

Log Message:
-----------
basic changes

Modified Paths:
--------------
    phenote/trunk/conf/birn2.cfg
    phenote/trunk/conf/zfin-standalone.cfg

Modified: phenote/trunk/conf/birn2.cfg
===================================================================
--- phenote/trunk/conf/birn2.cfg	2007-06-19 17:44:56 UTC (rev 666)
+++ phenote/trunk/conf/birn2.cfg	2007-06-19 21:45:36 UTC (rev 667)
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<phenote-configuration version="1.3-beta1" xmlns="phenote/config/xml" 
+<ns:phenote-configuration version="1.3-beta1" xmlns:ns="phenote/config/xml" 
 		       name="BIRN Test Config 2" 
 		       author="Nicole Washington"
 		       description="A test for finding a config for BIRN so I can test annotate from their spreadsheet.  It includes their converted brain subcellular anatomy ontology (SAO).">
@@ -7,65 +7,65 @@
 
   <!-- wipeout always means that the master will always wipeout the local copy
     in this mode modifying the local is useless -->
-  <master-to-local-config mode="WIPEOUT" when="ALWAYS" 
+  <ns:master-to-local-config mode="WIPEOUT" when="ALWAYS" 
      overriding-master-url="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/phenote/trunk/conf/birn2.cfg" />
 
   <!-- ********************* FILE ADAPTERS ************************** -->
   <!-- be sure to include at least one enabled file adapter -->                                      
-  <dataadapter name="phenote.dataadapter.phenosyntax.PhenoSyntaxFileAdapter" enable="true"/>
-  <dataadapter name="phenote.dataadapter.delimited.DelimitedFileAdapter" enable="true"/>
-  <dataadapter name="phenote.dataadapter.phenoxml.PhenoXmlAdapter" enable="true"/>
+  <ns:dataadapter name="phenote.dataadapter.phenosyntax.PhenoSyntaxFileAdapter" enable="true"/>
+  <ns:dataadapter name="phenote.dataadapter.delimited.DelimitedFileAdapter" enable="true"/>
+  <ns:dataadapter name="phenote.dataadapter.phenoxml.PhenoXmlAdapter" enable="true"/>
 
 
   <!-- ******************** FIELD DEFINITIONS *********************** --> 
-  <field name="Pub" syntax-abbrev="PUB" enable="true" desc="The provenance for this data"/>
-  <field name="Image" enable="true" desc="An image ID for reference"/>
-  <field name="Organism" enable="true" syntax-abbrev="GT" desc="This is like the genotype; its probably a
+  <ns:field name="Pub" syntax-abbrev="PUB" enable="true" desc="The provenance for this data"/>
+  <ns:field name="Image" enable="true" desc="An image ID for reference"/>
+  <ns:field name="Organism" enable="true" syntax-abbrev="GT" desc="This is like the genotype; its probably a
     mouse strain or some other identifying factor"/>
-  <field name="Phenotypic Character" enable="true" desc="This is a free-text field for phenotype characters for now, not exactly sure what this captures; it might be just a grouping or it might be conclusions, or something else entirely"/>
-  <field name="Entity" syntax-abbrev="E" enable="true">
-     <ontology name="Relationship" is-postcomp-rel="true"
+  <ns:field name="Phenotypic Character" enable="true" desc="This is a free-text field for phenotype characters for now, not exactly sure what this captures; it might be just a grouping or it might be conclusions, or something else entirely"/>
+  <ns:field name="Entity" syntax-abbrev="E" enable="true">
+     <ns:ontology name="Relationship" is-postcomp-rel="true"
       file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo"/>
-    <ontology name="SAO" file="SAO.obo"/>
-    <ontology name="FMA" file="fma_obo.obo"/>
-    <ontology name="Mouse" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/mouse/adult_mouse_anatomy.obo"/>
-    <ontology name="GO"
+    <ns:ontology name="SAO" file="SAO.obo"/>
+    <ns:ontology name="FMA" file="fma_obo.obo"/>
+    <ns:ontology name="Mouse" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/mouse/adult_mouse_anatomy.obo"/>
+    <ns:ontology name="GO"
        file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene_ontology.obo"/>
-    <ontology name="CL"
+    <ns:ontology name="CL"
         file="http://www.berkeleybop.org/ontologies/obo-all/cell/cell.obo" />
-    <ontology name="CHEBI"
+    <ns:ontology name="CHEBI"
        file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/chemical/chebi.obo"/>
-  </field>
+  </ns:field>
 
-  <field name="Quality" syntax-abbrev="Q" enable="true">
-    <ontology file="http://www.berkeleybop.org/ontologies/obo-all/quality/quality.obo"/>
-  </field>
+  <ns:field name="Quality" syntax-abbrev="Q" enable="true">
+    <ns:ontology file="http://www.berkeleybop.org/ontologies/obo-all/quality/quality.obo"/>
+  </ns:field>
 
-  <field name="Add'l Entity" syntax-abbrev="E2" enable="true">
-     <ontology name="Relationship" is-postcomp-rel="true"
+  <ns:field name="Add'l Entity" syntax-abbrev="E2" enable="true">
+     <ns:ontology name="Relationship" is-postcomp-rel="true"
       file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo"/>
-    <ontology name="SAO" file="SAO.obo"/>
-    <ontology name="FMA" file="fma_obo.obo"/>
-    <ontology name="Mouse" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/mouse/adult_mouse_anatomy.obo"/>
-    <ontology name="GO"
+    <ns:ontology name="SAO" file="SAO.obo"/>
+    <ns:ontology name="FMA" file="fma_obo.obo"/>
+    <ns:ontology name="Mouse" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/mouse/adult_mouse_anatomy.obo"/>
+    <ns:ontology name="GO"
      file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene_ontology.obo"/>
-    <ontology name="CL"
+    <ns:ontology name="CL"
         file="http://www.berkeleybop.org/ontologies/obo-all/cell/cell.obo" />
-    <ontology name="CHEBI"
+    <ns:ontology name="CHEBI"
        file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/chemical/chebi.obo"/>
-  </field>
+  </ns:field>
 
-  <field name="Compare To" syntax-abbrev="Compar" enable="true"/>
+  <ns:field name="Compare To" syntax-abbrev="Compar" enable="true"/>
 
-  <field name="Description" syntax-abbrev="Desc" enable="true"/>
+  <ns:field name="Description" syntax-abbrev="Desc" enable="true"/>
 
 
   <!-- *********************** SETTINGS **************************** -->
-  <uvic-graph enable="false"/>
-  <term-history enable="false"/>
-  <auto-update-ontologies enable="true"/>  <!--true=update; false=don't update-->
+  <ns:uvic-graph enable="false"/>
+  <ns:term-history enable="false"/>
+  <ns:auto-update-ontologies enable="true"/>  <!--true=update; false=don't update-->
   <!--set to 0 if you want to bypass the check; time in seconds-->
-  <update-timer timer="10"/>
+  <ns:update-timer timer="10"/>
 
 
-</phenote-configuration>
+</ns:phenote-configuration>

Modified: phenote/trunk/conf/zfin-standalone.cfg
===================================================================
--- phenote/trunk/conf/zfin-standalone.cfg	2007-06-19 17:44:56 UTC (rev 666)
+++ phenote/trunk/conf/zfin-standalone.cfg	2007-06-19 21:45:36 UTC (rev 667)
@@ -1,4 +1,4 @@
-<?xml version="1.3.1" encoding="UTF-8"?>
+<?xml version="1.4.1" encoding="UTF-8"?>
 <!-- *********************** CONFIG INFO ************************** -->
 <ns:phenote-configuration xmlns:ns="phenote/config/xml"
 			  name="Zebrafish Community"
@@ -6,7 +6,7 @@
 			  description="This configuration is for the curators and research community working with Zebrafish.  This tools provides for phenotype annotation.  It updates to the current ontologies.">
 
   <!-- *********************** SETTINGS **************************** -->
-  <ns:master-to-local-config mode="UPDATE" when="ON_VERSION_CHANGE" 
+  <ns:master-to-local-config mode="WIPEOUT" when="ALWAYS" 
      overriding-master-url="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/phenote/trunk/conf/zfin-standalone.cfg" />
 
   <ns:log config-file="conf/log4j-standalone.xml"/>
@@ -29,6 +29,8 @@
 
   <ns:field name="Genotype" syntax-abbrev="GT" enable="true"/>
 
+  <ns:field name="Image File" enable="true" desc="The image filename to attribute this phenotype character."/>
+
   <ns:field name="Genetic Context" syntax-abbrev="GC" enable="true">
     <ns:ontology name="Genetic Context" file="context.obo"/>
   </ns:field>
@@ -74,5 +76,7 @@
        removed the nexus adapter...it won't ever be used by this group.
        Changed GO to gene_ontology_edit.obo file (nlw) 
        Added in autocompletion setting defaults; Terms&Synonyms -->
+  <!-- 06.14.07 - Added 'image name' free-text field as an additional provenance field
+       changed settings to ALWAYS WIPEOUT in master-to-local config option --> 
 
 </ns:phenote-configuration>
\ No newline at end of file


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[Obo-svn-commit] SF.net SVN: obo: [666] phenote/trunk/src/java/phenote/util/HtmlUtil.java

[<nl...@us...>]

Revision: 666
          http://svn.sourceforge.net/obo/?rev=666&view=rev
Author:   nlw
Date:     2007-06-19 10:44:56 -0700 (Tue, 19 Jun 2007)

Log Message:
-----------
Added dbxrefs to TermInfo display.

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/util/HtmlUtil.java

Modified: phenote/trunk/src/java/phenote/util/HtmlUtil.java
===================================================================
--- phenote/trunk/src/java/phenote/util/HtmlUtil.java	2007-06-08 23:18:25 UTC (rev 665)
+++ phenote/trunk/src/java/phenote/util/HtmlUtil.java	2007-06-19 17:44:56 UTC (rev 666)
@@ -14,6 +14,8 @@
 import org.geneontology.oboedit.datamodel.Synonym;
 import org.geneontology.oboedit.datamodel.ObsoletableObject;
 import org.geneontology.oboedit.datamodel.IdentifiedObject;
+import org.geneontology.oboedit.datamodel.Dbxref;
+import org.geneontology.oboedit.datamodel.impl.DbxrefImpl;
 
 
 public class HtmlUtil {
@@ -82,44 +84,21 @@
 		sb.append(makeRow(makeLeftCol(bold("ONTOLOGY"))+makeRightCol(oboClass.getNamespace().toString())));
 		if (oboClass.isObsolete()) {
 			sb.append(makeRow(makeLeftCol(bold("TERM"))+makeRightCol(bold(oboClass.getName())+colorFont(bold("   (OBSOLETE)"), "red"))));
+			sb.append(makeObsLinks(oboClass));
 		}
 		else {
 			sb.append(makeRow(makeLeftCol(bold("TERM"))+makeRightCol(bold(oboClass.getName()))));
 		}
-		if (oboClass.isObsolete()) {
-			Set obsReplacements = oboClass.getReplacedBy();
-			StringBuffer replace = new StringBuffer();
-			boolean replaceFlag = false;
-			boolean considerFlag = false;
-			ObsoletableObject obsObj;
-			for (Iterator it = obsReplacements.iterator(); it.hasNext(); ) {
-				obsObj = (ObsoletableObject)it.next();
-				replaceFlag = true;
-				if (obsObj!=null) {
-					replace.append(termLink(obsObj)+"<br>");
-				}
-			}
-			if (replaceFlag)			
-				sb.append(makeRow(makeLeftCol(bold(italic("Replaced by:")))+makeRightCol(replace.toString())));
 
-			Set obsConsiders = oboClass.getConsiderReplacements();
-			StringBuffer considers = new StringBuffer();
-			for (Iterator it = obsConsiders.iterator(); it.hasNext(); ) {
-				obsObj = (ObsoletableObject)it.next();
-				considerFlag = true;
-				if (obsObj!=null) {
-					considers.append(termLink(obsObj)+"<br>");
-				}
-			}
-			if (considerFlag)
-				sb.append(makeRow(makeLeftCol(bold(italic("Consider using:")))+makeRightCol(considers.toString())));	
-		}	
 		sb.append(makeRow(makeLeftCol(bold("ID"))+makeRightCol(oboClass.getID())));
 
 		String synonyms = makeSyns(true, oboClass.getSynonyms());
 		if (synonyms!=null) {
 			sb.append(synonyms);
 		}
+
+		sb.append(makeDbxrefs(oboClass));
+		
 		String definition = oboClass.getDefinition();
 
 		if ((definition != null) && !(definition.equals(""))) {
@@ -143,7 +122,63 @@
 		sb.append("</table>");
 		return sb.toString();
 	}
+	
+	private static String makeObsLinks(OBOClass oboClass) {
+		StringBuffer sb = new StringBuffer();
+		Set obsReplacements = oboClass.getReplacedBy();
+		StringBuffer replace = new StringBuffer();
+		boolean replaceFlag = false;
+		boolean considerFlag = false;
+		ObsoletableObject obsObj;
+		for (Iterator it = obsReplacements.iterator(); it.hasNext(); ) {
+			obsObj = (ObsoletableObject)it.next();
+			replaceFlag = true;
+			if (obsObj!=null) {
+				replace.append(termLink(obsObj)+"<br>");
+			}
+		}
+		if (replaceFlag)			
+			sb.append(makeRow(makeLeftCol(bold(italic("Replaced by:")))+makeRightCol(replace.toString())));
 
+		Set obsConsiders = oboClass.getConsiderReplacements();
+		StringBuffer considers = new StringBuffer();
+		for (Iterator it = obsConsiders.iterator(); it.hasNext(); ) {
+			obsObj = (ObsoletableObject)it.next();
+			considerFlag = true;
+			if (obsObj!=null) {
+				considers.append(termLink(obsObj)+"<br>");
+			}
+		}
+		if (considerFlag)
+			sb.append(makeRow(makeLeftCol(bold(italic("Consider using:")))+makeRightCol(considers.toString())));	
+		if (replaceFlag || considerFlag)
+			return sb.toString();
+		else
+			return "";
+	}	
+
+	private static String makeDbxrefs(OBOClass oboClass) {
+		Set dbxrefs = oboClass.getDbxrefs();
+		StringBuffer sb = new StringBuffer();
+		StringBuffer dbxrefString = new StringBuffer();
+		boolean dbxrefFlag = false;
+		if (dbxrefs != null) {
+			Dbxref dbxrefObj;
+			for (Iterator it = dbxrefs.iterator(); it.hasNext(); ) {
+				dbxrefObj = (Dbxref)it.next();
+				dbxrefFlag=true;
+				if (dbxrefObj!=null) {
+					dbxrefString.append(dbxrefObj.getDatabase()+":"+dbxrefObj.getID()+
+							"("+dbxrefObj.getType()+")<br>");
+				}
+			}
+		}
+		if (dbxrefFlag)
+			return makeRow(makeLeftCol(bold("X-refs"))+makeRightCol(dbxrefString.toString()));			
+		else	
+			return "";
+	}
+	
 	private static String makeSyns(boolean sortByScope, Set syns) {
 		//This method creates a table of synonyms for a term, sorted by scope as
 		//defined in the oboedit class Synonym


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[Obo-svn-commit] SF.net SVN: obo: [664] phenote/trunk/doc/phenote-website/phenote.jnlp

[<mg...@us...>]

Revision: 664
          http://svn.sourceforge.net/obo/?rev=664&view=rev
Author:   mgibson
Date:     2007-06-06 06:43:05 -0700 (Wed, 06 Jun 2007)

Log Message:
-----------
medial -> medical

Modified Paths:
--------------
    phenote/trunk/doc/phenote-website/phenote.jnlp

Modified: phenote/trunk/doc/phenote-website/phenote.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote.jnlp	2007-06-06 00:19:34 UTC (rev 663)
+++ phenote/trunk/doc/phenote-website/phenote.jnlp	2007-06-06 13:43:05 UTC (rev 664)
@@ -5,7 +5,7 @@
 href="phenote.jnlp">
 <information>
 	<title>Phenote 1.3</title>
-	<vendor>National Center for Biomedial Ontology</vendor>
+	<vendor>National Center for Biomedical Ontology</vendor>
 	<description>Phenote standalone app via webstart</description>
  	 <!-- Declares that the application can run without
          access to the server it was downloaded from -->


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[Obo-svn-commit] SF.net SVN: obo: [663] phenote/trunk/doc/phenote-website/irc_chat/ transcripts/PWG_irc_060507.html

[<nl...@us...>]

Revision: 663
          http://svn.sourceforge.net/obo/?rev=663&view=rev
Author:   nlw
Date:     2007-06-05 17:19:34 -0700 (Tue, 05 Jun 2007)

Log Message:
-----------
changed css for today's transcripts

Modified Paths:
--------------
    phenote/trunk/doc/phenote-website/irc_chat/transcripts/PWG_irc_060507.html

Modified: phenote/trunk/doc/phenote-website/irc_chat/transcripts/PWG_irc_060507.html
===================================================================
--- phenote/trunk/doc/phenote-website/irc_chat/transcripts/PWG_irc_060507.html	2007-06-05 19:32:22 UTC (rev 662)
+++ phenote/trunk/doc/phenote-website/irc_chat/transcripts/PWG_irc_060507.html	2007-06-06 00:19:34 UTC (rev 663)
@@ -3,20 +3,730 @@
 <head>
 
 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
-<meta name="description" content="Phenote Transcripts 05.01.2007" />
+<meta name="description" content="Phenote Transcripts 06.05.2007" />
 <meta name="keywords" content="Phenotype, Annotation, Phenote, NCBO, National Center for Biomedical Ontology, Ontology, Berkeley Bioinformatics and Ontology Project, BBOP, Curation, EQ model, entities and qualities, phenotype annotation, PATO, phenotype and trait ontology, OBO, Open Biomedical Ontologies" />
 
 <!-- TODO: need an icon -->
 <link rel="icon" href="" type="image/png" />
 <link rel="shortcut icon" href="" type="image/png" />
-<link rel="stylesheet" type="text/css" href="/css/colloquy.css" title="standard" />
+<link rel="stylesheet" type="text/css" href="/css/colloquy2.css" title="standard" />
 <title>Phenote Working Group IRC chat 06.05.2007</title>
 
 </head>
 
 <body>
-

@@ Diff output truncated at 100000 characters. @@

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[Obo-svn-commit] SF.net SVN: obo: [662] phenote/trunk/doc/phenote-website/css

[<nl...@us...>]

Revision: 662
          http://svn.sourceforge.net/obo/?rev=662&view=rev
Author:   nlw
Date:     2007-06-05 12:32:22 -0700 (Tue, 05 Jun 2007)

Log Message:
-----------
adding the actual style sheets

Added Paths:
-----------
    phenote/trunk/doc/phenote-website/css/colloquy.css
    phenote/trunk/doc/phenote-website/css/colloquy2.css

Added: phenote/trunk/doc/phenote-website/css/colloquy.css
===================================================================
--- phenote/trunk/doc/phenote-website/css/colloquy.css	                        (rev 0)
+++ phenote/trunk/doc/phenote-website/css/colloquy.css	2007-06-05 19:32:22 UTC (rev 662)
@@ -0,0 +1,68 @@
+/* Generic items for all styles, these can be overridden */
+body {
+	background-color: white;
+	color: black;
+	overflow-y: auto;
+	overflow-x: hidden;
+}
+
+.hidden {
+	position: fixed;
+	top: -900px;
+	left: -900px;
+}
+
+.ignore {
+	display: none;
+}
+
+.error {
+	color: #aaa;
+}
+
+.error:before {
+	content: "[";
+}
+
+.error:after {
+	content: "]";
+}
+
+.searchHighlight {
+	background-color: rgba( 255, 128, 0, 0.75 ) !important;
+}
+
+.hostmask {
+	display: none;
+}
+
+/* For the display mark */
+hr#mark {
+	width: 80%;
+	color: #222222;
+}
+
+/* The rest of this file is for scripts, this will change in the future!
+ * Having script specific things in Colloquy is bad, bad, bad! */
+
+/* For the iTunes script links */
+.itunes > * {
+	text-decoration: none !important;
+	color: inherit !important
+}
+
+.itunes > a:hover {
+	text-decoration: underline !important;
+}
+
+/* For the TracLinks script links */
+.traclink :link, .traclink :visited {
+	text-decoration: none;
+	color: #b00;
+	border-bottom: 1px dotted #bbb;
+}
+
+.traclink :link:hover, .traclink :visited:hover {
+	background-color: #eee;
+	color: #555;
+}

Added: phenote/trunk/doc/phenote-website/css/colloquy2.css
===================================================================
--- phenote/trunk/doc/phenote-website/css/colloquy2.css	                        (rev 0)
+++ phenote/trunk/doc/phenote-website/css/colloquy2.css	2007-06-05 19:32:22 UTC (rev 662)
@@ -0,0 +1,138 @@
+body {
+  margin: 0;
+}
+
+div.message {
+  padding: 0px 7px;
+  overflow: hidden;
+}
+
+div.text span.message {
+  color: black;
+}
+
+div.event {
+  color: #666;
+  font-size: 90%;
+  overflow: hidden;
+  padding-bottom: 0;
+  text-align: center;
+}
+
+div.action > span.member:before {
+  content: "*";
+  margin: 0 0.5ex 0 0.5ex;
+}
+
+div.later > div.text > span.member {
+  display: none;
+}
+
+div.later span.timestamp, div.action span.timestamp {
+  display: none;
+}
+
+a.member {
+  font: bold 90% "Lucida Grande";
+  color: inherit;
+  text-decoration: none;
+}
+
+a.member:link    { text-decoration: none; }
+a.member:visited { text-decoration: none; }
+a.member:active  { text-decoration: none; }
+a.member:hover   { text-decoration: underline; }
+
+/*
+ * Timestamp positioning
+ */
+div.first > div.text > span.timestamp {
+  float: left;
+  margin: 0 0.5ex 0 0;
+  font: bold 90% "Lucida Grande";
+}
+
+div.first > div.text > span.timestamp:after {
+  content: "";
+}
+
+div.first > div.text > span.member:after {
+  content: ":";
+  font: bold 90% "Lucida Grande";
+}
+
+/*
+ * Timestamp display formats
+ */
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+ */
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+}
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+}
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[Obo-svn-commit] SF.net SVN: obo: [661] phenote/trunk/doc/phenote-website/irc_chat/ transcripts

[<nl...@us...>]

Revision: 661
          http://svn.sourceforge.net/obo/?rev=661&view=rev
Author:   nlw
Date:     2007-06-05 12:31:11 -0700 (Tue, 05 Jun 2007)

Log Message:
-----------
adding css styles to irc chats

Modified Paths:
--------------
    phenote/trunk/doc/phenote-website/irc_chat/transcripts/PWG_irc_060507.html

Added Paths:
-----------
    phenote/trunk/doc/phenote-website/irc_chat/transcripts/PWG_irc_050107.html

Removed Paths:
-------------
    phenote/trunk/doc/phenote-website/irc_chat/transcripts/test.html

Copied: phenote/trunk/doc/phenote-website/irc_chat/transcripts/PWG_irc_050107.html (from rev 660, phenote/trunk/doc/phenote-website/irc_chat/transcripts/test.html)
===================================================================
--- phenote/trunk/doc/phenote-website/irc_chat/transcripts/PWG_irc_050107.html	                        (rev 0)
+++ phenote/trunk/doc/phenote-website/irc_chat/transcripts/PWG_irc_050107.html	2007-06-05 19:31:11 UTC (rev 661)
@@ -0,0 +1,802 @@
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en">
+
+<head>
+
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+<meta name="description" content="Phenote Transcripts 05.01.2007" />
+<meta name="keywords" content="Phenotype, Annotation, Phenote, NCBO, National Center for Biomedical Ontology, Ontology, Berkeley Bioinformatics and Ontology Project, BBOP, Curation, EQ model, entities and qualities, phenotype annotation, PATO, phenotype and trait ontology, OBO, Open Biomedical Ontologies" />
+
+<!-- TODO: need an icon -->
+<link rel="icon" href="" type="image/png" />
+<link rel="shortcut icon" href="" type="image/png" />
+<link rel="stylesheet" type="text/css" href="/css/colloquy2.css" title="standard" />
+<title>Phenote Working Group IRC chat 05.01.2007</title>
+
+</head>
+
+<body>
+
+<div id="ZGC9D5CIP71" class="first message colors">
+  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:17<span class="secs">:32</span></span><span class="ampm">08:17<span class="secs">:32</span>am</span>)</span> <span class="message">hello?</span></div>
+</div><div id="F0MA77BVQ71" class="later message colors">
+  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:18<span class="secs">:43</span></span><span class="ampm">08:18<span class="secs">:43</span>am</span>)</span> <span class="message">hey mark, can you add a couple of new features to the wiki?</span></div>
+</div><div id="MFIG1THVQ71" class="first message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:22<span class="secs">:41</span></span><span class="ampm">08:22<span class="secs">:41</span>am</span>)</span> <span class="message">hi</span></div>
+</div><div id="RNFWIXHVQ71" class="later message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:22<span class="secs">:45</span></span><span class="ampm">08:22<span class="secs">:45</span>am</span>)</span> <span class="message">what features</span></div>
+</div><div class="event"><span class="message"><message><span class="member">DavidOS</span> joined the chat room.</message></span> <span class="timestamp"><span class="tfh">08:28<span class="secs">:05</span></span><span class="ampm">08:28<span class="secs">:05</span>am</span></span></div><div id="T9LYJ8RVQ71" class="first message color6">
+  <div class="text"><span class="member"><a href="member:DavidOS" class="member">DavidOS</a></span><span class="timestamp">(<span class="tfh">08:28<span class="secs">:20</span></span><span class="ampm">08:28<span class="secs">:20</span>am</span>)</span> <span class="message">Hiya</span></div>
+</div><div id="T8NW7PRVQ71" class="first message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:28<span class="secs">:37</span></span><span class="ampm">08:28<span class="secs">:37</span>am</span>)</span> <span class="message">hey david!</span></div>
+</div><div class="event"><span class="message"><message><span class="member">Michael</span> joined the chat room.</message></span> <span class="timestamp"><span class="tfh">08:29<span class="secs">:14</span></span><span class="ampm">08:29<span class="secs">:14</span>am</span></span></div><div class="event"><span class="message"><message><span class="member">MelissaH</span> joined the chat room.</message></span> <span class="timestamp"><span class="tfh">08:29<span class="secs">:32</span></span><span class="ampm">08:29<span class="secs">:32</span>am</span></span></div><div id="CAQCBATVQ71" class="first message colors">
+  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:29<span class="secs">:34</span></span><span class="ampm">08:29<span class="secs">:34</span>am</span>)</span> <span class="message">hi david</span></div>
+</div><div class="event"><span class="message"><message><span class="member">Michael</span> left the chat room.</message></span> (Quit: Michael) <span class="timestamp"><span class="tfh">08:29<span class="secs">:35</span></span><span class="ampm">08:29<span class="secs">:35</span>am</span></span></div><div class="event"><span class="message"><message><span class="member">MichaelAshburner</span> joined the chat room.</message></span> <span class="timestamp"><span class="tfh">08:29<span class="secs">:36</span></span><span class="ampm">08:29<span class="secs">:36</span>am</span></span></div><div id="OCDRJKTVQ71" class="first message colors">
+  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:29<span class="secs">:44</span></span><span class="ampm">08:29<span class="secs">:44</span>am</span>)</span> <span class="message">and michael and melissa</span></div>
+</div><div id="IONVITTVQ71" class="first message color4">
+  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:29<span class="secs">:53</span></span><span class="ampm">08:29<span class="secs">:53</span>am</span>)</span> <span class="message">Hi there</span></div>
+</div><div id="YOLT8WTVQ71" class="first message colors">
+  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:29<span class="secs">:56</span></span><span class="ampm">08:29<span class="secs">:56</span>am</span>)</span> <span class="message">mark:  whatever you've been working on</span></div>
+</div><div id="XU6FJ8VVQ71" class="first message color6">
+  <div class="text"><span class="member"><a href="member:MichaelAshburner" class="member">MichaelAshburner</a></span><span class="timestamp">(<span class="tfh">08:30<span class="secs">:44</span></span><span class="ampm">08:30<span class="secs">:44</span>am</span>)</span> <span class="message">MichaelA is here but has no idea how to use this tool !</span></div>
+</div><div id="O0VD9HWVQ71" class="first message colors">
+  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:31<span class="secs">:29</span></span><span class="ampm">08:31<span class="secs">:29</span>am</span>)</span> <span class="message">just type exasperating expressions</span></div>
+</div><div id="D9WNFXWVQ71" class="first message color6">
+  <div class="text"><span class="member"><a href="member:MichaelAshburner" class="member">MichaelAshburner</a></span><span class="timestamp">(<span class="tfh">08:31<span class="secs">:45</span></span><span class="ampm">08:31<span class="secs">:45</span>am</span>)</span> <span class="message">do you mean I cannot hear yu'all?</span></div>
+</div><div id="S77JK4XVQ71" class="first message colors">
+  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:31<span class="secs">:52</span></span><span class="ampm">08:31<span class="secs">:52</span>am</span>)</span> <span class="message">you are correct</span></div>
+</div><div id="MX8H3GXVQ71" class="first message color6">
+  <div class="text"><span class="member"><a href="member:MichaelAshburner" class="member">MichaelAshburner</a></span><span class="timestamp">(<span class="tfh">08:32<span class="secs">:04</span></span><span class="ampm">08:32<span class="secs">:04</span>am</span>)</span> <span class="message">oh pooh, exasperated</span></div>
+</div><div id="MI40EMXVQ71" class="first message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:32<span class="secs">:10</span></span><span class="ampm">08:32<span class="secs">:10</span>am</span>)</span> <span class="message"><span class="highlight member">nicole</span> - i added some stuff</span></div>
+</div><div id="M9QGIPXVQ71" class="first message colors">
+  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:32<span class="secs">:13</span></span><span class="ampm">08:32<span class="secs">:13</span>am</span>)</span> <span class="message">great</span></div>
+</div><div id="RPRI3WXVQ71" class="first message color6">
+  <div class="text"><span class="member"><a href="member:MichaelAshburner" class="member">MichaelAshburner</a></span><span class="timestamp">(<span class="tfh">08:32<span class="secs">:20</span></span><span class="ampm">08:32<span class="secs">:20</span>am</span>)</span> <span class="message">what stuff</span></div>
+</div><div id="H1NB5ZXVQ71" class="later message color6">
+  <div class="text"><span class="member"><a href="member:MichaelAshburner" class="member">MichaelAshburner</a></span><span class="timestamp">(<span class="tfh">08:32<span class="secs">:23</span></span><span class="ampm">08:32<span class="secs">:23</span>am</span>)</span> <span class="message">?</span></div>
+</div><div id="ZFYYF9YVQ71" class="first message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:32<span class="secs">:33</span></span><span class="ampm">08:32<span class="secs">:33</span>am</span>)</span> <span class="message">to the wiki</span></div>
+</div><div id="EIMPCHYVQ71" class="later message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:32<span class="secs">:41</span></span><span class="ampm">08:32<span class="secs">:41</span>am</span>)</span> <span class="message">hi michael</span></div>
+</div><div id="A5GNBWYVQ71" class="first message color6">
+  <div class="text"><span class="member"><a href="member:DavidOS" class="member">DavidOS</a></span><span class="timestamp">(<span class="tfh">08:32<span class="secs">:56</span></span><span class="ampm">08:32<span class="secs">:56</span>am</span>)</span> <span class="message">agenda wiki?</span></div>
+</div><div id="TXD2KIZVQ71" class="first message colors">
+  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:33<span class="secs">:18</span></span><span class="ampm">08:33<span class="secs">:18</span>am</span>)</span> <span class="message">yep, we've put up a small agenda on the wiki:  <a href="http://www.bioontology.org/wiki/index.php/Phenote:Agenda:_May_1%2C_2007">http://www.bioontology.org/wiki/index.php/Phenote:Agenda:_May_1%2C_2007</a></span></div>
+</div><div id="W85I2LZVQ71" class="first message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:33<span class="secs">:21</span></span><span class="ampm">08:33<span class="secs">:21</span>am</span>)</span> <span class="message"><a href="http://www.bioontology.org/wiki/index.php/Phenote:Agenda:_May_1%2C_2007">http://www.bioontology.org/wiki/index.php/Phenote:Agenda:_May_1%2C_2007</a></span></div>
+</div><div id="TP0A7Q1WQ71" class="first message colors">
+  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:34<span class="secs">:38</span></span><span class="ampm">08:34<span class="secs">:38</span>am</span>)</span> <span class="message">well, i suppose we ought to get started.  we'll follow that agenda, somewhat loosely</span></div>
+</div><div id="J1BX5K2WQ71" class="first message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:35<span class="secs">:08</span></span><span class="ampm">08:35<span class="secs">:08</span>am</span>)</span> <span class="message">michael are you using phenote these days?</span></div>
+</div><div id="ATHEES2WQ71" class="later message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:35<span class="secs">:16</span></span><span class="ampm">08:35<span class="secs">:16</span>am</span>)</span> <span class="message">or david?</span></div>
+</div><div id="NASED63WQ71" class="first message color6">
+  <div class="text"><span class="member"><a href="member:MichaelAshburner" class="member">MichaelAshburner</a></span><span class="timestamp">(<span class="tfh">08:35<span class="secs">:30</span></span><span class="ampm">08:35<span class="secs">:30</span>am</span>)</span> <span class="message">got it - can MArk possibly expand on some of these, espec (for me) multipe differntiae and worm adapter</span></div>
+</div><div id="EOOBD73WQ71" class="first message color6">
+  <div class="text"><span class="member"><a href="member:DavidOS" class="member">DavidOS</a></span><span class="timestamp">(<span class="tfh">08:35<span class="secs">:31</span></span><span class="ampm">08:35<span class="secs">:31</span>am</span>)</span> <span class="message">I'm not - except for some testing.</span></div>
+</div><div id="XZL25K3WQ71" class="first message colors">
+  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:35<span class="secs">:44</span></span><span class="ampm">08:35<span class="secs">:44</span>am</span>)</span> <span class="message">mark and i have described the most recently added features to phenote.  </span></div>
+</div><div id="AAXD634WQ71" class="first message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:36<span class="secs">:03</span></span><span class="ampm">08:36<span class="secs">:03</span>am</span>)</span> <span class="message">so in the post composition window you can now add more than one differentia</span></div>
+</div><div id="GHCGK64WQ71" class="first message color6">
+  <div class="text"><span class="member"><a href="member:MichaelAshburner" class="member">MichaelAshburner</a></span><span class="timestamp">(<span class="tfh">08:36<span class="secs">:06</span></span><span class="ampm">08:36<span class="secs">:06</span>am</span>)</span> <span class="message">Mark - yes indeed tho I have been on the road so much for the last 3 weeks, and have now 10 days on E Coast - that I am behind but I am using it for OMI annotation</span></div>
+</div><div id="KEWZIB4WQ71" class="first message colors">
+  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:36<span class="secs">:11</span></span><span class="ampm">08:36<span class="secs">:11</span>am</span>)</span> <span class="message">there will be a new beta release coming out later today with these elements</span></div>
+</div><div id="J91H5O4WQ71" class="first message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:36<span class="secs">:24</span></span><span class="ampm">08:36<span class="secs">:24</span>am</span>)</span> <span class="message">previously it was just genus rel &amp; differentia term</span></div>
+</div><div id="ZCAGR4WQ71" class="first message color6">
+  <div class="text"><span class="member"><a href="member:MichaelAshburner" class="member">MichaelAshburner</a></span><span class="timestamp">(<span class="tfh">08:36<span class="secs">:27</span></span><span class="ampm">08:36<span class="secs">:27</span>am</span>)</span> <span class="message">what elements does <span class="highlight member">Nicole</span> mean</span></div>
+</div><div id="G8PKDQ5WQ71" class="first message colors">
+  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:37<span class="secs">:02</span></span><span class="ampm">08:37<span class="secs">:02</span>am</span>)</span> <span class="message">elements=features described on wiki</span></div>
+</div><div id="QUOCHV5WQ71" class="first message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:37<span class="secs">:07</span></span><span class="ampm">08:37<span class="secs">:07</span>am</span>)</span> <span class="message">but at the moment you can addd 3 different differentia</span></div>
+</div><div id="TWMZ966WQ71" class="later message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:37<span class="secs">:18</span></span><span class="ampm">08:37<span class="secs">:18</span>am</span>)</span> <span class="message">do yall use post comp?</span></div>
+</div><div id="DXPYKC6WQ71" class="later message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:37<span class="secs">:24</span></span><span class="ampm">08:37<span class="secs">:24</span>am</span>)</span> <span class="message">you do right melissa?</span></div>
+</div><div id="VFJXK6WQ71" class="later message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:37<span class="secs">:32</span></span><span class="ampm">08:37<span class="secs">:32</span>am</span>)</span> <span class="message">fly?</span></div>
+</div><div id="EZ8E6R6WQ71" class="first message color6">
+  <div class="text"><span class="member"><a href="member:MichaelAshburner" class="member">MichaelAshburner</a></span><span class="timestamp">(<span class="tfh">08:37<span class="secs">:39</span></span><span class="ampm">08:37<span class="secs">:39</span>am</span>)</span> <span class="message">yes i do</span></div>
+</div><div id="I16HAU6WQ71" class="first message color6">
+  <div class="text"><span class="member"><a href="member:DavidOS" class="member">DavidOS</a></span><span class="timestamp">(<span class="tfh">08:37<span class="secs">:42</span></span><span class="ampm">08:37<span class="secs">:42</span>am</span>)</span> <span class="message">so for multiple genus post composition - isn't there an issue with correct nesting ?</span></div>
+</div><div id="QDVBGZ6WQ71" class="first message colors">
+  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:37<span class="secs">:47</span></span><span class="ampm">08:37<span class="secs">:47</span>am</span>)</span> <span class="message">like membrane^part_of(spermatocyte^part_of(random_organism))</span></div>
+</div><div id="QFQ487WQ71" class="first message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:37<span class="secs">:56</span></span><span class="ampm">08:37<span class="secs">:56</span>am</span>)</span> <span class="message">so i should clarify</span></div>
+</div><div id="M87QFH7WQ71" class="later message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:38<span class="secs">:05</span></span><span class="ampm">08:38<span class="secs">:05</span>am</span>)</span> <span class="message">it doesnt yet do "nesting"</span></div>
+</div><div id="GX3NHP7WQ71" class="first message color4">
+  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:38<span class="secs">:13</span></span><span class="ampm">08:38<span class="secs">:13</span>am</span>)</span> <span class="message">yes we do for omim and zfish</span></div>
+</div><div id="L4R8GT7WQ71" class="first message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:38<span class="secs">:17</span></span><span class="ampm">08:38<span class="secs">:17</span>am</span>)</span> <span class="message">it only does multiple differentia of one genus</span></div>
+</div><div id="CFVI2Y7WQ71" class="later message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:38<span class="secs">:22</span></span><span class="ampm">08:38<span class="secs">:22</span>am</span>)</span> <span class="message">does that make sense?</span></div>
+</div><div id="MA1F348WQ71" class="first message color4">
+  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:38<span class="secs">:28</span></span><span class="ampm">08:38<span class="secs">:28</span>am</span>)</span> <span class="message">we don't use multiple though</span></div>
+</div><div id="QR3IJ48WQ71" class="first message color6">
+  <div class="text"><span class="member"><a href="member:DavidOS" class="member">DavidOS</a></span><span class="timestamp">(<span class="tfh">08:38<span class="secs">:28</span></span><span class="ampm">08:38<span class="secs">:28</span>am</span>)</span> <span class="message">I think so</span></div>
+</div><div id="XIEV3M8WQ71" class="first message color4">
+  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:38<span class="secs">:46</span></span><span class="ampm">08:38<span class="secs">:46</span>am</span>)</span> <span class="message">yes but still a little scary...</span></div>
+</div><div id="TK6BBU8WQ71" class="first message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:38<span class="secs">:54</span></span><span class="ampm">08:38<span class="secs">:54</span>am</span>)</span> <span class="message">so you can say A^rel(B)^rel(C)</span></div>
+</div><div id="HUJVK29WQ71" class="later message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:39<span class="secs">:02</span></span><span class="ampm">08:39<span class="secs">:02</span>am</span>)</span> <span class="message">but you cant say </span></div>
+</div><div id="YFTLBJ9WQ71" class="later message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:39<span class="secs">:19</span></span><span class="ampm">08:39<span class="secs">:19</span>am</span>)</span> <span class="message">A^rel(B^rel(C))</span></div>
+</div><div class="event"><span class="message"><message><span class="member">MichaelAshburner</span> left the chat room.</message></span> () <span class="timestamp"><span class="tfh">08:39<span class="secs">:25</span></span><span class="ampm">08:39<span class="secs">:25</span>am</span></span></div><div id="TMZV6P9WQ71" class="first message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:39<span class="secs">:25</span></span><span class="ampm">08:39<span class="secs">:25</span>am</span>)</span> <span class="message">which are not equivalent</span></div>
+</div><div id="KJ3U8Q9WQ71" class="first message color4">
+  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:39<span class="secs">:26</span></span><span class="ampm">08:39<span class="secs">:26</span>am</span>)</span> <span class="message">in zfish, we only have A^part_of^B</span></div>
+</div><div id="VS7K11AWQ71" class="first message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:39<span class="secs">:37</span></span><span class="ampm">08:39<span class="secs">:37</span>am</span>)</span> <span class="message">michael had enough!</span></div>
+</div><div id="QIPRKHAWQ71" class="later message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:39<span class="secs">:53</span></span><span class="ampm">08:39<span class="secs">:53</span>am</span>)</span> <span class="message">does anyone have a need for multiple differentia at this point?</span></div>
+</div><div id="KVQ7DQAWQ71" class="first message colors">
+  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:40<span class="secs">:02</span></span><span class="ampm">08:40<span class="secs">:02</span>am</span>)</span> <span class="message">so the biggest user of this feature is Chris and those doing cross product composition</span></div>
+</div><div id="H37C3VAWQ71" class="first message color4">
+  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:40<span class="secs">:07</span></span><span class="ampm">08:40<span class="secs">:07</span>am</span>)</span> <span class="message"><span class="highlight member">Nicole</span>, was your OMIM annotations driving this feature?</span></div>
+</div><div id="TKHZDWAWQ71" class="first message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:40<span class="secs">:08</span></span><span class="ampm">08:40<span class="secs">:08</span>am</span>)</span> <span class="message">does anyone have a need for nested differentia?</span></div>
+</div><div id="LWGPXAWQ71" class="first message colors">
+  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:40<span class="secs">:09</span></span><span class="ampm">08:40<span class="secs">:09</span>am</span>)</span> <span class="message">i don't think other communities are using it</span></div>
+</div><div id="YOUDD5BWQ71" class="first message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:40<span class="secs">:17</span></span><span class="ampm">08:40<span class="secs">:17</span>am</span>)</span> <span class="message">yea chris really needed the multie diff</span></div>
+</div><div id="V6B8ICBWQ71" class="later message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:40<span class="secs">:24</span></span><span class="ampm">08:40<span class="secs">:24</span>am</span>)</span> <span class="message">as he was using phenote to do mapping</span></div>
+</div><div class="event"><span class="message"><message><span class="member">MichaelAshburner</span> joined the chat room.</message></span> <span class="timestamp"><span class="tfh">08:40<span class="secs">:26</span></span><span class="ampm">08:40<span class="secs">:26</span>am</span></span></div><div id="JXG4FMBWQ71" class="first message colors">
+  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:40<span class="secs">:34</span></span><span class="ampm">08:40<span class="secs">:34</span>am</span>)</span> <span class="message">no, not really.  there might have been one time that i wanted multi-differentia, but...</span></div>
+</div><div id="WUWJCTBWQ71" class="first message color6">
+  <div class="text"><span class="member"><a href="member:MichaelAshburner" class="member">MichaelAshburner</a></span><span class="timestamp">(<span class="tfh">08:40<span class="secs">:41</span></span><span class="ampm">08:40<span class="secs">:41</span>am</span>)</span> <span class="message">I lost you and hand to restart</span></div>
+</div><div id="YJLWBCWQ71" class="first message color6">
+  <div class="text"><span class="member"><a href="member:DavidOS" class="member">DavidOS</a></span><span class="timestamp">(<span class="tfh">08:40<span class="secs">:59</span></span><span class="ampm">08:40<span class="secs">:59</span>am</span>)</span> <span class="message">We may do - I'll have to look into our existing post-composed terms.  They are old and not implemented properly yet - may be examples of both nested and not in there.</span></div>
+</div><div id="S1M8IWCWQ71" class="first message colors">
+  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:41<span class="secs">:20</span></span><span class="ampm">08:41<span class="secs">:20</span>am</span>)</span> <span class="message">i think annotations can often be much better only using a single differentia...sometimes the multiple comes in if you're lazy and can' t think of how to say it more consicely</span></div>
+</div><div class="event"><span class="message"><message><span class="member">Anon363</span> joined the chat room.</message></span> <span class="timestamp"><span class="tfh">08:41<span class="secs">:31</span></span><span class="ampm">08:41<span class="secs">:31</span>am</span></span></div><div id="YVHICLDWQ71" class="first message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:41<span class="secs">:45</span></span><span class="ampm">08:41<span class="secs">:45</span>am</span>)</span> <span class="message">hey <span class="member">anon363</span> do a /nick</span></div>
+</div><div id="C2K0IYDWQ71" class="first message color4">
+  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:41<span class="secs">:58</span></span><span class="ampm">08:41<span class="secs">:58</span>am</span>)</span> <span class="message">I worry a bit about having the whole RO allowed for post-comp, because it may be that rules are needed about what can be post-comp with what.</span></div>
+</div><div id="QTO471EWQ71" class="first message color6">
+  <div class="text"><span class="member"><a href="member:DavidOS" class="member">DavidOS</a></span><span class="timestamp">(<span class="tfh">08:42<span class="secs">:01</span></span><span class="ampm">08:42<span class="secs">:01</span>am</span>)</span> <span class="message">"differentia...sometimes the multiple comes in if you're lazy and can' t think of how to say it more consicely </span></div>
+</div><div id="F978DTEWQ71" class="first message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:42<span class="secs">:29</span></span><span class="ampm">08:42<span class="secs">:29</span>am</span>)</span> <span class="message">we should probably have a phenote RO slim </span></div>
+</div><div id="STMBJ2FWQ71" class="later message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:42<span class="secs">:38</span></span><span class="ampm">08:42<span class="secs">:38</span>am</span>)</span> <span class="message">for those relations we want to restrict to</span></div>
+</div><div id="T2VK2FFWQ71" class="first message color3">
+  <div class="text"><span class="member"><a href="member:Anon363" class="member">Anon363</a></span><span class="timestamp">(<span class="tfh">08:42<span class="secs">:51</span></span><span class="ampm">08:42<span class="secs">:51</span>am</span>)</span> <span class="message">yes that would be a good idea</span></div>
+</div><div id="PG977TFWQ71" class="first message color6">
+  <div class="text"><span class="member"><a href="member:DavidOS" class="member">DavidOS</a></span><span class="timestamp">(<span class="tfh">08:43<span class="secs">:05</span></span><span class="ampm">08:43<span class="secs">:05</span>am</span>)</span> <span class="message">I agree with Melissa.  I only see us using part_of - at least at first.</span></div>
+</div><div id="VKJ2HYFWQ71" class="first message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:43<span class="secs">:10</span></span><span class="ampm">08:43<span class="secs">:10</span>am</span>)</span> <span class="message"><span class="member">anon363</span> who are you?</span></div>
+</div><div id="UOA78GWQ71" class="first message color4">
+  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:43<span class="secs">:20</span></span><span class="ampm">08:43<span class="secs">:20</span>am</span>)</span> <span class="message">so right now we only use part_of between continuants, and part_of between occurrents</span></div>
+</div><div id="II7568GWQ71" class="first message colors">
+  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:43<span class="secs">:20</span></span><span class="ampm">08:43<span class="secs">:20</span>am</span>)</span> <span class="message">is that really a slim or just limiting to part_of?  </span></div>
+</div><div class="event"><span class="message"><message><span class="member">Suzi</span> joined the chat room.</message></span> <span class="timestamp"><span class="tfh">08:43<span class="secs">:33</span></span><span class="ampm">08:43<span class="secs">:33</span>am</span></span></div><div id="HYU7AQGWQ71" class="first message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:43<span class="secs">:38</span></span><span class="ampm">08:43<span class="secs">:38</span>am</span>)</span> <span class="message">thats a very slim slim</span></div>
+</div><div id="QYJX1TGWQ71" class="first message color3">
+  <div class="text"><span class="member"><a href="member:Anon363" class="member">Anon363</a></span><span class="timestamp">(<span class="tfh">08:43<span class="secs">:41</span></span><span class="ampm">08:43<span class="secs">:41</span>am</span>)</span> <span class="message"><span class="member">anon363</span> seems to be Michael Ashburner, me !</span></div>
+</div><div id="G9W138HWQ71" class="first message color4">
+  <div class="text"><span class="member"><a href="member:Suzi" class="member">Suzi</a></span><span class="timestamp">(<span class="tfh">08:43<span class="secs">:56</span></span><span class="ampm">08:43<span class="secs">:56</span>am</span>)</span> <span class="message">I'm here too (<span class="member">Suzi</span>)</span></div>
+</div><div id="K2CC2CHWQ71" class="first message colors">
+  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:44<span class="secs">:00</span></span><span class="ampm">08:44<span class="secs">:00</span>am</span>)</span> <span class="message">hi <span class="member">suzi</span></span></div>
+</div><div id="O146IGHWQ71" class="first message color4">
+  <div class="text"><span class="member"><a href="member:Suzi" class="member">Suzi</a></span><span class="timestamp">(<span class="tfh">08:44<span class="secs">:04</span></span><span class="ampm">08:44<span class="secs">:04</span>am</span>)</span> <span class="message">Is there sound?</span></div>
+</div><div id="ZK0U7MHWQ71" class="first message colors">
+  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:44<span class="secs">:10</span></span><span class="ampm">08:44<span class="secs">:10</span>am</span>)</span> <span class="message">(no siund)</span></div>
+</div><div id="FPYO3OHWQ71" class="later message colors">
+  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:44<span class="secs">:12</span></span><span class="ampm">08:44<span class="secs">:12</span>am</span>)</span> <span class="message">sound</span></div>
+</div><div id="XE4JBXHWQ71" class="first message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:44<span class="secs">:21</span></span><span class="ampm">08:44<span class="secs">:21</span>am</span>)</span> <span class="message">if its just one relation that could be configured</span></div>
+</div><div id="RHDY14IWQ71" class="first message color4">
+  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:44<span class="secs">:28</span></span><span class="ampm">08:44<span class="secs">:28</span>am</span>)</span> <span class="message">(good then you can't hear me eating my breakfast)</span></div>
+</div><div id="YLURF9IWQ71" class="first message color6">
+  <div class="text"><span class="member"><a href="member:DavidOS" class="member">DavidOS</a></span><span class="timestamp">(<span class="tfh">08:44<span class="secs">:33</span></span><span class="ampm">08:44<span class="secs">:33</span>am</span>)</span> <span class="message">Limiting to part_of would be just fine for FB for now I think - michael?</span></div>
+</div><div id="XDPDCKIWQ71" class="first message color3">
+  <div class="text"><span class="member"><a href="member:Anon363" class="member">Anon363</a></span><span class="timestamp">(<span class="tfh">08:44<span class="secs">:44</span></span><span class="ampm">08:44<span class="secs">:44</span>am</span>)</span> <span class="message">yes ! Michael</span></div>
+</div><div id="Y34NC2JWQ71" class="first message colors">
+  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:45<span class="secs">:02</span></span><span class="ampm">08:45<span class="secs">:02</span>am</span>)</span> <span class="message">i think we talked about this when i visited zfin...  how high of a priority is configuring the limitation to be O rel O and C rel C?</span></div>
+</div><div id="UCNF18JWQ71" class="first message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:45<span class="secs">:08</span></span><span class="ampm">08:45<span class="secs">:08</span>am</span>)</span> <span class="message">so melissa zf curators only use partof and ignore the other relations?</span></div>
+</div><div id="GJHH89JWQ71" class="first message color4">
+  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:45<span class="secs">:09</span></span><span class="ampm">08:45<span class="secs">:09</span>am</span>)</span> <span class="message"><span class="highlight member">nicole</span>, have you used any other relation besides part_of? I think you were the one who initially configured that field in phenote, right?</span></div>
+</div><div id="ZJ5BCJWQ71" class="first message colors">
+  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:45<span class="secs">:12</span></span><span class="ampm">08:45<span class="secs">:12</span>am</span>)</span> <span class="message">rel=part_of</span></div>
+</div><div id="QWWL9HJWQ71" class="first message color4">
+  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:45<span class="secs">:17</span></span><span class="ampm">08:45<span class="secs">:17</span>am</span>)</span> <span class="message">yes</span></div>
+</div><div id="MMJO8TJWQ71" class="first message color3">
+  <div class="text"><span class="member"><a href="member:Anon363" class="member">Anon363</a></span><span class="timestamp">(<span class="tfh">08:45<span class="secs">:29</span></span><span class="ampm">08:45<span class="secs">:29</span>am</span>)</span> <span class="message">fb too</span></div>
+</div><div id="IFLJHTJWQ71" class="first message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:45<span class="secs">:29</span></span><span class="ampm">08:45<span class="secs">:29</span>am</span>)</span> <span class="message">i dont get nicoles question</span></div>
+</div><div id="JFAXCDKWQ71" class="later message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:45<span class="secs">:49</span></span><span class="ampm">08:45<span class="secs">:49</span>am</span>)</span> <span class="message">chris uses the other relations - but this can be a configurable</span></div>
+</div><div id="NUQV7KKWQ71" class="first message colors">
+  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:45<span class="secs">:56</span></span><span class="ampm">08:45<span class="secs">:56</span>am</span>)</span> <span class="message">oh, i did use other relationships, but i might not have used them right.  phenote doesn't display the defs of relations, so i didn't always use them properly btwn Cs or Os or CandO</span></div>
+</div><div id="BM4V0LWQ71" class="later message colors">
+  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:46<span class="secs">:12</span></span><span class="ampm">08:46<span class="secs">:12</span>am</span>)</span> <span class="message">C=continuant; O=occurant</span></div>
+</div><div id="XRSI8OLWQ71" class="first message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:46<span class="secs">:36</span></span><span class="ampm">08:46<span class="secs">:36</span>am</span>)</span> <span class="message">yea i havent yet done the constraints with that - todo</span></div>
+</div><div id="A4973MWQ71" class="first message color4">
+  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:46<span class="secs">:51</span></span><span class="ampm">08:46<span class="secs">:51</span>am</span>)</span> <span class="message">yes, for mapping I can see the need, but for standard phenotype annotations I think part_of is sufficient for now.</span></div>
+</div><div id="DC5TJAMWQ71" class="first message color6">
+  <div class="text"><span class="member"><a href="member:DavidOS" class="member">DavidOS</a></span><span class="timestamp">(<span class="tfh">08:46<span class="secs">:58</span></span><span class="ampm">08:46<span class="secs">:58</span>am</span>)</span> <span class="message">Important to have that constraint in place.</span></div>
+</div><div id="Y6Q49MMWQ71" class="first message colors">
+  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:47<span class="secs">:10</span></span><span class="ampm">08:47<span class="secs">:10</span>am</span>)</span> <span class="message">i think i did do some annotations that had process^contained_in(cell) or something like that, but i think that you guys at zfin don't allow that at the moment, right?</span></div>
+</div><div id="ARBSJPMWQ71" class="later message colors">
+  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:47<span class="secs">:13</span></span><span class="ampm">08:47<span class="secs">:13</span>am</span>)</span> <span class="message">what about fly?</span></div>
+</div><div id="MGUQGRMWQ71" class="first message color4">
+  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:47<span class="secs">:15</span></span><span class="ampm">08:47<span class="secs">:15</span>am</span>)</span> <span class="message">as you say <span class="highlight member">nicole</span>, its too easy to misuse them, in either context.</span></div>
+</div><div id="UR4OBNWQ71" class="later message color4">
+  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:47<span class="secs">:35</span></span><span class="ampm">08:47<span class="secs">:35</span>am</span>)</span> <span class="message">right</span></div>
+</div><div id="G0E75QNWQ71" class="first message color6">
+  <div class="text"><span class="member"><a href="member:DavidOS" class="member">DavidOS</a></span><span class="timestamp">(<span class="tfh">08:47<span class="secs">:50</span></span><span class="ampm">08:47<span class="secs">:50</span>am</span>)</span> <span class="message">We only use part_of</span></div>
+</div><div id="I6GW7RNWQ71" class="first message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:47<span class="secs">:51</span></span><span class="ampm">08:47<span class="secs">:51</span>am</span>)</span> <span class="message">for just 1 relation it can be a configurable i suppose</span></div>
+</div><div id="WJ1NE0OWQ71" class="first message colors">
+  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:48<span class="secs">:00</span></span><span class="ampm">08:48<span class="secs">:00</span>am</span>)</span> <span class="message">so chris has created an experimental file that bridges BFO and GO, so we can experiment with using those files to determine constraints</span></div>
+</div><div id="XE6C3OWQ71" class="first message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:48<span class="secs">:03</span></span><span class="ampm">08:48<span class="secs">:03</span>am</span>)</span> <span class="message">but as we allow more relations it should be a slim</span></div>
+</div><div id="B9LTDBOWQ71" class="first message color4">
+  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:48<span class="secs">:11</span></span><span class="ampm">08:48<span class="secs">:11</span>am</span>)</span> <span class="message">We had decided last august when Chris, David and Mark were here not to post-compose between continuants and occurrents</span></div>
+</div><div id="Q51J2OOWQ71" class="first message color3">
+  <div class="text"><span class="member"><a href="member:Anon363" class="member">Anon363</a></span><span class="timestamp">(<span class="tfh">08:48<span class="secs">:24</span></span><span class="ampm">08:48<span class="secs">:24</span>am</span>)</span> <span class="message">Sorry guys I have to go, I have another call in 10 mins and need to prepare </span></div>
+</div><div id="VI899QOWQ71" class="first message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:48<span class="secs">:26</span></span><span class="ampm">08:48<span class="secs">:26</span>am</span>)</span> <span class="message">and since its gonna go that way anyway maybe it should just be a slim to begin with</span></div>
+</div><div id="X2ZE2VOWQ71" class="first message colors">
+  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:48<span class="secs">:31</span></span><span class="ampm">08:48<span class="secs">:31</span>am</span>)</span> <span class="message">bye michael</span></div>
+</div><div class="event"><span class="message"><message><span class="member">Anon363</span> left the chat room.</message></span> (Quit: Anon363) <span class="timestamp"><span class="tfh">08:48<span class="secs">:37</span></span><span class="ampm">08:48<span class="secs">:37</span>am</span></span></div><div id="W0EWG5PWQ71" class="first message color6">
+  <div class="text"><span class="member"><a href="member:DavidOS" class="member">DavidOS</a></span><span class="timestamp">(<span class="tfh">08:48<span class="secs">:41</span></span><span class="ampm">08:48<span class="secs">:41</span>am</span>)</span> <span class="message">bye michael</span></div>
+</div><div id="SNDZ59PWQ71" class="later message color6">
+  <div class="text"><span class="member"><a href="member:DavidOS" class="member">DavidOS</a></span><span class="timestamp">(<span class="tfh">08:48<span class="secs">:45</span></span><span class="ampm">08:48<span class="secs">:45</span>am</span>)</span> <span class="message">too late</span></div>
+</div><div class="event"><span class="message"><message><span class="member">MichaelAshburner</span> left the chat room.</message></span> (Quit: MichaelAshburner) <span class="timestamp"><span class="tfh">08:48<span class="secs">:49</span></span><span class="ampm">08:48<span class="secs">:49</span>am</span></span></div><div id="S59CHPQWQ71" class="first message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:49<span class="secs">:37</span></span><span class="ampm">08:49<span class="secs">:37</span>am</span>)</span> <span class="message">hey melissa i know you are in active use right?</span></div>
+</div><div id="XJ5L7WQWQ71" class="first message colors">
+  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:49<span class="secs">:44</span></span><span class="ampm">08:49<span class="secs">:44</span>am</span>)</span> <span class="message">"not to post-compose between continuants and occurrents"</span></div>
+</div><div id="QXHBHWQWQ71" class="first message color4">
+  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:49<span class="secs">:44</span></span><span class="ampm">08:49<span class="secs">:44</span>am</span>)</span> <span class="message">yes</span></div>
+</div><div id="OQ6Y4ZQWQ71" class="first message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:49<span class="secs">:47</span></span><span class="ampm">08:49<span class="secs">:47</span>am</span>)</span> <span class="message">any issues that are humdingers - annoyances</span></div>
+</div><div id="I6OO5GRWQ71" class="first message colors">
+  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:50<span class="secs">:04</span></span><span class="ampm">08:50<span class="secs">:04</span>am</span>)</span> <span class="message">now that's because we can't do the deductive querying on that yet, right?</span></div>
+</div><div id="FUXPFKRWQ71" class="first message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:50<span class="secs">:08</span></span><span class="ampm">08:50<span class="secs">:08</span>am</span>)</span> <span class="message">i just fixed the sticky free text bug</span></div>
+</div><div id="WTBIENSWQ71" class="later message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:50<span class="secs">:47</span></span><span class="ampm">08:50<span class="secs">:47</span>am</span>)</span> <span class="message">deductive querying?</span></div>
+</div><div id="PARPKWSWQ71" class="first message color4">
+  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:50<span class="secs">:56</span></span><span class="ampm">08:50<span class="secs">:56</span>am</span>)</span> <span class="message">its because there is no link between the anatomy present in GO processes and the anatomy of an organism. CARO is still insufficient for this type of reasoning, and there is no way to synchronize. so we double annotate.</span></div>
+</div><div id="J72WMTWQ71" class="first message colors">
+  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:51<span class="secs">:22</span></span><span class="ampm">08:51<span class="secs">:22</span>am</span>)</span> <span class="message">yes yes</span></div>
+</div><div id="DJNGEPTWQ71" class="first message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:51<span class="secs">:25</span></span><span class="ampm">08:51<span class="secs">:25</span>am</span>)</span> <span class="message">what do you double annotate - whats an example</span></div>
+</div><div id="N0AN6IUWQ71" class="first message color4">
+  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:51<span class="secs">:54</span></span><span class="ampm">08:51<span class="secs">:54</span>am</span>)</span> <span class="message">brain development arrested AND brain small size</span></div>
+</div><div id="A8RX93VWQ71" class="first message colors">
+  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:52<span class="secs">:15</span></span><span class="ampm">08:52<span class="secs">:15</span>am</span>)</span> <span class="message">right... there's no link between brain development and brain the organ</span></div>
+</div><div id="TR4VJCVWQ71" class="first message color4">
+  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:52<span class="secs">:24</span></span><span class="ampm">08:52<span class="secs">:24</span>am</span>)</span> <span class="message">we annotate the processes separate from the anatomy</span></div>
+</div><div id="JLUZ5TVWQ71" class="first message colors">
+  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:52<span class="secs">:41</span></span><span class="ampm">08:52<span class="secs">:41</span>am</span>)</span> <span class="message">that will be a nice day when you don't have to</span></div>
+</div><div id="SAFJGVVWQ71" class="first message color7">
+  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:52<span class="secs">:43</span></span><span class="ampm">08:52<span class="secs">:43</span>am</span>)</span> <span class="message">how would you annotate together - with post comp?</span></div>
+</div><div id="MHK2LLWWQ71" class="first message color4">
+  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:53<span class="secs">:09</span></span><span class="ampm">08:53<span class="secs">:09</span>am</span>)</span> <span class="message">maybe midbrain development part_of brain process arrested</span></div>
+</div><div id="OYSAAUWWQ71" class="first message color6">
+  <div class="text"><span class="member"><a href="member:DavidOS" class="member">DavidOS</a></span><span class="timestamp">(<span class="tfh">08:53<span class="secs">:18</span></span><span class="ampm">08:53<span class="secs">:18</span>am</span>)</span> <span class="message">Strictly, those two are not equivalent.  One makes a statement about development, the other about the adult structure that result from that development.</span></div>
+</div><div id="C1JV1ZWWQ71" class="first message color4">
+  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:53<span class="secs">:23</span></span><span class="ampm">08:53<span class="secs">:23</span>am</span>)</span> <span class="message">or something like that</span></div>
+</div><div id="F6OLDCXWQ71" class="first message colors">
+  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:53<span class="secs">:36</span></span><span class="ampm">08:53<span class="secs">:36</span>am</span>)</span> <span class="message">or maybe some kind of "conclusion" statement...brain development leads_to brain size small ?</span></div>
+</div><div id="QOAJMXWQ71" class="first message color4">
+  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:53<span class="secs">:46</span></span><span class="ampm">08:53<span class="secs">:46</span>am</span>)</span> <span class="message">yes</span></div>
+</div><div id="P612JRXWQ71" class="later message color4">
+  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:53<span class="secs">:51</span></span><span class="ampm">08:53<span class="secs">:51</span>am</span>)</span> <span class="message">to david</span></div>
+</div><div id="KWVZ2VXWQ71" class="...
 
[truncated message content]

[Obo-svn-commit] SF.net SVN: obo: [660] phenote/trunk/doc/phenote-website/irc_chat/ transcripts

[<nl...@us...>]

Revision: 660
          http://svn.sourceforge.net/obo/?rev=660&view=rev
Author:   nlw
Date:     2007-06-05 12:29:16 -0700 (Tue, 05 Jun 2007)

Log Message:
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playing around with the transcript files for irc chat

Added Paths:
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    phenote/trunk/doc/phenote-website/irc_chat/transcripts/test.html

Removed Paths:
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    phenote/trunk/doc/phenote-website/irc_chat/transcripts/PWG_irc_050107.html

Deleted: phenote/trunk/doc/phenote-website/irc_chat/transcripts/PWG_irc_050107.html
===================================================================
--- phenote/trunk/doc/phenote-website/irc_chat/transcripts/PWG_irc_050107.html	2007-06-05 19:11:10 UTC (rev 659)
+++ phenote/trunk/doc/phenote-website/irc_chat/transcripts/PWG_irc_050107.html	2007-06-05 19:29:16 UTC (rev 660)
@@ -1,781 +0,0 @@
-<div id="ZGC9D5CIP71" class="first message colors">
-  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:17<span class="secs">:32</span></span><span class="ampm">08:17<span class="secs">:32</span>am</span>)</span> <span class="message">hello?</span></div>
-</div><div id="F0MA77BVQ71" class="later message colors">
-  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:18<span class="secs">:43</span></span><span class="ampm">08:18<span class="secs">:43</span>am</span>)</span> <span class="message">hey mark, can you add a couple of new features to the wiki?</span></div>
-</div><div id="MFIG1THVQ71" class="first message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:22<span class="secs">:41</span></span><span class="ampm">08:22<span class="secs">:41</span>am</span>)</span> <span class="message">hi</span></div>
-</div><div id="RNFWIXHVQ71" class="later message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:22<span class="secs">:45</span></span><span class="ampm">08:22<span class="secs">:45</span>am</span>)</span> <span class="message">what features</span></div>
-</div><div class="event"><span class="message"><message><span class="member">DavidOS</span> joined the chat room.</message></span> <span class="timestamp"><span class="tfh">08:28<span class="secs">:05</span></span><span class="ampm">08:28<span class="secs">:05</span>am</span></span></div><div id="T9LYJ8RVQ71" class="first message color6">
-  <div class="text"><span class="member"><a href="member:DavidOS" class="member">DavidOS</a></span><span class="timestamp">(<span class="tfh">08:28<span class="secs">:20</span></span><span class="ampm">08:28<span class="secs">:20</span>am</span>)</span> <span class="message">Hiya</span></div>
-</div><div id="T8NW7PRVQ71" class="first message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:28<span class="secs">:37</span></span><span class="ampm">08:28<span class="secs">:37</span>am</span>)</span> <span class="message">hey david!</span></div>
-</div><div class="event"><span class="message"><message><span class="member">Michael</span> joined the chat room.</message></span> <span class="timestamp"><span class="tfh">08:29<span class="secs">:14</span></span><span class="ampm">08:29<span class="secs">:14</span>am</span></span></div><div class="event"><span class="message"><message><span class="member">MelissaH</span> joined the chat room.</message></span> <span class="timestamp"><span class="tfh">08:29<span class="secs">:32</span></span><span class="ampm">08:29<span class="secs">:32</span>am</span></span></div><div id="CAQCBATVQ71" class="first message colors">
-  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:29<span class="secs">:34</span></span><span class="ampm">08:29<span class="secs">:34</span>am</span>)</span> <span class="message">hi david</span></div>
-</div><div class="event"><span class="message"><message><span class="member">Michael</span> left the chat room.</message></span> (Quit: Michael) <span class="timestamp"><span class="tfh">08:29<span class="secs">:35</span></span><span class="ampm">08:29<span class="secs">:35</span>am</span></span></div><div class="event"><span class="message"><message><span class="member">MichaelAshburner</span> joined the chat room.</message></span> <span class="timestamp"><span class="tfh">08:29<span class="secs">:36</span></span><span class="ampm">08:29<span class="secs">:36</span>am</span></span></div><div id="OCDRJKTVQ71" class="first message colors">
-  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:29<span class="secs">:44</span></span><span class="ampm">08:29<span class="secs">:44</span>am</span>)</span> <span class="message">and michael and melissa</span></div>
-</div><div id="IONVITTVQ71" class="first message color4">
-  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:29<span class="secs">:53</span></span><span class="ampm">08:29<span class="secs">:53</span>am</span>)</span> <span class="message">Hi there</span></div>
-</div><div id="YOLT8WTVQ71" class="first message colors">
-  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:29<span class="secs">:56</span></span><span class="ampm">08:29<span class="secs">:56</span>am</span>)</span> <span class="message">mark:  whatever you've been working on</span></div>
-</div><div id="XU6FJ8VVQ71" class="first message color6">
-  <div class="text"><span class="member"><a href="member:MichaelAshburner" class="member">MichaelAshburner</a></span><span class="timestamp">(<span class="tfh">08:30<span class="secs">:44</span></span><span class="ampm">08:30<span class="secs">:44</span>am</span>)</span> <span class="message">MichaelA is here but has no idea how to use this tool !</span></div>
-</div><div id="O0VD9HWVQ71" class="first message colors">
-  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:31<span class="secs">:29</span></span><span class="ampm">08:31<span class="secs">:29</span>am</span>)</span> <span class="message">just type exasperating expressions</span></div>
-</div><div id="D9WNFXWVQ71" class="first message color6">
-  <div class="text"><span class="member"><a href="member:MichaelAshburner" class="member">MichaelAshburner</a></span><span class="timestamp">(<span class="tfh">08:31<span class="secs">:45</span></span><span class="ampm">08:31<span class="secs">:45</span>am</span>)</span> <span class="message">do you mean I cannot hear yu'all?</span></div>
-</div><div id="S77JK4XVQ71" class="first message colors">
-  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:31<span class="secs">:52</span></span><span class="ampm">08:31<span class="secs">:52</span>am</span>)</span> <span class="message">you are correct</span></div>
-</div><div id="MX8H3GXVQ71" class="first message color6">
-  <div class="text"><span class="member"><a href="member:MichaelAshburner" class="member">MichaelAshburner</a></span><span class="timestamp">(<span class="tfh">08:32<span class="secs">:04</span></span><span class="ampm">08:32<span class="secs">:04</span>am</span>)</span> <span class="message">oh pooh, exasperated</span></div>
-</div><div id="MI40EMXVQ71" class="first message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:32<span class="secs">:10</span></span><span class="ampm">08:32<span class="secs">:10</span>am</span>)</span> <span class="message"><span class="highlight member">nicole</span> - i added some stuff</span></div>
-</div><div id="M9QGIPXVQ71" class="first message colors">
-  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:32<span class="secs">:13</span></span><span class="ampm">08:32<span class="secs">:13</span>am</span>)</span> <span class="message">great</span></div>
-</div><div id="RPRI3WXVQ71" class="first message color6">
-  <div class="text"><span class="member"><a href="member:MichaelAshburner" class="member">MichaelAshburner</a></span><span class="timestamp">(<span class="tfh">08:32<span class="secs">:20</span></span><span class="ampm">08:32<span class="secs">:20</span>am</span>)</span> <span class="message">what stuff</span></div>
-</div><div id="H1NB5ZXVQ71" class="later message color6">
-  <div class="text"><span class="member"><a href="member:MichaelAshburner" class="member">MichaelAshburner</a></span><span class="timestamp">(<span class="tfh">08:32<span class="secs">:23</span></span><span class="ampm">08:32<span class="secs">:23</span>am</span>)</span> <span class="message">?</span></div>
-</div><div id="ZFYYF9YVQ71" class="first message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:32<span class="secs">:33</span></span><span class="ampm">08:32<span class="secs">:33</span>am</span>)</span> <span class="message">to the wiki</span></div>
-</div><div id="EIMPCHYVQ71" class="later message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:32<span class="secs">:41</span></span><span class="ampm">08:32<span class="secs">:41</span>am</span>)</span> <span class="message">hi michael</span></div>
-</div><div id="A5GNBWYVQ71" class="first message color6">
-  <div class="text"><span class="member"><a href="member:DavidOS" class="member">DavidOS</a></span><span class="timestamp">(<span class="tfh">08:32<span class="secs">:56</span></span><span class="ampm">08:32<span class="secs">:56</span>am</span>)</span> <span class="message">agenda wiki?</span></div>
-</div><div id="TXD2KIZVQ71" class="first message colors">
-  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:33<span class="secs">:18</span></span><span class="ampm">08:33<span class="secs">:18</span>am</span>)</span> <span class="message">yep, we've put up a small agenda on the wiki:  <a href="http://www.bioontology.org/wiki/index.php/Phenote:Agenda:_May_1%2C_2007">http://www.bioontology.org/wiki/index.php/Phenote:Agenda:_May_1%2C_2007</a></span></div>
-</div><div id="W85I2LZVQ71" class="first message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:33<span class="secs">:21</span></span><span class="ampm">08:33<span class="secs">:21</span>am</span>)</span> <span class="message"><a href="http://www.bioontology.org/wiki/index.php/Phenote:Agenda:_May_1%2C_2007">http://www.bioontology.org/wiki/index.php/Phenote:Agenda:_May_1%2C_2007</a></span></div>
-</div><div id="TP0A7Q1WQ71" class="first message colors">
-  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:34<span class="secs">:38</span></span><span class="ampm">08:34<span class="secs">:38</span>am</span>)</span> <span class="message">well, i suppose we ought to get started.  we'll follow that agenda, somewhat loosely</span></div>
-</div><div id="J1BX5K2WQ71" class="first message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:35<span class="secs">:08</span></span><span class="ampm">08:35<span class="secs">:08</span>am</span>)</span> <span class="message">michael are you using phenote these days?</span></div>
-</div><div id="ATHEES2WQ71" class="later message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:35<span class="secs">:16</span></span><span class="ampm">08:35<span class="secs">:16</span>am</span>)</span> <span class="message">or david?</span></div>
-</div><div id="NASED63WQ71" class="first message color6">
-  <div class="text"><span class="member"><a href="member:MichaelAshburner" class="member">MichaelAshburner</a></span><span class="timestamp">(<span class="tfh">08:35<span class="secs">:30</span></span><span class="ampm">08:35<span class="secs">:30</span>am</span>)</span> <span class="message">got it - can MArk possibly expand on some of these, espec (for me) multipe differntiae and worm adapter</span></div>
-</div><div id="EOOBD73WQ71" class="first message color6">
-  <div class="text"><span class="member"><a href="member:DavidOS" class="member">DavidOS</a></span><span class="timestamp">(<span class="tfh">08:35<span class="secs">:31</span></span><span class="ampm">08:35<span class="secs">:31</span>am</span>)</span> <span class="message">I'm not - except for some testing.</span></div>
-</div><div id="XZL25K3WQ71" class="first message colors">
-  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:35<span class="secs">:44</span></span><span class="ampm">08:35<span class="secs">:44</span>am</span>)</span> <span class="message">mark and i have described the most recently added features to phenote.  </span></div>
-</div><div id="AAXD634WQ71" class="first message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:36<span class="secs">:03</span></span><span class="ampm">08:36<span class="secs">:03</span>am</span>)</span> <span class="message">so in the post composition window you can now add more than one differentia</span></div>
-</div><div id="GHCGK64WQ71" class="first message color6">
-  <div class="text"><span class="member"><a href="member:MichaelAshburner" class="member">MichaelAshburner</a></span><span class="timestamp">(<span class="tfh">08:36<span class="secs">:06</span></span><span class="ampm">08:36<span class="secs">:06</span>am</span>)</span> <span class="message">Mark - yes indeed tho I have been on the road so much for the last 3 weeks, and have now 10 days on E Coast - that I am behind but I am using it for OMI annotation</span></div>
-</div><div id="KEWZIB4WQ71" class="first message colors">
-  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:36<span class="secs">:11</span></span><span class="ampm">08:36<span class="secs">:11</span>am</span>)</span> <span class="message">there will be a new beta release coming out later today with these elements</span></div>
-</div><div id="J91H5O4WQ71" class="first message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:36<span class="secs">:24</span></span><span class="ampm">08:36<span class="secs">:24</span>am</span>)</span> <span class="message">previously it was just genus rel &amp; differentia term</span></div>
-</div><div id="ZCAGR4WQ71" class="first message color6">
-  <div class="text"><span class="member"><a href="member:MichaelAshburner" class="member">MichaelAshburner</a></span><span class="timestamp">(<span class="tfh">08:36<span class="secs">:27</span></span><span class="ampm">08:36<span class="secs">:27</span>am</span>)</span> <span class="message">what elements does <span class="highlight member">Nicole</span> mean</span></div>
-</div><div id="G8PKDQ5WQ71" class="first message colors">
-  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:37<span class="secs">:02</span></span><span class="ampm">08:37<span class="secs">:02</span>am</span>)</span> <span class="message">elements=features described on wiki</span></div>
-</div><div id="QUOCHV5WQ71" class="first message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:37<span class="secs">:07</span></span><span class="ampm">08:37<span class="secs">:07</span>am</span>)</span> <span class="message">but at the moment you can addd 3 different differentia</span></div>
-</div><div id="TWMZ966WQ71" class="later message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:37<span class="secs">:18</span></span><span class="ampm">08:37<span class="secs">:18</span>am</span>)</span> <span class="message">do yall use post comp?</span></div>
-</div><div id="DXPYKC6WQ71" class="later message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:37<span class="secs">:24</span></span><span class="ampm">08:37<span class="secs">:24</span>am</span>)</span> <span class="message">you do right melissa?</span></div>
-</div><div id="VFJXK6WQ71" class="later message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:37<span class="secs">:32</span></span><span class="ampm">08:37<span class="secs">:32</span>am</span>)</span> <span class="message">fly?</span></div>
-</div><div id="EZ8E6R6WQ71" class="first message color6">
-  <div class="text"><span class="member"><a href="member:MichaelAshburner" class="member">MichaelAshburner</a></span><span class="timestamp">(<span class="tfh">08:37<span class="secs">:39</span></span><span class="ampm">08:37<span class="secs">:39</span>am</span>)</span> <span class="message">yes i do</span></div>
-</div><div id="I16HAU6WQ71" class="first message color6">
-  <div class="text"><span class="member"><a href="member:DavidOS" class="member">DavidOS</a></span><span class="timestamp">(<span class="tfh">08:37<span class="secs">:42</span></span><span class="ampm">08:37<span class="secs">:42</span>am</span>)</span> <span class="message">so for multiple genus post composition - isn't there an issue with correct nesting ?</span></div>
-</div><div id="QDVBGZ6WQ71" class="first message colors">
-  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:37<span class="secs">:47</span></span><span class="ampm">08:37<span class="secs">:47</span>am</span>)</span> <span class="message">like membrane^part_of(spermatocyte^part_of(random_organism))</span></div>
-</div><div id="QFQ487WQ71" class="first message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:37<span class="secs">:56</span></span><span class="ampm">08:37<span class="secs">:56</span>am</span>)</span> <span class="message">so i should clarify</span></div>
-</div><div id="M87QFH7WQ71" class="later message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:38<span class="secs">:05</span></span><span class="ampm">08:38<span class="secs">:05</span>am</span>)</span> <span class="message">it doesnt yet do "nesting"</span></div>
-</div><div id="GX3NHP7WQ71" class="first message color4">
-  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:38<span class="secs">:13</span></span><span class="ampm">08:38<span class="secs">:13</span>am</span>)</span> <span class="message">yes we do for omim and zfish</span></div>
-</div><div id="L4R8GT7WQ71" class="first message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:38<span class="secs">:17</span></span><span class="ampm">08:38<span class="secs">:17</span>am</span>)</span> <span class="message">it only does multiple differentia of one genus</span></div>
-</div><div id="CFVI2Y7WQ71" class="later message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:38<span class="secs">:22</span></span><span class="ampm">08:38<span class="secs">:22</span>am</span>)</span> <span class="message">does that make sense?</span></div>
-</div><div id="MA1F348WQ71" class="first message color4">
-  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:38<span class="secs">:28</span></span><span class="ampm">08:38<span class="secs">:28</span>am</span>)</span> <span class="message">we don't use multiple though</span></div>
-</div><div id="QR3IJ48WQ71" class="first message color6">
-  <div class="text"><span class="member"><a href="member:DavidOS" class="member">DavidOS</a></span><span class="timestamp">(<span class="tfh">08:38<span class="secs">:28</span></span><span class="ampm">08:38<span class="secs">:28</span>am</span>)</span> <span class="message">I think so</span></div>
-</div><div id="XIEV3M8WQ71" class="first message color4">
-  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:38<span class="secs">:46</span></span><span class="ampm">08:38<span class="secs">:46</span>am</span>)</span> <span class="message">yes but still a little scary...</span></div>
-</div><div id="TK6BBU8WQ71" class="first message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:38<span class="secs">:54</span></span><span class="ampm">08:38<span class="secs">:54</span>am</span>)</span> <span class="message">so you can say A^rel(B)^rel(C)</span></div>
-</div><div id="HUJVK29WQ71" class="later message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:39<span class="secs">:02</span></span><span class="ampm">08:39<span class="secs">:02</span>am</span>)</span> <span class="message">but you cant say </span></div>
-</div><div id="YFTLBJ9WQ71" class="later message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:39<span class="secs">:19</span></span><span class="ampm">08:39<span class="secs">:19</span>am</span>)</span> <span class="message">A^rel(B^rel(C))</span></div>
-</div><div class="event"><span class="message"><message><span class="member">MichaelAshburner</span> left the chat room.</message></span> () <span class="timestamp"><span class="tfh">08:39<span class="secs">:25</span></span><span class="ampm">08:39<span class="secs">:25</span>am</span></span></div><div id="TMZV6P9WQ71" class="first message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:39<span class="secs">:25</span></span><span class="ampm">08:39<span class="secs">:25</span>am</span>)</span> <span class="message">which are not equivalent</span></div>
-</div><div id="KJ3U8Q9WQ71" class="first message color4">
-  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:39<span class="secs">:26</span></span><span class="ampm">08:39<span class="secs">:26</span>am</span>)</span> <span class="message">in zfish, we only have A^part_of^B</span></div>
-</div><div id="VS7K11AWQ71" class="first message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:39<span class="secs">:37</span></span><span class="ampm">08:39<span class="secs">:37</span>am</span>)</span> <span class="message">michael had enough!</span></div>
-</div><div id="QIPRKHAWQ71" class="later message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:39<span class="secs">:53</span></span><span class="ampm">08:39<span class="secs">:53</span>am</span>)</span> <span class="message">does anyone have a need for multiple differentia at this point?</span></div>
-</div><div id="KVQ7DQAWQ71" class="first message colors">
-  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:40<span class="secs">:02</span></span><span class="ampm">08:40<span class="secs">:02</span>am</span>)</span> <span class="message">so the biggest user of this feature is Chris and those doing cross product composition</span></div>
-</div><div id="H37C3VAWQ71" class="first message color4">
-  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:40<span class="secs">:07</span></span><span class="ampm">08:40<span class="secs">:07</span>am</span>)</span> <span class="message"><span class="highlight member">Nicole</span>, was your OMIM annotations driving this feature?</span></div>
-</div><div id="TKHZDWAWQ71" class="first message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:40<span class="secs">:08</span></span><span class="ampm">08:40<span class="secs">:08</span>am</span>)</span> <span class="message">does anyone have a need for nested differentia?</span></div>
-</div><div id="LWGPXAWQ71" class="first message colors">
-  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:40<span class="secs">:09</span></span><span class="ampm">08:40<span class="secs">:09</span>am</span>)</span> <span class="message">i don't think other communities are using it</span></div>
-</div><div id="YOUDD5BWQ71" class="first message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:40<span class="secs">:17</span></span><span class="ampm">08:40<span class="secs">:17</span>am</span>)</span> <span class="message">yea chris really needed the multie diff</span></div>
-</div><div id="V6B8ICBWQ71" class="later message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:40<span class="secs">:24</span></span><span class="ampm">08:40<span class="secs">:24</span>am</span>)</span> <span class="message">as he was using phenote to do mapping</span></div>
-</div><div class="event"><span class="message"><message><span class="member">MichaelAshburner</span> joined the chat room.</message></span> <span class="timestamp"><span class="tfh">08:40<span class="secs">:26</span></span><span class="ampm">08:40<span class="secs">:26</span>am</span></span></div><div id="JXG4FMBWQ71" class="first message colors">
-  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:40<span class="secs">:34</span></span><span class="ampm">08:40<span class="secs">:34</span>am</span>)</span> <span class="message">no, not really.  there might have been one time that i wanted multi-differentia, but...</span></div>
-</div><div id="WUWJCTBWQ71" class="first message color6">
-  <div class="text"><span class="member"><a href="member:MichaelAshburner" class="member">MichaelAshburner</a></span><span class="timestamp">(<span class="tfh">08:40<span class="secs">:41</span></span><span class="ampm">08:40<span class="secs">:41</span>am</span>)</span> <span class="message">I lost you and hand to restart</span></div>
-</div><div id="YJLWBCWQ71" class="first message color6">
-  <div class="text"><span class="member"><a href="member:DavidOS" class="member">DavidOS</a></span><span class="timestamp">(<span class="tfh">08:40<span class="secs">:59</span></span><span class="ampm">08:40<span class="secs">:59</span>am</span>)</span> <span class="message">We may do - I'll have to look into our existing post-composed terms.  They are old and not implemented properly yet - may be examples of both nested and not in there.</span></div>
-</div><div id="S1M8IWCWQ71" class="first message colors">
-  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:41<span class="secs">:20</span></span><span class="ampm">08:41<span class="secs">:20</span>am</span>)</span> <span class="message">i think annotations can often be much better only using a single differentia...sometimes the multiple comes in if you're lazy and can' t think of how to say it more consicely</span></div>
-</div><div class="event"><span class="message"><message><span class="member">Anon363</span> joined the chat room.</message></span> <span class="timestamp"><span class="tfh">08:41<span class="secs">:31</span></span><span class="ampm">08:41<span class="secs">:31</span>am</span></span></div><div id="YVHICLDWQ71" class="first message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:41<span class="secs">:45</span></span><span class="ampm">08:41<span class="secs">:45</span>am</span>)</span> <span class="message">hey <span class="member">anon363</span> do a /nick</span></div>
-</div><div id="C2K0IYDWQ71" class="first message color4">
-  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:41<span class="secs">:58</span></span><span class="ampm">08:41<span class="secs">:58</span>am</span>)</span> <span class="message">I worry a bit about having the whole RO allowed for post-comp, because it may be that rules are needed about what can be post-comp with what.</span></div>
-</div><div id="QTO471EWQ71" class="first message color6">
-  <div class="text"><span class="member"><a href="member:DavidOS" class="member">DavidOS</a></span><span class="timestamp">(<span class="tfh">08:42<span class="secs">:01</span></span><span class="ampm">08:42<span class="secs">:01</span>am</span>)</span> <span class="message">"differentia...sometimes the multiple comes in if you're lazy and can' t think of how to say it more consicely </span></div>
-</div><div id="F978DTEWQ71" class="first message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:42<span class="secs">:29</span></span><span class="ampm">08:42<span class="secs">:29</span>am</span>)</span> <span class="message">we should probably have a phenote RO slim </span></div>
-</div><div id="STMBJ2FWQ71" class="later message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:42<span class="secs">:38</span></span><span class="ampm">08:42<span class="secs">:38</span>am</span>)</span> <span class="message">for those relations we want to restrict to</span></div>
-</div><div id="T2VK2FFWQ71" class="first message color3">
-  <div class="text"><span class="member"><a href="member:Anon363" class="member">Anon363</a></span><span class="timestamp">(<span class="tfh">08:42<span class="secs">:51</span></span><span class="ampm">08:42<span class="secs">:51</span>am</span>)</span> <span class="message">yes that would be a good idea</span></div>
-</div><div id="PG977TFWQ71" class="first message color6">
-  <div class="text"><span class="member"><a href="member:DavidOS" class="member">DavidOS</a></span><span class="timestamp">(<span class="tfh">08:43<span class="secs">:05</span></span><span class="ampm">08:43<span class="secs">:05</span>am</span>)</span> <span class="message">I agree with Melissa.  I only see us using part_of - at least at first.</span></div>
-</div><div id="VKJ2HYFWQ71" class="first message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:43<span class="secs">:10</span></span><span class="ampm">08:43<span class="secs">:10</span>am</span>)</span> <span class="message"><span class="member">anon363</span> who are you?</span></div>
-</div><div id="UOA78GWQ71" class="first message color4">
-  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:43<span class="secs">:20</span></span><span class="ampm">08:43<span class="secs">:20</span>am</span>)</span> <span class="message">so right now we only use part_of between continuants, and part_of between occurrents</span></div>
-</div><div id="II7568GWQ71" class="first message colors">
-  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:43<span class="secs">:20</span></span><span class="ampm">08:43<span class="secs">:20</span>am</span>)</span> <span class="message">is that really a slim or just limiting to part_of?  </span></div>
-</div><div class="event"><span class="message"><message><span class="member">Suzi</span> joined the chat room.</message></span> <span class="timestamp"><span class="tfh">08:43<span class="secs">:33</span></span><span class="ampm">08:43<span class="secs">:33</span>am</span></span></div><div id="HYU7AQGWQ71" class="first message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:43<span class="secs">:38</span></span><span class="ampm">08:43<span class="secs">:38</span>am</span>)</span> <span class="message">thats a very slim slim</span></div>
-</div><div id="QYJX1TGWQ71" class="first message color3">
-  <div class="text"><span class="member"><a href="member:Anon363" class="member">Anon363</a></span><span class="timestamp">(<span class="tfh">08:43<span class="secs">:41</span></span><span class="ampm">08:43<span class="secs">:41</span>am</span>)</span> <span class="message"><span class="member">anon363</span> seems to be Michael Ashburner, me !</span></div>
-</div><div id="G9W138HWQ71" class="first message color4">
-  <div class="text"><span class="member"><a href="member:Suzi" class="member">Suzi</a></span><span class="timestamp">(<span class="tfh">08:43<span class="secs">:56</span></span><span class="ampm">08:43<span class="secs">:56</span>am</span>)</span> <span class="message">I'm here too (<span class="member">Suzi</span>)</span></div>
-</div><div id="K2CC2CHWQ71" class="first message colors">
-  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:44<span class="secs">:00</span></span><span class="ampm">08:44<span class="secs">:00</span>am</span>)</span> <span class="message">hi <span class="member">suzi</span></span></div>
-</div><div id="O146IGHWQ71" class="first message color4">
-  <div class="text"><span class="member"><a href="member:Suzi" class="member">Suzi</a></span><span class="timestamp">(<span class="tfh">08:44<span class="secs">:04</span></span><span class="ampm">08:44<span class="secs">:04</span>am</span>)</span> <span class="message">Is there sound?</span></div>
-</div><div id="ZK0U7MHWQ71" class="first message colors">
-  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:44<span class="secs">:10</span></span><span class="ampm">08:44<span class="secs">:10</span>am</span>)</span> <span class="message">(no siund)</span></div>
-</div><div id="FPYO3OHWQ71" class="later message colors">
-  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:44<span class="secs">:12</span></span><span class="ampm">08:44<span class="secs">:12</span>am</span>)</span> <span class="message">sound</span></div>
-</div><div id="XE4JBXHWQ71" class="first message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:44<span class="secs">:21</span></span><span class="ampm">08:44<span class="secs">:21</span>am</span>)</span> <span class="message">if its just one relation that could be configured</span></div>
-</div><div id="RHDY14IWQ71" class="first message color4">
-  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:44<span class="secs">:28</span></span><span class="ampm">08:44<span class="secs">:28</span>am</span>)</span> <span class="message">(good then you can't hear me eating my breakfast)</span></div>
-</div><div id="YLURF9IWQ71" class="first message color6">
-  <div class="text"><span class="member"><a href="member:DavidOS" class="member">DavidOS</a></span><span class="timestamp">(<span class="tfh">08:44<span class="secs">:33</span></span><span class="ampm">08:44<span class="secs">:33</span>am</span>)</span> <span class="message">Limiting to part_of would be just fine for FB for now I think - michael?</span></div>
-</div><div id="XDPDCKIWQ71" class="first message color3">
-  <div class="text"><span class="member"><a href="member:Anon363" class="member">Anon363</a></span><span class="timestamp">(<span class="tfh">08:44<span class="secs">:44</span></span><span class="ampm">08:44<span class="secs">:44</span>am</span>)</span> <span class="message">yes ! Michael</span></div>
-</div><div id="Y34NC2JWQ71" class="first message colors">
-  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:45<span class="secs">:02</span></span><span class="ampm">08:45<span class="secs">:02</span>am</span>)</span> <span class="message">i think we talked about this when i visited zfin...  how high of a priority is configuring the limitation to be O rel O and C rel C?</span></div>
-</div><div id="UCNF18JWQ71" class="first message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:45<span class="secs">:08</span></span><span class="ampm">08:45<span class="secs">:08</span>am</span>)</span> <span class="message">so melissa zf curators only use partof and ignore the other relations?</span></div>
-</div><div id="GJHH89JWQ71" class="first message color4">
-  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:45<span class="secs">:09</span></span><span class="ampm">08:45<span class="secs">:09</span>am</span>)</span> <span class="message"><span class="highlight member">nicole</span>, have you used any other relation besides part_of? I think you were the one who initially configured that field in phenote, right?</span></div>
-</div><div id="ZJ5BCJWQ71" class="first message colors">
-  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:45<span class="secs">:12</span></span><span class="ampm">08:45<span class="secs">:12</span>am</span>)</span> <span class="message">rel=part_of</span></div>
-</div><div id="QWWL9HJWQ71" class="first message color4">
-  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:45<span class="secs">:17</span></span><span class="ampm">08:45<span class="secs">:17</span>am</span>)</span> <span class="message">yes</span></div>
-</div><div id="MMJO8TJWQ71" class="first message color3">
-  <div class="text"><span class="member"><a href="member:Anon363" class="member">Anon363</a></span><span class="timestamp">(<span class="tfh">08:45<span class="secs">:29</span></span><span class="ampm">08:45<span class="secs">:29</span>am</span>)</span> <span class="message">fb too</span></div>
-</div><div id="IFLJHTJWQ71" class="first message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:45<span class="secs">:29</span></span><span class="ampm">08:45<span class="secs">:29</span>am</span>)</span> <span class="message">i dont get nicoles question</span></div>
-</div><div id="JFAXCDKWQ71" class="later message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:45<span class="secs">:49</span></span><span class="ampm">08:45<span class="secs">:49</span>am</span>)</span> <span class="message">chris uses the other relations - but this can be a configurable</span></div>
-</div><div id="NUQV7KKWQ71" class="first message colors">
-  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:45<span class="secs">:56</span></span><span class="ampm">08:45<span class="secs">:56</span>am</span>)</span> <span class="message">oh, i did use other relationships, but i might not have used them right.  phenote doesn't display the defs of relations, so i didn't always use them properly btwn Cs or Os or CandO</span></div>
-</div><div id="BM4V0LWQ71" class="later message colors">
-  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:46<span class="secs">:12</span></span><span class="ampm">08:46<span class="secs">:12</span>am</span>)</span> <span class="message">C=continuant; O=occurant</span></div>
-</div><div id="XRSI8OLWQ71" class="first message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:46<span class="secs">:36</span></span><span class="ampm">08:46<span class="secs">:36</span>am</span>)</span> <span class="message">yea i havent yet done the constraints with that - todo</span></div>
-</div><div id="A4973MWQ71" class="first message color4">
-  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:46<span class="secs">:51</span></span><span class="ampm">08:46<span class="secs">:51</span>am</span>)</span> <span class="message">yes, for mapping I can see the need, but for standard phenotype annotations I think part_of is sufficient for now.</span></div>
-</div><div id="DC5TJAMWQ71" class="first message color6">
-  <div class="text"><span class="member"><a href="member:DavidOS" class="member">DavidOS</a></span><span class="timestamp">(<span class="tfh">08:46<span class="secs">:58</span></span><span class="ampm">08:46<span class="secs">:58</span>am</span>)</span> <span class="message">Important to have that constraint in place.</span></div>
-</div><div id="Y6Q49MMWQ71" class="first message colors">
-  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:47<span class="secs">:10</span></span><span class="ampm">08:47<span class="secs">:10</span>am</span>)</span> <span class="message">i think i did do some annotations that had process^contained_in(cell) or something like that, but i think that you guys at zfin don't allow that at the moment, right?</span></div>
-</div><div id="ARBSJPMWQ71" class="later message colors">
-  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:47<span class="secs">:13</span></span><span class="ampm">08:47<span class="secs">:13</span>am</span>)</span> <span class="message">what about fly?</span></div>
-</div><div id="MGUQGRMWQ71" class="first message color4">
-  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:47<span class="secs">:15</span></span><span class="ampm">08:47<span class="secs">:15</span>am</span>)</span> <span class="message">as you say <span class="highlight member">nicole</span>, its too easy to misuse them, in either context.</span></div>
-</div><div id="UR4OBNWQ71" class="later message color4">
-  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:47<span class="secs">:35</span></span><span class="ampm">08:47<span class="secs">:35</span>am</span>)</span> <span class="message">right</span></div>
-</div><div id="G0E75QNWQ71" class="first message color6">
-  <div class="text"><span class="member"><a href="member:DavidOS" class="member">DavidOS</a></span><span class="timestamp">(<span class="tfh">08:47<span class="secs">:50</span></span><span class="ampm">08:47<span class="secs">:50</span>am</span>)</span> <span class="message">We only use part_of</span></div>
-</div><div id="I6GW7RNWQ71" class="first message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:47<span class="secs">:51</span></span><span class="ampm">08:47<span class="secs">:51</span>am</span>)</span> <span class="message">for just 1 relation it can be a configurable i suppose</span></div>
-</div><div id="WJ1NE0OWQ71" class="first message colors">
-  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:48<span class="secs">:00</span></span><span class="ampm">08:48<span class="secs">:00</span>am</span>)</span> <span class="message">so chris has created an experimental file that bridges BFO and GO, so we can experiment with using those files to determine constraints</span></div>
-</div><div id="XE6C3OWQ71" class="first message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:48<span class="secs">:03</span></span><span class="ampm">08:48<span class="secs">:03</span>am</span>)</span> <span class="message">but as we allow more relations it should be a slim</span></div>
-</div><div id="B9LTDBOWQ71" class="first message color4">
-  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:48<span class="secs">:11</span></span><span class="ampm">08:48<span class="secs">:11</span>am</span>)</span> <span class="message">We had decided last august when Chris, David and Mark were here not to post-compose between continuants and occurrents</span></div>
-</div><div id="Q51J2OOWQ71" class="first message color3">
-  <div class="text"><span class="member"><a href="member:Anon363" class="member">Anon363</a></span><span class="timestamp">(<span class="tfh">08:48<span class="secs">:24</span></span><span class="ampm">08:48<span class="secs">:24</span>am</span>)</span> <span class="message">Sorry guys I have to go, I have another call in 10 mins and need to prepare </span></div>
-</div><div id="VI899QOWQ71" class="first message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:48<span class="secs">:26</span></span><span class="ampm">08:48<span class="secs">:26</span>am</span>)</span> <span class="message">and since its gonna go that way anyway maybe it should just be a slim to begin with</span></div>
-</div><div id="X2ZE2VOWQ71" class="first message colors">
-  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:48<span class="secs">:31</span></span><span class="ampm">08:48<span class="secs">:31</span>am</span>)</span> <span class="message">bye michael</span></div>
-</div><div class="event"><span class="message"><message><span class="member">Anon363</span> left the chat room.</message></span> (Quit: Anon363) <span class="timestamp"><span class="tfh">08:48<span class="secs">:37</span></span><span class="ampm">08:48<span class="secs">:37</span>am</span></span></div><div id="W0EWG5PWQ71" class="first message color6">
-  <div class="text"><span class="member"><a href="member:DavidOS" class="member">DavidOS</a></span><span class="timestamp">(<span class="tfh">08:48<span class="secs">:41</span></span><span class="ampm">08:48<span class="secs">:41</span>am</span>)</span> <span class="message">bye michael</span></div>
-</div><div id="SNDZ59PWQ71" class="later message color6">
-  <div class="text"><span class="member"><a href="member:DavidOS" class="member">DavidOS</a></span><span class="timestamp">(<span class="tfh">08:48<span class="secs">:45</span></span><span class="ampm">08:48<span class="secs">:45</span>am</span>)</span> <span class="message">too late</span></div>
-</div><div class="event"><span class="message"><message><span class="member">MichaelAshburner</span> left the chat room.</message></span> (Quit: MichaelAshburner) <span class="timestamp"><span class="tfh">08:48<span class="secs">:49</span></span><span class="ampm">08:48<span class="secs">:49</span>am</span></span></div><div id="S59CHPQWQ71" class="first message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:49<span class="secs">:37</span></span><span class="ampm">08:49<span class="secs">:37</span>am</span>)</span> <span class="message">hey melissa i know you are in active use right?</span></div>
-</div><div id="XJ5L7WQWQ71" class="first message colors">
-  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:49<span class="secs">:44</span></span><span class="ampm">08:49<span class="secs">:44</span>am</span>)</span> <span class="message">"not to post-compose between continuants and occurrents"</span></div>
-</div><div id="QXHBHWQWQ71" class="first message color4">
-  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:49<span class="secs">:44</span></span><span class="ampm">08:49<span class="secs">:44</span>am</span>)</span> <span class="message">yes</span></div>
-</div><div id="OQ6Y4ZQWQ71" class="first message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:49<span class="secs">:47</span></span><span class="ampm">08:49<span class="secs">:47</span>am</span>)</span> <span class="message">any issues that are humdingers - annoyances</span></div>
-</div><div id="I6OO5GRWQ71" class="first message colors">
-  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:50<span class="secs">:04</span></span><span class="ampm">08:50<span class="secs">:04</span>am</span>)</span> <span class="message">now that's because we can't do the deductive querying on that yet, right?</span></div>
-</div><div id="FUXPFKRWQ71" class="first message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:50<span class="secs">:08</span></span><span class="ampm">08:50<span class="secs">:08</span>am</span>)</span> <span class="message">i just fixed the sticky free text bug</span></div>
-</div><div id="WTBIENSWQ71" class="later message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:50<span class="secs">:47</span></span><span class="ampm">08:50<span class="secs">:47</span>am</span>)</span> <span class="message">deductive querying?</span></div>
-</div><div id="PARPKWSWQ71" class="first message color4">
-  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:50<span class="secs">:56</span></span><span class="ampm">08:50<span class="secs">:56</span>am</span>)</span> <span class="message">its because there is no link between the anatomy present in GO processes and the anatomy of an organism. CARO is still insufficient for this type of reasoning, and there is no way to synchronize. so we double annotate.</span></div>
-</div><div id="J72WMTWQ71" class="first message colors">
-  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:51<span class="secs">:22</span></span><span class="ampm">08:51<span class="secs">:22</span>am</span>)</span> <span class="message">yes yes</span></div>
-</div><div id="DJNGEPTWQ71" class="first message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:51<span class="secs">:25</span></span><span class="ampm">08:51<span class="secs">:25</span>am</span>)</span> <span class="message">what do you double annotate - whats an example</span></div>
-</div><div id="N0AN6IUWQ71" class="first message color4">
-  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:51<span class="secs">:54</span></span><span class="ampm">08:51<span class="secs">:54</span>am</span>)</span> <span class="message">brain development arrested AND brain small size</span></div>
-</div><div id="A8RX93VWQ71" class="first message colors">
-  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:52<span class="secs">:15</span></span><span class="ampm">08:52<span class="secs">:15</span>am</span>)</span> <span class="message">right... there's no link between brain development and brain the organ</span></div>
-</div><div id="TR4VJCVWQ71" class="first message color4">
-  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:52<span class="secs">:24</span></span><span class="ampm">08:52<span class="secs">:24</span>am</span>)</span> <span class="message">we annotate the processes separate from the anatomy</span></div>
-</div><div id="JLUZ5TVWQ71" class="first message colors">
-  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:52<span class="secs">:41</span></span><span class="ampm">08:52<span class="secs">:41</span>am</span>)</span> <span class="message">that will be a nice day when you don't have to</span></div>
-</div><div id="SAFJGVVWQ71" class="first message color7">
-  <div class="text"><span class="member"><a href="member:mark-gibson" class="member">mark-gibson</a></span><span class="timestamp">(<span class="tfh">08:52<span class="secs">:43</span></span><span class="ampm">08:52<span class="secs">:43</span>am</span>)</span> <span class="message">how would you annotate together - with post comp?</span></div>
-</div><div id="MHK2LLWWQ71" class="first message color4">
-  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:53<span class="secs">:09</span></span><span class="ampm">08:53<span class="secs">:09</span>am</span>)</span> <span class="message">maybe midbrain development part_of brain process arrested</span></div>
-</div><div id="OYSAAUWWQ71" class="first message color6">
-  <div class="text"><span class="member"><a href="member:DavidOS" class="member">DavidOS</a></span><span class="timestamp">(<span class="tfh">08:53<span class="secs">:18</span></span><span class="ampm">08:53<span class="secs">:18</span>am</span>)</span> <span class="message">Strictly, those two are not equivalent.  One makes a statement about development, the other about the adult structure that result from that development.</span></div>
-</div><div id="C1JV1ZWWQ71" class="first message color4">
-  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:53<span class="secs">:23</span></span><span class="ampm">08:53<span class="secs">:23</span>am</span>)</span> <span class="message">or something like that</span></div>
-</div><div id="F6OLDCXWQ71" class="first message colors">
-  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:53<span class="secs">:36</span></span><span class="ampm">08:53<span class="secs">:36</span>am</span>)</span> <span class="message">or maybe some kind of "conclusion" statement...brain development leads_to brain size small ?</span></div>
-</div><div id="QOAJMXWQ71" class="first message color4">
-  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:53<span class="secs">:46</span></span><span class="ampm">08:53<span class="secs">:46</span>am</span>)</span> <span class="message">yes</span></div>
-</div><div id="P612JRXWQ71" class="later message color4">
-  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:53<span class="secs">:51</span></span><span class="ampm">08:53<span class="secs">:51</span>am</span>)</span> <span class="message">to david</span></div>
-</div><div id="KWVZ2VXWQ71" class="first message color6">
-  <div class="text"><span class="member"><a href="member:DavidOS" class="member">DavidOS</a></span><span class="timestamp">(<span class="tfh">08:53<span class="secs">:55</span></span><span class="ampm">08:53<span class="secs">:55</span>am</span>)</span> <span class="message">In the unlikely(?) event that your brain shrank you could have one without the other.</span></div>
-</div><div id="C83V52YWQ71" class="first message colors">
-  <div class="text"><span class="member self"><a href="member:nicole" class="member">nicole</a></span><span class="timestamp">(<span class="tfh">08:54<span class="secs">:02</span></span><span class="ampm">08:54<span class="secs">:02</span>am</span>)</span> <span class="message">true</span></div>
-</div><div id="H4XK39YWQ71" class="first message color4">
-  <div class="text"><span class="member"><a href="member:MelissaH" class="member">MelissaH</a></span><span class="timestamp">(<span class="tfh">08:54<span class="secs">:09<...
 
[truncated message content]

[Obo-svn-commit] SF.net SVN: obo: [659] phenote/trunk/doc/phenote-website/irc_chat/ transcripts/PWG_irc_060507.html

[<nl...@us...>]

Revision: 659
          http://svn.sourceforge.net/obo/?rev=659&view=rev
Author:   nlw
Date:     2007-06-05 12:11:10 -0700 (Tue, 05 Jun 2007)

Log Message:
-----------
adding today's working group chat transcript

Added Paths:
-----------
    phenote/trunk/doc/phenote-website/irc_chat/transcripts/PWG_irc_060507.html

Added: phenote/trunk/doc/phenote-website/irc_chat/transcripts/PWG_irc_060507.html
===================================================================
--- phenote/trunk/doc/phenote-website/irc_chat/transcripts/PWG_irc_060507.html	                        (rev 0)
+++ phenote/trunk/doc/phenote-website/irc_chat/transcripts/PWG_irc_060507.html	2007-06-05 19:11:10 UTC (rev 659)
@@ -0,0 +1 @@

@@ Diff output truncated at 100000 characters. @@

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Obo-svn-commit] SF.net SVN: obo: [658] phenote/trunk/data/birn-test.xls

[<nl...@us...>]

Revision: 658
          http://svn.sourceforge.net/obo/?rev=658&view=rev
Author:   nlw
Date:     2007-06-04 17:08:36 -0700 (Mon, 04 Jun 2007)

Log Message:
-----------
adding some test data for the BIRN project
this is for the birn2.cfg configuration

Added Paths:
-----------
    phenote/trunk/data/birn-test.xls

Added: phenote/trunk/data/birn-test.xls
===================================================================
--- phenote/trunk/data/birn-test.xls	                        (rev 0)
+++ phenote/trunk/data/birn-test.xls	2007-06-05 00:08:36 UTC (rev 658)
@@ -0,0 +1,47 @@
+Pub	Image	Organism	Phenotypic Character	Entity ID	Entity Name	Quality ID	Quality Name	Add'l Entity ID	Add'l Entity Name	Compare To	Description	
+PD_data_annot_spread2:10		Mouse Strain (D-Line)	colocated expression of human alpha synuclein and mGlur5	sao:Glutamate_Receptor^OBO_REL:located_in(MA:0000950)	Glutamate_Receptor that located_in hippocampus CA1	PATO:0001162	increased concentration			non-transgenic animals	mGlur5 expression increased in Area CA1	
+PD_data_annot_spread2:11		Mouse Strain (D-Line)	colocated expression of human alpha synuclein and mGlur5	sao:Glutamate_Receptor^OBO_REL:located_in(MA:0000952)	Glutamate_Receptor that located_in hippocampus CA3	PATO:0001162	increased concentration			non-transgenic animals	mGlur5 expression increased in Area CA3	
+PD_data_annot_spread2:12		Mouse Strain (D-Line)	colocated expression of human alpha synuclein and mGlur5	sao:Glutamate_Receptor^OBO_REL:located_in(MA:0000190)	Glutamate_Receptor that located_in dentate gyrus	PATO:0001162	increased concentration			non-transgenic animals	mGlur5 expression increased	
+PD_data_annot_spread2:14		Mouse Strain (D-Line)	colocated expression of human alpha synuclein and mGlur5	sao:Protein^OBO_REL:located_in(MA:0000907)	Protein that located_in primary motor cortex	PATO:0001162	increased concentration			non-transgenic animals	human alpha synuclein expression increased	
+PD_data_annot_spread2:15		Mouse Strain (D-Line)	colocated expression of human alpha synuclein and mGlur5	sao:Protein^OBO_REL:located_in(MA:0000978)	Protein that located_in piriform cortex	PATO:0001162	increased concentration			non-transgenic animals	human alpha synuclein expression increased	
+PD_data_annot_spread2:16		Mouse Strain (D-Line)	colocated expression of human alpha synuclein and mGlur5	sao:Protein^OBO_REL:located_in(MA:0000891)	Protein that located_in striatum	PATO:0001162	increased concentration			non-transgenic animals	human alpha synuclein expression increased	
+PD_data_annot_spread2:17		Mouse Strain (D-Line)	colocated expression of human alpha synuclein and mGlur5	sao:Protein^OBO_REL:located_in(MA:0000210)	Protein that located_in substantia nigra	PATO:0001162	increased concentration			non-transgenic animals	human alpha synuclein expression increased	
+PD_data_annot_spread2:18		Mouse Strain (D-Line)	colocated expression of human alpha synuclein and mGlur5	sao:Protein^OBO_REL:located_in(MA:0000950)	Protein that located_in hippocampus CA1	PATO:0001162	increased concentration			non-transgenic animals	human alpha synuclein expression increased	
+PD_data_annot_spread2:19		Mouse Strain (D-Line)	colocated expression of human alpha synuclein and mGlur5	sao:Protein^OBO_REL:located_in(MA:0000952)	Protein that located_in hippocampus CA3	PATO:0001162	increased concentration			non-transgenic animals	human alpha synuclein expression increased	
+PD_data_annot_spread2:20		Mouse Strain (D-Line)	colocated expression of human alpha synuclein and mGlur5	sao:Protein^OBO_REL:located_in(MA:0000190)	Protein that located_in dentate gyrus	PATO:0001162	increased concentration			non-transgenic animals	human alpha synuclein expression increased	
+PD_data_annot_spread2:22		Mouse Strain (D-Line)	Dopamine Receptor (D1) Expression	FMA:61986^OBO_REL:located_in(MA:0000891)	D1 receptor that located_in striatum	PATO:0001162	increased concentration			non-transgenic animals	D1 receptor expression in dorsal medial striatum	
+PD_data_annot_spread2:3		Mouse Strain (D-Line)	cognitive deficit	GO:0007613	memory	PATO:0000762	impaired					
+PD_data_annot_spread2:3		Mouse Strain (D-Line)	cognitive deficit	GO:0050890	cognition	PATO:0000762	impaired					
+PD_data_annot_spread2:4		Mouse Strain (D-Line)	motor deficit	GO:0008344	adult locomotory behavior	PATO:0000188	coordination			non-transgenic animals	decreased coordination	
+PD_data_annot_spread2:4		Mouse Strain (D-Line)	motor deficit	GO:0008344	adult locomotory behavior	PATO:0001779	decreased strength			non-transgenic animals		
+PD_data_annot_spread2:4		Mouse Strain (D-Line)	motor deficit	GO:0008344	adult locomotory behavior	PATO:0000762	impaired			non-transgenic animals		
+PD_data_annot_spread2:5		Mouse Strain (D-Line)+MPEP	mGluR5 antagonism mediated via MPEP	GO:0008344	adult locomotory behavior	PATO:0000188	coordination			pre-MPEP D-Line animals	increased coordination	
+PD_data_annot_spread2:5		Mouse Strain (D-Line)+MPEP	mGluR5 antagonism mediated via MPEP	GO:0008344	adult locomotory behavior	PATO:0001778	increased strength			pre-MPEP D-Line animals		
+PD_data_annot_spread2:6		Mouse Strain (D-Line)	colocated expression of human alpha synuclein and mGlur5	sao:Glutamate_Receptor^OBO_REL:located_in(MA:0000907)	Glutamate_Receptor that located_in primary motor cortex	PATO:0001162	increased concentration			non-transgenic animals	mGlur5 expression increased	
+PD_data_annot_spread2:7		Mouse Strain (D-Line)	colocated expression of human alpha synuclein and mGlur5	sao:Glutamate_Receptor^OBO_REL:located_in(MA:0000978)	Glutamate_Receptor that located_in piriform cortex	PATO:0001162	increased concentration			non-transgenic animals	mGlur5 expression increased	
+PD_data_annot_spread2:8		Mouse Strain (D-Line)	colocated expression of human alpha synuclein and mGlur5	sao:Glutamate_Receptor^OBO_REL:located_in(MA:0000891)	Glutamate_Receptor that located_in striatum	PATO:0001162	increased concentration			non-transgenic animals	mGlur5 expression increased in neostriatum	
+PD_data_annot_spread2:9		Mouse Strain (D-Line)	colocated expression of human alpha synuclein and mGlur5	sao:Glutamate_Receptor^OBO_REL:located_in(MA:0000210)	Glutamate_Receptor that located_in substantia nigra	PATO:0001162	increased concentration			non-transgenic animals	mGlur5 expression increased in neostriatum	
+inclusion_body_test_case_v1:4		human	Lewy Neurite (LN) - Inclusion Body	sao:Subregional_part_of_neuron_process^OBO_REL:contains(sao:Terminal_Bouton)	Subregional_part_of_neuron_process that contains Terminal_Bouton	PATO:0001409	spindle-shaped					
+inclusion_body_test_case_v1:5		human	Lewy Neurite (LN) - Inclusion Body	sao:Subregional_part_of_neuron_process^OBO_REL:contains(sao:Terminal_Bouton)	Subregional_part_of_neuron_process that contains Terminal_Bouton	PATO:0000052	shape				thread-like shape	
+inclusion_body_test_case_v1:6		human	Lewy Neurite (LN) - Inclusion Body	sao:Subregional_part_of_neuron_process^OBO_REL:contains(sao:Terminal_Bouton)	Subregional_part_of_neuron_process that contains Terminal_Bouton	PATO:0000402	branched					
+inclusion_body_test_case_v1:9		human	Lewy Body (LB) - Inclusion Body	sao:Somatic_Spine	Somatic_Spine	PATO:0001759	granular					
+inclusion_body_test_case_v1:9		human	Lewy Body (LB) - Inclusion Body	sao:Somatic_Spine	Somatic_Spine	PATO:0001629	aggregated				contains 'granular aggregate' - chosen quality not quite right	
+inclusion_body_test_case_v1:10		human	Lewy Body (LB) - Inclusion Body	sao:Somatic_Spine	Somatic_Spine	PATO:0001499	spherical				spherical pale body	
+inclusion_body_test_case_v1:10		human	Lewy Body (LB) - Inclusion Body	sao:Somatic_Spine	Somatic_Spine	PATO:0000328	pale				spherical pale body	
+inclusion_body_test_case_v1:14		human	LB & LN - Inclusion Body	GO:0016234	inclusion body	PATO:0000025	composition	sao:Protein	Protein		alpha-synuclein	
+inclusion_body_test_case_v1:18		human	LB & LN - Inclusion Body	GO:0016234	inclusion body	PATO:0000025	composition	sao:Protein	Protein		synphilin-1	
+inclusion_body_test_case_v1:19		human	LB & LN - Inclusion Body	GO:0016234	inclusion body	PATO:0000025	composition	sao:Neurofilament^OBO_REL:contains(GO:0006468)	Neurofilament that contains protein amino acid phosphorylation		trying to represent 'phosphorylated neurofilament'...but there's nothing that captures this properly	
+inclusion_body_test_case_v1:20		human	LB & LN - Inclusion Body	GO:0016234	inclusion body	PATO:0000025	composition	GO:0016567	protein ubiquitination		ubiquitin - not really a term for the molecule in an ontology anywhere!	
+inclusion_body_test_case_v1:15		human	LB & LN - Inclusion Body	GO:0016234	inclusion body	PATO:0000025	composition	sao:Protein	Protein		alpha-synuclein - can't figure out how to say non-membrane bound!	
+inclusion_body_test_case_v1:15		human	LB & LN - Inclusion Body	sao:Protein	Protein	PATO:0000141	structure	sao:Protein	Protein		alpha-synuclein - can't figure out how to say pleated	
+inclusion_body_test_case_v1:25		human	Susceptible cell type	FMA:67310	Projection neuron	PATO:0000467	present				cell type = projection neuron	
+inclusion_body_test_case_v1:26		human	Susceptible cell type	FMA:67308^OBO_REL:part_of(FMA:67310)	Axon^part_of(Projection neuron)	PATO:0001154	elongated				cell type = projection neuron	
+inclusion_body_test_case_v1:26		human	Susceptible cell type	FMA:67308^OBO_REL:part_of(FMA:67310)	Axon^part_of(Projection neuron)	PATO:0001470	proportionality to	FMA:67301^OBO_REL:part_of(FMA:67310)	Cell body^part_of(Projection neuron)		axon length disproportionate to size of cell soma	
+inclusion_body_test_case_v1:27		human	Susceptible cell type	FMA:67308^OBO_REL:part_of(FMA:67310)	Axon^part_of(Projection neuron)	PATO:0000592	decreased thickness				thin axon	
+inclusion_body_test_case_v1:28		human	Susceptible cell type	FMA:67308^OBO_REL:part_of(FMA:67310)	Axon^part_of(Projection neuron)	PATO:0001557	lacking physical part	sao:Myelin_Sheath	Myelin_Sheath		unmyelinated	
+inclusion_body_test_case_v1:29		human	Susceptible cell type	FMA:67308^OBO_REL:part_of(FMA:67310)	Axon^part_of(Projection neuron)	PATO:0001163	decreased concentration	sao:Myelin_Sheath	Myelin_Sheath		poorly myelinated	
+inclusion_body_test_case_v1:30		human	Susceptible cell type	GO:0019226^OBO_REL:located_in(FMA:67310)	transmission of nerve impulse^located_in(Projection neuron)	PATO:0001839	increased flow				high energy output	
+inclusion_body_test_case_v1:32		human	Susceptible cell type	GO:0048668^OBO_REL:located_in(FMA:67310)	collateral sprouting^located_in(Projection neuron)	PATO:0000420	increased number				increased pathological sprouting (how to use pathological?)	
+inclusion_body_test_case_v1:33		human	Susceptible cell type	sao:Neuromelanin^OBO_REL:part_of(FMA:67310)^OBO_REL:part_of(FMA:62907)	Neuromelanin^part_of(Projection neuron)^part_of(Substantia nigra pars compacta)	PATO:0000467	present				melanized projection nneuron of pars compacta of the substantia nigra	
+inclusion_body_test_case_v1:34		human	Susceptible cell type	FMA:67310^OBO_REL:located_in(FMA:84039)^OBO_REL:located_in(FMA:63867)	Projection neuron^located_in(Mesocortex)^located_in(Temporal part of head)	PATO:0000587	decreased size				small projection neurons of temporal mesocortex deep layers	
+inclusion_body_test_case_v1:35		human	Susceptible cell type	sao:Neuron^OBO_REL:contains(FMA:62295)^OBO_REL:part_of(FMA:67947)	Neuron^contains(Melanin)^part_of(Substantia nigra)	PATO:0001154	elongated				melanoneurons of substantia nigra	


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[Obo-svn-commit] SF.net SVN: obo: [657] phenote/trunk/src/java/phenote

[<nl...@us...>]

Revision: 657
          http://svn.sourceforge.net/obo/?rev=657&view=rev
Author:   nlw
Date:     2007-05-31 19:15:41 -0700 (Thu, 31 May 2007)

Log Message:
-----------
*Added right-click editing functionality to free-text fields.
*Added right-click copy functionality to table.  Will copy ontology terms as free-text.
*These edits to not go into transaction table...to do.

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/config/Config.java
    phenote/trunk/src/java/phenote/config/ConfigFileQueryGui.java
    phenote/trunk/src/java/phenote/gui/CharacterTablePanel.java
    phenote/trunk/src/java/phenote/gui/field/FreeTextField.java

Added Paths:
-----------
    phenote/trunk/src/java/phenote/gui/FieldRightClickMenu.java
    phenote/trunk/src/java/phenote/gui/TableRightClickMenu.java

Modified: phenote/trunk/src/java/phenote/config/Config.java
===================================================================
--- phenote/trunk/src/java/phenote/config/Config.java	2007-05-30 22:17:15 UTC (rev 656)
+++ phenote/trunk/src/java/phenote/config/Config.java	2007-06-01 02:15:41 UTC (rev 657)
@@ -60,9 +60,9 @@
   //private int updateTimer = 0; //default is to not wait
   //private String reposUrlDir;
   private String version;
-  private String configName;
-  private String configDesc;
-  private String configAuthor;
+//  private String configName;
+//  private String configDesc;
+//  private String configAuthor;
   //private String masterToLocalConfigMode;
   //private MasterToLocalConfig masterToLocalBean;
   private PhenoteConfigurationDocument phenoDocBean;
@@ -86,13 +86,14 @@
   public void setConfigModified(boolean setting) { configModified = setting; }
 
   public void saveModifiedConfig() {
-    // this is the "species" conf file - eg ~/.phenote/conf/flybase.cfg
-  	System.out.println(configFile);
+  	//If settings during the Phenote session are modified (such as search
+  	//parameters, term history view, col widths (and others, eventually)
+  	//then this function will rewrite the config file with whatever the
+  	//current settings are (presumably they are changed)
     File localFile = new File(configFile);
+    new ConfigWriter().writeConfig(this,localFile);
 
-    new ConfigWriter().writeConfig(this,localFile);
-    
-		setConfigModified(false);  //in case if the person doesn't quit
+    setConfigModified(false);  //in case if the person doesn't quit
     return;
   }
   /** This is setting config file with nothing to do with personal config
@@ -810,14 +811,14 @@
 
       version = phenoConfigBean.getVersion();
       
-      configName = phenoConfigBean.getName();
+//      configName = phenoConfigBean.getName();
       
-      configDesc = phenoConfigBean.getDescription();
+//      configDesc = phenoConfigBean.getDescription();
       
-      configAuthor = phenoConfigBean.getAuthor();
+//      configAuthor = phenoConfigBean.getAuthor();
 
-      System.out.println("version:  "+version+"\nname:  "+configName+"\nDesc:  "+
-      		configDesc+"\nAuthor:  "+configAuthor);
+//      System.out.println("version:  "+version+"\nname:  "+configName+"\nDesc:  "+
+//      		configDesc+"\nAuthor:  "+getConfigAuthor());
       //MasterToLocalConfig m 
 //         = phenoConfigBean.getMasterToLocalConfig();
 //       if (m != null && m.getMode() != null)
@@ -960,9 +961,30 @@
     phenoConfigBean.setFieldArray(index,fc.getFieldBean());
   }
   
-  public String getConfigName() {	return configName;  }
-  public String getConfigDesc() { return configDesc; }
-  public String getConfigAuthor() { return configAuthor; }
+  public String getConfigName() {	
+  	String name = phenoConfigBean.getName();
+  	return name;  
+  	}
+  public void setConfigName(String name) {
+  	phenoConfigBean.setName(name);
+  	return;
+  }
+  public String getConfigDesc() { 
+  	String desc = phenoConfigBean.getDescription();
+  	return desc; 
+  	}
+  public void setConfigDesc(String desc) {
+  	phenoConfigBean.setDescription(desc);
+  	return;
+  }
+  public String getConfigAuthor() { 
+  	String author = phenoConfigBean.getAuthor();
+    return author;
+  }
+  public void setConfigAuthor(String author) {
+  	phenoConfigBean.setAuthor(author);
+  	return;
+  }
   
 }
 

Modified: phenote/trunk/src/java/phenote/config/ConfigFileQueryGui.java
===================================================================
--- phenote/trunk/src/java/phenote/config/ConfigFileQueryGui.java	2007-05-30 22:17:15 UTC (rev 656)
+++ phenote/trunk/src/java/phenote/config/ConfigFileQueryGui.java	2007-06-01 02:15:41 UTC (rev 657)
@@ -29,6 +29,7 @@
 import javax.swing.AbstractAction;
 import javax.swing.BoxLayout;
 import javax.swing.JDialog;
+import javax.swing.JOptionPane;
 import javax.swing.JLabel;
 import javax.swing.JPanel;
 import javax.swing.JButton;
@@ -46,6 +47,7 @@
   //private String selection;
   private String selectedFile;
   private JDialog dialog;
+  private JPanel infoPanel;
   //private boolean okPressed = false;
   private ButtonGroup buttonGroup;
   private boolean hasCancelButton = false;
@@ -82,7 +84,7 @@
     JLabel text = new JLabel("Please pick a configuration for Phenote: ");
     int center = GridBagConstraints.CENTER;
     GridBagConstraints gbc = GridBagUtil.makeAnchorConstraint(0,0,center);
-    gbc.gridwidth=2;
+    gbc.gridwidth=3;
     dialog.add(text,gbc);
 
     JPanel buttonPanel = new JPanel();
@@ -92,7 +94,7 @@
     String currentConfig = null;
     try { currentConfig = Config.inst().getMyPhenoteConfigString(); }
     catch (IOException e) { doFirst = true; }
-    for (String cfg : getConfigNames()) {
+   for (String cfg : getConfigNames()) {
       JRadioButton b = new JRadioButton(new BtnAction(cfg));
       buttonPanel.add(b);
       // select current myphenote if exists, else select first
@@ -117,11 +119,19 @@
       ++gbc.gridx;
       dialog.add(cancel,gbc);
     }
+    JButton info = new JButton("Info...");
+    info.addActionListener(new InfoActionListener());
+    ++gbc.gridx;
+    dialog.add(info,gbc);
     dialog.pack();
     centerOnScreen(dialog);
     dialog.addWindowListener(new WindowCancel());
     dialog.setVisible(true);
   }
+  
+  private void updateInfoPanel() {
+  	
+  }
 
   private class OkActionListener implements ActionListener {
     public void actionPerformed(ActionEvent e) {
@@ -135,9 +145,20 @@
   private class CancelActionListener implements ActionListener {
     public void actionPerformed(ActionEvent e) {
       isCancelled = true;
+      
       dialog.dispose();
     }
   }
+  private class InfoActionListener implements ActionListener {
+    public void actionPerformed(ActionEvent e) {
+    	System.out.println("info button pressed");
+    	String m = "This feature will display some basic information about \na configuration. " +
+    			"It is not yet enabled.";
+      JOptionPane.showMessageDialog(null, m, "Config Info",
+              JOptionPane.INFORMATION_MESSAGE);
+    	return;
+    }
+  }
   private class WindowCancel extends WindowAdapter {
     public void windowClosing(WindowEvent e) {
       // should this do a System.exit if we are at startup?
@@ -154,6 +175,7 @@
       super(makeDisplayFromFile(configFilename));
       //putValue("filename",configFilename);
       this.configFilename = configFilename;
+      updateInfoPanel();
     }
     public void actionPerformed(ActionEvent e) {
       selectedFile = configFilename;
@@ -161,7 +183,7 @@
   }
   private String makeDisplayFromFile(String f) {
     f = f.replaceAll(".cfg","");
-    f = f.replaceAll("-"," ");
+    //f = f.replaceAll("-"," ");
     return f;
   }
 

Modified: phenote/trunk/src/java/phenote/gui/CharacterTablePanel.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/CharacterTablePanel.java	2007-05-30 22:17:15 UTC (rev 656)
+++ phenote/trunk/src/java/phenote/gui/CharacterTablePanel.java	2007-06-01 02:15:41 UTC (rev 657)
@@ -12,6 +12,7 @@
 import java.awt.event.ActionListener;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
 
 import javax.swing.Box;
 import javax.swing.JButton;
@@ -19,6 +20,9 @@
 import javax.swing.JScrollBar;
 import javax.swing.JScrollPane;
 import javax.swing.JTable;
+import javax.swing.JPopupMenu;
+import javax.swing.JOptionPane;
+import javax.swing.JMenuItem;
 import javax.swing.ListSelectionModel;
 import javax.swing.event.ChangeEvent;
 import javax.swing.event.ChangeListener;
@@ -38,14 +42,16 @@
 import phenote.config.Config;
 import phenote.gui.selection.SelectionManager;
 import phenote.dataadapter.LoadSaveManager;
+import phenote.gui.TableRightClickMenu;
 
   /** Character panel has character table and del add copy buttons to manipulate
    *  table. Modifications to fields modify columns in selected row in table
    * for now no explicit commit - may be configurable later */
 public class CharacterTablePanel extends JPanel {
 
-  private JTable charJTable;
-  private CharacterTableModel characterTableModel;
+  private CharacterTableModel characterTableModel = new CharacterTableModel();
+  private JTable charJTable = new JTable(characterTableModel);
+
   //private FieldPanel fieldPanel;
   //private JButton newButton;
   private JButton copyButton;
@@ -56,6 +62,7 @@
   private JScrollBar verticalScrollBar;
   private boolean scrollToNewLastRowOnRepaint = false;
   private boolean ignoreSelectionChange = false;
+  private Point currentMousePoint = new Point(0,0);
   
   //private int selectedRow;
   // get from file menu?
@@ -65,6 +72,7 @@
 
   public CharacterTablePanel() { //TermPanel tp) {
     //fieldPanel = tp;
+  	super();    
     init();
   }
 
@@ -76,8 +84,6 @@
     setPreferredSize(new Dimension(1400,500));
     //setMinimumSize(new Dimension(1400,630)); // 630   
 
-    characterTableModel = new CharacterTableModel();
-    charJTable = new JTable(characterTableModel);
     //charJTable.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
     charJTable.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
     CharacterSelectionListener isl = new CharacterSelectionListener();
@@ -93,6 +99,12 @@
     charJTable.setPreferredScrollableViewportSize(new Dimension(500, 600));//150
 
     GridBagConstraints gbc = GridBagUtil.makeFillingConstraint(0,0);
+
+    //Add listener to components that can bring up popup menus.
+    JPopupMenu popup = new TableRightClickMenu();
+    MouseListener popupListener = new PopupListener(popup);
+    charJTable.addMouseListener(popupListener);
+
     add(tableScroll,gbc);
 
     // add in buttons
@@ -146,10 +158,17 @@
     return getSelectedRow() != -1;
   }
 
-  private int getSelectedRow() {
+  public int getSelectedRow() {
     return charJTable.getSelectedRow();
   }
   
+  public String getCellString(int row, int col) {
+  	Object s = charJTable.getValueAt(row,col);
+  	if (s==null) {
+  		return ("");
+  	} else return s.toString();
+  }
+  
   /** row number is zero based for tables */
   private void selectRow(int row) {
     if (charJTable == null) return;
@@ -402,7 +421,67 @@
       
     }
   }
+  private void setPoint (Point p) {
+  	currentMousePoint= p;
+  	return;
+  }
+  public Point getPoint() {
+  	return currentMousePoint;
+  }
+  
+  public Point getTableCoord() {
+  	Point coord;
+  	int col = charJTable.getTableHeader().columnAtPoint(currentMousePoint);
+    int row = charJTable.rowAtPoint(currentMousePoint);
+    coord = new Point(row,col);
+    return (coord);
+  }
+  
+  private class PopupListener extends MouseAdapter {
+  	JPopupMenu popup;
+  	int col; int row;
+  	Point p;
+  	PopupListener(JPopupMenu popupMenu) {
+  		popup = popupMenu;
+  	}
 
+  	public void mousePressed(MouseEvent e) {
+//  		super.mousePressed(e);
+  		maybeShowPopup(e);
+  	}
+
+  	public void mouseReleased(MouseEvent e) {
+//  		super.mouseReleased(e);
+  		maybeShowPopup(e);
+  	}
+
+  	private void maybeShowPopup(MouseEvent e) {
+  		String m="";
+  		col=e.getX();
+  		row=e.getY();
+  		p= e.getPoint();
+      col = charJTable.getTableHeader().columnAtPoint(p);
+      row = charJTable.rowAtPoint(p);
+      setPoint(p);
+//      System.out.println("col="+col+" row= "+row);
+//  		System.out.println("button="+e.getButton());
+//  		System.out.println(e.paramString());
+//  		System.out.println("popuptrigger="+e.isPopupTrigger());
+//  		if(e.getButton()==MouseEvent.BUTTON3) {
+  		if (e.isPopupTrigger()) {
+    		m = "popuptrigger!";
+    		popup.show(e.getComponent(),
+  					e.getX(), e.getY());
+  		}
+//  		else {
+//  			m="no trigger, its "+e.paramString()+"!";
+//  		}
+//  		JOptionPane.showMessageDialog(null, m, "Phenote Help",
+//    			JOptionPane.INFORMATION_MESSAGE);
+//  		e.consume();
+  	}
+  }
+
   // for test
   void pressCommitButtonTest() {
     commitButton.doClick();

Added: phenote/trunk/src/java/phenote/gui/FieldRightClickMenu.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/FieldRightClickMenu.java	                        (rev 0)
+++ phenote/trunk/src/java/phenote/gui/FieldRightClickMenu.java	2007-06-01 02:15:41 UTC (rev 657)
@@ -0,0 +1,46 @@
+package phenote.gui;
+
+//import java.awt.event.ActionEvent;
+//import java.awt.event.ActionListener;
+//import java.awt.event.MouseAdapter;
+//import java.awt.event.MouseEvent;
+import java.awt.event.KeyEvent;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JPopupMenu;
+import javax.swing.text.DefaultEditorKit;
+
+
+public class FieldRightClickMenu extends JPopupMenu {
+	//this menu does the basic editing functionality cut/copy/paste 
+	//for free text fields
+	//this in some way needs to link up to the undo/redo transaction 
+	//history i think.
+	
+	public FieldRightClickMenu() {
+		super();
+		init();
+	}
+
+	private void init() {
+//		Create the popup menu.
+		JMenuItem menuItem;
+		menuItem = new JMenuItem(new DefaultEditorKit.CopyAction());
+		menuItem.setText("Copy");
+		menuItem.setMnemonic(KeyEvent.VK_C);
+		menuItem.setEnabled(true);
+		add(menuItem);
+		menuItem = new JMenuItem(new DefaultEditorKit.CutAction());
+		menuItem.setText("Cut");
+		menuItem.setEnabled(true);
+		menuItem.setMnemonic(KeyEvent.VK_X);
+		add(menuItem);
+//		menuItem = new JMenuItem();
+		menuItem = new JMenuItem(new DefaultEditorKit.PasteAction());
+		//		menuItem.addActionListener(new PasteActionListener());
+		menuItem.setText("Paste");
+		menuItem.setEnabled(true);
+		menuItem.setMnemonic(KeyEvent.VK_V);
+		add(menuItem);
+	}
+}

Added: phenote/trunk/src/java/phenote/gui/TableRightClickMenu.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/TableRightClickMenu.java	                        (rev 0)
+++ phenote/trunk/src/java/phenote/gui/TableRightClickMenu.java	2007-06-01 02:15:41 UTC (rev 657)
@@ -0,0 +1,84 @@
+package phenote.gui;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+//import java.awt.event.MouseListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.event.KeyEvent;
+import java.awt.Point;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.ClipboardOwner;
+import java.awt.datatransfer.Transferable;
+import java.awt.datatransfer.StringSelection;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.UnsupportedFlavorException;
+import java.awt.Toolkit;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+//import javax.swing.JOptionPane;
+import javax.swing.JPopupMenu;
+import javax.swing.JTable;
+//import javax.swing.text.DefaultEditorKit;
+
+
+
+import phenote.gui.CharacterTablePanel;
+import phenote.gui.CharacterTableModel;
+import phenote.main.Phenote;
+
+
+
+class TableRightClickMenu extends JPopupMenu {
+	//currently this menu set can only copy free text, or ontology 
+	//field content as free text.  it will need to get smart to the charfields
+
+	TableRightClickMenu() {
+		super();
+		init();
+	}
+
+	private void init() {
+//		Create the popup menu.
+		JMenuItem menuItem;
+		menuItem = new JMenuItem();
+		menuItem.setText("Copy");
+		menuItem.setMnemonic(KeyEvent.VK_C);
+		menuItem.addActionListener(new CopyActionListener());
+		add(menuItem);
+		menuItem = new JMenuItem();
+//		menuItem.addActionListener(new CutActionListener());
+		menuItem.setText("Cut");
+		menuItem.setEnabled(false);
+		menuItem.setMnemonic(KeyEvent.VK_X);
+		add(menuItem);
+		menuItem = new JMenuItem();
+//		menuItem.addActionListener(new PasteActionListener());
+		menuItem.setText("Paste");
+		menuItem.setEnabled(false);
+		menuItem.setMnemonic(KeyEvent.VK_V);
+		add(menuItem);
+	}
+
+	private class CopyActionListener implements ActionListener {
+		public void actionPerformed(ActionEvent e) {
+			CharacterTablePanel table = Phenote.getPhenote().getCharacterTablePanel();
+			Point coord = table.getTableCoord();
+			int row = (int) coord.getX();
+			int col = (int) coord.getY();
+			String s = table.getCellString(row, col);
+			//System.out.println("copied ("+row+","+col+") "+s);
+			Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+			//System.out.println("system clipboard="+c.getContents(null));
+			StringSelection stringSelection = new StringSelection( s );
+			c.setContents( stringSelection , null);
+		}
+	}
+
+	private class PasteActionListener implements ActionListener {
+		public void actionPerformed(ActionEvent e) {
+
+			return;
+		}
+	}
+}

Modified: phenote/trunk/src/java/phenote/gui/field/FreeTextField.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/FreeTextField.java	2007-05-30 22:17:15 UTC (rev 656)
+++ phenote/trunk/src/java/phenote/gui/field/FreeTextField.java	2007-06-01 02:15:41 UTC (rev 657)
@@ -10,11 +10,21 @@
 import java.awt.datatransfer.Transferable;
 import java.awt.event.KeyAdapter;
 import java.awt.event.KeyEvent;
-
 import java.awt.event.InputEvent;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
 import javax.swing.KeyStroke;
 import javax.swing.text.DefaultEditorKit;
+import javax.swing.JPopupMenu;
+import javax.swing.JMenuItem;
+import java.awt.Point;
 
+
+
+
 import javax.swing.text.JTextComponent;
 import javax.swing.JTextField;
 import javax.swing.text.Keymap;
@@ -30,7 +40,9 @@
 import phenote.edit.EditManager;
 import phenote.gui.selection.CharSelectionEvent;
 import phenote.gui.selection.SelectionManager;
+import phenote.gui.FieldRightClickMenu;
 
+
 // should this be a subclass of charfieldGui? maybe?
 class FreeTextField extends CharFieldGui {
 
@@ -50,6 +62,11 @@
     textField.setEditable(true);
     textField.getDocument().addDocumentListener(new TextFieldDocumentListener());
     textField.addFocusListener(new FreeFocusListener());
+     //Add listener to components that can bring up popup menus.
+    JPopupMenu popup = new FieldRightClickMenu();
+    MouseListener popupListener = new PopupListener(popup);
+    textField.addMouseListener(popupListener);
+
     //textField.addKeyListener(new TextKeyListener());
     loadKeyMap(); // mac cut copy paste
   }
@@ -133,7 +150,46 @@
       }
     }
   }
+  
+  private class PopupListener extends MouseAdapter {
+  	JPopupMenu popup;
+  	
+  	int col; int row;
+  	Point p;
+  	PopupListener(JPopupMenu popupMenu) {
+  		popup = popupMenu;
+  	}
 
+  	public void mousePressed(MouseEvent e) {
+//  		super.mousePressed(e);
+  		maybeShowPopup(e);
+  	}
+
+  	public void mouseReleased(MouseEvent e) {
+//  		super.mouseReleased(e);
+  		maybeShowPopup(e);
+  	}
+
+  	private void maybeShowPopup(MouseEvent e) {
+//  		String m="";
+//  		col=e.getX();
+//  		row=e.getY();
+//       System.out.println("col="+col+" row= "+row);
+//  		System.out.println("button="+e.getButton());
+//  		System.out.println(e.paramString());
+//  		System.out.println("popuptrigger="+e.isPopupTrigger());
+//  		if(e.getButton()==MouseEvent.BUTTON3) {
+  		if (e.isPopupTrigger()) {
+//    		m = "popuptrigger!";
+    		popup.show(e.getComponent(),
+  					e.getX(), e.getY());
+  		}
+//  		else {
+////  			m="no trigger, its "+e.paramString()+"!";
+//  		}
+  	}
+  }
+
   /** if the focus has changed and the gui has been edited then edit the model */
   private class FreeFocusListener implements FocusListener {
     public void focusGained(FocusEvent e) {}


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[Obo-svn-commit] SF.net SVN: obo: [656] phenote/trunk/conf/worm.cfg

[<azu...@us...>]

Revision: 656
          http://svn.sourceforge.net/obo/?rev=656&view=rev
Author:   azurebrd
Date:     2007-05-30 15:17:15 -0700 (Wed, 30 May 2007)

Log Message:
-----------
re-removed   <obo-repository url-dir="http://www.berkeleybop.org/ontologies/obo-all/"/>

Modified Paths:
--------------
    phenote/trunk/conf/worm.cfg

Modified: phenote/trunk/conf/worm.cfg
===================================================================
--- phenote/trunk/conf/worm.cfg	2007-05-30 22:06:47 UTC (rev 655)
+++ phenote/trunk/conf/worm.cfg	2007-05-30 22:17:15 UTC (rev 656)
@@ -21,9 +21,7 @@
   <update-timer timer="0"/><!--set to 0 if you want to bypass the check; time in seconds-->
   
 
-  <obo-repository url-dir="http://www.berkeleybop.org/ontologies/obo-all/"/>
 
-
   <field name="Object Type" enable="true"/>
 
   <field name="Object Name" enable="true"/>


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[Obo-svn-commit] SF.net SVN: obo: [655] phenote/trunk

[<azu...@us...>]

Revision: 655
          http://svn.sourceforge.net/obo/?rev=655&view=rev
Author:   azurebrd
Date:     2007-05-30 15:06:47 -0700 (Wed, 30 May 2007)

Log Message:
-----------
Added Genetic Intx Desc field for Gary.

Fixed postgres query of Object Type and other tables that have no alp_column

Modified Paths:
--------------
    phenote/trunk/conf/worm.cfg
    phenote/trunk/src/java/phenote/dataadapter/worm/WormAdapter.java

Modified: phenote/trunk/conf/worm.cfg
===================================================================
--- phenote/trunk/conf/worm.cfg	2007-05-30 19:59:45 UTC (rev 654)
+++ phenote/trunk/conf/worm.cfg	2007-05-30 22:06:47 UTC (rev 655)
@@ -21,6 +21,9 @@
   <update-timer timer="0"/><!--set to 0 if you want to bypass the check; time in seconds-->
   
 
+  <obo-repository url-dir="http://www.berkeleybop.org/ontologies/obo-all/"/>
+
+
   <field name="Object Type" enable="true"/>
 
   <field name="Object Name" enable="true"/>
@@ -29,20 +32,22 @@
          <ontology name="Pub" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/paper_obo.cgi"/>
   </field>
 
-  <field name="Reference Remark" syntax-abbrev="OtherRemark" enable="true"/>
-
   <field name="Person" syntax-abbrev="T" enable="true">
          <ontology name="Person" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/person_obo.cgi"/>
   </field>
   
   <field name="NBP" syntax-abbrev="PhenotypeTextRemark" enable="true"/>
 
+  <field name="Reference Remark" syntax-abbrev="OtherRemark" enable="true"/>
+
+  <field name="Genetic Intx Desc" syntax-abbrev="IntxDesc" enable="true"/>
+
   <field name="Curator" syntax-abbrev="Curator" enable="true"/>             
 
   <field name="NOT" enable="true"/> <!-- Boolean checkbox -->
 
   <field name="Phenotype" syntax-abbrev="T" enable="true">
-         <ontology name="Person" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/phenotype_ontology_obo.cgi"/>
+         <ontology name="Phenotype" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/phenotype_ontology_obo.cgi"/>
   </field>
 
   <field name="Phenotype Remark" syntax-abbrev="PhenotypeRemark" enable="true"/>

Modified: phenote/trunk/src/java/phenote/dataadapter/worm/WormAdapter.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/worm/WormAdapter.java	2007-05-30 19:59:45 UTC (rev 654)
+++ phenote/trunk/src/java/phenote/dataadapter/worm/WormAdapter.java	2007-05-30 22:06:47 UTC (rev 655)
@@ -315,7 +315,17 @@
     } catch (SQLException se) {
       System.out.println("Couldn't connect: print out a stack trace and exit.");
       se.printStackTrace();
-      System.exit(1);
+      System.out.println("Couldn't connect: stack trace done.");
+      String getMessage = se.getMessage();
+      getMessage = getMessage + " \nYour IP is not recognized by the postgres database, please contact he...@wo... if you're a valid Phenotype WormBase curator.";
+      JOptionPane.showMessageDialog(null,getMessage,"Postgres connection error",JOptionPane.INFORMATION_MESSAGE);
+//       Throwable throwCause = se.getCause();
+//       String getCause = throwCause.toString();
+//       JOptionPane.showMessageDialog(null,getCause,"getCause",JOptionPane.INFORMATION_MESSAGE);
+//       String m = "Your IP is not recognized by the postgres database, please contact he...@wo... if you're a valid Phenotype WormBase curator.";
+//       JOptionPane.showMessageDialog(null,m,"Worm stub",JOptionPane.INFORMATION_MESSAGE);
+      // System.exit(1);
+      // System.out.println("Couldn't connect: exit done.");
     }
     if (c != null)
       System.out.println("Hooray! We connected to the database!");
@@ -335,13 +345,20 @@
       try { while (rs.next()) { default_value = rs.getString(4); } }		// assign the new term value
       catch (SQLException se) {
         System.out.println("We got an exception while getting a "+postgres_table+" result:this shouldn't happen: we've done something really bad."); se.printStackTrace(); System.exit(1); } }
-    else {
+    else if (boxI > 0) {
       try { rs = s.executeQuery("SELECT * FROM "+postgres_table+" WHERE joinkey = '"+query+"' AND app_box='"+boxI+"' ORDER BY app_timestamp"); }
       catch (SQLException se) {
         System.out.println("We got an exception while executing our "+postgres_table+" query: that probably means our term SQL is invalid"); se.printStackTrace(); System.exit(1); }
       try { while (rs.next()) { default_value = rs.getString(3); } }		// assign the new term value
       catch (SQLException se) {
         System.out.println("We got an exception while getting a "+postgres_table+" result:this shouldn't happen: we've done something really bad."); se.printStackTrace(); System.exit(1); } }
+    else {
+      try { rs = s.executeQuery("SELECT * FROM "+postgres_table+" WHERE joinkey = '"+query+"' ORDER BY app_timestamp"); }
+      catch (SQLException se) {
+        System.out.println("We got an exception while executing our "+postgres_table+" query: that probably means our term SQL is invalid"); se.printStackTrace(); System.exit(1); }
+      try { while (rs.next()) { default_value = rs.getString(2); } }		// assign the new term value
+      catch (SQLException se) {
+        System.out.println("We got an exception while getting a "+postgres_table+" result:this shouldn't happen: we've done something really bad."); se.printStackTrace(); System.exit(1); } }
 //    System.out.println("Added in function charList term "+query+" column "+colI+".");		// comment out later
     if (default_value == null) { default_value = "postgres value is null"; }
     if (default_value == "") { default_value = "postgres value is blank"; }
@@ -361,10 +378,12 @@
       if (phenotype_match != null) { postgres_value = phenotype_match; }		// query for this, otherwise keep the default value
       if (postgres_value == "No postgres value assigned") { } else { c1.setValue("Phenotype",postgres_value); }					// assign the queried value
 //       c1.setValue("Phenotype",postgres_value);					// assign the queried value
-      postgres_table = "app_curator"; postgres_value = "No postgres value assigned";
-      postgres_value = queryPostgresCharacter(s, postgres_table, postgres_value, joinkey, boxI, colI);
-      c1.setValue("Curator",postgres_value);					// assign the queried value
-
+      postgres_table = "app_type"; postgres_value = "No postgres value assigned";
+      postgres_value = queryPostgresCharacter(s, postgres_table, postgres_value, joinkey, 0, 0);
+      c1.setValue("Object Type",postgres_value);					// assign the queried value
+      postgres_table = "app_intx_desc"; postgres_value = "No postgres value assigned";
+      postgres_value = queryPostgresCharacter(s, postgres_table, postgres_value, joinkey, boxI, 0);
+      c1.setValue("Genetic Intx Desc",postgres_value);					// assign the queried value
       postgres_table = "app_paper"; postgres_value = "No postgres value assigned";
       postgres_value = queryPostgresCharacter(s, postgres_table, postgres_value, joinkey, boxI, 0);
       String paper_match = find("(WBPaper[0-9]*)", postgres_value);		// Find a WBPaper followed by any amount of digits
@@ -377,11 +396,15 @@
       if (person_match != null) { postgres_value = person_match; }	// query for this, otherwise keep the default value
       if (postgres_value == "No postgres value assigned") { } else { c1.setValue("Person",postgres_value); }					// assign the queried value
       postgres_table = "app_phenotype"; postgres_value = "No postgres value assigned";
-      postgres_value = queryPostgresCharacter(s, postgres_table, postgres_value, joinkey, boxI, colI);
+      postgres_value = queryPostgresCharacter(s, postgres_table, postgres_value, joinkey, boxI, 0);
       c1.setValue("NBP",postgres_value);					// assign the queried value
       postgres_table = "app_remark"; postgres_value = "No postgres value assigned";
+      postgres_value = queryPostgresCharacter(s, postgres_table, postgres_value, joinkey, boxI, 0);
+      c1.setValue("Reference Remark",postgres_value);					// assign the queried value
+
+      postgres_table = "app_curator"; postgres_value = "No postgres value assigned";
       postgres_value = queryPostgresCharacter(s, postgres_table, postgres_value, joinkey, boxI, colI);
-      c1.setValue("Reference Remark",postgres_value);					// assign the queried value
+      c1.setValue("Curator",postgres_value);					// assign the queried value
       postgres_table = "app_phen_remark"; postgres_value = "No postgres value assigned";
       postgres_value = queryPostgresCharacter(s, postgres_table, postgres_value, joinkey, boxI, colI);
       c1.setValue("Phenotype Remark",postgres_value);				// assign the queried value


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[Obo-svn-commit] SF.net SVN: obo: [654] phenote/trunk

[<nl...@us...>]

Revision: 654
          http://svn.sourceforge.net/obo/?rev=654&view=rev
Author:   nlw
Date:     2007-05-30 12:59:45 -0700 (Wed, 30 May 2007)

Log Message:
-----------
*Adding in the help docs to work *inside* of phenote.  its not smart yet to detect what you might be needing help on, but it'll at least bring up the help.  search works.

Modified Paths:
--------------
    phenote/trunk/doc/phenote-website/help/toc.html
    phenote/trunk/doc/phenote-website/help/toc_generator.xsl
    phenote/trunk/src/java/phenote/gui/HelpMenu.java

Added Paths:
-----------
    phenote/trunk/src/java/phenote/main/HelpManager.java

Modified: phenote/trunk/doc/phenote-website/help/toc.html
===================================================================
--- phenote/trunk/doc/phenote-website/help/toc.html	2007-05-30 19:49:19 UTC (rev 653)
+++ phenote/trunk/doc/phenote-website/help/toc.html	2007-05-30 19:59:45 UTC (rev 654)
@@ -1,351 +1,362 @@
 <html>
 <head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<META http-equiv="Content-Type" content="text/html; charset=UTF-8">
 <title>Table of Contents</title>
 </head>
-<body><small><font face="Arial"><p><center><strong>Contents</strong></center></p>
+<body>
+<small><font face="Arial">
+<p>
+<center>
+<strong>Contents</strong>
+</center>
+</p>
 
-<table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Phenote User's Guide
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">What is Phenote?</font></td>
-</tr></table>
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Advantages to Annotation with Ontolgies</font></td>
-</tr></table>
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Bugs and Troubleshooting</font></td>
-</tr></table>
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Licensing Information</font></td>
-</tr></table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Phenote User's Guide
+     <table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">What is Phenote?</font></td>
+</tr>
+</table>
+     
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Advantages to Annotation with Ontolgies</font></td>
+</tr>
+</table>
+     
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Bugs and Troubleshooting</font></td>
+</tr>
+</table>
+     
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Licensing Information</font></td>
+</tr>
+</table>
+
 </font></td>
-</tr></table>
-<table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Getting Started
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Phenote Webstart</font></td>
-</tr></table>
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Phenote from the Command Line</font></td>
-</tr></table>
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Ontologies included with Phenote</font></td>
-</tr></table>
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Running Phenote for the First Time</font></td>
-</tr></table>
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Exiting Phenote</font></td>
-</tr></table>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Getting Started
+     <table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Phenote Webstart</font></td>
+</tr>
+</table>
+     
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Phenote from the Command Line</font></td>
+</tr>
+</table>
+     
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Ontologies included with Phenote</font></td>
+</tr>
+</table>
+     
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Running Phenote for the First Time</font></td>
+</tr>
+</table>
+     
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Exiting Phenote</font></td>
+</tr>
+</table>
+
 </font></td>
-</tr></table>
-<table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The Phenote Interface
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Menu Bars</font></td>
-</tr></table>
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Data Entry</font></td>
-</tr></table>
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Term Info</font></td>
-</tr></table>
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Annotation Spreadsheet</font></td>
-</tr></table>
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Changing your Configuration</font></td>
-</tr></table>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">The Phenote Interface
+     <table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Menu Bars</font></td>
+</tr>
+</table>
+     
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Data Entry</font></td>
+</tr>
+</table>
+     
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Term Info</font></td>
+</tr>
+</table>
+     
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Annotation Spreadsheet</font></td>
+</tr>
+</table>
+     
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Changing your Configuration</font></td>
+</tr>
+</table>
+
 </font></td>
-</tr></table>
-<table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Loading/Saving Annotations
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Introduction to Data Adapters</font></td>
-</tr></table>
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Loading &amp; Saving</font></td>
-</tr></table>
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The PhenoXML adapter</font></td>
-</tr></table>
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The PhenoSyntax Adapter</font></td>
-</tr></table>
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The Tag-Value Adapter</font></td>
-</tr></table>
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The Tab-Delimited Adapter</font></td>
-</tr></table>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Loading/Saving Annotations
+     <table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Introduction to Data Adapters</font></td>
+</tr>
+</table>
+     
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Loading &amp; Saving</font></td>
+</tr>
+</table>
+     
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">The PhenoXML adapter</font></td>
+</tr>
+</table>
+     
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">The PhenoSyntax Adapter</font></td>
+</tr>
+</table>
+     
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">The Tag-Value Adapter</font></td>
+</tr>
+</table>
+     
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">The Tab-Delimited Adapter</font></td>
+</tr>
+</table>
+
 </font></td>
-</tr></table>
-<table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Creating Annotations
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Editing Functions</font></td>
-</tr></table>
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Entering data into Free-Text fields</font></td>
-</tr></table>
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Entering data into Ontology Fields</font></td>
-</tr></table>
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Term Composition/Refinement</font></td>
-</tr></table>
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Changing your Autocompletion Settings</font></td>
-</tr></table>
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Sample Annotations</font></td>
-</tr></table>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Creating Annotations
+     <table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Editing Functions</font></td>
+</tr>
+</table>
+     
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Entering data into Free-Text fields</font></td>
+</tr>
+</table>
+     
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Entering data into Ontology Fields</font></td>
+</tr>
+</table>
+     
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Term Composition/Refinement</font></td>
+</tr>
+</table>
+     
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Changing your Autocompletion Settings</font></td>
+</tr>
+</table>
+     
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Sample Annotations</font></td>
+</tr>
+</table>
+
 </font></td>
-</tr></table>
-<table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Information for Developers
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Writing a Data Adapter</font></td>
-</tr></table>
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Connecting to a Database</font></td>
-</tr></table>
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Adding configurability</font></td>
-</tr></table>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Information for Developers
+     <table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Writing a Data Adapter</font></td>
+</tr>
+</table>
+     
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Connecting to a Database</font></td>
+</tr>
+</table>
+     
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Adding configurability</font></td>
+</tr>
+</table>
+
 </font></td>
-</tr></table>
-<table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">What to do after Phenote
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">I've entered my data, now what?</font></td>
-</tr></table>
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Other Uses for Phenote</font></td>
-</tr></table>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">What to do after Phenote
+     <table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">I've entered my data, now what?</font></td>
+</tr>
+</table>
+     
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Other Uses for Phenote</font></td>
+</tr>
+</table>
+
 </font></td>
-</tr></table>
-<table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Customizing Phenote
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">What is a Configuration?</font></td>
-</tr></table>
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">How To Edit a Configuration File</font></td>
-</tr></table>
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Sample Configuration 1</font></td>
-</tr></table>
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Sample Configuration 2</font></td>
-</tr></table>
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">XML skeleton</font></td>
-</tr></table>
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The &lt;phenote-configuration&gt; Tag</font></td>
-</tr></table>
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The &lt;tab&gt; Tag</font></td>
-</tr></table>
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The &lt;dataadapter&gt; Tag</font></td>
-</tr></table>
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The &lt;master-to-local-config&gt; Tag</font></td>
-</tr></table>
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The &lt;field&gt; Tag</font></td>
-</tr></table>
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The &lt;ontology&gt; Tag</font></td>
-</tr></table>
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The &lt;auto-update-ontologies&gt; Tag</font></td>
-</tr></table>
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The &lt;update-timer&gt; Tag</font></td>
-</tr></table>
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The &lt;term-history&gt; Tag</font></td>
-</tr></table>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Customizing Phenote
+     <table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">What is a Configuration?</font></td>
+</tr>
+</table>
+     
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">How To Edit a Configuration File</font></td>
+</tr>
+</table>
+     
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Sample Configuration 1</font></td>
+</tr>
+</table>
+     
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Sample Configuration 2</font></td>
+</tr>
+</table>
+     
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">XML skeleton</font></td>
+</tr>
+</table>
+     
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">The &lt;phenote-configuration&gt; Tag</font></td>
+</tr>
+</table>
+     
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">The &lt;tab&gt; Tag</font></td>
+</tr>
+</table>
+     
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">The &lt;dataadapter&gt; Tag</font></td>
+</tr>
+</table>
+     
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">The &lt;master-to-local-config&gt; Tag</font></td>
+</tr>
+</table>
+     
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">The &lt;field&gt; Tag</font></td>
+</tr>
+</table>
+     
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">The &lt;ontology&gt; Tag</font></td>
+</tr>
+</table>
+     
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">The &lt;auto-update-ontologies&gt; Tag</font></td>
+</tr>
+</table>
+     
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">The &lt;update-timer&gt; Tag</font></td>
+</tr>
+</table>
+     
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">The &lt;term-history&gt; Tag</font></td>
+</tr>
+</table>
+
 </font></td>
-</tr></table>
-<table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Appendix
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">An Introduction to OBO Ontologies</font></td>
-</tr></table>
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Basic Concepts and Vocabulary</font></td>
-</tr></table>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Appendix
+     <table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">An Introduction to OBO Ontologies</font></td>
+</tr>
+</table>
+     
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Basic Concepts and Vocabulary</font></td>
+</tr>
+</table>
+
 </font></td>
-</tr></table>
-<table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">from OBOedit
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Working with Data Adapters
-          <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The Basic Flat File Interface</font></td>
-</tr></table>
-          <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The OBO Adapter</font></td>
-</tr></table>
-          <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The GO Flat File Adapter</font></td>
-</tr></table>
-          <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The Serial Adapter</font></td>
-</tr></table>
-          <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Custom Data Adapters</font></td>
-</tr></table>
-     </font></td>
-</tr></table>
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Customizing the Interface
-          <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Working with XML Layouts</font></td>
-</tr></table>
-          <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Common Parameters</font></td>
-</tr></table>
-          <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The &lt;glue&gt; Tag</font></td>
-</tr></table>
-          <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The &lt;spacer&gt; Tag</font></td>
-</tr></table>
-          <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The &lt;label&gt; Tag</font></td>
-</tr></table>
-          <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The &lt;box&gt; Tag</font></td>
-</tr></table>
-          <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The &lt;grid&gt; Tag</font></td>
-</tr></table>
-          <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The &lt;panel&gt; Tag</font></td>
-</tr></table>
-          <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The &lt;compactgrid&gt; Tag</font></td>
-</tr></table>
-          <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The &lt;divider&gt; Tag</font></td>
-</tr></table>
-          <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The &lt;tabs&gt; Tag</font></td>
-</tr></table>
-          <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The &lt;window&gt; Tag</font></td>
-</tr></table>
-          <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The &lt;if&gt; Tag</font></td>
-</tr></table>
-          <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The &lt;component&gt; Tag</font></td>
-</tr></table>
-          <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Example Layouts
-               <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The Default Layout</font></td>
-</tr></table>
-          </font></td>
-</tr></table>
-     </font></td>
-</tr></table>
-     <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Customizing OBO-Edit
-          <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The Configuration Plugin</font></td>
-</tr></table>
-     </font></td>
-</tr></table>
-</font></td>
-</tr></table>
-</font></small></body>
+</tr>
+</table>
+
+</font></small>
+</body>
 </html>

Modified: phenote/trunk/doc/phenote-website/help/toc_generator.xsl
===================================================================
--- phenote/trunk/doc/phenote-website/help/toc_generator.xsl	2007-05-30 19:49:19 UTC (rev 653)
+++ phenote/trunk/doc/phenote-website/help/toc_generator.xsl	2007-05-30 19:59:45 UTC (rev 654)
@@ -1,6 +1,6 @@
 <xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform">
 
-<xsl:param name="mapfile" select='/phenote/doc/phenote-website/help/Phenote.jhm'/>
+<xsl:param name="mapfile" select='Phenote.jhm'/>
 
 <xsl:template match="toc">
   <html>

Modified: phenote/trunk/src/java/phenote/gui/HelpMenu.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/HelpMenu.java	2007-05-30 19:49:19 UTC (rev 653)
+++ phenote/trunk/src/java/phenote/gui/HelpMenu.java	2007-05-30 19:59:45 UTC (rev 654)
@@ -8,6 +8,7 @@
 import javax.swing.JMenuItem;
 import javax.swing.JOptionPane;
 import javax.swing.ImageIcon;
+import javax.help.CSH;
 
 import phenote.dataadapter.CharacterListManager;
 import phenote.dataadapter.DataAdapterI;
@@ -18,6 +19,7 @@
 //import phenote.gui.prefswindow.PrefsWindowController; ???
 import phenote.gui.SplashScreen;
 import phenote.main.PhenoteVersion;
+import phenote.main.HelpManager;
 
 class HelpMenu extends JMenu {
 
@@ -38,7 +40,9 @@
     help = new JMenuItem("Phenote Help");
     help.setEnabled(Config.inst().hasDataAdapters());
     help.setActionCommand("help");
-    help.addActionListener(actionListener);
+ 		help.addActionListener(new CSH.DisplayHelpFromSource(HelpManager
+				.getHelpBroker()));
+//    help.addActionListener(actionListener);
     add(help); 
 
     JMenuItem about = new JMenuItem("About");
@@ -57,7 +61,7 @@
     		JOptionPane.showMessageDialog(null, m, "Phenote Help",
     			JOptionPane.INFORMATION_MESSAGE);
     		System.out.println("help selected");	
-    	}
+     	}
     	else if (e.getActionCommand().equals("about")) {
     		//throw up splash screen here.  make sure to make different pic.
 //    	  String m = "This is Phenote v (version here)....[more to come]";

Added: phenote/trunk/src/java/phenote/main/HelpManager.java
===================================================================
--- phenote/trunk/src/java/phenote/main/HelpManager.java	                        (rev 0)
+++ phenote/trunk/src/java/phenote/main/HelpManager.java	2007-05-30 19:59:45 UTC (rev 654)
@@ -0,0 +1,29 @@
+package phenote.main;
+
+import java.io.File;
+
+import javax.help.HelpBroker;
+import javax.help.HelpSet;
+
+public class HelpManager {
+	protected static HelpBroker helpBroker;
+	protected static String helpsetPath = "doc/phenote-website/help/Phenote.hs";
+
+	public static HelpBroker getHelpBroker() {
+		if (helpBroker == null) {
+			HelpSet hs;
+			File docsDir = new File(helpsetPath);
+
+			try {
+				hs = new HelpSet(null, docsDir.toURL());
+			} catch (Exception ee) {
+				System.out.println("HelpSet " + ee.getMessage());
+				System.out.println("HelpSet " + docsDir + " not found");
+				return null;
+			}
+			helpBroker = hs.createHelpBroker();
+		}
+
+		return helpBroker;
+	}
+}
\ No newline at end of file


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Obo-svn-commit] SF.net SVN: obo: [652] phenote/trunk/doc/phenote-website/help/ JavaHelpSearch/

[<nl...@us...>]

Revision: 652
          http://svn.sourceforge.net/obo/?rev=652&view=rev
Author:   nlw
Date:     2007-05-30 12:06:30 -0700 (Wed, 30 May 2007)

Log Message:
-----------
getting rid of this directory because its causing a headache with the help search stuff

Removed Paths:
-------------
    phenote/trunk/doc/phenote-website/help/JavaHelpSearch/


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.