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[Obo-svn-commit] SF.net SVN: obo: [544] phenote/trunk/doc/phenote-website/content

From: <nl...@us...> - 2007-05-02 22:05:39

Revision: 544
          http://svn.sourceforge.net/obo/?rev=544&view=rev
Author:   nlw
Date:     2007-05-02 15:05:39 -0700 (Wed, 02 May 2007)

Log Message:
-----------
adding new phenote 1.2 links

Modified Paths:
--------------
    phenote/trunk/doc/phenote-website/content/howtos/index.shtml
    phenote/trunk/doc/phenote-website/content/software/index.shtml

Modified: phenote/trunk/doc/phenote-website/content/howtos/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/content/howtos/index.shtml	2007-05-02 21:02:47 UTC (rev 543)
+++ phenote/trunk/doc/phenote-website/content/howtos/index.shtml	2007-05-02 22:05:39 UTC (rev 544)
@@ -12,7 +12,7 @@
 <p>
 Phenote is a Java application, which can be launched from the web using "Webstart".  Simply click on the link below, and this  will download the application to your computer and run.  Future clicks on the link should recognize that you've already downloaded the application, and it will simply start the software.</p>
 <p>
-Webstart:  <a href="http://toy.lbl.gov:9010/phenote/1.1/phenote.jnlp">Phenote v1.1</a>
+Webstart:  <a href="http://toy.lbl.gov:9010/phenote/1.2/phenote.jnlp">Phenote v1.1</a>
 </p>
 <p>
 Phenote can also be launched from our <a href="/content/software/">Downloads</a> page.  There you will also find any newer versions under development.
@@ -27,7 +27,7 @@
 
 <h4><a name="install">Downloading and Installing Phenote</a></h4>
 <p>The most up-to-date version of phenote can be checked out with subversion using: <br />
-svn co https://phenote.svn.sourceforge.net/svnroot/obo/phenote/trunk phenote
+svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/trunk phenote
 <br />
 </p>
 <p>

Modified: phenote/trunk/doc/phenote-website/content/software/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/content/software/index.shtml	2007-05-02 21:02:47 UTC (rev 543)
+++ phenote/trunk/doc/phenote-website/content/software/index.shtml	2007-05-02 22:05:39 UTC (rev 544)
@@ -8,7 +8,7 @@
 
 <h2>Phenote Software</h2>
 
-<h3><a name="current">Current Release: 1.1</a> [<a href="http://toy.lbl.gov:9010/phenote/1.1/phenote.jnlp">Webstart</a>] </h3>
+<h3><a name="current">Current Release: 1.2</a> [<a href="http://toy.lbl.gov:9010/phenote/1.2/phenote.jnlp">Webstart</a>] </h3>
 Newest Features:
 <ul>
 <li>Can now search ALL ontologies of a field without having to change the pull-down menu</li>
@@ -29,7 +29,7 @@
 
 <p>
 To download this version with subversion, use the command:
-svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/release-1.1/ phenote
+svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/release-1.2/ phenote
 </p>
 
 <h3><a name="devel">Development Version</a></h3>


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[Obo-svn-commit] SF.net SVN: obo: [543] phenote/trunk/src/java/phenote/datamodel/Ontology. java

From: <mg...@us...> - 2007-05-02 21:02:45

Revision: 543
          http://svn.sourceforge.net/obo/?rev=543&view=rev
Author:   mgibson
Date:     2007-05-02 14:02:47 -0700 (Wed, 02 May 2007)

Log Message:
-----------
took out printlns

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/datamodel/Ontology.java

Modified: phenote/trunk/src/java/phenote/datamodel/Ontology.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/Ontology.java	2007-05-02 20:00:54 UTC (rev 542)
+++ phenote/trunk/src/java/phenote/datamodel/Ontology.java	2007-05-02 21:02:47 UTC (rev 543)
@@ -310,12 +310,12 @@
     // BUG - this includes obsoletes!
     nsQuery.setAllowObsoletes(false);
     sortedTerms = engine.query(nsQuery, false);
-     System.out.println("Non-obsolete: got " + sortedTerms.size()+" namespace hits in " + (System.currentTimeMillis() - time)+ "ms # of namespaces: "+spaces.size()+" printing terms in order: ");
+    //System.out.println("Non-obsolete: got " + sortedTerms.size()+" namespace hits in " + (System.currentTimeMillis() - time)+ "ms # of namespaces: "+spaces.size()+" printing terms in order: ");
 
     nsQuery.setAllowObsoletes(true);
     nsQuery.setAllowNonObsoletes(false);
     sortedObsoleteTerms = engine.query(nsQuery, false);
-     System.out.println("Obsolete: got " + sortedTerms.size()+" namespace hits in " + (System.currentTimeMillis() - time)+ "ms # of namespaces: "+spaces.size()+" printing terms in order: ");
+    //System.out.println("Obsolete: got " + sortedTerms.size()+" namespace hits in " + (System.currentTimeMillis() - time)+ "ms # of namespaces: "+spaces.size()+" printing terms in order: ");
 
     if (hasSlim()) {
       CategoryQuery catQuery = new CategoryQuery(slim);


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[Obo-svn-commit] SF.net SVN: obo: [542] phenote/trunk

From: <mg...@us...> - 2007-05-02 20:01:43

Revision: 542
          http://svn.sourceforge.net/obo/?rev=542&view=rev
Author:   mgibson
Date:     2007-05-02 13:00:54 -0700 (Wed, 02 May 2007)

Log Message:
-----------
fixed obsolete bug - search param for obsolete i broke with new query from obo
session - but john just added obsolete param to query and it grooves now

Modified Paths:
--------------
    phenote/trunk/jars/oboedit.jar
    phenote/trunk/src/java/phenote/datamodel/Ontology.java

Modified: phenote/trunk/jars/oboedit.jar
===================================================================
(Binary files differ)

Modified: phenote/trunk/src/java/phenote/datamodel/Ontology.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/Ontology.java	2007-05-02 18:59:04 UTC (rev 541)
+++ phenote/trunk/src/java/phenote/datamodel/Ontology.java	2007-05-02 20:00:54 UTC (rev 542)
@@ -41,7 +41,7 @@
   private String version;
   private OBOSession oboSession;
   private Collection<OBOClass> sortedTerms; // was List
-  private List<OBOClass> sortedObsoleteTerms;
+  private Collection<OBOClass> sortedObsoleteTerms;
   private List<OBOProperty> sortedRelations;
   private String slim; 
   private String filterOutString;
@@ -184,7 +184,7 @@
     return sortedTerms;
   }
 
-  public List<OBOClass> getSortedObsoleteTerms() {
+  public Collection<OBOClass> getSortedObsoleteTerms() {
     return sortedObsoleteTerms;
   }
 
@@ -297,7 +297,8 @@
     
     // for now just grab 1st namespace as namespacequery only takes 1 namespace
     //Namespace ns = spaces.toArray(new Namespace[0])[0];
-    Query<OBOClass, OBOClass> nsQuery =
+    //Query<OBOClass, OBOClass> nsQuery =
+    NamespaceQuery nsQuery =
       new NamespaceQuery(spaces.toArray(new Namespace[0]));
     // create a new query engine on the session we just loaded
     QueryEngine engine = new QueryEngine(oboSession);
@@ -305,24 +306,27 @@
     // run the namespace query and cache the results
     long time = System.currentTimeMillis();
     //Collection<OBOClass> 
-    // true -> cache result
+    // true -> cache result ??? do we need to cache - i dont think so
     // BUG - this includes obsoletes!
-    sortedTerms = engine.query(nsQuery, true);
-    System.out.println("got " + sortedTerms.size()
-                       + " namespace hits in " + (System.currentTimeMillis() - time)
-                       + "ms # of namespaces: "+spaces.size()+" printing terms in order: ");
+    nsQuery.setAllowObsoletes(false);
+    sortedTerms = engine.query(nsQuery, false);
+     System.out.println("Non-obsolete: got " + sortedTerms.size()+" namespace hits in " + (System.currentTimeMillis() - time)+ "ms # of namespaces: "+spaces.size()+" printing terms in order: ");
 
+    nsQuery.setAllowObsoletes(true);
+    nsQuery.setAllowNonObsoletes(false);
+    sortedObsoleteTerms = engine.query(nsQuery, false);
+     System.out.println("Obsolete: got " + sortedTerms.size()+" namespace hits in " + (System.currentTimeMillis() - time)+ "ms # of namespaces: "+spaces.size()+" printing terms in order: ");
+
     if (hasSlim()) {
       CategoryQuery catQuery = new CategoryQuery(slim);
       time = System.currentTimeMillis();
-      sortedTerms = engine.query(sortedTerms,catQuery, true);
-      System.out.println("Category query (" +slim+ ") got "
-                         + sortedTerms.size()
-                         + " in " + (System.currentTimeMillis() - time) + "ms");
-
+      sortedTerms = engine.query(sortedTerms,catQuery, false);
+//      System.out.println("Category query (" +slim+ ") got "+sortedTerms.size()+" in " + (System.currentTimeMillis() - time) + "ms");
+      // obsoletes?
+      sortedObsoleteTerms = engine.query(sortedObsoleteTerms,catQuery,false);
     }
 
-    for (Namespace n : spaces) System.out.println(n);
+    //for (Namespace n : spaces) System.out.println(n);
     //for (OBOClass o : sortedTerms) System.out.println(o);
     
   }


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[Obo-svn-commit] SF.net SVN: obo: [541] phenote/trunk/doc/phenote-website/phenote.html

From: <mg...@us...> - 2007-05-02 18:59:09

Revision: 541
          http://svn.sourceforge.net/obo/?rev=541&view=rev
Author:   mgibson
Date:     2007-05-02 11:59:04 -0700 (Wed, 02 May 2007)

Log Message:
-----------
dev comment

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

Modified: phenote/trunk/doc/phenote-website/phenote.html
===================================================================
--- phenote/trunk/doc/phenote-website/phenote.html	2007-05-02 18:55:27 UTC (rev 540)
+++ phenote/trunk/doc/phenote-website/phenote.html	2007-05-02 18:59:04 UTC (rev 541)
@@ -240,7 +240,7 @@
 <br>
 
 
-[In development - the bleeding edge if you will:<a href="1.1/phenote.jnlp"> Phenote 1.2</a> coming soon]<br>
+[In development - the bleeding edge if you will:<a href="1.3/phenote.jnlp"> Phenote 1.3</a> coming soon]<br>
 
 
 


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[Obo-svn-commit] SF.net SVN: obo: [540] phenote/trunk

From: <mg...@us...> - 2007-05-02 18:55:28

Revision: 540
          http://svn.sourceforge.net/obo/?rev=540&view=rev
Author:   mgibson
Date:     2007-05-02 11:55:27 -0700 (Wed, 02 May 2007)

Log Message:
-----------
webstart to 1.2

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

Modified: phenote/trunk/build.xml
===================================================================
--- phenote/trunk/build.xml	2007-05-02 18:37:03 UTC (rev 539)
+++ phenote/trunk/build.xml	2007-05-02 18:55:27 UTC (rev 540)
@@ -415,6 +415,27 @@
 <!-- need to test if PHENOTE_VERSION is defined - possible?? -->
     <target name="webstart" depends="webstart-jars,webstart-webpages,copy-jnlps"/>
 
+
+    <target name="webstart-jars"
+            depends="build-all,jar,copy-webstart-jars,sign-webstart-jars"/> 
+
+    <target name="copy-webstart-jars">
+      <echo message="Env Var PHENOTE VERSION is set to ${env.PHENOTE_VERSION}" />
+      <mkdir dir="phenote-webstart/${env.PHENOTE_VERSION}"/>
+      <copy todir="phenote-webstart/${env.PHENOTE_VERSION}/jars">
+        <fileset file="${lib}/*.jar"/>
+      </copy>
+    </target>
+
+    <target name="sign-webstart-jars">
+       <signjar keystore="plumpkey" alias="signFiles"
+                storepass="plumper" keypass="plumper">
+         <fileset dir="phenote-webstart/${env.PHENOTE_VERSION}/jars">
+            <include name="*.jar"/>
+         </fileset>
+       </signjar>
+    </target>   
+
     <target name="webstart-webpages">
       <copy todir="phenote-webstart">
          <!-- fileset file="doc/phenote-website/*.html"/ -->
@@ -436,26 +457,8 @@
       </copy>
     </target>    
 
-    <target name="webstart-jars"
-            depends="build-all,jar,copy-webstart-jars,sign-webstart-jars"/> 
 
-    <target name="copy-webstart-jars">
-      <echo message="Env Var PHENOTE VERSION is set to ${env.PHENOTE_VERSION}" />
-      <mkdir dir="phenote-webstart/${env.PHENOTE_VERSION}"/>
-      <copy todir="phenote-webstart/${env.PHENOTE_VERSION}/jars">
-        <fileset file="${lib}/*.jar"/>
-      </copy>
-    </target>
 
-    <target name="sign-webstart-jars">
-       <signjar keystore="plumpkey" alias="signFiles"
-                storepass="plumper" keypass="plumper">
-         <fileset dir="phenote-webstart/${env.PHENOTE_VERSION}/jars">
-            <include name="*.jar"/>
-         </fileset>
-       </signjar>
-    </target>   
-
     <target name="webstart-just-phenote-jar" depends="build-all,jar">
        <copy file="${lib}/phenote.jar"
              todir="phenote-webstart/${env.PHENOTE_VERSION}/jars"/>

Modified: phenote/trunk/doc/phenote-website/phenote.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote.jnlp	2007-05-02 18:37:03 UTC (rev 539)
+++ phenote/trunk/doc/phenote-website/phenote.jnlp	2007-05-02 18:55:27 UTC (rev 540)
@@ -1,10 +1,10 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <jnlp
 spec="1.0+"
-codebase="http://toy.lbl.gov:9010/phenote/1.1"
+codebase="http://toy.lbl.gov:9010/phenote/1.2"
 href="phenote.jnlp">
 <information>
-	<title>Phenote 1.1</title>
+	<title>Phenote 1.2</title>
 	<vendor>National Center for Biomedial Ontology</vendor>
 	<description>Phenote standalone app via webstart</description>
  	 <!-- Declares that the application can run without


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[Obo-svn-commit] SF.net SVN: obo: [539] phenote/trunk

From: <mg...@us...> - 2007-05-02 18:37:09

Revision: 539
          http://svn.sourceforge.net/obo/?rev=539&view=rev
Author:   mgibson
Date:     2007-05-02 11:37:03 -0700 (Wed, 02 May 2007)

Log Message:
-----------
docs for release

Modified Paths:
--------------
    phenote/trunk/doc/phenote-website/phenote-release-notes.html
    phenote/trunk/doc/phenote-website/phenote.html
    phenote/trunk/src/java/phenote/datamodel/Ontology.java

Modified: phenote/trunk/doc/phenote-website/phenote-release-notes.html
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-release-notes.html	2007-05-02 18:26:05 UTC (rev 538)
+++ phenote/trunk/doc/phenote-website/phenote-release-notes.html	2007-05-02 18:37:03 UTC (rev 539)
@@ -3,13 +3,17 @@
 <head>
 
 
+
   
   
+  
   <meta content="text/html; charset=ISO-8859-1" http-equiv="content-type">
 
 
+
   
   
+  
   <title>Phenote Release Notes</title>
 </head>
 
@@ -17,241 +21,329 @@
 <body>
 
 
+
 <h1>Phenote Release Notes</h1>
 
 
-1.2
-will probably come out in May<br>
 
+1.3
+will probably come out in June<br>
+<br>
+<h2><span style="text-decoration: underline;">1.2</span></h2>
+<a href="1.2/phenote.jnlp">Phenote 1.2</a><br>
+<br>
+
+
 Features:
-Can post-compose with >2 terms <br>
+Can post-compose with &gt;2 terms <br>
+
 Term history display can be toggled on/off <br>
+
 Synonym types display in term info<br>
+
 Obsolete replacements displayed in term info<br>
+
 Search filters moved into menu <br>
+
 Loading splash screen <br>
+Can configure by namespace for ontologies<br>
 
-Bug Fixes:
 
+Bug Fixes: Free text field text not "sticking"
+
 <h2><span style="text-decoration: underline;">1.1</span></h2>
+
 <a href="1.1/phenote.jnlp">Phenote 1.1</a><br>
+
 <br>
+
 March 28, 2007<br>
+
 <br>
+
 Phenote will merge its default configuration with users configuration,
 preserving users changes as well as adding anything new from phenote
 upgrade.<br>
+
 User can select configuration they want to use at initialization or
 subsequently from file menu &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;
 &nbsp;&nbsp;&nbsp; (currently requires phenote restart).<br>
+
 Tab delimited data adapter - thank you nicole!<br>
+
 Beginnings of term history - thank you nicole!<br>
+
 Tabbed main field panel if more than 12 fields.<br>
+
 QueryableDataAdapter interface for adding a database data adapter that
 can be queried. The data adapter specifies queryable fields, which get
 a retrieve button.<br>
+
 Layout improved<br>
+
 Can now search ALL ontologies of a field<br>
+
 Retrieve obo from web if more up to date or no local found<br>
+
 Refactored code for field guis<br>
+
 Ontology chooser reflects current term (bug fix)
 <h2><span style="text-decoration: underline;">1.0</span></h2>
 
+
 <a href="1.0/phenote-flybase.jnlp">Phenote 1.0 for fly</a><br>
 
 
+
 <a href="1.0/phenote-zfin.jnlp">Phenote 1.0 for zfin</a><br>
 
+
 <a href="http://165.124.152.194/db/cgi-bin/dictyBase/curation/phenotypeCuration.pl">DichtyBase
 webby phenote</a><br>
 
+
 <a href="http://reaper.lbl.gov/phenote/html/ncbo.html">Webby
 Phenote(components used by Zfin)</a><br>
 
+
 <br>
 
+
 January 12, 2007<br>
 
+
 <br>
 
+
 The main improvement here is the ability to add any field you like, not
 just E,Q,GC,GT,Pub. In the configured webstarts Stage, Evidence,
 Description, Abnormal, and Absent have been added through this new
 mechanism. This entailed a refactoring of the datamodel.<br>
 
+
 <br>
 
+
 Webby phenote is now using JSP and Spring.<br>
 
+
 <br>
 
+
 There has been some recent work with UVictoria for ontology graph
 visualization. This is coming along well and hopefully will be seen in
 the next release.
 <h2><span style="text-decoration: underline;">0.9</span></h2>
 
 
+
 <a href="0.9/phenote-flybase.jnlp">Phenote 0.9 for fly</a><br>
 
 
+
 <a href="0.9/phenote-zfin.jnlp">Phenote (standalone) 0.9 for zfin</a><br>
 
 
+
 <a href="http://165.124.152.194/web/html/interface.html">DichtyBase
 webby phenote</a><br>
 
 
+
 <br>
 
 
+
 mid November 2006<br>
 
 
+
 <br>
 
 
+
 Undo<br>
 
 
+
 Christian Pich(Zfin) has added a Quartz scheduler to phenote, which
 zfin takes advantage of, to schedule when to check for new obo files.<br>
 
 
+
 Also Christian Pich upgraded the PhenoteServlet to the Spring framework
 - much nicer!<br>
 
 
+
 Synonyms are now returned from auto complete with [syn] and when
 selected the term goes in the field (webby &amp; standalone), obsoletes
 hits with [obs]<br>
 
 
+
 Bulk update &amp; copy in standalone.<br>
 
 
+
 Jim Balhoff(Nescent) changed radio buttons to checkboxes, and file
 saver says save not load and recognizes adapter by file extensions,
 psx-&gt;phenosyntax, .xml -&gt; phenoxml <br>
 
 
+
 Single quotes escaped for javascript fns.<br>
 
 
+
 <h2><span style="text-decoration: underline;">0.8</span></h2>
 
 
+
 <a href="0.8/phenote-flybase.jnlp">Phenote 0.8 for fly.</a><br>
 
 
+
 <a href="0.8/phenote-zfin.jnlp">Phenote (standalone) 0.8 for zfin</a><br>
 
 
+
 <a href="http://165.124.152.194/web/html/interface.html">DichtyBase
 webby phenote</a><br>
 
 
+
 <br>
 
 
+
 10/2/06<br>
 
 
+
 Added post composition to standalone phenote. Logging for both
 webby/servlet &amp; standalone.<br>
 
 
+
 Pheno-xml reader (thanks to Jim Balhoff) and improvements to pheno-xml
 writer (does pub &amp; genetic context)<br>
 
 
+
 Command line reading &amp; writing of phenoxml &amp; phenosyntax.<br>
 
 
+
 Application exits on window exit (unless servlet)<br>
 
 
+
 Can filter out stage terms from zfin anatomy<br>
 
 
+
 <h2><span style="text-decoration: underline;">0.7</span></h2>
 
 
+
 <a href="0.7/phenote-flybase.jnlp">Phenote 0.7 for fly.</a><br>
 
 
+
 <a href="0.7/phenote-zfin.jnlp">Phenote (standalone) 0.7 for zfin</a><br>
 
 
+
 <a href="http://165.124.152.194/web/html/interface.html">DichtyBase
 webby phenote</a><br>
 
 
+
 <br>
 
 
+
 Web: entity chooser, can configure to check for new obo files and load
 them. (These are installed at zfin, if anyone would like to see them
 publicly let me know). Entity field and term info installed into zfin
 phenotype site. term info &amp; completion are scrollable.<br>
 
 
+
 Standalone: can read &amp; write pheno-syntax with ids &amp; term names
 in comments, entity chooser, pub field, use button in term info, sort
 table by clicking on headers, personal config file gets copied out of
 jar, paste mac bug fixed, file load/save remembered,layout fixed<br>
 
 
+
 <br>
 
 
+
 <h2><span style="font-weight: bold;"><span style="text-decoration: underline;">0.6</span></span></h2>
 
 
+
 <a href="http://reaper.lbl.gov/phenote/html/ncbo.html">Webby Phenote
 (0.6)</a><br>
 
 
+
 <a href="0.6/phenote-flybase.jnlp">Phenote 0.6 with fly anatomy</a><br>
 
 
+
 <a href="0.6/phenote-zfin.jnlp">Phenote 0.6 with zebrafish anatomy</a><br>
 
 
+
 <br>
 
 
+
 The main feature of release 0.6 is a webby phenote. This is in its
 extremely early stages (very little functionality and buggy). At this
 point it only does Entity and Quality fields and term info and thats
 it, and even thats buggy, but more coming soon! <br>
 
 
+
 <br>
 
 
+
 Not much new in the stand alone phenote (as Ive been working on the
 webby phenote). Mainly it can write pheno-xml, and it uses the latest
 pato (as of July 28, 2006).<br>
 
 
+
 <h2><span style="font-weight: bold;"><span style="text-decoration: underline;">0.5</span></span></h2>
 
 
+
 <br>
 
 
+
 <a href="0.5/phenote-flybase.jnlp">Phenote 0.5 webstart for FlyBase</a><br>
 
 
+
 <a href="0.5/phenote-zfin.jnlp">Phenote 0.5 webstart for ZFIN</a><br>
 
 
+
 <br>
 
 
+
 5/12/06<br>
 
 
+
 No&nbsp; new additions to the gui here. In preparation for my visit to
 Cambridge/FlyBase, I worked on a FlyBase dataadapter. This is phenote
 first data adapter so I also laid down the foundations for data
@@ -265,30 +357,39 @@
 character strings.<br>
 
 
+
 <h2><span style="text-decoration: underline;">0.4</span></h2>
 
 
+
 <a href="0.4/phenote-flybase.jnlp">0.4 flybase webstart</a><br>
 
 
+
 <a href="0.4/phenote-zfin.jnlp">0.4 zfin webstart</a><br>
 
 
+
 <br>
 
 
+
 4/26/06<br>
 
 
+
 Added Genetic Context field.<br>
 
 
+
 Parent &amp; child terms in term info are now clickable/navigable.<br>
 
 
+
 Links in descriptions are clickable (should bring up default browser)<br>
 
 
+
 Added configuration to configure ontologies &amp; fields. This is
 currently at a devloper level (xml file) not a user level(gui - todo).
 There is a command line argument for which configuration file to use.
@@ -298,16 +399,20 @@
 todo is to have a gui configuration for users.<br>
 
 
+
 Minor bugs:&nbsp; cant delete to 0 rows anymore, synonym search
 duplicates taken out<br>
 
 
+
 <br>
 
 
+
 Dev stuff:<br>
 
 
+
 Refactored for configuration &amp; adding field. Made the internal code
 much more generic for adding new fields from configuration, got rid of
 a lot of hard wiring.&nbsp; Part of this was instituring
@@ -316,187 +421,244 @@
 plop a web gui on top of the current phenote model &amp; controller.<br>
 
 
+
 Renamed Phenotype to Character. Added Character interface CharacterI.<br>
 
 
+
 Added tests to test suite.<br>
 
 
+
 <br>
 
 
+
 <h2><span style="text-decoration: underline;">0.3.1 (CToL)<br>
 
 
+
 </span></h2>
 
 
+
 <a href="0.3.1/phenote-webstart.jnlp">0.3.1 phenote webstart (for CToL)</a><br>
 
 
+
 <br>
 
 
+
 4/7/06<br>
 
 
+
 0.3.1 is identical to 0.3 except that it has ontologies for CToL
 (fish evolution group). In particular it uses a fish taxonomy<br>
 
 
+
 ontology for the id (in this taxonomy) choosing. On the todo is the
 ability to configure ontologies, but not there yet, so for now need to
 hardwire with seaparate jar file. This clearly makes the todo item a
 bit more pressing.<br>
 
 
+
 <h2><span style="text-decoration: underline;">0.3</span></h2>
 
 
+
 <a href="0.3/phenote-webstart.jnlp">0.3 phenote webstart</a><br>
 
 
+
 <br>
 
 
+
 4/7/06<br>
 
 
+
 Release for NESCent fish eveolution meeting. No major new functionality
 here. Cleaned up and fixed a lot of the bugs in 0.2, which was rather
 buggy.<br>
 
 
+
 <br>
 
 
+
 Completion terms now sorted alphabeitcally.<br>
 
 
+
 Obsolete is now in addition to regular terms, not in lieu of.<br>
 
 
+
 Filtering out attribute values (todo: change to actually filter in
 values)<br>
 
 
+
 Html formatting of term info (todo: make terms selectable)<br>
 
 
+
 Children relations are in term info<br>
 
 
+
 Term info layout greatly improved<br>
 
 
+
 Term info in scroller<br>
 
 
+
 Border with label around term info<br>
 
 
+
 Put definition at end of term info<br>
 
 
+
 <br>
 
 
+
 Fixed bugs:<br>
 
 
+
 Backspace in ontology combo box<br>
 
 
+
 Selection of item in comp list causing exception, not going in term box<br>
 
 
+
 No terms with just 1 char<br>
 
 
+
 Popup was staying up after selection<br>
 
 
+
 <br>
 
 
+
 Dev stuff:<br>
 
 
+
 Test suite added! (todo: add more tests)<br>
 
 
+
 Migrated to jdk 1.5 (which caused some of the bugs above)<br>
 
 
+
 Ant file made build.xml.<br>
 
 
+
 CompletionList refactored into Ontology (prompted by sorting)<br>
 
 
+
 <br>
 
 
+
 <br>
 
 
+
 <h2><span style="text-decoration: underline;">0.2</span></h2>
 
 
+
 <a href="0.2/phenote-webstart.jnlp">0.2 phenote webstart</a><br>
 
 
+
 <br>
 
 
+
 3/27/06<br>
 
 
+
 Added the ability to do term completion on Synonyms, Definitions, and
 Obsoletes. Also can mouse over a term in a completion list and get
 information about it in the term info text area. <br>
 
 
+
 <br>
 
 
+
 The term info area needs a lot of work.<br>
 
 
+
 TODO:<br>
 
 
+
 &nbsp;layout, scrollbar, border w title, ordering &amp; lumping parents
 &amp; children, formatting. <br>
 
 
+
 Also perhaps have children &amp; parents be clickable in some fashion
 either html-like clickable text or as buttons.<br>
 
 
+
 Theres also bugs in term completion boxes. If you start backspacing it
 gets wacky for instance.<br>
 
 
+
 <br>
 
 
+
 <a href="0.2/phenote-webstart.jnlp"><br>
 
 
+
 </a>
 <h2><span style="text-decoration: underline;">0.1</span></h2>
 
 
+
 <a href="0.1/phenote-webstart.jnlp">0.1 phenote webstart</a><br>
 
 
+
 <br>
 
 
+
 &nbsp;3/1/06<br>
 
 
+
 0.1 was the initial phenote release (known briefly as the plumper at
 the time).&nbsp; It just had a genotype, anatomy and pato fields, where
 anatomy and pato did term completion (just on term names) with there
@@ -505,20 +667,26 @@
 limited functionality was demo'd at the cbio meeting 3/3/06 at Stanford.<br>
 
 
+
 <br>
 
 
+
 <a href="0.2/phenote-webstart.jnlp"></a><br>
 
 
+
 <br>
 
 
+
 <br>
 
 
+
 <a href="phenote.html">Phenote main page</a><br>
 
 
+
 </body>
 </html>

Modified: phenote/trunk/doc/phenote-website/phenote.html
===================================================================
--- phenote/trunk/doc/phenote-website/phenote.html	2007-05-02 18:26:05 UTC (rev 538)
+++ phenote/trunk/doc/phenote-website/phenote.html	2007-05-02 18:37:03 UTC (rev 539)
@@ -8,6 +8,7 @@
 
 
 
+
   
   
   
@@ -15,6 +16,7 @@
   
   
   
+  
   <meta content="text/html; charset=ISO-8859-1" http-equiv="content-type">
 
 
@@ -23,6 +25,7 @@
 
 
 
+
   
   
   
@@ -30,6 +33,7 @@
   
   
   
+  
   <title>Phenote</title>
 </head>
 
@@ -42,6 +46,7 @@
 
 
 
+
 <h1 style="text-align: left;"><span style="font-weight: bold;"></span>Phenote<br>
 
 
@@ -50,6 +55,7 @@
 
 
 
+
 </h1>
 
 
@@ -58,6 +64,7 @@
 
 
 
+
 <br>
 
 
@@ -66,6 +73,7 @@
 
 
 
+
 Phenote is a tool to annotate phenotypes using the Entity Quality
 paradigm. It takes advantage of
 ontologies. It uses term completion to allow curators quick access to
@@ -77,6 +85,7 @@
 
 
 
+
 <br>
 
 
@@ -84,10 +93,14 @@
 
 
 
-<a href="1.1/phenote.jnlp">Phenote 1.1</a><br>
 
+<a href="1.2/phenote.jnlp">Phenote 1.2</a><br>
 <br>
 
+
+<br>
+
+
 After phenote downloads the java jar files (takes a while) it will ask
 you what configuration you would like to use, fly, zfin, human,worm....<br>
 
@@ -97,12 +110,14 @@
 
 
 
+
 <br>
 
+
 Recent addditions include the ability to update config while preserving
 your changes, change config, tab delimited format, tabbed field panel,
 retrieve ontologies from web, retrieve from field to database, search
-ALL ontols, add any field you like, post compose terms, bulk
+ALL ontols, add any field you like, post compose terms with multiple diff, bulk
 update, undo, spring framework, and
 synonyms now are shown in the completion list.<br>
 
@@ -112,6 +127,7 @@
 
 
 
+
 <br>
 
 
@@ -120,6 +136,7 @@
 
 
 
+
 Zebrafish requires
 components of phenote(to plug into their non-public
 website), not a full web app. Here is a proof of concept of some of
@@ -132,6 +149,7 @@
 
 
 
+
 <br>
 
 
@@ -140,6 +158,7 @@
 
 
 
+
 <a href="http://reaper.lbl.gov/phenote/html/ncbo.html">Webby
 Phenote(components used by Zfin)</a><br>
 
@@ -149,6 +168,7 @@
 
 
 
+
 <br>
 
 
@@ -157,6 +177,7 @@
 
 
 
+
 Webby phenote is a collaboration with Sohel Merchant at dictyBase.
 Here is what they have done:<br>
 
@@ -166,6 +187,7 @@
 
 
 
+
 <br>
 
 
@@ -174,6 +196,7 @@
 
 
 
+
 <a href="http://165.124.152.194/db/cgi-bin/dictyBase/curation/phenotypeCuration.pl">DictyBase
 webby phenote</a><br>
 
@@ -183,6 +206,7 @@
 
 
 
+
 <br>
 
 
@@ -191,6 +215,7 @@
 
 
 
+
 <br>
 
 
@@ -199,6 +224,7 @@
 
 
 
+
 We are doing these
 releases to get feedback. Please report any bugs (ideally through the <a href="https://sourceforge.net/tracker/?group_id=76834&amp;atid=887913">bug
 tracker</a>) and let us know what you
@@ -210,8 +236,10 @@
 
 
 
+
 <br>
 
+
 [In development - the bleeding edge if you will:<a href="1.1/phenote.jnlp"> Phenote 1.2</a> coming soon]<br>
 
 
@@ -220,6 +248,7 @@
 
 
 
+
 <h4>Phenote links:<br>
 
 
@@ -228,6 +257,7 @@
 
 
 
+
 </h4>
 
 
@@ -236,6 +266,7 @@
 
 
 
+
 <a href="https://lists.sourceforge.net/lists/listinfo/obo-phenote">Phenote
 email list</a><br>
 
@@ -245,6 +276,7 @@
 
 
 
+
 <a href="https://sourceforge.net/tracker/?group_id=76834&amp;atid=887913">Phenote
 bug tracker</a><br>
 
@@ -254,6 +286,7 @@
 
 
 
+
 <a href="https://lists.sourceforge.net/lists/listinfo/obo-phenote-bug-tracker">Bug
 tracker email list</a><br>
 
@@ -263,6 +296,7 @@
 
 
 
+
 <a href="https://sourceforge.net/svn/?group_id=76834">Phenote source
 code (obo sourceforge svn)</a><br>
 
@@ -272,6 +306,7 @@
 
 
 
+
 <a href="https://lists.sourceforge.net/lists/listinfo/obo-svn-commit">Phenote
 svn commit email list</a><br>
 
@@ -281,6 +316,7 @@
 
 
 
+
 <a href="http://wiki.dictybase.org/dictywiki/index.php/Phenotype_Curation_Tool_Documentation#Usage">Dicty
 webby phenote wiki developer docs</a><br>
 
@@ -290,11 +326,14 @@
 
 
 
+
 <a href="http://www.bioontology.org/wiki-internal/index.php/Phenotype_Annotation_Tool">Phenote
 ncbo internal wiki (ncbo folk only)</a><br>
 
 
+
 <a href="developer-docs/dataadapter.html">Phenote dataadapter developer doc</a><br>
+
 <a href="developer-docs/developer-docs.html">More developer docs</a><br>
 
 
@@ -303,6 +342,7 @@
 
 
 
+
 <br>
 
 
@@ -311,6 +351,7 @@
 
 
 
+
 <a href="phenote-release-notes.html">Phenote Release Notes and old
 webstart releases</a><br>
 
@@ -320,6 +361,7 @@
 
 
 
+
 <br>
 
 
@@ -328,6 +370,7 @@
 
 
 
+
 If the Phenote webstart link fails to do anything, then there are
 probably problems
 with webstart and/or java(has to be jdk 1.5). Take a look at the&nbsp; <a href="webstart-troubleshooting.html">webstart troubleshooting</a><br>
@@ -338,6 +381,7 @@
 
 
 
+
 page.<br>
 
 
@@ -346,6 +390,7 @@
 
 
 
+
 <br>
 
 
@@ -354,6 +399,7 @@
 
 
 
+
 Click here for <a href="phenote-java-requirements.html">phenote java
 requirements</a><br>
 
@@ -363,6 +409,7 @@
 
 
 
+
 <br>
 
 
@@ -371,6 +418,7 @@
 
 
 
+
 <br>
 
 
@@ -379,6 +427,7 @@
 
 
 
+
 <br>
 
 
@@ -387,6 +436,7 @@
 
 
 
+
 Old releases: <br>
 
 
@@ -395,6 +445,8 @@
 
 
 
+
+<a href="1.1/phenote.jnlp">Phenote 1.1</a><br>
 <a href="1.0/phenote-flybase.jnlp">Phenote 1.0 for fly</a><br>
 
 
@@ -403,6 +455,7 @@
 
 
 
+
 <a href="1.0/phenote-zfin.jnlp">Phenote 1.0 for zfin</a><br>
 
 
@@ -410,11 +463,13 @@
 
 
 
+
 <a href="1.0/phenote-human.jnlp">Phenote 1.0 for human</a><br>
 
 
 
 
+
 <br>
 
 
@@ -423,6 +478,7 @@
 
 
 
+
 <a href="0.9/phenote-flybase.jnlp">Phenote 0.9 for fly</a><br>
 
 
@@ -431,6 +487,7 @@
 
 
 
+
 <a href="0.9/phenote-zfin.jnlp">Phenote (standalone) 0.9 for zfin</a><br>
 
 
@@ -438,6 +495,7 @@
 
 
 
+
 <br>
 
 
@@ -445,6 +503,7 @@
 
 
 
+
 <a href="0.8/phenote-flybase.jnlp">Phenote 0.8 for fly.</a><br>
 
 
@@ -453,6 +512,7 @@
 
 
 
+
 <a href="0.8/phenote-zfin.jnlp">Phenote (standalone) 0.8 for zfin</a><br>
 
 
@@ -461,6 +521,7 @@
 
 
 
+
 <br>
 
 
@@ -469,6 +530,7 @@
 
 
 
+
 <a href="0.7/phenote-flybase.jnlp">Phenote 0.7 for fly.</a><br>
 
 
@@ -477,6 +539,7 @@
 
 
 
+
 <a href="0.7/phenote-zfin.jnlp">Phenote (standalone) 0.7 for zfin</a><br>
 
 
@@ -485,6 +548,7 @@
 
 
 
+
 <br>
 
 
@@ -493,6 +557,7 @@
 
 
 
+
 <a href="0.6/phenote-flybase.jnlp">Phenote 0.6 with fly anatomy</a><br>
 
 
@@ -501,6 +566,7 @@
 
 
 
+
 <br>
 
 
@@ -509,6 +575,7 @@
 
 
 
+
 <a href="0.6/phenote-zfin.jnlp">Phenote 0.6 with zebrafish anatomy</a><br>
 
 
@@ -517,6 +584,7 @@
 
 
 
+
 <br>
 
 
@@ -525,6 +593,7 @@
 
 
 
+
 <a href="0.5/phenote-flybase.jnlp">Phenote 0.5 webstart for FlyBase</a><br>
 
 
@@ -533,6 +602,7 @@
 
 
 
+
 <br>
 
 
@@ -541,6 +611,7 @@
 
 
 
+
 <a href="0.5/phenote-zfin.jnlp">Phenote 0.5 webstart for ZFIN</a><br>
 
 
@@ -549,6 +620,7 @@
 
 
 
+
 <br>
 
 
@@ -557,6 +629,7 @@
 
 
 
+
 <a href="0.4/phenote-flybase.jnlp">Phenote 0.4 webstart for FlyBase</a><br>
 
 
@@ -565,6 +638,7 @@
 
 
 
+
 <br>
 
 
@@ -573,6 +647,7 @@
 
 
 
+
 <a href="0.4/phenote-zfin.jnlp">Phenote 0.4 webstart for ZFIN</a><br>
 
 
@@ -581,6 +656,7 @@
 
 
 
+
 <br>
 
 
@@ -589,6 +665,7 @@
 
 
 
+
 <a href="0.3.1/phenote-webstart.jnlp">Phenote for CToL group (0.3.1)</a>&nbsp;&nbsp;
 (a special release for the CToL group that uses fish
 taxonomy)<br>
@@ -599,6 +676,7 @@
 
 
 
+
 <br>
 
 
@@ -607,6 +685,7 @@
 
 
 
+
 <a href="0.3/phenote-webstart.jnlp">Phenote 0.3</a><br>
 
 
@@ -615,6 +694,7 @@
 
 
 
+
 <br>
 
 
@@ -623,6 +703,7 @@
 
 
 
+
 <a href="0.2/phenote-webstart.jnlp">Phenote 0.2</a><br>
 
 
@@ -631,6 +712,7 @@
 
 
 
+
 <br>
 
 
@@ -639,6 +721,7 @@
 
 
 
+
 <a href="0.1/phenote-webstart.jnlp">Phenote 0.1</a><br>
 
 
@@ -647,6 +730,7 @@
 
 
 
+
 <br>
 
 
@@ -655,6 +739,7 @@
 
 
 
+
 <br>
 
 
@@ -663,5 +748,6 @@
 
 
 
+
 </body>
 </html>

Modified: phenote/trunk/src/java/phenote/datamodel/Ontology.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/Ontology.java	2007-05-02 18:26:05 UTC (rev 538)
+++ phenote/trunk/src/java/phenote/datamodel/Ontology.java	2007-05-02 18:37:03 UTC (rev 539)
@@ -306,6 +306,7 @@
     long time = System.currentTimeMillis();
     //Collection<OBOClass> 
     // true -> cache result
+    // BUG - this includes obsoletes!
     sortedTerms = engine.query(nsQuery, true);
     System.out.println("got " + sortedTerms.size()
                        + " namespace hits in " + (System.currentTimeMillis() - time)


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[Obo-svn-commit] SF.net SVN: obo: [538] phenote/trunk/src/java/phenote/gui/SettingsMenu.java

From: <nl...@us...> - 2007-05-02 18:26:04

Revision: 538
          http://svn.sourceforge.net/obo/?rev=538&view=rev
Author:   nlw
Date:     2007-05-02 11:26:05 -0700 (Wed, 02 May 2007)

Log Message:
-----------
moved the search parameters directly into the settings menu item

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

Modified: phenote/trunk/src/java/phenote/gui/SettingsMenu.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/SettingsMenu.java	2007-05-02 18:17:01 UTC (rev 537)
+++ phenote/trunk/src/java/phenote/gui/SettingsMenu.java	2007-05-02 18:26:05 UTC (rev 538)
@@ -14,7 +14,7 @@
   private final int ITEM_PLAIN = 0;  // Item types
   private final int ITEM_CHECK = 1;
   private final int ITEM_RADIO = 2;
-  private JMenu menuSearchFilter;
+//  private JMenu menuSearchFilter;
   private JMenuItem menuSearchFilterTerm;
   private JMenuItem menuSearchFilterSynonym;
   private JMenuItem menuSearchFilterDefinition;
@@ -32,26 +32,29 @@
   private void init() {
 
     // Build the search types sub-menu
-    menuSearchFilter = new JMenu("Search Filters");
-    menuSearchFilter.setMnemonic('F');
+//    menuSearchFilter = new JMenu("Search Filters");
+//    menuSearchFilter.setMnemonic('F');
 
     //set defaults
     getSearchParams().setParam(SearchFilterType.TERM, true); //default Term = on
     getSearchParams().setParam(SearchFilterType.SYN, true); //default Syn = on
+    getSearchParams().setParam(SearchFilterType.DEF, false); //default Def = off
+    getSearchParams().setParam(SearchFilterType.OBS, false); //default Obs = off
+    
 
     // Create property items based on status
-    menuSearchFilterTerm = CreateMenuItem(menuSearchFilter, ITEM_CHECK,
-            SearchFilterType.TERM.getName(), null, 'T', "Look for partial matches within Term Names",
-            getSearchParams().getParam(SearchFilterType.TERM));
-    menuSearchFilterSynonym = CreateMenuItem(menuSearchFilter, ITEM_CHECK,
+    menuSearchFilterTerm = CreateMenuItem(this, ITEM_CHECK,
+        SearchFilterType.TERM.getName(), null, 'T', "Look for partial matches within Term Names",
+        getSearchParams().getParam(SearchFilterType.TERM));
+    menuSearchFilterSynonym = CreateMenuItem(this, ITEM_CHECK,
             SearchFilterType.SYN.getName(), null, 'S', "Look for partial matches within Synonyms of Terms",
             getSearchParams().getParam(SearchFilterType.SYN));
-    menuSearchFilterDefinition = CreateMenuItem(menuSearchFilter, ITEM_CHECK,
+    menuSearchFilterDefinition = CreateMenuItem(this, ITEM_CHECK,
             SearchFilterType.DEF.getName(), null, 'D', "Look for partial matches within the Definition of Terms",
             getSearchParams().getParam(SearchFilterType.DEF));
 
-    addSeparator();  //obs are in a class by themselves.
-    menuSearchFilterObsolete = CreateMenuItem(menuSearchFilter, ITEM_CHECK,
+//    addSeparator();  //obs are in a class by themselves.
+    menuSearchFilterObsolete = CreateMenuItem(this, ITEM_CHECK,
             SearchFilterType.OBS.getName(), null, 'O', "Look for partial matches within Obsolete Term Names",
             getSearchParams().getParam(SearchFilterType.OBS));
 
@@ -61,7 +64,7 @@
 ////    searchSettings.setEnabled(Config.inst().hasDataAdapters());
 //    searchSettings.setActionCommand("search");
 //    searchSettings.addActionListener(actionListener);
-    add(menuSearchFilter);
+//    add(menuSearchFilter);
 
     addSeparator();
 


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[Obo-svn-commit] SF.net SVN: obo: [537] phenote/trunk/src/java/phenote/main/PhenoteVersion. java

From: <mg...@us...> - 2007-05-02 18:16:59

Revision: 537
          http://svn.sourceforge.net/obo/?rev=537&view=rev
Author:   mgibson
Date:     2007-05-02 11:17:01 -0700 (Wed, 02 May 2007)

Log Message:
-----------
release 1.2

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/main/PhenoteVersion.java

Modified: phenote/trunk/src/java/phenote/main/PhenoteVersion.java
===================================================================
--- phenote/trunk/src/java/phenote/main/PhenoteVersion.java	2007-05-02 00:26:50 UTC (rev 536)
+++ phenote/trunk/src/java/phenote/main/PhenoteVersion.java	2007-05-02 18:17:01 UTC (rev 537)
@@ -9,7 +9,7 @@
 
   //private static final float MAJOR_VERSION_NUM = 0.8f;
   //private static final float SUB_VERSION_NUM = .3f;
-  private static final String VERSION = "1.2-beta3"; // ??
+  private static final String VERSION = "1.2 release"; // ??
   // type is "dev" or "release" 
   //private static final String type = " dev"; // "release"
 
@@ -19,7 +19,7 @@
   }
 
   public static Date getDateOfVersion(){
-    GregorianCalendar cal = new GregorianCalendar(2007, GregorianCalendar.MARCH, 16);
+    GregorianCalendar cal = new GregorianCalendar(2007, GregorianCalendar.MAY, 2);
     return cal.getTime();
   }
 


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[Obo-svn-commit] SF.net SVN: obo: [536] phenote/trunk/doc/phenote-website/help

From: <nl...@us...> - 2007-05-02 00:26:48

Revision: 536
          http://svn.sourceforge.net/obo/?rev=536&view=rev
Author:   nlw
Date:     2007-05-01 17:26:50 -0700 (Tue, 01 May 2007)

Log Message:
-----------
modifying the tab delimited help page

Modified Paths:
--------------
    phenote/trunk/doc/phenote-website/help/Phenote.hs
    phenote/trunk/doc/phenote-website/help/Phenote.hs.bak
    phenote/trunk/doc/phenote-website/help/Phenote.prj
    phenote/trunk/doc/phenote-website/help/PhenoteTOC.xml
    phenote/trunk/doc/phenote-website/help/html/Changing_your_Configuration.htm
    phenote/trunk/doc/phenote-website/help/html/Introduction_to_Adapters.htm
    phenote/trunk/doc/phenote-website/help/html/Loading___Saving.htm
    phenote/trunk/doc/phenote-website/help/html/The_Tab_Delimited_Adapter.htm
    phenote/trunk/doc/phenote-website/help/html/What_is_Phenote_.htm
    phenote/trunk/doc/phenote-website/help/report/report.htm

Modified: phenote/trunk/doc/phenote-website/help/Phenote.hs
===================================================================
--- phenote/trunk/doc/phenote-website/help/Phenote.hs	2007-05-01 23:27:18 UTC (rev 535)
+++ phenote/trunk/doc/phenote-website/help/Phenote.hs	2007-05-02 00:26:50 UTC (rev 536)
@@ -9,7 +9,7 @@
 
 <!-- maps -->
 <maps>
-    <homeID>FirstTopic</homeID>
+    <homeID>What_is_Phenote</homeID>
     <mapref location="Phenote.jhm" />
 </maps>
 

Modified: phenote/trunk/doc/phenote-website/help/Phenote.hs.bak
===================================================================
--- phenote/trunk/doc/phenote-website/help/Phenote.hs.bak	2007-05-01 23:27:18 UTC (rev 535)
+++ phenote/trunk/doc/phenote-website/help/Phenote.hs.bak	2007-05-02 00:26:50 UTC (rev 536)
@@ -9,7 +9,7 @@
 
 <!-- maps -->
 <maps>
-    <homeID>FirstTopic</homeID>
+    <homeID>What_is_Phenote</homeID>
     <mapref location="Phenote.jhm" />
 </maps>
 

Modified: phenote/trunk/doc/phenote-website/help/Phenote.prj
===================================================================
--- phenote/trunk/doc/phenote-website/help/Phenote.prj	2007-05-01 23:27:18 UTC (rev 535)
+++ phenote/trunk/doc/phenote-website/help/Phenote.prj	2007-05-02 00:26:50 UTC (rev 536)
@@ -1,12 +1,12 @@
 [Settings]
-html=
+html=html
 images=images
 ccs=htmlhelp.css
 i=phenote.hhk
 last_path=C:\Documents and Settings\Nicole\Desktop\phenote-helper\html
 prefix list=IDH_,
 preview=1
-css=C:\Documents and Settings\Nicole\Desktop\phenote-helper\javahelp.css
+css=C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\javahelp.css
 t=PhenoteTOC.xml
 web_dhtml=1
 web_indxpg=PhenoteWebIndex.html

Modified: phenote/trunk/doc/phenote-website/help/PhenoteTOC.xml
===================================================================
--- phenote/trunk/doc/phenote-website/help/PhenoteTOC.xml	2007-05-01 23:27:18 UTC (rev 535)
+++ phenote/trunk/doc/phenote-website/help/PhenoteTOC.xml	2007-05-02 00:26:50 UTC (rev 536)
@@ -29,7 +29,7 @@
      <tocitem text="Loading &amp; Saving" target="Loading___Saving"/>
      <tocitem text="The PhenoXML adapter" target="Data_Formats"/>
      <tocitem text="The PhenoSyntax Adapter" target="The_PhenoSyntax_Adapter"/>
-     <tocitem text="The Tab-Value Adapter" target="The_tag_value_adapter"/>
+     <tocitem text="The Tag-Value Adapter" target="The_tag_value_adapter"/>
      <tocitem text="The Tab-Delimited Adapter" target="The_Tab_Delimited_Adapter"/>
 </tocitem>
 <tocitem text="Creating Annotations">

Modified: phenote/trunk/doc/phenote-website/help/html/Changing_your_Configuration.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/Changing_your_Configuration.htm	2007-05-01 23:27:18 UTC (rev 535)
+++ phenote/trunk/doc/phenote-website/help/html/Changing_your_Configuration.htm	2007-05-02 00:26:50 UTC (rev 536)
@@ -7,7 +7,17 @@
 </HEAD>
 <BODY BGCOLOR=#ffffff>
 <H1>Changing your Configuration</H1>
+<P>If you would like to select a different Phenote configuration, this can be 
+accomplished from inside of Phenote.</P>
+<P>Select the menu item Settings-&gt;Configuration...</P>
+<P>This will popup a menu of choices, with many configurations that come 
+pre-packaged with phenote.&nbsp; The radio button next to your currently loaded 
+configuration will be highlighted:</P>
 <P><IMG hspace=0 src="../images/change_config.png" 
 border=0></P>
+<P>To select the new configuration, click on the radio button next to the 
+configuration of your choice, and click OK.&nbsp; </P>
+<P>You will need to quit and restart Phenote for the changes to take effect.</P>
+<P>&nbsp;</P>
 </BODY>
 </HTML>
\ No newline at end of file

Modified: phenote/trunk/doc/phenote-website/help/html/Introduction_to_Adapters.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/Introduction_to_Adapters.htm	2007-05-01 23:27:18 UTC (rev 535)
+++ phenote/trunk/doc/phenote-website/help/html/Introduction_to_Adapters.htm	2007-05-02 00:26:50 UTC (rev 536)
@@ -11,10 +11,10 @@
 <STRONG>data adapters.</STRONG> Data adapters are little code modules that know 
 how to get data into or out of Phenote. A data adapter may read data from a 
 formatted file on a hard drive, write data to a relational database, or download 
-a file from CVS.</P>
+a file from SVN/CVS.</P>
 <P>Every file format/database schema/whatever is different. Many 
 data adapters have complex options, particularly when saving data. Phenote has 
-three data adapters built-in:&nbsp; PhenoXML, PhenoSyntax, and a tab-delimited format.f&nbsp; (And soon will have 
+three data adapters built-in:&nbsp; PhenoXML, PhenoSyntax, and a tab-delimited format.&nbsp; (And soon will have 
 an OBO-edit 1.3 annotation format adapter.)</P>
 <P>This section provides a general overview of how to load and save, and then an 
 in-depth discussion of each of Phenote's built-in data 

Modified: phenote/trunk/doc/phenote-website/help/html/Loading___Saving.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/Loading___Saving.htm	2007-05-01 23:27:18 UTC (rev 535)
+++ phenote/trunk/doc/phenote-website/help/html/Loading___Saving.htm	2007-05-02 00:26:50 UTC (rev 536)
@@ -31,7 +31,7 @@
 operating under the "demo" configuration.&nbsp; However, since then, you 
 switched your configuration to "my_new_config".&nbsp; Since these configurations 
 might not match, you are unable to load in the data.&nbsp; Try <A 
-href="Changing_your_Configuration.htm">changing your configuration</a>              
+href="Changing_your_Configuration.htm">changing your configuration</A>              
                
         back to "demo" and 
 then retry loading the annotation file.&nbsp;</p>
@@ -61,5 +61,12 @@
                
             
      &nbsp;</p>
+<P>Warning:&nbsp; If you give an extension to a filename that is not valid for 
+that selected format, you may encounter problems during loading.&nbsp; For 
+example, if you save your file as "example.xls" but the format you tell it to 
+save as is PhenoSyntax, then when the file is loaded it might try to use the 
+tab-delimited adapter instead of the phenosyntax adapter, resulting in your data 
+hangin' in space.&nbsp; Be sure to use the appropriate combination of extension 
+and adapter.</P>
 </body>
 </html>
\ No newline at end of file

Modified: phenote/trunk/doc/phenote-website/help/html/The_Tab_Delimited_Adapter.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/The_Tab_Delimited_Adapter.htm	2007-05-01 23:27:18 UTC (rev 535)
+++ phenote/trunk/doc/phenote-website/help/html/The_Tab_Delimited_Adapter.htm	2007-05-02 00:26:50 UTC (rev 536)
@@ -7,6 +7,37 @@
 </HEAD>
 <BODY BGCOLOR=#ffffff>
 <H1>The Tab-Delimited Adapter</H1>
+<P>Purpose:&nbsp; For loading and saving annotation data in a 
+easy-to-read format.</P>
+<P>Extensions:&nbsp; <STRONG>.xls</STRONG> 
+<STRONG>.tab</STRONG></P>
+<P>Notes:&nbsp; These files can be directly imported to external spreadsheet 
+applications like Microsoft Excel.</P>
+<P>You must make sure that you are using the same Phenote configuration when 
+loading a file as was used to save it.&nbsp; For example, if you had "demo" 
+configuration loaded when you saved your data file, then you must have the demo 
+configuration loaded when you try opening your data file.&nbsp; If, in the 
+meantime, you have changed your configuration, you must change it back.</P>
 <P>&nbsp;</P>
+<P>When saving your annotations, the first line of the file will contain the 
+column headings.&nbsp; These column headings are derived from the field names 
+specified in the configuration file.</P>
+<P>&nbsp;</P>
+<P>There is a field called "Pub" which&nbsp;is a free text field.&nbsp; This 
+will translate to a single column in the file, with the column heading of 
+Pub.</P>
+<P>&nbsp;</P>
+<P>There is a field called "Entity" which is an 
+ontology-based field.&nbsp; This will translate into two columns in the 
+file.&nbsp; The column headings will take the name, Entity, and follow it with 
+ID and Name, respectively.&nbsp; In this case, you'd have the column headings 
+"Entity ID" and "Entity Name".&nbsp; The former will contain the ID of the term 
+from the OBO file, and the latter will contain the TermName from the obo 
+file.&nbsp; These are both placed in the file as a conveniece to read 
+for&nbsp;the user.</P>
+<P>Upon reading the file, only the ID column is used and the 
+"Name" column is skipped over; column headings are thrown out.</P>
+<P>You can generate your own tab-delimited files from 
+external applications so long as they follow this format.</P>
 </BODY>
 </HTML>
\ No newline at end of file

Modified: phenote/trunk/doc/phenote-website/help/html/What_is_Phenote_.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/What_is_Phenote_.htm	2007-05-01 23:27:18 UTC (rev 535)
+++ phenote/trunk/doc/phenote-website/help/html/What_is_Phenote_.htm	2007-05-02 00:26:50 UTC (rev 536)
@@ -7,9 +7,9 @@
 </head>
 <body bgcolor="#ffffff">
 <h1>What is Phenote?</h1>
-<P>Phenote&nbsp;is a general-purpose open source platform-independent 
-application to facilitate data annotation&nbsp;using&nbsp;ontologies.</P>
-<P>Originally developed as a literature curation tool for biomedical phenotype 
+<p>Phenote&nbsp;is a general-purpose open source platform-independent 
+application to facilitate data annotation&nbsp;using&nbsp;ontologies.</p>
+<p>Originally developed as a literature curation tool for biomedical phenotype 
 annotation, Phenote can be customized to suit any user-specified domain 
 requiring ontology-based annotation. The all-in-one interface allows users to 
 quickly search and view corresponding metadata for relevant ontology terms 
@@ -17,10 +17,10 @@
 the data annotations in a spreadsheet-like window. Data recorded with Phenote 
 can be ported to any external application or database using one of its built-in 
 data adapters, or by plugging in a custom data adapter generated with the 
-API.</P>
-<P>Phenote development is funded by the National Center for Biomedical Ontology 
-(<A href="http://www.bioontology.org">www.bioontology.org</A>), which is an NIH 
+API.</p>
+<p>Phenote development is funded by the National Center for Biomedical Ontology 
+(<a href="http://www.bioontology.org">www.bioontology.org</a>), which is an NIH 
 Roadmap Intiative through the National Centers for Biomedical 
-Computing.</P>
+Computing.</p>
 </body>
 </html>
\ No newline at end of file

Modified: phenote/trunk/doc/phenote-website/help/report/report.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/report/report.htm	2007-05-01 23:27:18 UTC (rev 535)
+++ phenote/trunk/doc/phenote-website/help/report/report.htm	2007-05-02 00:26:50 UTC (rev 536)
@@ -7,7 +7,7 @@
 <i>To print this report, right click and choose "Print" from the pop-up context menu.</i><p>
 <p><i> You can use the Contents, Topics, and Index tabs on the left to navigate within the report.</i>
 <p><i> This HTML file and also a tab-delimited text file are available in the \report subdirectory below your project directory.</i>
-<p>&nbsp;</p><p><b>Report Date/Time:</b> 4/30/2007 5:17:02 PM
+<p>&nbsp;</p><p><b>Report Date/Time:</b> 5/1/2007 4:57:09 PM
 <p><b>Total Number of Topics: </b> 163
 <p><b>Number of Index Entries: </b> 0
 <p>&nbsp;</p>
@@ -15,7 +15,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Adding configurability</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Adding_configurability</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Adding_configurability.htm" target=_blank>html\Adding_configurability.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Adding_configurability.htm" target=_blank>html\Adding_configurability.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -23,7 +23,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Adding New Relationships</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Adding_New_Relationships</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Adding_New_Relationships.htm" target=_blank>html\Adding_New_Relationships.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Adding_New_Relationships.htm" target=_blank>html\Adding_New_Relationships.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -31,7 +31,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Adding New Terms</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Adding_New_Terms</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Adding_New_Terms.htm" target=_blank>html\Adding_New_Terms.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Adding_New_Terms.htm" target=_blank>html\Adding_New_Terms.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -39,7 +39,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Advantages to Annotation with Ontolgies</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Advantages_to_Annotation_with_Ontolgies</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Advantages_to_Annotation_with_Ontolgies.htm" target=_blank>html\Advantages_to_Annotation_with_Ontolgies.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Advantages_to_Annotation_with_Ontolgies.htm" target=_blank>html\Advantages_to_Annotation_with_Ontolgies.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -47,7 +47,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> An Introduction to OBO Ontologies</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> An_Introduction_to_OBO_Ontologies</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\An_Introduction_to_OBO_Ontologies.htm" target=_blank>html\An_Introduction_to_OBO_Ontologies.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\An_Introduction_to_OBO_Ontologies.htm" target=_blank>html\An_Introduction_to_OBO_Ontologies.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -55,7 +55,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Annotation Spreadsheet</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Annotation_Spreadsheet</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Annotation_Spreadsheet.htm" target=_blank>html\Annotation_Spreadsheet.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Annotation_Spreadsheet.htm" target=_blank>html\Annotation_Spreadsheet.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -63,7 +63,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Assigning New Roots</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Assigning_New_Roots</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Assigning_New_Roots.htm" target=_blank>html\Assigning_New_Roots.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Assigning_New_Roots.htm" target=_blank>html\Assigning_New_Roots.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -71,7 +71,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Assigning Replacement Terms</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Assigning_Replacement_Terms</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Assigning_Replacement_Terms.htm" target=_blank>html\Assigning_Replacement_Terms.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Assigning_Replacement_Terms.htm" target=_blank>html\Assigning_Replacement_Terms.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -79,7 +79,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Backtick Expressions</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Backtick_Expressions</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Backtick_Expressions.htm" target=_blank>html\Backtick_Expressions.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Backtick_Expressions.htm" target=_blank>html\Backtick_Expressions.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -87,7 +87,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Basic Concepts and Vocabulary</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Basic_Concepts_and_Vocabulary</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Basic_Concepts_and_Vocabulary.htm" target=_blank>html\Basic_Concepts_and_Vocabulary.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Basic_Concepts_and_Vocabulary.htm" target=_blank>html\Basic_Concepts_and_Vocabulary.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -95,7 +95,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Bugs and Troubleshooting</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Bugs_and_Troubleshooting</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Bugs_and_Troubleshooting.htm" target=_blank>html\Bugs_and_Troubleshooting.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Bugs_and_Troubleshooting.htm" target=_blank>html\Bugs_and_Troubleshooting.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -103,7 +103,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Building a Filter</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Building_a_Filter</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Building_a_Filter.htm" target=_blank>html\Building_a_Filter.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Building_a_Filter.htm" target=_blank>html\Building_a_Filter.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -111,7 +111,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Building Filters</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Building_Filters</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Building_Filters.htm" target=_blank>html\Building_Filters.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Building_Filters.htm" target=_blank>html\Building_Filters.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -119,7 +119,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Changing Link Attributes</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Changing_Link_Attributes</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Changing_Link_Attributes.htm" target=_blank>html\Changing_Link_Attributes.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Changing_Link_Attributes.htm" target=_blank>html\Changing_Link_Attributes.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -127,7 +127,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Changing Relationship Types</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Changing_Relationship_Types</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Changing_Relationship_Types.htm" target=_blank>html\Changing_Relationship_Types.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Changing_Relationship_Types.htm" target=_blank>html\Changing_Relationship_Types.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -135,7 +135,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Changing your Configuration</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Changing_your_Configuration</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Changing_your_Configuration.htm" target=_blank>html\Changing_your_Configuration.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Changing_your_Configuration.htm" target=_blank>html\Changing_your_Configuration.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -143,7 +143,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Classes</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Classes</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Classes.htm" target=_blank>html\Classes.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Classes.htm" target=_blank>html\Classes.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -151,7 +151,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Cloning</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Cloning</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Cloning.htm" target=_blank>html\Cloning.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Cloning.htm" target=_blank>html\Cloning.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -159,7 +159,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Common Parameters</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Common_Parameters</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Common_Parameters.htm" target=_blank>html\Common_Parameters.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Common_Parameters.htm" target=_blank>html\Common_Parameters.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -167,7 +167,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Compound Filtering</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Compound_Filtering</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Compound_Filtering.htm" target=_blank>html\Compound_Filtering.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Compound_Filtering.htm" target=_blank>html\Compound_Filtering.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -175,7 +175,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Connecting to a Database</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Connecting_to_a_Database</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Connecting_to_a_Database.htm" target=_blank>html\Connecting_to_a_Database.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Connecting_to_a_Database.htm" target=_blank>html\Connecting_to_a_Database.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -183,7 +183,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Creating Your Own GO Slim in OBO-Edit</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Creating_Your_Own_GO_Slim_in_OBO_Edit</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Creating_Your_Own_GO_Slim_in_OBO_Edit.htm" target=_blank>html\Creating_Your_Own_GO_Slim_in_OBO_Edit.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Creating_Your_Own_GO_Slim_in_OBO_Edit.htm" target=_blank>html\Creating_Your_Own_GO_Slim_in_OBO_Edit.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -191,7 +191,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Cross Products</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Cross_Products</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Cross_Products.htm" target=_blank>html\Cross_Products.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Cross_Products.htm" target=_blank>html\Cross_Products.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -199,7 +199,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Cross Products By Hand</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Cross_Products_By_Hand</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Cross_Products_By_Hand.htm" target=_blank>html\Cross_Products_By_Hand.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Cross_Products_By_Hand.htm" target=_blank>html\Cross_Products_By_Hand.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -207,7 +207,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Cross Products in the Text Editor</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Cross_Products_in_the_Text_Editor</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Cross_Products_in_the_Text_Editor.htm" target=_blank>html\Cross_Products_in_the_Text_Editor.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Cross_Products_in_the_Text_Editor.htm" target=_blank>html\Cross_Products_in_the_Text_Editor.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -215,7 +215,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Custom Data Adapters</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Custom_Data_Adapters</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Custom_Data_Adapters.htm" target=_blank>html\Custom_Data_Adapters.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Custom_Data_Adapters.htm" target=_blank>html\Custom_Data_Adapters.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -223,7 +223,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Dangling Intersection Check</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Dangling_Intersection_Check</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Dangling_Intersection_Check.htm" target=_blank>html\Dangling_Intersection_Check.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Dangling_Intersection_Check.htm" target=_blank>html\Dangling_Intersection_Check.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -231,7 +231,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Data Entry</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Data_Entry</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Data_Entry.htm" target=_blank>html\Data_Entry.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Data_Entry.htm" target=_blank>html\Data_Entry.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -239,7 +239,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Data Formats</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Data_Formats</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Data_Formats.htm" target=_blank>html\Data_Formats.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Data_Formats.htm" target=_blank>html\Data_Formats.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -247,7 +247,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Dbxref Check</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Dbxref_Check</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Dbxref_Check.htm" target=_blank>html\Dbxref_Check.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Dbxref_Check.htm" target=_blank>html\Dbxref_Check.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -255,7 +255,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Definition Check</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Definition_Check</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Definition_Check.htm" target=_blank>html\Definition_Check.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Definition_Check.htm" target=_blank>html\Definition_Check.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -263,7 +263,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Deleting</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Deleting</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Deleting.htm" target=_blank>html\Deleting.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Deleting.htm" target=_blank>html\Deleting.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -271,7 +271,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Destroying</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Destroying</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Destroying.htm" target=_blank>html\Destroying.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Destroying.htm" target=_blank>html\Destroying.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -279,7 +279,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Disjointedness Check</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Disjointedness_Check</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Disjointedness_Check.htm" target=_blank>html\Disjointedness_Check.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Disjointedness_Check.htm" target=_blank>html\Disjointedness_Check.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -287,7 +287,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Editing</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Editing</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Editing.htm" target=_blank>html\Editing.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Editing.htm" target=_blank>html\Editing.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -295,7 +295,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Editing Obsoletes</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Editing_Obsoletes</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Editing_Obsoletes.htm" target=_blank>html\Editing_Obsoletes.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Editing_Obsoletes.htm" target=_blank>html\Editing_Obsoletes.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -303,7 +303,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Example Layouts</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Example_Layouts</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Example_Layouts.htm" target=_blank>html\Example_Layouts.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Example_Layouts.htm" target=_blank>html\Example_Layouts.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -311,7 +311,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Example Scripts</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Example_Scripts</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Example_Scripts.htm" target=_blank>html\Example_Scripts.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Example_Scripts.htm" target=_blank>html\Example_Scripts.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -319,7 +319,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Exiting Phenote</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Exiting_Phenote</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Exiting_Phenote.htm" target=_blank>html\Exiting_Phenote.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Exiting_Phenote.htm" target=_blank>html\Exiting_Phenote.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -327,7 +327,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Expression Syntax</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Expression_Syntax</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Expression_Syntax.htm" target=_blank>html\Expression_Syntax.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Expression_Syntax.htm" target=_blank>html\Expression_Syntax.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -335,7 +335,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Filtering</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Filtering</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Filtering.htm" target=_blank>html\Filtering.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Filtering.htm" target=_blank>html\Filtering.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -343,7 +343,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Filters</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Filters</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Filters.htm" target=_blank>html\Filters.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Filters.htm" target=_blank>html\Filters.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -351,7 +351,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Frequently Asked Questions</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Frequently_Asked_Questions</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Frequently_Asked_Questions.htm" target=_blank>html\Frequently_Asked_Questions.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Frequently_Asked_Questions.htm" target=_blank>html\Frequently_Asked_Questions.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -359,7 +359,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Getting Phenote Started</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Getting_Phenote_Started</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Getting_Phenote_Started.htm" target=_blank>html\Getting_Phenote_Started.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Getting_Phenote_Started.htm" target=_blank>html\Getting_Phenote_Started.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -367,7 +367,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Getting Started</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Getting_Started</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Getting_Started.htm" target=_blank>html\Getting_Started.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Getting_Started.htm" target=_blank>html\Getting_Started.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -375,7 +375,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Global Filters & Renderers</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Global_Filters___Renderers</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Global_Filters___Renderers.htm" target=_blank>html\Global_Filters___Renderers.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Global_Filters___Renderers.htm" target=_blank>html\Global_Filters___Renderers.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -383,7 +383,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> How Do I Find Terms Without an is_a Parent?</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> How_Do_I_Find_Terms_Without_an_is_a_Parent_</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\How_Do_I_Find_Terms_Without_an_is_a_Parent_.htm" target=_blank>html\How_Do_I_Find_Terms_Without_an_is_a_Parent_.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\How_Do_I_Find_Terms_Without_an_is_a_Parent_.htm" target=_blank>html\How_Do_I_Find_Terms_Without_an_is_a_Parent_.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -391,7 +391,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> How Do I Make a "Slim" Ontology?</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> How_Do_I_Make_a__Slim__Ontology_</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\How_Do_I_Make_a__Slim__Ontology_.htm" target=_blank>html\How_Do_I_Make_a__Slim__Ontology_.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\How_Do_I_Make_a__Slim__Ontology_.htm" target=_blank>html\How_Do_I_Make_a__Slim__Ontology_.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -399,7 +399,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> How Do I Not Search Obsoletes?</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> How_Do_I_Not_Search_Obsoletes_</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\How_Do_I_Not_Search_Obsoletes_.htm" target=_blank>html\How_Do_I_Not_Search_Obsoletes_.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\How_Do_I_Not_Search_Obsoletes_.htm" target=_blank>html\How_Do_I_Not_Search_Obsoletes_.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -407,7 +407,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> How Do I Search a Specific Ontology?</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> How_Do_I_Search_a_Specific_Ontology_</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\How_Do_I_Search_a_Specific_Ontology_.htm" target=_blank>html\How_Do_I_Search_a_Specific_Ontology_.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\How_Do_I_Search_a_Specific_Ontology_.htm" target=_blank>html\How_Do_I_Search_a_Specific_Ontology_.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -415,7 +415,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> How Do I Spell Check?</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> How_Do_I_Spell_Check_</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\How_Do_I_Spell_Check_.htm" target=_blank>html\How_Do_I_Spell_Check_.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\How_Do_I_Spell_Check_.htm" target=_blank>html\How_Do_I_Spell_Check_.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -423,7 +423,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> How ID Generation Works</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> How_ID_Generation_Works</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\How_ID_Generation_Works.htm" target=_blank>html\How_ID_Generation_Works.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\How_ID_Generation_Works.htm" target=_blank>html\How_ID_Generation_Works.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -431,7 +431,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> How OBO-Edit Understands Histories</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> How_OBO_Edit_Understands_Histories</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\How_OBO_Edit_Understands_Histories.htm" target=_blank>html\How_OBO_Edit_Understands_Histories.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\How_OBO_Edit_Understands_Histories.htm" target=_blank>html\How_OBO_Edit_Understands_Histories.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -439,7 +439,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> How To Edit a Configuration File</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> How_To_Edit_a_Configuration_File</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\How_To_Edit_a_Configuration_File.htm" target=_blank>html\How_To_Edit_a_Configuration_File.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\How_To_Edit_a_Configuration_File.htm" target=_blank>html\How_To_Edit_a_Configuration_File.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -447,7 +447,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Instances</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Instances</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Instances.htm" target=_blank>html\Instances.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Instances.htm" target=_blank>html\Instances.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -455,7 +455,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Intersections</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Intersections</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Intersections.htm" target=_blank>html\Intersections.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Intersections.htm" target=_blank>html\Intersections.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -463,7 +463,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Introduction to Adapters</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Introduction_to_Adapters</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Introduction_to_Adapters.htm" target=_blank>html\Introduction_to_Adapters.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Introduction_to_Adapters.htm" target=_blank>html\Introduction_to_Adapters.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -471,7 +471,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Introduction to Cross Products</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Introduction_to_Cross_Products</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Introduction_to_Cross_Products.htm" target=_blank>html\Introduction_to_Cross_Products.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Introduction_to_Cross_Products.htm" target=_blank>html\Introduction_to_Cross_Products.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -479,7 +479,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Introduction to Expressions</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Introduction_to_Expressions</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Introduction_to_Expressions.htm" target=_blank>html\Introduction_to_Expressions.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Introduction_to_Expressions.htm" target=_blank>html\Introduction_to_Expressions.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -487,7 +487,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Introduction to Plugins</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Introduction_to_Plugins</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Introduction_to_Plugins.htm" target=_blank>html\Introduction_to_Plugins.htm</a></td></tr>
+<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-help-docs\html\Introduction_to_Plugins.htm" target=_blank>html\Introduction_to_Plugins.htm</a></td></tr>
 <tr><td bgcolor=#FFFFFF><b>Index Keywords:</b> </td></tr>
 <tr><td bgcolor=#FFFFFF><b>Status:</b> Not Specified<br><b>Notes: </b></td></tr>
 </table><br>
@@ -495,7 +495,7 @@
 <table border=0 width=100% cellpadding=4 cellspacing=1 bgcolor=#808080>
 <tr><td bgcolor=#D7D7D7><b>Topic Title:</b> Introduction to Verification</td></tr>
 <tr><td bgcolor=#FFFFFF><b>MapID:</b> Introduction_to_Verification</td></tr>
-<tr><td bgcolor=#FFFFFF><b>File Path:</b> <a href="C:\Documents and Settings\Nicole\Desktop\phenote-helper\html\Introduction_to_Verification.htm"...
 
[truncated message content]

[Obo-svn-commit] SF.net SVN: obo: [535] phenote/trunk/doc/phenote-website/help/html/ Term_Info.htm

From: <nl...@us...> - 2007-05-01 23:27:16

Revision: 535
          http://svn.sourceforge.net/obo/?rev=535&view=rev
Author:   nlw
Date:     2007-05-01 16:27:18 -0700 (Tue, 01 May 2007)

Log Message:
-----------
changed a file; testing svn on windows on my mac

Modified Paths:
--------------
    phenote/trunk/doc/phenote-website/help/html/Term_Info.htm

Modified: phenote/trunk/doc/phenote-website/help/html/Term_Info.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/Term_Info.htm	2007-05-01 18:58:04 UTC (rev 534)
+++ phenote/trunk/doc/phenote-website/help/html/Term_Info.htm	2007-05-01 23:27:18 UTC (rev 535)
@@ -1,44 +1,44 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
-<HTML>
-<HEAD>
-<META NAME="GENERATOR" CONTENT="Solutionsoft HelpBreeze JavaHelp Edition">
-<TITLE>Term Info</TITLE>
-<LINK REL="stylesheet" TYPE="text/css" HREF=../javahelp.css>
-</HEAD>
-<BODY BGCOLOR=#ffffff>
-<H1>Term Info</H1>
-<P><IMG hspace=0 src="../images/term_info.png" 
-border=0></P>
-<P>&nbsp;</P>
-<P>The Term Info window is a text-based ontology browser.&nbsp; This window will 
+<html>
+<head>
+<meta name="GENERATOR" content="Solutionsoft HelpBreeze JavaHelp Edition">
+<title>Term Info</title>
+<link rel="stylesheet" type="text/css" href="../javahelp.css">
+</head>
+<body bgcolor="#ffffff">
+<h1>Term Info</h1>
+<p><IMG hspace=0 src="../images/term_info.png" 
+border=0></p>
+<p>&nbsp;</p>
+<p>The Term Info window is a text-based ontology browser.&nbsp; This window will 
 display any relevant metadata about an ontology term selected in the Data Entry 
-frame, such as:</P>
-<P><STRONG>Ontology</STRONG> - the name of the Ontology from which the term 
-comes, in this case the Biological Process ontology from the Gene Ontology.</P>
-<P><STRONG>Term</STRONG> - the actual name of the term</P>
-<P><STRONG>ID</STRONG> - the official alphanumeric identifier for the 
+frame, such as:</p>
+<p><strong>Ontology</strong> - the name of the Ontology from which the term 
+comes, in this case the Biological Process ontology from the Gene Ontology.</p>
+<p><strong>Term</strong> - the actual name of the term</p>
+<p><strong>ID</strong> - the official alphanumeric identifier for the 
 term.&nbsp; It is often presented in the id:####### format.&nbsp; The id part 
 before the colon usually reflects the abbreviation for the ontology and should 
-be unique.</P>
-<P><STRONG>Synonyms</STRONG> - many terms have synonyms, especially between 
+be unique.</p>
+<p><strong>Synonyms</strong> - many terms have synonyms, especially between 
 different communities.&nbsp; If no synonyms are present, this section will not 
-appear.</P>
-<P><STRONG>Definition</STRONG> - the definition for the term is displayed</P>
-<P>&nbsp;</P>
-<H3>Navigating an Ontology in Term Info</H3>
-<P>Each term in an ontology is related to at least one other term.&nbsp; Those 
+appear.</p>
+<p><strong>Definition</strong> - the definition for the term is displayed</p>
+<p>&nbsp;</p>
+<h3>Navigating an Ontology in Term Info</h3>
+<p>Each term in an ontology is related to at least one other term.&nbsp; Those 
 terms, and their relationships are displayed in the Term Info window as 
-well.&nbsp; In the example above, the term <EM>sensory perception of sound</EM> 
-<STRONG>is a</STRONG> child of <EM>sensory perception of mechanical 
-stimulus</EM>.&nbsp; Each term is&nbsp;a hyperlink.&nbsp; Clicking on these 
+well.&nbsp; In the example above, the term <em>sensory perception of sound</em> 
+<strong>is a</strong> child of <em>sensory perception of mechanical 
+stimulus</em>.&nbsp; Each term is&nbsp;a hyperlink.&nbsp; Clicking on these 
 terms will load that new information into the Term Info window.&nbsp; If I were 
-to select the <EM>sensory perception of mechanical stimulus</EM> link, the Term 
-Info window would look like:</P>
-<P><IMG hspace=0 src="../Images/term_info_linked.png" border=0></P>
-<P>and if&nbsp;I move the slider to see the rest of the window, I will see a 
-link from where we just came:&nbsp;<EM>sensory perception of sound</EM></P>
-<P><IMG height=0 hspace=0 src="../Images/term_info_linked2.png" width=0 
-border=0><IMG hspace=0 src="../Images/term_info_linked2.png" 
-border=0></P>
-</BODY>
-</HTML>
\ No newline at end of file
+to select the <em>sensory perception of mechanical stimulus</em> link, the Term 
+Info window would look like:</p>
+<p><IMG hspace=0 src="../images/term_info_linked.png" border=0></p>
+<p>and if&nbsp;I move the slider to see the rest of the window, I will see a 
+link from where we just came:&nbsp;<em>sensory perception of sound</em></p>
+<p><IMG height=0 hspace=0 src="../images/term_info_linked2.png" width=0 
+border=0><IMG hspace=0 src="../images/term_info_linked2.png" 
+border=0></p>
+</body>
+</html>
\ No newline at end of file


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[Obo-svn-commit] SF.net SVN: obo: [534] obo-database/trunk/sql/obd-core-schema.sql

From: <cmu...@us...> - 2007-05-01 18:58:03

Revision: 534
          http://svn.sourceforge.net/obo/?rev=534&view=rev
Author:   cmungall
Date:     2007-05-01 11:58:04 -0700 (Tue, 01 May 2007)

Log Message:
-----------


Modified Paths:
--------------
    obo-database/trunk/sql/obd-core-schema.sql

Modified: obo-database/trunk/sql/obd-core-schema.sql
===================================================================
--- obo-database/trunk/sql/obd-core-schema.sql	2007-05-01 18:13:12 UTC (rev 533)
+++ obo-database/trunk/sql/obd-core-schema.sql	2007-05-01 18:58:04 UTC (rev 534)
@@ -6,7 +6,6 @@
 	uid VARCHAR NOT NULL DEFAULT '__internal:_' || nextval('node_node_uid_seq'),
 	label VARCHAR,
 	uri VARCHAR,
-        -- one of: C, R or I. Can also be unknown
         metatype        CHAR(1),
 	is_anonymous BOOLEAN NOT NULL DEFAULT 'f',
 	is_transitive BOOLEAN NOT NULL DEFAULT 'f',


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[Obo-svn-commit] SF.net SVN: obo: [533] phenote/trunk/src/java/phenote

From: <mg...@us...> - 2007-05-01 18:13:11

Revision: 533
          http://svn.sourceforge.net/obo/?rev=533&view=rev
Author:   mgibson
Date:     2007-05-01 11:13:12 -0700 (Tue, 01 May 2007)

Log Message:
-----------
fixed bug where if select a row free text just entered was going in
seems to still be a problem for multi select

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/gui/field/CharFieldGui.java
    phenote/trunk/src/java/phenote/gui/field/FreeTextField.java
    phenote/trunk/src/java/phenote/gui/selection/CharSelectionEvent.java
    phenote/trunk/src/java/phenote/gui/selection/SelectionManager.java
    phenote/trunk/src/java/phenote/main/PhenoteVersion.java

Modified: phenote/trunk/src/java/phenote/gui/field/CharFieldGui.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/CharFieldGui.java	2007-05-01 16:49:37 UTC (rev 532)
+++ phenote/trunk/src/java/phenote/gui/field/CharFieldGui.java	2007-05-01 18:13:12 UTC (rev 533)
@@ -435,20 +435,29 @@
 
   private class FieldCharSelectListener implements CharSelectionListener {
     public void charactersSelected(CharSelectionEvent e) {
-      // if multi select then clear out fields - alternatively could do first char
-      // or only show fields that are all same? 
-      if (e.isMultiSelect()) {
-        setGuiForMultiSelect();
-        return;
-      }
-      if (e.getChars() == null || e.getChars().isEmpty()) return;
-      updateGuiOnly = true; // selection should not cause an edit/transaction!
-      setValueFromChar(e.getChars().get(0));
-      updateGuiOnly = false;
+      CharFieldGui.this.charactersSelected(e);
     }
   }
 
+  /** FreeTextField both overrides and calls this as it needs to edit model
+      on focus change */
+  protected void charactersSelected(CharSelectionEvent e) {
+    // if multi select then clear out fields - alternatively could do first char
+    // or only show fields that are all same? 
+    if (e.isMultiSelect()) {
+      setGuiForMultiSelect();
+      return;
+    }
+    if (e.getChars() == null || e.getChars().isEmpty()) return;
+    updateGuiOnly = true; // selection should not cause an edit/transaction!
+    setValueFromChar(e.getChars().get(0));
+    updateGuiOnly = false;
+  }
 
+  /** overridden by FreeTextField, for selection to tell free text field that
+      focus was lost before selection goes through and rubs out change */
+  //protected void focusLost() {}
+
 //   /** I think post-comp should only be closeable if its empty (in expand collapse
 //    inframe case - now window) */ --> TermCompList
 //   private class PostCompListener implements ActionListener {

Modified: phenote/trunk/src/java/phenote/gui/field/FreeTextField.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/FreeTextField.java	2007-05-01 16:49:37 UTC (rev 532)
+++ phenote/trunk/src/java/phenote/gui/field/FreeTextField.java	2007-05-01 18:13:12 UTC (rev 533)
@@ -28,6 +28,7 @@
 //import phenote.datamodel.CharFieldEnum; // phase out
 import phenote.edit.CompoundTransaction;
 import phenote.edit.EditManager;
+import phenote.gui.selection.CharSelectionEvent;
 import phenote.gui.selection.SelectionManager;
 
 // should this be a subclass of charfieldGui? maybe?
@@ -136,31 +137,45 @@
   private class FreeFocusListener implements FocusListener {
     public void focusGained(FocusEvent e) {}
     public void focusLost(FocusEvent e) {
-      updateModel();
+      //updateModel();
+      FreeTextField.this.focusLost();
     }
   }
 
+  protected void focusLost() { updateModel(); }
+
+  /** update model using currently selected chars */
   private void updateModel() {
+    List<CharacterI> chars = getSelectedChars();
+    updateModel(chars);
+  }
+
+  private void updateModel(List<CharacterI> chars) {
     // if only updating gui (multi select clear) then dont update model
     if (updateGuiOnly()) return;
     if (!guiTextHasChanged) return; // gui hasnt been edited
-    List<CharacterI> chars = getSelectedChars();
+
     String v = getText();
     //CompoundTransaction ct = new CompoundTransaction(chars,getCharFieldEnum(),v);
     CompoundTransaction ct = CompoundTransaction.makeUpdate(chars,getCharField(),v);
     EditManager.inst().updateModel(this,ct);//charFieldGui,ct); // cfg source
     guiTextHasChanged = false; // reset flag
+
   }
+
+  /** selection (from table) comes in before focus lost! update model with
+      previous selection */
+  protected void charactersSelected(CharSelectionEvent e) {
+    if (e.hasPreviouslySelectedChars())
+      updateModel(e.getPreviouslySelectedChars());
+    super.charactersSelected(e); // CharFieldGui
+  }
   
   private List<CharacterI> getSelectedChars() {
     return SelectionManager.inst().getSelectedChars();
   }
   
-  //private CharFieldEnum getCharFieldEnum() { return charFieldGui.getCharFieldEnum(); }
-  
-  
 
-
   /** This is where it is noted that the gui has been edited, only update  
     the model on focus change if the gui has been actually edited */
   private class TextFieldDocumentListener implements DocumentListener {

Modified: phenote/trunk/src/java/phenote/gui/selection/CharSelectionEvent.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/selection/CharSelectionEvent.java	2007-05-01 16:49:37 UTC (rev 532)
+++ phenote/trunk/src/java/phenote/gui/selection/CharSelectionEvent.java	2007-05-01 18:13:12 UTC (rev 533)
@@ -8,14 +8,22 @@
 public class CharSelectionEvent extends EventObject {
 
   private List<CharacterI> charList;
+  private List<CharacterI> previouslySelectedChars;
 
-  CharSelectionEvent(Object source, List<CharacterI> chars) {
+  CharSelectionEvent(Object source, List<CharacterI> chars, List<CharacterI> prev) {
     super(source);
     this.charList= chars;
+    this.previouslySelectedChars = prev;
   }
 
   public List<CharacterI> getChars() { return charList; }
 
   public boolean isMultiSelect() { return charList.size() > 1; }
 
+  public boolean hasPreviouslySelectedChars() {
+    return previouslySelectedChars != null && !previouslySelectedChars.isEmpty();
+  }
+
+  public List<CharacterI> getPreviouslySelectedChars() { return previouslySelectedChars; }
+
 }

Modified: phenote/trunk/src/java/phenote/gui/selection/SelectionManager.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/selection/SelectionManager.java	2007-05-01 16:49:37 UTC (rev 532)
+++ phenote/trunk/src/java/phenote/gui/selection/SelectionManager.java	2007-05-01 18:13:12 UTC (rev 533)
@@ -18,6 +18,7 @@
   // phase out for list...
   private CharacterI selectedCharacter;
   private List<CharacterI> selectedCharList;
+  private List<CharacterI> previouslySelectedChars;
 
   public static SelectionManager inst() {
     if (singleton == null) singleton = new SelectionManager();
@@ -29,6 +30,8 @@
     charListenerList = new ArrayList<CharSelectionListener>(4);
   }
 
+  // TERM SELECTION
+
   public void addTermSelectionListener(TermSelectionListener l) {
     termListenerList.add(l);
   }
@@ -39,27 +42,27 @@
 	  boolean isMouseOver = false;
 	  boolean isHyperlink = true;
 	  TermSelectionEvent e = makeTermEvent(source, oboClass, l, isMouseOver, isHyperlink);
-	  fireSelect(e);
+	  fireTermSelect(e);
   }
   
   public void selectMouseOverTerm(Object source, OBOClass oboClass,UseTermListener l) {
 	boolean isMouseOver = true;
 	boolean isHyperlink = false;
     TermSelectionEvent e = makeTermEvent(source,oboClass,l,isMouseOver,isHyperlink);
-    fireSelect(e);
+    fireTermSelect(e);
   }
   
   public void selectTerm(Object source,OBOClass oboClass, boolean isHyperlink) {
 	boolean isMouseOver = false;
 //	System.out.println("ishyperlink="+isHyperlink);
 	TermSelectionEvent e = makeTermEvent(source,oboClass,null,isMouseOver, isHyperlink);
-    if (!isHyperlink) fireSelect(e);
+    if (!isHyperlink) fireTermSelect(e);
   }
 
-  private void fireSelect(TermSelectionEvent e) {
+  private void fireTermSelect(TermSelectionEvent e) {
     Iterator<TermSelectionListener> it = termListenerList.iterator();
     while(it.hasNext())
-      it.next().termSelected(e);   
+      it.next().termSelected(e);
   }
   
   
@@ -69,6 +72,8 @@
     return new TermSelectionEvent(src,oc,l,mouse,link);
   }
 
+  // CHARACTER SELECTION
+
   public CharacterI getFirstSelectedCharacter() {
     if (selectedCharList == null || selectedCharList.isEmpty())
       return null; // ex?
@@ -89,9 +94,10 @@
   public void selectCharacters(Object src, List<CharacterI> chars) {
     selectedCharList = chars;
     //if (chars.size() == 1) { selectCharacter(src,chars.get(0)); return; }
-    CharSelectionEvent e = new CharSelectionEvent(src,chars);
+    CharSelectionEvent e = new CharSelectionEvent(src,chars,previouslySelectedChars);
     for (CharSelectionListener l : charListenerList)
       l.charactersSelected(e);
+    previouslySelectedChars = selectedCharList;
   }
  
 

Modified: phenote/trunk/src/java/phenote/main/PhenoteVersion.java
===================================================================
--- phenote/trunk/src/java/phenote/main/PhenoteVersion.java	2007-05-01 16:49:37 UTC (rev 532)
+++ phenote/trunk/src/java/phenote/main/PhenoteVersion.java	2007-05-01 18:13:12 UTC (rev 533)
@@ -9,7 +9,7 @@
 
   //private static final float MAJOR_VERSION_NUM = 0.8f;
   //private static final float SUB_VERSION_NUM = .3f;
-  private static final String VERSION = "1.2-beta2"; // ??
+  private static final String VERSION = "1.2-beta3"; // ??
   // type is "dev" or "release" 
   //private static final String type = " dev"; // "release"
 


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[Obo-svn-commit] SF.net SVN: obo: [532] phenote/trunk/doc/phenote-website/irc_chat

From: <nl...@us...> - 2007-05-01 16:49:36

Revision: 532
          http://svn.sourceforge.net/obo/?rev=532&view=rev
Author:   nlw
Date:     2007-05-01 09:49:37 -0700 (Tue, 01 May 2007)

Log Message:
-----------
added transcript from today's IRC chat

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

Added: phenote/trunk/doc/phenote-website/irc_chat/transcripts/PWG_irc_050107.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	2007-05-01 16:49:37 UTC (rev 532)
@@ -0,0 +1,781 @@
+<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</span></span><span class="ampm">08:54<span class="secs">:0...
 
[truncated message content]

[Obo-svn-commit] SF.net SVN: obo: [531] phenote/trunk/doc/phenote-website/help/html

From: <nl...@us...> - 2007-05-01 03:19:38

Revision: 531
          http://svn.sourceforge.net/obo/?rev=531&view=rev
Author:   nlw
Date:     2007-04-30 20:19:38 -0700 (Mon, 30 Apr 2007)

Log Message:
-----------
changed "Images" to "images" in pathnames

Modified Paths:
--------------
    phenote/trunk/doc/phenote-website/help/html/Annotation_Spreadsheet.htm
    phenote/trunk/doc/phenote-website/help/html/Changing_your_Configuration.htm
    phenote/trunk/doc/phenote-website/help/html/Data_Entry.htm
    phenote/trunk/doc/phenote-website/help/html/Loading___Saving.htm
    phenote/trunk/doc/phenote-website/help/html/Running_Phenote_for_the_First_Time.htm
    phenote/trunk/doc/phenote-website/help/html/Term_Info.htm

Modified: phenote/trunk/doc/phenote-website/help/html/Annotation_Spreadsheet.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/Annotation_Spreadsheet.htm	2007-05-01 03:13:51 UTC (rev 530)
+++ phenote/trunk/doc/phenote-website/help/html/Annotation_Spreadsheet.htm	2007-05-01 03:19:38 UTC (rev 531)
@@ -8,7 +8,7 @@
 <BODY BGCOLOR=#ffffff>
 <H1>Annotation Spreadsheet</H1>
 <P><IMG hspace=0 
-src="../Images/annotation_spreadsheet_blank.png" width="100%" 
+src="../images/annotation_spreadsheet_blank.png" width="100%" 
 border=0></P>
 <P>&nbsp;</P>
 <P>In the bottom half of the Phenote window occupies the Annotation 

Modified: phenote/trunk/doc/phenote-website/help/html/Changing_your_Configuration.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/Changing_your_Configuration.htm	2007-05-01 03:13:51 UTC (rev 530)
+++ phenote/trunk/doc/phenote-website/help/html/Changing_your_Configuration.htm	2007-05-01 03:19:38 UTC (rev 531)
@@ -7,7 +7,7 @@
 </HEAD>
 <BODY BGCOLOR=#ffffff>
 <H1>Changing your Configuration</H1>
-<P><IMG hspace=0 src="../Images/change_config.png" 
+<P><IMG hspace=0 src="../images/change_config.png" 
 border=0></P>
 </BODY>
 </HTML>
\ No newline at end of file

Modified: phenote/trunk/doc/phenote-website/help/html/Data_Entry.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/Data_Entry.htm	2007-05-01 03:13:51 UTC (rev 530)
+++ phenote/trunk/doc/phenote-website/help/html/Data_Entry.htm	2007-05-01 03:19:38 UTC (rev 531)
@@ -1,21 +1,21 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
-<HTML>
-<HEAD>
-<META NAME="GENERATOR" CONTENT="Solutionsoft HelpBreeze JavaHelp Edition">
-<TITLE>Data Entry</TITLE>
-<LINK REL="stylesheet" TYPE="text/css" HREF=../javahelp.css>
-</HEAD>
-<BODY BGCOLOR=#ffffff>
-<H1>Data Entry</H1>
-<P><IMG height=0 hspace=0 
-src="../Images/data_entry_blank.png" width=0 border=0><IMG hspace=0 
-src="../Images/data_entry_blank.png" border=0></P>
-<P>The data entry section of Phenote is where the user will enter each 
+<html>
+<head>
+<meta name="GENERATOR" content="Solutionsoft HelpBreeze JavaHelp Edition">
+<title>Data Entry</title>
+<link rel="stylesheet" type="text/css" href="../javahelp.css">
+</head>
+<body bgcolor="#ffffff">
+<h1>Data Entry</h1>
+<p><IMG height=0 hspace=0 
+src="../images/data_entry_blank.png" width=0 border=0><IMG hspace=0 
+src="../images/data_entry_blank.png" border=0></p>
+<p>The data entry section of Phenote is where the user will enter each 
 annotation.&nbsp; The data entered here will be displayed in a single row of the 
 Annotation Spreadsheet.&nbsp; When a user selects a row within the spreadsheet, 
 this section will be updated with that information, and the user can change that 
-information. </P>
-<P>Please read the Creating Annotations section for more 
-information.</P>
-</BODY>
-</HTML>
\ No newline at end of file
+information. </p>
+<p>Please read the Creating Annotations section for more 
+information.</p>
+</body>
+</html>
\ No newline at end of file

Modified: phenote/trunk/doc/phenote-website/help/html/Loading___Saving.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/Loading___Saving.htm	2007-05-01 03:13:51 UTC (rev 530)
+++ phenote/trunk/doc/phenote-website/help/html/Loading___Saving.htm	2007-05-01 03:19:38 UTC (rev 531)
@@ -1,65 +1,65 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
-<HTML>
-<HEAD>
-<META NAME="GENERATOR" CONTENT="Solutionsoft HelpBreeze JavaHelp Edition">
-<TITLE>Loading & Saving</TITLE>
-<LINK REL="stylesheet" TYPE="text/css" HREF=../javahelp.css>
-</HEAD>
-<BODY BGCOLOR=#ffffff>
-<H1>Loading &amp; Saving</H1>
-<H3>        Loading Annotations</H3>
-<P>    Choose File-&gt;Open... A dialog like this will appear:</P>
-<P><IMG hspace=0 src="../Images/open_dialog.png" 
-border=0></P>
-<P>&nbsp;</P>
-<P>  The drop down "Files of Type" box contains a list of data 
+<html>
+<head>
+<meta name="GENERATOR" content="Solutionsoft HelpBreeze JavaHelp Edition">
+<title>Loading & Saving</title>
+<link rel="stylesheet" type="text/css" href="../javahelp.css">
+</head>
+<body bgcolor="#ffffff">
+<h1>Loading &amp; Saving</h1>
+<h3>        Loading Annotations</h3>
+<p>    Choose File-&gt;Open... A dialog like this will appear:</p>
+<p><IMG hspace=0 src="../images/open_dialog.png" 
+border=0></p>
+<p>&nbsp;</p>
+<p>  The drop down "Files of Type" box contains a list of data 
 adapters.&nbsp; To choose a different data adapter, click on the little upside-down triangle, and select 
 it from the dropdown list.&nbsp; The list of valid extensions for each 
-data adapter is also listed shown.</P>
-<P><IMG hspace=0 src="../Images/data_adapter_open_list.png" 
+data adapter is also listed shown.</p>
+<p><IMG hspace=0 src="../images/data_adapter_open_list.png" 
 border=0>              
                
             
-     </P>
-<P>When opening an Annotation file, if "All Files" is selected 
+     </p>
+<p>When opening an Annotation file, if "All Files" is selected 
 and your file has an extension appropriate for the data type, the data adapter will 
 be applied automatically.&nbsp; For example if your filename is "example.xls", the tab-delimited 
-data adapter will be automatically used.</P>
-<P>If your current configuration does not match that used 
+data adapter will be automatically used.</p>
+<p>If your current configuration does not match that used 
 when the file was previously saved, then you might encounter an error during 
 loading.&nbsp; For example, when you saved this file the last time, you were 
 operating under the "demo" configuration.&nbsp; However, since then, you 
 switched your configuration to "my_new_config".&nbsp; Since these configurations 
 might not match, you are unable to load in the data.&nbsp; Try <A 
-href="Changing_your_Configuration.htm">changing your configuration</A>              
+href="Changing_your_Configuration.htm">changing your configuration</a>              
                
         back to "demo" and 
-then retry loading the annotation file.&nbsp;</P>
-<P>              
+then retry loading the annotation file.&nbsp;</p>
+<p>              
                
             
-     &nbsp;</P>
-<H3>              
+     &nbsp;</p>
+<h3>              
                
             
-    Saving Annotations</H3>
-<P>              
+    Saving Annotations</h3>
+<p>              
            To save a file, 
 select the appropriate output format, type in the name of the file 
-(including the extension), and click "Save".&nbsp;</P>
-<P>              
+(including the extension), and click "Save".&nbsp;</p>
+<p>              
     Note that you can also select a filename that already exists 
 which will overwrite the file. (There is no warning in the software 
-itself, so this is your warning.)</P>
-<P><IMG height=0 hspace=0 
-src="../Images/data_adapter_listing.png" width=0 border=0><IMG hspace=0 
-src="../Images/data_adapter_listing.png" border=0>              
+itself, so this is your warning.)</p>
+<p><IMG height=0 hspace=0 
+src="../images/data_adapter_listing.png" width=0 border=0><IMG hspace=0 
+src="../images/data_adapter_listing.png" border=0>              
                
             
-     </P>
-<P>              
+     </p>
+<p>              
                
             
-     &nbsp;</P>
-</BODY>
-</HTML>
\ No newline at end of file
+     &nbsp;</p>
+</body>
+</html>
\ No newline at end of file

Modified: phenote/trunk/doc/phenote-website/help/html/Running_Phenote_for_the_First_Time.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/Running_Phenote_for_the_First_Time.htm	2007-05-01 03:13:51 UTC (rev 530)
+++ phenote/trunk/doc/phenote-website/help/html/Running_Phenote_for_the_First_Time.htm	2007-05-01 03:19:38 UTC (rev 531)
@@ -10,8 +10,8 @@
 <H2>Choosing the Configuration</H2>
 <P>The very first time you start phenote, a window will 
 popup and ask you to choose a configuration:</P>
-<P><IMG height=0 hspace=0 src="../Images/config-screenshot.png" width=0 
-border=0><IMG hspace=0 src="../Images/config-screenshot.png" border=0></P>
+<P><IMG height=0 hspace=0 src="../images/config-screenshot.png" width=0 
+border=0><IMG hspace=0 src="../images/config-screenshot.png" border=0></P>
 <P>&nbsp;</P>
 <P>For demonstration purposes, we will work with the "demo" configuration.&nbsp; 
 Select this option and press OK.&nbsp; Phenote will continue to load.&nbsp; It 

Modified: phenote/trunk/doc/phenote-website/help/html/Term_Info.htm
===================================================================
--- phenote/trunk/doc/phenote-website/help/html/Term_Info.htm	2007-05-01 03:13:51 UTC (rev 530)
+++ phenote/trunk/doc/phenote-website/help/html/Term_Info.htm	2007-05-01 03:19:38 UTC (rev 531)
@@ -7,7 +7,7 @@
 </HEAD>
 <BODY BGCOLOR=#ffffff>
 <H1>Term Info</H1>
-<P><IMG hspace=0 src="../Images/term_info.png" 
+<P><IMG hspace=0 src="../images/term_info.png" 
 border=0></P>
 <P>&nbsp;</P>
 <P>The Term Info window is a text-based ontology browser.&nbsp; This window will 


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[Obo-svn-commit] SF.net SVN: obo: [530] phenote/trunk/doc/phenote-website/help/Phenote.prj

From: <nl...@us...> - 2007-05-01 03:13:50

Revision: 530
          http://svn.sourceforge.net/obo/?rev=530&view=rev
Author:   nlw
Date:     2007-04-30 20:13:51 -0700 (Mon, 30 Apr 2007)

Log Message:
-----------
modifications to the project

Modified Paths:
--------------
    phenote/trunk/doc/phenote-website/help/Phenote.prj

Modified: phenote/trunk/doc/phenote-website/help/Phenote.prj
===================================================================
--- phenote/trunk/doc/phenote-website/help/Phenote.prj	2007-05-01 00:26:58 UTC (rev 529)
+++ phenote/trunk/doc/phenote-website/help/Phenote.prj	2007-05-01 03:13:51 UTC (rev 530)
@@ -1,6 +1,6 @@
 [Settings]
 html=
-images=Images
+images=images
 ccs=htmlhelp.css
 i=phenote.hhk
 last_path=C:\Documents and Settings\Nicole\Desktop\phenote-helper\html


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[Obo-svn-commit] SF.net SVN: obo: [528] phenote/trunk/src/java/phenote/gui/field

From: <mg...@us...> - 2007-04-30 23:45:49

Revision: 528
          http://svn.sourceforge.net/obo/?rev=528&view=rev
Author:   mgibson
Date:     2007-04-30 16:45:50 -0700 (Mon, 30 Apr 2007)

Log Message:
-----------
fixed bug where text from free text fields was "sticking" when selecting a new
character with no text in that field

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java
    phenote/trunk/src/java/phenote/gui/field/CharFieldGui.java
    phenote/trunk/src/java/phenote/gui/field/FreeTextField.java

Modified: phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java	2007-04-30 23:18:38 UTC (rev 527)
+++ phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java	2007-04-30 23:45:50 UTC (rev 528)
@@ -124,6 +124,7 @@
 
   protected void setSearchParams(SearchParamsI sp) {
     searchParams = sp;
+    // this assumes that its set up initially with ALL - presumptious?
     compListSearcher = new CompListSearcher(getCharField().getOntologyList());
   }
 

Modified: phenote/trunk/src/java/phenote/gui/field/CharFieldGui.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/CharFieldGui.java	2007-04-30 23:18:38 UTC (rev 527)
+++ phenote/trunk/src/java/phenote/gui/field/CharFieldGui.java	2007-04-30 23:45:50 UTC (rev 528)
@@ -44,14 +44,6 @@
     details of the gui - just a field that gives text 
     should there be subclasses for free text, term, & relations? hmmmm */
 abstract class CharFieldGui {
-  //private AutoComboBox comboBox;
-  //private AbstractAutoCompList comboBox; // ???
-  //private RelationCompList relCompList;
-  //private TermCompList termCompList;
-  //private CompListSearcher compListSearcher;
-  //private JTextField textField;
-  //private FreeTextField freeTextField;
-  //private boolean isCompList = false;
   private CharField charField;
   //private FieldPanel fieldPanel;
   //private JComboBox ontologyChooserCombo;
@@ -75,13 +67,6 @@
       t.enableListeners(true);
       t.allowPostCompButton(true);
       return t;
-      //return createCompList(charField,sp);
-//       if (charField.isRelationship()) {
-//         return new RelationCompList(searcher,editModel,charField);
-//       }
-//       else {
-//         return new TermCompList(searcher,editModel,charField);
-//       }
     }
     else {
       FreeTextField f = new FreeTextField(charField);
@@ -90,19 +75,7 @@
     }
   }
 
-//   private static CharFieldGui createCompList(CharField charField, SearchParamsI sp) {
-//     // enableListeners - if false then ACB wont directly edit model (post comp)
-//     //compListSearcher = new CompListSearcher(charField.getOntologyList(),sp);
-//       //new CompListSearcher(charField.getFirstOntology(),fieldPanel.getSearchParams());
-//     if (charField.isRelationshipList()) {
-//       return new RelationCompList(sp,enableListeners,charField);
-//     }
-//     else {
-//       return new TermCompList(sp,enableListeners);
-//     }
-//   }
 
-  // private static CharFieldGui createFreeTextField() {} ??
 
   /** createPostCompRelationList - will relation lists ever be in main window and if
       so will they ever have listeners enabled - maybe, probably not */
@@ -134,36 +107,8 @@
   protected CharFieldGui(CharField charField) {
     init(charField);
   }
-//   protected CharFieldGui(CharField charField,String label) {
-//     init(charField,label);
-//   }
 
-//   protected CharFieldGui(CharField charField,boolean enableListeners) {
-//     //this.enableListeners = enableListeners;
-//     enableListeners(enableListeners);
-//     init(charField);
-//   }
-    
 
-//   CharFieldGui(CharField charField, FieldPanel tp) {/*Container parent,*/
-//     init(charField,tp);
-//   }
-
-//   /** @param enableListeners - a catchall flag for disabling editing model, listening
-//       to model edits, & litening to selection - postcompGui handles these and sets
-//       this false, in main window this is true - rename? more flags? subclass?
-//       postCompGui mode?
-//       @param addCompButton if false override configuration and dont show
-//       post comp button */
-//   CharFieldGui(CharField cf,FieldPanel tp,String label,boolean enableListeners,
-//                boolean addCompButton) {
-//     this.label = label;
-//     this.enableListeners = enableListeners;
-//     this.addCompButton = addCompButton; // post comp button
-//     init(cf,tp);
-//   }
-
-
   private void init(CharField cf) { //, FieldPanel tp) {
     charField = cf;
     //fieldPanel = tp;
@@ -560,3 +505,60 @@
     return log;
   }
 }
+
+  // private static CharFieldGui createFreeTextField() {} ??
+
+//   private static CharFieldGui createCompList(CharField charField, SearchParamsI sp) {
+//     // enableListeners - if false then ACB wont directly edit model (post comp)
+//     //compListSearcher = new CompListSearcher(charField.getOntologyList(),sp);
+//       //new CompListSearcher(charField.getFirstOntology(),fieldPanel.getSearchParams());
+//     if (charField.isRelationshipList()) {
+//       return new RelationCompList(sp,enableListeners,charField);
+//     }
+//     else {
+//       return new TermCompList(sp,enableListeners);
+//     }
+//   }
+      //return createCompList(charField,sp);
+//       if (charField.isRelationship()) {
+//         return new RelationCompList(searcher,editModel,charField);
+//       }
+//       else {
+//         return new TermCompList(searcher,editModel,charField);
+//       }
+  //private AutoComboBox comboBox;
+  //private AbstractAutoCompList comboBox; // ???
+  //private RelationCompList relCompList;
+  //private TermCompList termCompList;
+  //private CompListSearcher compListSearcher;
+  //private JTextField textField;
+  //private FreeTextField freeTextField;
+  //private boolean isCompList = false;
+//   protected CharFieldGui(CharField charField,String label) {
+//     init(charField,label);
+//   }
+
+//   protected CharFieldGui(CharField charField,boolean enableListeners) {
+//     //this.enableListeners = enableListeners;
+//     enableListeners(enableListeners);
+//     init(charField);
+//   }
+    
+
+//   CharFieldGui(CharField charField, FieldPanel tp) {/*Container parent,*/
+//     init(charField,tp);
+//   }
+
+//   /** @param enableListeners - a catchall flag for disabling editing model, listening
+//       to model edits, & litening to selection - postcompGui handles these and sets
+//       this false, in main window this is true - rename? more flags? subclass?
+//       postCompGui mode?
+//       @param addCompButton if false override configuration and dont show
+//       post comp button */
+//   CharFieldGui(CharField cf,FieldPanel tp,String label,boolean enableListeners,
+//                boolean addCompButton) {
+//     this.label = label;
+//     this.enableListeners = enableListeners;
+//     this.addCompButton = addCompButton; // post comp button
+//     init(cf,tp);
+//   }

Modified: phenote/trunk/src/java/phenote/gui/field/FreeTextField.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/FreeTextField.java	2007-04-30 23:18:38 UTC (rev 527)
+++ phenote/trunk/src/java/phenote/gui/field/FreeTextField.java	2007-04-30 23:45:50 UTC (rev 528)
@@ -93,8 +93,11 @@
       return;
     }
     //String v = charField.getCharFieldEnum().getValue(chr).getName();
-    if (!chr.hasValue(getCharField()))
+    //if (!chr.hasValue(getCharField())) return;
+    if (!chr.hasValue(getCharField())) {
+      setText(""); // ?? null?
       return;
+    }
     String v = chr.getValue(getCharField()).getName();
     setText(v);
   }


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[Obo-svn-commit] SF.net SVN: obo: [527] phenote/trunk/src/java/phenote

From: <mg...@us...> - 2007-04-30 23:18:39

Revision: 527
          http://svn.sourceforge.net/obo/?rev=527&view=rev
Author:   mgibson
Date:     2007-04-30 16:18:38 -0700 (Mon, 30 Apr 2007)

Log Message:
-----------
fixed all bug - in char field refactor lst initialization to all ontologies

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java
    phenote/trunk/src/java/phenote/gui/field/CompListSearcher.java
    phenote/trunk/src/java/phenote/gui/field/TermCompList.java
    phenote/trunk/src/java/phenote/servlet/PhenoteController.java

Modified: phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java	2007-04-30 22:37:06 UTC (rev 526)
+++ phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java	2007-04-30 23:18:38 UTC (rev 527)
@@ -124,7 +124,7 @@
 
   protected void setSearchParams(SearchParamsI sp) {
     searchParams = sp;
-    compListSearcher = new CompListSearcher(getCharField().getFirstOntology(),sp);
+    compListSearcher = new CompListSearcher(getCharField().getOntologyList());
   }
 
   protected SearchParamsI getSearchParams() { return searchParams; }

Modified: phenote/trunk/src/java/phenote/gui/field/CompListSearcher.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/CompListSearcher.java	2007-04-30 22:37:06 UTC (rev 526)
+++ phenote/trunk/src/java/phenote/gui/field/CompListSearcher.java	2007-04-30 23:18:38 UTC (rev 527)
@@ -27,21 +27,19 @@
   //private Ontology ontology;
   //private boolean searchAll=false;
   private List<Ontology> ontologyList = new ArrayList<Ontology>(3);
-  private SearchParamsI searchParams = SearchParams.inst();
+  private SearchParamsI searchParams = SearchParams.inst(); // singleton
 
   /** Ontology - the initial ontology to search, setOntology changes this,
       initially only searches the one ontology (not ALL) - used by servlet which
       currently doesnt do ALL */
-  public CompListSearcher(Ontology o,SearchParamsI sp) {
+  public CompListSearcher(Ontology o) {
     setOntology(o);
-//    searchParams = sp;
   }
 
   /** l - initial list of ontologies to search, as in ALL. used by CharFieldGui
       to set list to all ontols in field as initial setting is ALL - is this funny? */
-  public CompListSearcher(List<Ontology> l,SearchParamsI sp) {
+  public CompListSearcher(List<Ontology> l) {
     setOntologies(l);
-//    searchParams = sp;
   }
 
   //void setSearchAll(boolean s) { searchAll = s; }

Modified: phenote/trunk/src/java/phenote/gui/field/TermCompList.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/TermCompList.java	2007-04-30 22:37:06 UTC (rev 526)
+++ phenote/trunk/src/java/phenote/gui/field/TermCompList.java	2007-04-30 23:18:38 UTC (rev 527)
@@ -32,54 +32,13 @@
     init();
   }
 
-//   protected TermCompList(CharField cf, boolean addCompButton) {
-//     super(cf);
-//     this.addCompButton = addCompButton;
-//     init();
-//   }
 
-  // pase?
-//   protected TermCompList(CharField cf, SearchParamsI sp, boolean editModel) {
-//     this(cf,sp,editModel,true,null); // true - dont supress configured comp button
-// //     super(sp,editModel,cf);  protected CharFieldGui(CharField charField,String label) {
-//     init(charField,label);
-//   }
-
-// //     enableTermInfoListening();
-// //     if (hasMoreThanOneOntology()) // super AACL
-// //       initOntologyChooser(getCharField());
-// //     if (charField.postCompAllowed() && addCompButton) {
-// //       JButton postCompButton = new JButton("Comp"); // ???
-// //       postCompButton.addActionListener(new PostCompListener());
-// //       //fieldPanel.addPostCompButton(postCompButton);
-// //     } 
-//   }
-
-//   protected TermCompList(CharField cf, SearchParamsI sp, boolean editModel,
-//                          boolean addCompButton, String label) {
-//     super(sp,editModel,cf,label);
-//     init();
-//   }
-
   private void init() {
     enableTermInfoListening();
     if (hasMoreThanOneOntology()) // super AACL
       initOntologyChooser(getCharField());
-//     if (charField.postCompAllowed() && addCompButton) {
-//       JButton postCompButton = new JButton("Comp"); // ???
-//       postCompButton.addActionListener(new PostCompListener());
-//       //fieldPanel.addPostCompButton(postCompButton);
-//     } 
   }
 
-  // pase i think
-//   TermCompList(CompListSearcher s,boolean editModel,CharFieldGui cfg) {
-//     super(s,editModel,cfg.getCharField());
-//     this.charFieldGui = cfg; // pass to super? AACL subclass CFG?
-//     enableTermInfoListening();
-//     if (hasMoreThanOneOntology()) // super AACL
-//       initOntologyChooser(getCharField());
-//   }
 
   protected boolean isTermCompList() {
     return true;
@@ -381,5 +340,47 @@
     }
   }
 
+}
+//     if (charField.postCompAllowed() && addCompButton) {
+//       JButton postCompButton = new JButton("Comp"); // ???
+//       postCompButton.addActionListener(new PostCompListener());
+//       //fieldPanel.addPostCompButton(postCompButton);
+//     } 
 
-}
+  // pase i think
+//   TermCompList(CompListSearcher s,boolean editModel,CharFieldGui cfg) {
+//     super(s,editModel,cfg.getCharField());
+//     this.charFieldGui = cfg; // pass to super? AACL subclass CFG?
+//     enableTermInfoListening();
+//     if (hasMoreThanOneOntology()) // super AACL
+//       initOntologyChooser(getCharField());
+//   }
+
+//   protected TermCompList(CharField cf, boolean addCompButton) {
+//     super(cf);
+//     this.addCompButton = addCompButton;
+//     init();
+//   }
+
+  // pase?
+//   protected TermCompList(CharField cf, SearchParamsI sp, boolean editModel) {
+//     this(cf,sp,editModel,true,null); // true - dont supress configured comp button
+// //     super(sp,editModel,cf);  protected CharFieldGui(CharField charField,String label) {
+//     init(charField,label);
+//   }
+
+// //     enableTermInfoListening();
+// //     if (hasMoreThanOneOntology()) // super AACL
+// //       initOntologyChooser(getCharField());
+// //     if (charField.postCompAllowed() && addCompButton) {
+// //       JButton postCompButton = new JButton("Comp"); // ???
+// //       postCompButton.addActionListener(new PostCompListener());
+// //       //fieldPanel.addPostCompButton(postCompButton);
+// //     } 
+//   }
+
+//   protected TermCompList(CharField cf, SearchParamsI sp, boolean editModel,
+//                          boolean addCompButton, String label) {
+//     super(sp,editModel,cf,label);
+//     init();
+//   }

Modified: phenote/trunk/src/java/phenote/servlet/PhenoteController.java
===================================================================
--- phenote/trunk/src/java/phenote/servlet/PhenoteController.java	2007-04-30 22:37:06 UTC (rev 526)
+++ phenote/trunk/src/java/phenote/servlet/PhenoteController.java	2007-04-30 23:18:38 UTC (rev 527)
@@ -136,7 +136,7 @@
     SearchParams searchParams = SearchParams.inst();
     searchParams.setParam(SearchFilterType.TERM, true);
     searchParams.setParam(SearchFilterType.SYN, true);
-    return new CompListSearcher(getOntology(ontologyName), searchParams);
+    return new CompListSearcher(getOntology(ontologyName));
   }
 
   /**


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[Obo-svn-commit] SF.net SVN: obo: [526] phenote/trunk/doc/phenote-website/irc_chat

From: <nl...@us...> - 2007-04-30 22:37:09

Revision: 526
          http://svn.sourceforge.net/obo/?rev=526&view=rev
Author:   nlw
Date:     2007-04-30 15:37:06 -0700 (Mon, 30 Apr 2007)

Log Message:
-----------
added instructions for getting irc clients, with a link

Modified Paths:
--------------
    phenote/trunk/doc/phenote-website/irc_chat/index.shtml

Added Paths:
-----------
    phenote/trunk/doc/phenote-website/irc_chat/irc_clients.shtml

Modified: phenote/trunk/doc/phenote-website/irc_chat/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/irc_chat/index.shtml	2007-04-30 22:13:46 UTC (rev 525)
+++ phenote/trunk/doc/phenote-website/irc_chat/index.shtml	2007-04-30 22:37:06 UTC (rev 526)
@@ -8,8 +8,9 @@
 
 When: First Tuesday of every month; 8:30am <br/>
 
-<p>You will need an IRC client to visit our chats.  You can download any number of free clients to do this.  You'll need to connect to the <b>irc.sf.net</b> and join the <b>#phenote</b> channel. </p>
+<p>You will need an IRC client to visit our chats.  You can download any number of <a href="/irc_chat/irc_clients.shtml">free clients</a> to do this.  You'll need to connect to the <b>irc.sf.net</b> and join the <b>#phenote</b> channel. </p>
 
+<hr />
 <p>Alternatively, you can connect to the Phenote IRC chat using the applet at the bottom of this page. Simply enter a name to be used during the chat.  If the name you enter is already being used by someone else, an 'anonymous' one will be assigned to you. (but you can change it once you're logged on by typing the command "/nick newname") </p>
 
   <form method="post" name="launcher">
@@ -20,7 +21,7 @@
     <td style="width: 327px;"><input size="40" name="username"></td>
   </tr>
   <tr>
-    <td colspan="2" rowspan="1" style="height: 25px; color: rgb(0, 0, 0); text-align: center; width: 327px;"><input name="appletbutton" value="Start Applets" style="color: rgb(0, 0, 0); "onclick="startApplets()" type="button"><br>
+    <td colspan="2" rowspan="1" style="height: 25px; color: rgb(0, 0, 0); text-align: center; width: 327px;"><input name="appletbutton" value="Join IRC chat" style="color: rgb(0, 0, 0); "onclick="startApplets()" type="button"><br>
     </td>
   </tr>
 

Added: phenote/trunk/doc/phenote-website/irc_chat/irc_clients.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/irc_chat/irc_clients.shtml	                        (rev 0)
+++ phenote/trunk/doc/phenote-website/irc_chat/irc_clients.shtml	2007-04-30 22:37:06 UTC (rev 526)
@@ -0,0 +1,46 @@
+<!--#include virtual="/ssi/header.html" -->
+<div id="page_body">
+
+<!--#include virtual="/ssi/navi_home.html" -->
+
+<div id="main_content">
+<h2>Free IRC Clients</h2>
+
+<p>There are several Internet Relay Chat (IRC) software clients available for every computer platform, such as: </p>
+  <table border="1" height="40" width="500">
+    <tbody>
+      <tr>
+	<td align="center" width="159"><b>Mac</b></td>
+	<td align="center" width="159"><b>Windows</b></td>
+	<td align="center" width="160"><b>Linux</b></td>
+      </tr>
+      <tr>
+	<td align="center" width="159">
+	  <a href="http://homepage.mac.com/philrobin/conversation/">Conversation</a> <br />
+	  <a href="http://www.snak.com/Snak.html">Snak</a><br />
+	  <a href="http://www.ircle.com/">ircle</a>
+	</td>
+	<td align="center" width="159">
+	  <a href="http://www.mirc.com/">mIRC</a><br />
+	  <a href="http://www.xircon.com/">Xircon</a><br />
+	  <span style="color: rgb(0, 0, 0);"><span
+	    style="color: rgb(0, 0, 0);">
+	  <a href="http://www.xchat.org/">xchat</a></span></span>
+	</td>
+	<td align="center" width="160">
+	  <a href="http://konversation.kde.org/">Konversation</a><br />
+	  <a href="http://www.xchat.org/">xchat</a><br />
+	  <a href="http://www.bitchx.org/">BitchX</a>
+	</td>
+      </tr>
+    </tbody>
+  </table>
+  <br />
+<p>  Although we won't be using most IRC features during the Working Group chats, there are dozens and dozens of commands and special IRC features. If you want to read up, take a look at the IRC primer at
+  <a href="http://www.irchelp.org/irchelp/ircprimer.html">http://www.irchelp.org/irchelp/ircprimer.html</a></p>
+
+</div>
+</div>
+
+<!--#include virtual="/ssi/footer.shtml" -->
+


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[Obo-svn-commit] SF.net SVN: obo: [525] phenote/trunk/doc/phenote-website

From: <nl...@us...> - 2007-04-30 22:13:44

Revision: 525
          http://svn.sourceforge.net/obo/?rev=525&view=rev
Author:   nlw
Date:     2007-04-30 15:13:46 -0700 (Mon, 30 Apr 2007)

Log Message:
-----------
removed the vnc client applet, and added text to describe changing nickname during chats

Modified Paths:
--------------
    phenote/trunk/doc/phenote-website/irc_chat/index.shtml
    phenote/trunk/doc/phenote-website/javascript/irc_script.js

Modified: phenote/trunk/doc/phenote-website/irc_chat/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/irc_chat/index.shtml	2007-04-30 22:00:15 UTC (rev 524)
+++ phenote/trunk/doc/phenote-website/irc_chat/index.shtml	2007-04-30 22:13:46 UTC (rev 525)
@@ -10,7 +10,7 @@
 
 <p>You will need an IRC client to visit our chats.  You can download any number of free clients to do this.  You'll need to connect to the <b>irc.sf.net</b> and join the <b>#phenote</b> channel. </p>
 
-<p>Alternatively, you can connect to the Phenote IRC chat using the applet at the bottom of this page. </p>
+<p>Alternatively, you can connect to the Phenote IRC chat using the applet at the bottom of this page. Simply enter a name to be used during the chat.  If the name you enter is already being used by someone else, an 'anonymous' one will be assigned to you. (but you can change it once you're logged on by typing the command "/nick newname") </p>
 
   <form method="post" name="launcher">
  <table style="text-align: left; margin-left: auto; margin-right: auto; width: 524px; height: 84px;" width="100%">

Modified: phenote/trunk/doc/phenote-website/javascript/irc_script.js
===================================================================
--- phenote/trunk/doc/phenote-website/javascript/irc_script.js	2007-04-30 22:00:15 UTC (rev 524)
+++ phenote/trunk/doc/phenote-website/javascript/irc_script.js	2007-04-30 22:13:46 UTC (rev 525)
@@ -13,7 +13,7 @@
      vncwindow = null;
    }
 
-   vcnwindow = window.open("http://frizzled.lbl.gov:5801", "VNC", "status=no,width=1100,height=800");
+   //   vcnwindow = window.open("http://frizzled.lbl.gov:5801", "VNC", "status=no,width=1100,height=800");
    ircwindow = window.open("about:blank", "My window", "scrollbars=no,status=no,width=510,height=430");
 
    var html = "";


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[Obo-svn-commit] SF.net SVN: obo: [524] phenote/trunk/doc/phenote-website/javascript

From: <nl...@us...> - 2007-04-30 22:00:15

Revision: 524
          http://svn.sourceforge.net/obo/?rev=524&view=rev
Author:   nlw
Date:     2007-04-30 15:00:15 -0700 (Mon, 30 Apr 2007)

Log Message:
-----------
moving js into this dir

Added Paths:
-----------
    phenote/trunk/doc/phenote-website/javascript/irc_script.js
    phenote/trunk/doc/phenote-website/javascript/script.js

Added: phenote/trunk/doc/phenote-website/javascript/irc_script.js
===================================================================
--- phenote/trunk/doc/phenote-website/javascript/irc_script.js	                        (rev 0)
+++ phenote/trunk/doc/phenote-website/javascript/irc_script.js	2007-04-30 22:00:15 UTC (rev 524)
@@ -0,0 +1,37 @@
+var ircwindow = null;
+var vncwindow = null;
+
+function startApplets() {
+
+   if (ircwindow != null) {
+     ircwindow.close();
+     ircwindow = null;
+   }
+
+   if (vncwindow != null) {
+     vncwindow.close();
+     vncwindow = null;
+   }
+
+   vcnwindow = window.open("http://frizzled.lbl.gov:5801", "VNC", "status=no,width=1100,height=800");
+   ircwindow = window.open("about:blank", "My window", "scrollbars=no,status=no,width=510,height=430");
+
+   var html = "";
+
+   html += "<html><body>\n";
+   html += "<applet code=\"IRCApplet.class\" archive=\"irc.jar,pixx.jar\" width=475 height=400>\n";
+   html += "<param name=\"CABINETS\" value=\"irc.cab,securedirc.cab,pixx.cab\">\n";
+   html += "<param name=\"nick\" value='"+document.forms["launcher"].username.value+"'>\n";
+   html += "<param name=\"fullname\" value='"+document.forms["launcher"].username.value+"'>\n";
+
+   html += "<param name=\"alternatenick\" value=\"Anon???\">\n";
+   html += "<param name=\"host\" value=\"irc.sf.net\">\n";
+   html += "<param name=\"command1\" value=\"/join #phenote\">\n";
+   html += "<param name=\"gui\" value=\"pixx\">\n";
+   html += "</applet>\n";
+   html += "</body></html>";
+
+//   alert(html);
+   ircwindow.document.writeln(html);
+   ircwindow.document.close();
+}

Added: phenote/trunk/doc/phenote-website/javascript/script.js
===================================================================
--- phenote/trunk/doc/phenote-website/javascript/script.js	                        (rev 0)
+++ phenote/trunk/doc/phenote-website/javascript/script.js	2007-04-30 22:00:15 UTC (rev 524)
@@ -0,0 +1,37 @@
+var ircwindow = null;
+var vncwindow = null;
+
+function startApplets() {
+
+   if (ircwindow != null) {
+     ircwindow.close();
+     ircwindow = null;
+   }
+
+   if (vncwindow != null) {
+     vncwindow.close();
+     vncwindow = null;
+   }
+
+   vcnwindow = window.open("http://frizzled.lbl.gov:5801", "VNC", "status=no,width=1100,height=800");
+   ircwindow = window.open("about:blank", "My window", "scrollbars=no,status=no,width=510,height=430");
+
+   var html = "";
+
+   html += "<html><body>\n";
+   html += "<applet code=\"IRCApplet.class\" archive=\"irc.jar,pixx.jar\" width=475 height=400>\n";
+   html += "<param name=\"CABINETS\" value=\"irc.cab,securedirc.cab,pixx.cab\">\n";
+   html += "<param name=\"nick\" value='"+document.forms["launcher"].username.value+"'>\n";
+   html += "<param name=\"fullname\" value='"+document.forms["launcher"].username.value+"'>\n";
+
+   html += "<param name=\"alternatenick\" value=\"Anon???\">\n";
+   html += "<param name=\"host\" value=\"irc.sf.net\">\n";
+   html += "<param name=\"command1\" value=\"/join #oboedit\">\n";
+   html += "<param name=\"gui\" value=\"pixx\">\n";
+   html += "</applet>\n";
+   html += "</body></html>";
+
+//   alert(html);
+   ircwindow.document.writeln(html);
+   ircwindow.document.close();
+}
\ No newline at end of file


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[Obo-svn-commit] SF.net SVN: obo: [523] phenote/trunk/doc/phenote-website

From: <nl...@us...> - 2007-04-30 21:57:18

Revision: 523
          http://svn.sourceforge.net/obo/?rev=523&view=rev
Author:   nlw
Date:     2007-04-30 14:57:20 -0700 (Mon, 30 Apr 2007)

Log Message:
-----------
making changes to the header

Modified Paths:
--------------
    phenote/trunk/doc/phenote-website/irc_chat/index.shtml
    phenote/trunk/doc/phenote-website/ssi/header.html

Modified: phenote/trunk/doc/phenote-website/irc_chat/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/irc_chat/index.shtml	2007-04-30 21:51:18 UTC (rev 522)
+++ phenote/trunk/doc/phenote-website/irc_chat/index.shtml	2007-04-30 21:57:20 UTC (rev 523)
@@ -1,5 +1,4 @@
 <!--#include virtual="/ssi/header.html" -->
-  <script language="JavaScript" src="/irc_script.js"><!-- --></script>
 <div id="page_body">
 
 <!--#include virtual="/ssi/navi_home.html" -->

Modified: phenote/trunk/doc/phenote-website/ssi/header.html
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/header.html	2007-04-30 21:51:18 UTC (rev 522)
+++ phenote/trunk/doc/phenote-website/ssi/header.html	2007-04-30 21:57:20 UTC (rev 523)
@@ -14,6 +14,7 @@
 <link rel="stylesheet" type="text/css" href="/phenote/css/style.css" title="standard" />
 
 <script type="text/javascript" src="/javascript/obfuscate.js"></script>
+<script type="text/javascript" src="/javascript/irc_script.js"></script>
 
 <title>Phenote: A Phenotype Annotation Tool using Ontologies</title>
 


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[Obo-svn-commit] SF.net SVN: obo: [522] phenote/trunk/src/java/phenote

From: <mg...@us...> - 2007-04-30 21:51:17

Revision: 522
          http://svn.sourceforge.net/obo/?rev=522&view=rev
Author:   mgibson
Date:     2007-04-30 14:51:18 -0700 (Mon, 30 Apr 2007)

Log Message:
-----------
i broke reloading of ontologies for servlet/OntologyUpdateJob - as now an
obosesion is all of the ontologies not just one - so need to actually
reload the whole obo session and all ontologies
christian - can you make sure this works for you - thanks

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java
    phenote/trunk/src/java/phenote/jobs/OntologyUpdateJob.java

Modified: phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java	2007-04-30 21:43:29 UTC (rev 521)
+++ phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java	2007-04-30 21:51:18 UTC (rev 522)
@@ -517,9 +517,15 @@
   /** The ontology has been determined to be out of date (by quartz) and thus directed
       to reload itself from its file - in other words there is a new obo file to load 
       in place of old one */
-  public void reloadOntology(Ontology ont) throws OntologyException {
-    URL url = findFile(ont.getSource()); // ex
-    loadOboSessionFromUrl(ont,url,ont.getSource()); // throws ex
+//   public void reloadOntology(Ontology ont) throws OntologyException {
+//     URL url = findFile(ont.getSource()); // ex
+//     loadOboSessionFromUrl(ont,url,ont.getSource()); // throws ex
+//   }
+  public void reloadOntologies() throws OntologyException {
+    fileToOntologyCache = new HashMap<String,Ontology>();
+    // i dont think we need to clear out ontologies from OntMans char field as they
+    // will just get replaced
+    initOntologies();
   }
 
   // eventually move to util class

Modified: phenote/trunk/src/java/phenote/jobs/OntologyUpdateJob.java
===================================================================
--- phenote/trunk/src/java/phenote/jobs/OntologyUpdateJob.java	2007-04-30 21:43:29 UTC (rev 521)
+++ phenote/trunk/src/java/phenote/jobs/OntologyUpdateJob.java	2007-04-30 21:51:18 UTC (rev 522)
@@ -1,108 +1,111 @@
-package phenote.jobs;
-
-import org.apache.log4j.Logger;
-import org.quartz.JobExecutionContext;
-import org.quartz.JobExecutionException;
-import org.springframework.scheduling.quartz.QuartzJobBean;
-import phenote.dataadapter.OntologyDataAdapter;
-import phenote.datamodel.Ontology;
-import phenote.datamodel.OntologyManager;
-
-import java.io.File;
-import java.util.Date;
-
-/**
- * Job that reloads and archives a specified ontology. This job is scheduled via Quartz.
- * The job is defined in the spring configuration file.
- */
-public class OntologyUpdateJob extends QuartzJobBean {
-
-  public static final Logger LOG = Logger.getLogger(OntologyUpdateJob.class);
-  public static final long MILLISECONDS_PER_DAY = (24 * 60 * 60 * 1000);
-
-  // set by spring
-  private String ontologyName;
-  private String archiveDirectory;
-  private double purgePeriodInDays;
-
-
-  protected void executeInternal(JobExecutionContext context) throws JobExecutionException {
-    LOG.info("Started Ontology Update Job: " + ontologyName);
-
-
-    Ontology ontology = OntologyManager.inst().getOntologyForName(ontologyName);
-    if (ontology == null) {
-      // In case no ontology has ever been loaded.
-      // we assume we run in lazy initialization mode
-      // and need to initialize first.
-      OntologyDataAdapter.initialize();
-      ontology = OntologyManager.inst().getOntologyForName(ontologyName);
-      // Check if ontology by this name is found
-      if (ontology == null)
-        LOG.warn("No Ontology with name :" + ontologyName + " found!");
-      // we can return here in either case: If ontology was found it read the latest version
-      // if it could not be found no more action needed.
-      return;
-    }
-
-    try {
-      File newFile = newOntologyFile(ontology);
-      if (newFile != null) {
-        OntologyDataAdapter ontReader = OntologyDataAdapter.getInstance();
-        ontReader.reloadOntology(ontology);
-
-/*
-        File archiveFile = FileUtil.archiveFile(newFile, PhenoteWebConfiguration.getInstance().getWebRoot(), archiveDirectory);
-        long purgePeriodInMilliseconds = (long) (purgePeriodInDays * MILLISECONDS_PER_DAY );
-        FileUtil.purgeArchiveDirectory(archiveFile.getParentFile(), purgePeriodInMilliseconds);
-*/
-      }
-    } catch (Exception e) {
-      LOG.error(e.getMessage(), e);
-    }
-  }
-
-  /*
-   * Retrieve the new ontology file if available.
-   * It checks the time stamps of the new file and the file
-   * from which it was loaded (save in the Ontology object)
-   */
-  private File newOntologyFile(Ontology ontology) {
-    String fileName = ontology.getSource();
-    File file = new File(fileName);
-    long timestamp = file.lastModified();
-    long timestampOldFile = ontology.getTimestamp();
-    if (timestamp > timestampOldFile) {
-      LOG.debug("New File  " + file.getAbsolutePath() + " found. ");
-      return file;
-    } else {
-      Date date = new Date(timestampOldFile);
-      LOG.debug("The file  " + file.getAbsolutePath() + " has not changed since the last load: " + date);
-      return null;
-    }
-  }
-
-  public String getOntologyName() {
-    return ontologyName;
-  }
-
-  public void setOntologyName(String ontologyName) {
-    this.ontologyName = ontologyName;
-  }
-
-  public String getArchiveDirectory() {
-    return archiveDirectory;
-  }
-
-  public void setArchiveDirectory(String archiveDirectory) {
-    this.archiveDirectory = archiveDirectory;
-  }
-
-  public double getPurgePeriodInDays() {
-    return purgePeriodInDays;
-  }
-
-  public void setPurgePeriodInDays(double purgePeriodInDays) {
-    this.purgePeriodInDays = purgePeriodInDays;
-  }
-}
+package phenote.jobs;
+
+import org.apache.log4j.Logger;
+import org.quartz.JobExecutionContext;
+import org.quartz.JobExecutionException;
+import org.springframework.scheduling.quartz.QuartzJobBean;
+import phenote.dataadapter.OntologyDataAdapter;
+import phenote.datamodel.Ontology;
+import phenote.datamodel.OntologyManager;
+
+import java.io.File;
+import java.util.Date;
+
+/**
+ * Job that reloads and archives a specified ontology. This job is scheduled via Quartz.
+ * The job is defined in the spring configuration file.
+ */
+public class OntologyUpdateJob extends QuartzJobBean {
+
+  public static final Logger LOG = Logger.getLogger(OntologyUpdateJob.class);
+  public static final long MILLISECONDS_PER_DAY = (24 * 60 * 60 * 1000);
+
+  // set by spring
+  private String ontologyName;
+  private String archiveDirectory;
+  private double purgePeriodInDays;
+
+
+  protected void executeInternal(JobExecutionContext context) throws JobExecutionException {
+    LOG.info("Started Ontology Update Job: " + ontologyName);
+
+
+    Ontology ontology = OntologyManager.inst().getOntologyForName(ontologyName);
+    if (ontology == null) {
+      // In case no ontology has ever been loaded.
+      // we assume we run in lazy initialization mode
+      // and need to initialize first.
+      OntologyDataAdapter.initialize();
+      ontology = OntologyManager.inst().getOntologyForName(ontologyName);
+      // Check if ontology by this name is found
+      if (ontology == null)
+        LOG.warn("No Ontology with name :" + ontologyName + " found!");
+      // we can return here in either case: If ontology was found it read the latest version
+      // if it could not be found no more action needed.
+      return;
+    }
+
+    try {
+      File newFile = newOntologyFile(ontology);
+      if (newFile != null) {
+        OntologyDataAdapter ontReader = OntologyDataAdapter.getInstance();
+        //ontReader.reloadOntology(ontology);
+         // have to now reload all of the ontologies as they are all in 1 oboSession
+        ontReader.reloadOntologies();
+
+/*
+        File archiveFile = FileUtil.archiveFile(newFile, PhenoteWebConfiguration.getInstance().getWebRoot(), archiveDirectory);
+        long purgePeriodInMilliseconds = (long) (purgePeriodInDays * MILLISECONDS_PER_DAY );
+        FileUtil.purgeArchiveDirectory(archiveFile.getParentFile(), purgePeriodInMilliseconds);
+*/
+      }
+    } catch (Exception e) {
+      LOG.error(e.getMessage(), e);
+    }
+  }
+
+  /*
+   * Retrieve the new ontology file if available.
+   * It checks the time stamps of the new file and the file
+   * from which it was loaded (save in the Ontology object)
+   */
+  private File newOntologyFile(Ontology ontology) {
+    String fileName = ontology.getSource();
+    File file = new File(fileName);
+    long timestamp = file.lastModified();
+    long timestampOldFile = ontology.getTimestamp();
+    if (timestamp > timestampOldFile) {
+      LOG.debug("New File  " + file.getAbsolutePath() + " found. ");
+      return file;
+    } else {
+      Date date = new Date(timestampOldFile);
+      LOG.debug("The file  " + file.getAbsolutePath() + " has not changed since the last load: " + date);
+      return null;
+    }
+  }
+
+  public String getOntologyName() {
+    return ontologyName;
+  }
+
+  public void setOntologyName(String ontologyName) {
+    this.ontologyName = ontologyName;
+  }
+
+  public String getArchiveDirectory() {
+    return archiveDirectory;
+  }
+
+  public void setArchiveDirectory(String archiveDirectory) {
+    this.archiveDirectory = archiveDirectory;
+  }
+
+  public double getPurgePeriodInDays() {
+    return purgePeriodInDays;
+  }
+
+  public void setPurgePeriodInDays(double purgePeriodInDays) {
+    this.purgePeriodInDays = purgePeriodInDays;
+  }
+}
+


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: [521] phenote/trunk/doc/phenote-website/irc_chat

From: <nl...@us...> - 2007-04-30 21:43:27

Revision: 521
          http://svn.sourceforge.net/obo/?rev=521&view=rev
Author:   nlw
Date:     2007-04-30 14:43:29 -0700 (Mon, 30 Apr 2007)

Log Message:
-----------
removing the oboedit webinar page, renaming the ircchat page to index

Added Paths:
-----------
    phenote/trunk/doc/phenote-website/irc_chat/index.shtml

Removed Paths:
-------------
    phenote/trunk/doc/phenote-website/irc_chat/index.html
    phenote/trunk/doc/phenote-website/irc_chat/irc_chat.shtml

Deleted: phenote/trunk/doc/phenote-website/irc_chat/index.html
===================================================================
--- phenote/trunk/doc/phenote-website/irc_chat/index.html	2007-04-30 21:34:47 UTC (rev 520)
+++ phenote/trunk/doc/phenote-website/irc_chat/index.html	2007-04-30 21:43:29 UTC (rev 521)
@@ -1,133 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html>
-<head>
-  <meta content="text/html; charset=ISO-8859-1"
- http-equiv="content-type">
-  <title>OBO-Edit Webinar Overview</title>
-  <link rel="stylesheet" href="style.css" type="text/css">
-  <script language="JavaScript" src="script.js"><!-- --></script>
-</head>
-<body>
-<br>
-<table style="width: 776px; height: 617px;" cellpadding="10"
- cellspacing="0">
-  <tbody>
-    <tr>
-      <td
- style="width: 200px; height: 149px; background-color: rgb(109, 150, 202); direction: ltr;"><img
- style="width: 200px; height: 138px;" alt="OBO-Edit Logo"
- src="images/splash.jpg"></td>
-      <td
- style="text-align: center; width: 568px; height: 149px; background-color: rgb(109, 150, 202); font-family: Helvetica,Arial,sans-serif;">
-      <font color="white">
-      <h1>OBO-Edit
-Webinar</h1>
-      <h2>Overview</h2>
-      </font> </td>
-    </tr>
-    <tr>
-      <td
- style="vertical-align: top; background-color: rgb(109, 150, 202); height: 454px;">
-      <ul>
-        <li style="color: rgb(255, 255, 255);">Overview</li>
-        <li><a href="technologies.html">Technologies</a></li>
-        <ul>
-          <li><a href="vnc.html">VNC</a></li>
-          <li><a href="irc.html">IRC</a></li>
-          <li><a href="gizmo.html">The Gizmo Project</a></li>
-          <li><a href="oboedit.html">OBO-Edit</a></li>
-        </ul>
-        <li><a href="etiquette.html">Etiquette</a></li>
-        <li><a href="contact.html">Contact</a></li>
-      </ul>
-      </td>
-      <td
- style="background-color: rgb(198, 203, 228); width: 568px; vertical-align: top; height: 454px;">
-      <table height="361" width="491">
-        <tbody>
-          <tr>
-            <td style="vertical-align: top;"><span
- style="color: rgb(0, 0, 0); font-weight: bold;">What:</span></td>
-            <td style="color: rgb(0, 0, 0); vertical-align: top;">OBO-Edit
-Tutorial</td>
-          </tr>
-          <tr>
-            <td style="width: 67px; vertical-align: top;"><span
- style="color: rgb(0, 0, 0); font-weight: bold;">When:</span></td>
-            <td
- style="color: rgb(0, 0, 0); width: 411px; vertical-align: top;"><span
- style="color: rgb(0, 0, 0);">February 6th - <i>9:00AM - 9:30AM PST</i>
-- Technology test<br>
-February 7th - </span><span
- style="font-style: italic; color: rgb(0, 0, 0);">9:00AM
-- 3:00PM PST</span><br style="color: rgb(0, 0, 0);">
-            <span style="color: rgb(0, 0, 0);">February 8th - </span><span
- style="font-style: italic; color: rgb(0, 0, 0);">1:00PM
-- 3:00PM PST (revised time!)</span></td>
-          </tr>
-          <tr>
-            <td style="width: 67px; vertical-align: top;"><span
- style="font-weight: bold; color: rgb(0, 0, 0);">Where:</span></td>
-            <td style="width: 411px; vertical-align: top;"><span
- style="color: rgb(0, 0, 0);">The Internet</span></td>
-          </tr>
-          <tr>
-            <td style="vertical-align: top;"><span
- style="font-weight: bold; color: rgb(0, 0, 0);">Signups:</span></td>
-            <td style="vertical-align: top;"><span
- style="color: rgb(0, 0, 0);">Participation
-is
-currently limited to GO Consortium members only</span></td>
-          </tr>
-          <tr>
-            <td style="height: 132px;" colspan="2" rowspan="1">
-            <hr><span style="color: rgb(0, 0, 0);"><br>
-Participants
-should visit the Technologies section to learn how to download and
-install the programs you'll need to join the webinar. All of these
-technologies can be tested immediately; you do not need to wait until
-the webinar begins.</span><br style="color: rgb(0, 0, 0);">
-            <br style="color: rgb(0, 0, 0);">
-            <span style="color: rgb(0, 0, 0);">Voice chat can be
-accessed via The Gizmo Project using phone number <b>1-222-626-3348</b>
-(1-222-OBO-EDIT). Don't try to call from a regular phone; it won't work.<br>
-            <br>
-IRC
-and VNC can be accessed via Java applets. The VNC password is <b>oboedit_vnc</b>.<br>
-            <br>
-            </span>
-            <form method="post" name="launcher">
-              <table
- style="text-align: left; margin-left: auto; margin-right: auto; width: 524px; height: 84px;"
- width="100%">
-                <tbody>
-                  <tr>
-                    <td colspan="1" rowspan="1" width="156">IRC
-Nickname</td>
-                    <td style="width: 327px;"><input size="40"
- name="username"></td>
-                  </tr>
-                  <tr>
-                    <td colspan="2" rowspan="1"
- style="height: 25px; color: rgb(0, 0, 0); text-align: center; width: 327px;"><input
- name="appletbutton" value="Start Applets" style="color: rgb(0, 0, 0);"
- onclick="startApplets()" type="button"><br>
-                    </td>
-                  </tr>
-                </tbody>
-              </table>
-            </form>
-            <span style="color: rgb(0, 0, 0);">
-            <hr> </span></td>
-          </tr>
-        </tbody>
-      </table>
-      <br>
-      <span style="color: rgb(0, 0, 0);"><span
- style="color: rgb(0, 0, 0);"><br>
-      </span></span></td>
-    </tr>
-  </tbody>
-</table>
-</body>
-</html>

Copied: phenote/trunk/doc/phenote-website/irc_chat/index.shtml (from rev 520, phenote/trunk/doc/phenote-website/irc_chat/irc_chat.shtml)
===================================================================
--- phenote/trunk/doc/phenote-website/irc_chat/index.shtml	                        (rev 0)
+++ phenote/trunk/doc/phenote-website/irc_chat/index.shtml	2007-04-30 21:43:29 UTC (rev 521)
@@ -0,0 +1,36 @@
+<!--#include virtual="/ssi/header.html" -->
+  <script language="JavaScript" src="/irc_script.js"><!-- --></script>
+<div id="page_body">
+
+<!--#include virtual="/ssi/navi_home.html" -->
+
+<div id="main_content">
+<h2>Phenote Working Group IRC Chat</h2>
+
+When: First Tuesday of every month; 8:30am <br/>
+
+<p>You will need an IRC client to visit our chats.  You can download any number of free clients to do this.  You'll need to connect to the <b>irc.sf.net</b> and join the <b>#phenote</b> channel. </p>
+
+<p>Alternatively, you can connect to the Phenote IRC chat using the applet at the bottom of this page. </p>
+
+  <form method="post" name="launcher">
+ <table style="text-align: left; margin-left: auto; margin-right: auto; width: 524px; height: 84px;" width="100%">
+<tbody>
+  <tr>
+    <td colspan="1" rowspan="1" width="156">IRC Nickname</td>
+    <td style="width: 327px;"><input size="40" name="username"></td>
+  </tr>
+  <tr>
+    <td colspan="2" rowspan="1" style="height: 25px; color: rgb(0, 0, 0); text-align: center; width: 327px;"><input name="appletbutton" value="Start Applets" style="color: rgb(0, 0, 0); "onclick="startApplets()" type="button"><br>
+    </td>
+  </tr>
+
+</tbody>
+</table>
+</form>
+
+</div>
+</div>
+
+<!--#include virtual="/ssi/footer.shtml" -->
+

Deleted: phenote/trunk/doc/phenote-website/irc_chat/irc_chat.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/irc_chat/irc_chat.shtml	2007-04-30 21:34:47 UTC (rev 520)
+++ phenote/trunk/doc/phenote-website/irc_chat/irc_chat.shtml	2007-04-30 21:43:29 UTC (rev 521)
@@ -1,36 +0,0 @@
-<!--#include virtual="/ssi/header.html" -->
-  <script language="JavaScript" src="/irc_script.js"><!-- --></script>
-<div id="page_body">
-
-<!--#include virtual="/ssi/navi_home.html" -->
-
-<div id="main_content">
-<h2>Phenote Working Group IRC Chat</h2>
-
-When: First Tuesday of every month; 8:30am <br/>
-
-<p>You will need an IRC client to visit our chats.  You can download any number of free clients to do this.  You'll need to connect to the <b>irc.sf.net</b> and join the <b>#phenote</b> channel. </p>
-
-<p>Alternatively, you can connect to the Phenote IRC chat using the applet at the bottom of this page. </p>
-
-  <form method="post" name="launcher">
- <table style="text-align: left; margin-left: auto; margin-right: auto; width: 524px; height: 84px;" width="100%">
-<tbody>
-  <tr>
-    <td colspan="1" rowspan="1" width="156">IRC Nickname</td>
-    <td style="width: 327px;"><input size="40" name="username"></td>
-  </tr>
-  <tr>
-    <td colspan="2" rowspan="1" style="height: 25px; color: rgb(0, 0, 0); text-align: center; width: 327px;"><input name="appletbutton" value="Start Applets" style="color: rgb(0, 0, 0); "onclick="startApplets()" type="button"><br>
-    </td>
-  </tr>
-
-</tbody>
-</table>
-</form>
-
-</div>
-</div>
-
-<!--#include virtual="/ssi/footer.shtml" -->
-


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: [520] phenote/trunk/doc/phenote-website

From: <nl...@us...> - 2007-04-30 21:34:46

Revision: 520
          http://svn.sourceforge.net/obo/?rev=520&view=rev
Author:   nlw
Date:     2007-04-30 14:34:47 -0700 (Mon, 30 Apr 2007)

Log Message:
-----------
ok, i removed some of the irc files i added b/c it didn't work.  instead, i'm adding john's old webinar folder...pretty much in its entirety.  there's probably some stuff that shouldn't be here, but i'll figure that out after i get it working

Added Paths:
-----------
    phenote/trunk/doc/phenote-website/irc_chat/
    phenote/trunk/doc/phenote-website/irc_chat/EIRC-gfx.jar
    phenote/trunk/doc/phenote-website/irc_chat/EIRC.jar
    phenote/trunk/doc/phenote-website/irc_chat/IRCApplet.class
    phenote/trunk/doc/phenote-website/irc_chat/background.gif
    phenote/trunk/doc/phenote-website/irc_chat/blank.html
    phenote/trunk/doc/phenote-website/irc_chat/chat/
    phenote/trunk/doc/phenote-website/irc_chat/chat/EIRC-cfg.cab
    phenote/trunk/doc/phenote-website/irc_chat/chat/EIRC-cfg.jar
    phenote/trunk/doc/phenote-website/irc_chat/chat/EIRC.cab
    phenote/trunk/doc/phenote-website/irc_chat/chat/EIRC.jar
    phenote/trunk/doc/phenote-website/irc_chat/chat/index.html
    phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/
    phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Boink.au
    phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Boooh.au
    phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Boop.au
    phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Click.au
    phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Clock.au
    phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Drip.au
    phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Hit.au
    phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Magic.au
    phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Pipe.au
    phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Pouet.au
    phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Rifle.au
    phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Ringin.au
    phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Squish.au
    phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Train.au
    phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Warning.au
    phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Whistle.au
    phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Whoosh.au
    phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Yoo.au
    phenote/trunk/doc/phenote-website/irc_chat/contact.html
    phenote/trunk/doc/phenote-website/irc_chat/eirc.html
    phenote/trunk/doc/phenote-website/irc_chat/english.lng
    phenote/trunk/doc/phenote-website/irc_chat/etiquette.html
    phenote/trunk/doc/phenote-website/irc_chat/first.html
    phenote/trunk/doc/phenote-website/irc_chat/french.lng
    phenote/trunk/doc/phenote-website/irc_chat/gizmo.html
    phenote/trunk/doc/phenote-website/irc_chat/images/
    phenote/trunk/doc/phenote-website/irc_chat/images/splash.jpg
    phenote/trunk/doc/phenote-website/irc_chat/index.html
    phenote/trunk/doc/phenote-website/irc_chat/irc-unsigned.jar
    phenote/trunk/doc/phenote-website/irc_chat/irc.cab
    phenote/trunk/doc/phenote-website/irc_chat/irc.html
    phenote/trunk/doc/phenote-website/irc_chat/irc.jar
    phenote/trunk/doc/phenote-website/irc_chat/irc_chat.shtml
    phenote/trunk/doc/phenote-website/irc_chat/irc_script.js
    phenote/trunk/doc/phenote-website/irc_chat/junk.html
    phenote/trunk/doc/phenote-website/irc_chat/pbtn3.2.zip
    phenote/trunk/doc/phenote-website/irc_chat/pixx-english.lng
    phenote/trunk/doc/phenote-website/irc_chat/pixx-french.lng
    phenote/trunk/doc/phenote-website/irc_chat/pixx-readme.txt
    phenote/trunk/doc/phenote-website/irc_chat/pixx.cab
    phenote/trunk/doc/phenote-website/irc_chat/pixx.jar
    phenote/trunk/doc/phenote-website/irc_chat/pjirc.cfg
    phenote/trunk/doc/phenote-website/irc_chat/pjirc_2_2_1_bin.zip
    phenote/trunk/doc/phenote-website/irc_chat/script.js
    phenote/trunk/doc/phenote-website/irc_chat/securedirc-unsigned.cab
    phenote/trunk/doc/phenote-website/irc_chat/securedirc.cab
    phenote/trunk/doc/phenote-website/irc_chat/style.css
    phenote/trunk/doc/phenote-website/irc_chat/technologies.html
    phenote/trunk/doc/phenote-website/irc_chat/vnc.html

Removed Paths:
-------------
    phenote/trunk/doc/phenote-website/IRCApplet.class
    phenote/trunk/doc/phenote-website/irc.cab
    phenote/trunk/doc/phenote-website/irc.jar
    phenote/trunk/doc/phenote-website/irc_chat.shtml
    phenote/trunk/doc/phenote-website/irc_script.js
    phenote/trunk/doc/phenote-website/securedirc-unsigned.cab
    phenote/trunk/doc/phenote-website/securedirc.cab

Deleted: phenote/trunk/doc/phenote-website/IRCApplet.class
===================================================================
(Binary files differ)

Deleted: phenote/trunk/doc/phenote-website/irc.cab
===================================================================
(Binary files differ)

Deleted: phenote/trunk/doc/phenote-website/irc.jar
===================================================================
(Binary files differ)

Added: phenote/trunk/doc/phenote-website/irc_chat/EIRC-gfx.jar
===================================================================
(Binary files differ)


Property changes on: phenote/trunk/doc/phenote-website/irc_chat/EIRC-gfx.jar
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Added: phenote/trunk/doc/phenote-website/irc_chat/EIRC.jar
===================================================================
(Binary files differ)


Property changes on: phenote/trunk/doc/phenote-website/irc_chat/EIRC.jar
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Added: phenote/trunk/doc/phenote-website/irc_chat/IRCApplet.class
===================================================================
(Binary files differ)


Property changes on: phenote/trunk/doc/phenote-website/irc_chat/IRCApplet.class
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Added: phenote/trunk/doc/phenote-website/irc_chat/background.gif
===================================================================
(Binary files differ)


Property changes on: phenote/trunk/doc/phenote-website/irc_chat/background.gif
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Added: phenote/trunk/doc/phenote-website/irc_chat/blank.html
===================================================================
--- phenote/trunk/doc/phenote-website/irc_chat/blank.html	                        (rev 0)
+++ phenote/trunk/doc/phenote-website/irc_chat/blank.html	2007-04-30 21:34:47 UTC (rev 520)
@@ -0,0 +1,44 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html>
+<head>
+  <meta http-equiv="content-type"
+ content="text/html; charset=ISO-8859-1">
+  <title>OBO-Edit Webinar Overview</title>
+  <link type="text/css" href="style.css" rel="stylesheet">
+  <script language="JavaScript" src="script.js">
+</head>
+<body>
+<input><input> <br>
+<table style="width: 780px; height: 619px;" cellpadding="10"
+ cellspacing="0">
+  <tbody>
+    <tr>
+      <td
+ style="width: 200px; height: 149px; background-color: rgb(109, 150, 202); direction: ltr;"><img
+ style="width: 200px; height: 138px;" alt="OBO-Edit Logo"
+ src="images/splash.jpg"></td>
+      <td
+ style="text-align: center; width: 568px; height: 149px; background-color: rgb(109, 150, 202); font-family: Helvetica,Arial,sans-serif;">
+      <font color="white">
+      <h1>OBO-Edit
+Webinar</h1>
+      </font>
+      <h2><font color="white">Under construction</font></h2>
+      <font color="white"> </font> </td>
+    </tr>
+    <tr>
+      <td
+ style="vertical-align: top; background-color: rgb(109, 150, 202); height: 454px;">
+      <ul>
+      </ul>
+      </td>
+      <td
+ style="background-color: rgb(198, 203, 228); width: 568px; vertical-align: top; height: 454px;"><br>
+      <span style="color: rgb(0, 0, 0);"><span
+ style="color: rgb(0, 0, 0);"><font size="+2">Coming soon</font><br>
+      </span></span></td>
+    </tr>
+  </tbody>
+</table>
+</body>
+</html>

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Added: phenote/trunk/doc/phenote-website/irc_chat/chat/index.html
===================================================================
--- phenote/trunk/doc/phenote-website/irc_chat/chat/index.html	                        (rev 0)
+++ phenote/trunk/doc/phenote-website/irc_chat/chat/index.html	2007-04-30 21:34:47 UTC (rev 520)
@@ -0,0 +1,40 @@
+<HTML><HEAD>
+<TITLE>www.coolsmile.net - Chat sympa et gratuit</TITLE>
+</HEAD>
+
+<BODY style="background-color: #000000; margin: 1px; overflow: hidden;">
+<CENTER>
+<APPLET name="coolsmile" code="EIRC.class" width="100%" height="100%">
+	<PARAM name="archive" value="EIRC.jar,EIRC-cfg.jar">
+	<PARAM name="cabbase" value="EIRC.cab,EIRC-cfg.cab">
+	<PARAM name="server" value="irc.sf.net">
+	<PARAM name="port" value="6667">
+	<PARAM name="font_name" value="Helvetica">
+	<PARAM name="font_size" value="11">
+	<PARAM name="language" value="">
+	<PARAM name="mainbg" value="#809BDC">
+	<PARAM name="mainfg" value="#000000">
+	<PARAM name="textbg" value="#FFFFFF">
+	<PARAM name="textfg" value="#000000">
+	<PARAM name="selbg" value="#F0F0FF">
+	<PARAM name="selfg" value="#000000">
+	<PARAM name="join" value="#oboedit">
+	<PARAM name="username" value="cool">
+	<PARAM name="realname" value="20 H Internet">
+	<PARAM name="nickname" value="Hello??????">
+	<PARAM name="login" value="1">
+	<PARAM name="asl" value="1">
+	<PARAM name="spawn_frame" value="0">
+	<PARAM name="width" value="700">
+	<PARAM name="height" value="500">
+	<PARAM name="write_color" value="12">
+	<PARAM name="debug_traffic" value="0">
+	<PARAM name="boxmessage" value="Please wait while loading chat box...">
+	<PARAM name="boxbgcolor" value="blue">
+	<PARAM name="boxfgcolor" value="black">
+	<PARAM name="progressbar" value="true">
+	<PARAM name="progresscolor" value="red">
+	<B>You must enable or <A HREF="http://www.java.com">setup Java</A> in your web browser !</B>
+</APPLET>
+</CENTER>
+</BODY></HTML>
\ No newline at end of file

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Added: phenote/trunk/doc/phenote-website/irc_chat/contact.html
===================================================================
--- phenote/trunk/doc/phenote-website/irc_chat/contact.html	                        (rev 0)
+++ phenote/trunk/doc/phenote-website/irc_chat/contact.html	2007-04-30 21:34:47 UTC (rev 520)
@@ -0,0 +1,58 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html>
+<head>
+  <meta http-equiv="content-type"
+ content="text/html; charset=ISO-8859-1">
+  <title>OBO-Edit Webinar Contacts</title>
+  <link type="text/css" href="style.css" rel="stylesheet">
+</head>
+<body>
+<br>
+<table style="width: 780px; height: 619px;" cellpadding="10"
+ cellspacing="0">
+  <tbody>
+    <tr>
+      <td
+ style="width: 200px; height: 149px; background-color: rgb(109, 150, 202); direction: ltr;"><img
+ style="width: 200px; height: 138px;" alt="OBO-Edit Logo"
+ src="images/splash.jpg"></td>
+      <td
+ style="text-align: center; width: 568px; height: 149px; background-color: rgb(109, 150, 202); font-family: Helvetica,Arial,sans-serif;">
+      <font color="white">
+      <h1>OBO-Edit
+Webinar</h1>
+      <h2>Contact<br>
+      </h2>
+      </font> </td>
+    </tr>
+    <tr>
+      <td
+ style="vertical-align: top; background-color: rgb(109, 150, 202); height: 454px;">
+      <ul>
+        <li><a href="index.html">Overview</a></li>
+        <li><a href="technologies.html">Technologies</a><br>
+        </li>
+        <ul>
+          <li><a href="vnc.html">VNC</a></li>
+          <li><a href="irc.html">IRC</a></li>
+          <li><a href="gizmo.html">The Gizmo Project</a></li>
+          <li><a href="oboedit.html">OBO-Edit</a></li>
+        </ul>
+        <li><a href="etiquette.html">Etiquette</a></li>
+        <li style="color: rgb(255, 255, 255);">Contact</li>
+      </ul>
+      </td>
+      <td
+ style="background-color: rgb(198, 203, 228); width: 568px; vertical-align: top; height: 454px;">
+      <br>
+      <span style="color: rgb(0, 0, 0);"><span
+ style="color: rgb(0, 0, 0);">For more information,
+please contact John Day-Richter at <b>joh...@ay...</b>,
+or call him on The Gizmo Project with id <b>johnrichter.</b><br>
+      </span></span><span style="color: rgb(0, 0, 0);"><span
+ style="color: rgb(0, 0, 0);"> </span></span></td>
+    </tr>
+  </tbody>
+</table>
+</body>
+</html>

Added: phenote/trunk/doc/phenote-website/irc_chat/eirc.html
===================================================================
--- phenote/trunk/doc/phenote-website/irc_chat/eirc.html	                        (rev 0)
+++ phenote/trunk/doc/phenote-website/irc_chat/eirc.html	2007-04-30 21:34:47 UTC (rev 520)
@@ -0,0 +1,37 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+    "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+  <title>Eteria IRC Client</title>
+ </head>
+
+ <body>
+  <applet code="EIRC" archive="EIRC.jar,EIRC-gfx.jar" width="620" height="400">
+   <!-- Uncomment the line below to use signed CABs /-->
+   <!--param name="cabinets" value="EIRC.cab,EIRC-gfx.cab" /-->
+   <param name="server" value="irc.diboo.net" >
+   <!--param name="server" value="eu.undernet.org" /-->
+   <!--param name="port" value="6667" /-->
+   <!--param name="mainbg" value="#424242" /-->
+   <param name="mainbg" value="#C0C0C0" />
+   <param name="mainfg" value="#000000" />
+   <param name="textbg" value="#FFFFFF" />
+   <param name="textfg" value="#000000" />
+   <param name="selbg" value="#00007F" />
+   <param name="selfg" value="#FFFFFF" />
+   <param name="channel" value="#eirc" />
+   <param name="titleExtra" value=" - EIRC" />
+   <param name="nickname" value="Guest????" />
+   <param name="login" value="1" />
+   <!--param name="spawn_frame" value="1" /-->
+   <!--param name="frame_width" value="620" /-->
+   <!--param name="frame_height" value="400" /-->
+   <!--param name="language" value="en" /-->
+   <!--param name="country" value="US" /-->
+
+   <h1>Eteria IRC Client</h1>
+   <p>
+    Sorry, but you need a Java 1.1.x enabled browser to use EIRC.</p>
+  </applet>
+ </body>
+</html>

Added: phenote/trunk/doc/phenote-website/irc_chat/english.lng
===================================================================
--- phenote/trunk/doc/phenote-website/irc_chat/english.lng	                        (rev 0)
+++ phenote/trunk/doc/phenote-website/irc_chat/english.lng	2007-04-30 21:34:47 UTC (rev 520)
@@ -0,0 +1,93 @@
+#
+#         This java file is a part of the
+#
+#          -  Plouf's Java IRC Client  -
+#
+#      Copyright (C) 2004 Philippe Detournay
+#
+#   This file is licensed under the GPL license
+#
+#        All contacts : the...@ya...
+#
+#
+#  Syntax :
+#    Comments begin with the # character. This character must be the first character of the line.
+#    A data line has three parts : the data id, the data id description, the data string.
+#      - Data id : An hexadecimal figure identifying the string.
+#      - Data description : Begins by [ and ends by ]. The description is not parsed and
+#                           can be any string.
+#      - Data string : The string itself. Parameters are specified using the %i syntax.
+#
+#  Trailing spaces can be added using the \s escape character.
+
+0001 [INTERPRETOR_NOT_ON_CHANNEL] Not on a channel
+0002 [INTERPRETOR_UNKNOWN_DCC] %1 : unknown dcc subcommand
+0003 [INTERPRETOR_INSUFFICIENT_PARAMETERS] %1 : insufficient parameters
+0004 [INTERPRETOR_BAD_CONTEXT] %1 : unable to perform in current context
+0005 [INTERPRETOR_CANNOT_CTCP_IN_DCCCHAT] Cannot send CTCP codes via DCC Chat
+0006 [INTERPRETOR_UNKNOWN_CONFIG] %1 : unknown config subcommand
+0007 [INTERPRETOR_TIMESTAMP_ON] Timestamp enabled
+0008 [INTERPRETOR_TIMESTAMP_OFF] Timestamp disabled
+0009 [INTERPRETOR_SMILEYS_ON] Graphical smileys enabled
+000a [INTERPRETOR_SMILEYS_OFF] Graphical smileys disabled
+000b [INTERPRETOR_IGNORE_ON] Now ignoring %1
+000c [INTERPRETOR_IGNORE_OFF] Not ignoring %1 anymore
+000d [INTERPRETOR_MULTISERVER_DISABLED] Multiserver support is disabled
+  
+0101 [DCC_WAITING_INCOMING] Waiting for incoming connection...
+0102 [DCC_UNABLE_TO_OPEN_CONNECTION] Unable to open connection : %1
+0103 [DCC_CONNECTION_ESTABLISHED] DCC Connection established
+0104 [DCC_CONNECTION_CLOSED] Connection closed
+0105 [DCC_ERROR] Error : %1
+0106 [DCC_UNABLE_TO_SEND_TO] %1 : unable to send to %2
+0107 [DCC_BAD_CONTEXT] Unable to execute command from current context
+0108 [DCC_NOT_CONNECTED] Not connected
+0109 [DCC_UNABLE_PASSIVE_MODE] Unable to initialize passive mode
+010a [CTCP_PING_REPLY] [%1 PING reply] : %2 seconds
+010b [DCC_STREAM_CLOSED] Stream closed
+      
+0201 [IDENT_FAILED_LAUNCH] Failed to launch Ident server : %1
+0202 [IDENT_REQUEST] Ident request from %1
+0203 [IDENT_ERROR] Error occurred
+0204 [IDENT_REPLIED] Replied %1
+0205 [IDENT_DEFAULT_USER] default user
+0206 [IDENT_NO_USER] No user for request
+0207 [IDENT_RUNNING_ON_PORT] Ident server running on port %1
+0208 [IDENT_LEAVING] Ident server leaving : %1
+0209 [IDENT_NONE] none
+020a [IDENT_UNKNOWN] unknown
+020b [IDENT_UNDEFINED] Undefined result
+      
+0301 [FILE_SAVEAS] Save file as
+      
+0401 [ABOUT_ABOUT] About
+0402 [ABOUT_PROGRAMMING] Programming
+0403 [ABOUT_DESIGN] Design
+0404 [ABOUT_THANKS] Thanks to
+0405 [ABOUT_SUPPORT] for support, ideas and testing
+0406 [ABOUT_GPL] This software is licensed under the GPL license
+      
+0501 [SERVER_UNABLE_TO_CONNECT] Unable to connect : %1
+0502 [SERVER_UNABLE_TO_CONNECT_STILL] Unable to connect to %1 : currently trying to connect to %2
+0503 [SERVER_DISCONNECTING] Disconnecting from %1
+0504 [SERVER_CONNECTING] Connecting...
+0505 [SERVER_NOT_CONNECTED] Not connected
+0506 [SERVER_LOGIN] Logging in...
+0507 [SERVER_DISCONNECTED] Disconnected from %1
+0508 [SERVER_ERROR] Error : %1
+0509 [SERVER_AUTOREJOIN_ATTEMPT] Attempting to rejoin channel %1...
+050a [SERVER_AUTOREJOIN_FAILED] Unable to rejoin channel %1
+      
+071a [GUI_CHANGE_NICK] Change nick to
+071b [GUI_COPY_WINDOW] Copy text
+071c [GUI_DCC_CHAT_WARNING_TITLE] Warning
+071d [GUI_DCC_CHAT_WARNING_TEXT] Do you want to accept DCC chat from %1?
+
+0801 [ASL_MALE] Boy, %1 years old, %2
+0802 [ASL_FEMALE] Girl, %1 years old, %2
+0803 [ASL_UNKNOWN] %1 years old from %2
+
+0901 [REPLY_IDLE] %1 has been idle for %2
+0902 [REPLY_SIGNON] %1 connected on %2
+
+ffff [ERROR_NOT_DEFINED] Undefined string

Added: phenote/trunk/doc/phenote-website/irc_chat/etiquette.html
===================================================================
--- phenote/trunk/doc/phenote-website/irc_chat/etiquette.html	                        (rev 0)
+++ phenote/trunk/doc/phenote-website/irc_chat/etiquette.html	2007-04-30 21:34:47 UTC (rev 520)
@@ -0,0 +1,87 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html>
+<head>
+  <meta http-equiv="content-type"
+ content="text/html; charset=ISO-8859-1">
+  <title>OBO-Edit Webinar
+Technologies: OBO-Edit</title>
+  <link type="text/css" href="style.css" rel="stylesheet">
+</head>
+<body>
+<br>
+<table style="width: 780px; height: 619px;" cellpadding="10"
+ cellspacing="0">
+  <tbody>
+    <tr>
+      <td
+ style="width: 200px; height: 149px; background-color: rgb(109, 150, 202); direction: ltr;"><img
+ style="width: 200px; height: 138px;" alt="OBO-Edit Logo"
+ src="images/splash.jpg"></td>
+      <td
+ style="text-align: center; width: 568px; height: 149px; background-color: rgb(109, 150, 202); font-family: Helvetica,Arial,sans-serif;">
+      <font color="white">
+      <h1>OBO-Edit
+Webinar</h1>
+      <h2>Etiquette<br>
+      </h2>
+      </font> </td>
+    </tr>
+    <tr>
+      <td
+ style="vertical-align: top; background-color: rgb(109, 150, 202); height: 454px;">
+      <ul>
+        <li><a href="index.html">Overview</a></li>
+        <li><a href="technologies.html">Technologies</a><br>
+        </li>
+        <ul>
+          <li><a href="vnc.html">VNC</a></li>
+          <li><a href="irc.html">IRC</a></li>
+          <li><a href="gizmo.html">The Gizmo Project</a></li>
+          <li><a href="oboedit.html">OBO-Edit</a></li>
+        </ul>
+        <li style="color: rgb(255, 255, 255);">Etiquette</li>
+        <li><a href="contact.html">Contact</a></li>
+      </ul>
+      </td>
+      <td
+ style="background-color: rgb(198, 203, 228); width: 568px; vertical-align: top; height: 454px;">
+      <br>
+      <span style="color: rgb(0, 0, 0);"><span
+ style="color: rgb(0, 0, 0);">This
+is a new way of communicating for the Gene Ontology, and we're not sure
+how well it will work.<br>
+      <br>
+In order to make the whole process go more smoothly, here are some
+etiquette suggestions for the webinar...<br>
+      <br>
+      </span></span>
+      <ol>
+        <li><b>Please
+keep your phone muted. </b>The Gizmo Project teleconferencing software
+works well with many users as long as
+most users aren't transmitting data. If everyone keeps their phone
+except when asking a question, we should be fine.</li>
+        <li><b>Use
+IRC to raise your hand.</b> Before
+unmuting your phone, raise your hand in IRC and wait
+to be
+acknowledged. You can either raise your hand by typing "I have a
+question" (or something similar) or by typing "/me raises her hand".
+The second version will create a special message like "* Jane raises
+her hand"in the IRC room. I'll type "go ahead, Jane" in the IRC
+channel, and you can go ahead and ask your question.<br>
+        </li>
+        <li><b>Test
+your configuration beforehand!</b>
+Please make sure that all the tools work for you before we go into this
+seminar.&nbsp; We are bound to have technical problems the first
+day, but it would be nice to have as few as possible.</li>
+      </ol>
+      <span style="color: rgb(0, 0, 0);"><span
+ style="color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0);"><span
+ style="color: rgb(0, 0, 0);"> </span></span></span></span></td>
+    </tr>
+  </tbody>
+</table>
+</body>
+</html>

Added: phenote/trunk/doc/phenote-website/irc_chat/first.html
===================================================================
--- phenote/trunk/doc/phenote-website/irc_chat/first.html	                        (rev 0)
+++ phenote/trunk/doc/phenote-website/irc_chat/first.html	2007-04-30 21:34:47 UTC (rev 520)
@@ -0,0 +1,135 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html>
+<head>
+  <meta http-equiv="content-type"
+ content="text/html; charset=ISO-8859-1">
+  <title>OBO-Edit Webinar Overview</title>
+  <link type="text/css" href="style.css" rel="stylesheet">
+  <script language="JavaScript" src="script.js">
+</head>
+<body>
+<br>
+<table style="width: 780px; height: 619px;" cellpadding="10"
+ cellspacing="0">
+  <tbody>
+    <tr>
+      <td
+ style="width: 200px; height: 149px; background-color: rgb(109, 150, 202); direction: ltr;"><img
+ style="width: 200px; height: 138px;" alt="OBO-Edit Logo"
+ src="file:///home/jrichter/oboedit_webinar/images/splash.jpg"></td>
+      <td
+ style="text-align: center; width: 568px; height: 149px; background-color: rgb(109, 150, 202); font-family: Helvetica,Arial,sans-serif;">
+      <font color="white">
+      <h1>OBO-Edit
+Webinar</h1>
+      <h2>Overview</h2>
+      </font> </td>
+    </tr>
+    <tr>
+      <td
+ style="vertical-align: top; background-color: rgb(109, 150, 202); height: 454px;">
+      <ul>
+        <li>Overview</li>
+        <li><a href="technologies.html">Technologies</a></li>
+        <ul>
+          <li><a href="vnc.html">VNC</a></li>
+          <li><a href="irc.html">IRC</a></li>
+          <li><a href="gizmo.html">The Gizmo Project</a></li>
+          <li><a href="oboedit.html">OBO-Edit</a></li>
+        </ul>
+        <li><a href="contact.html">Contact</a></li>
+      </ul>
+      </td>
+      <td
+ style="background-color: rgb(198, 203, 228); width: 568px; vertical-align: top; height: 454px;">
+      <table style="width: 517px; height: 420px;">
+        <tbody>
+          <tr>
+            <td style="width: 67px; vertical-align: top;"><span
+ style="color: rgb(0, 0, 0); font-weight: bold;">What:</span></td>
+            <td
+ style="color: rgb(0, 0, 0); width: 411px; vertical-align: top;">OBO-Edit
+Tutorial</td>
+          </tr>
+          <tr>
+            <td style="width: 67px; vertical-align: top;"><span
+ style="color: rgb(0, 0, 0); font-weight: bold;">When:</span></td>
+            <td
+ style="color: rgb(0, 0, 0); width: 411px; vertical-align: top;"><span
+ style="color: rgb(0, 0, 0);">February 7th - </span><span
+ style="font-style: italic; color: rgb(0, 0, 0);">9:00AM
+- 3:00PM PST</span><br style="color: rgb(0, 0, 0);">
+            <span style="color: rgb(0, 0, 0);">February 8th - </span><span
+ style="font-style: italic; color: rgb(0, 0, 0);">12:00PM
+- 3:00PM PST</span></td>
+          </tr>
+          <tr>
+            <td style="width: 67px; vertical-align: top;"><span
+ style="font-weight: bold; color: rgb(0, 0, 0);">Where:</span></td>
+            <td style="width: 411px; vertical-align: top;"><span
+ style="color: rgb(0, 0, 0);">The Internet</span></td>
+          </tr>
+          <tr>
+            <td style="vertical-align: top;"><span
+ style="font-weight: bold; color: rgb(0, 0, 0);">Signups:</span></td>
+            <td style="vertical-align: top;"><span
+ style="color: rgb(0, 0, 0);">Participation is
+currently limited to GO Consortium members only</span></td>
+          </tr>
+          <tr>
+            <td style="height: 132px;" colspan="2" rowspan="1">
+            <hr><span style="color: rgb(0, 0, 0);"><br>
+Participants
+should visit the Technologies section to learn how to download and
+install the programs you'll need to join the webinar.</span><br
+ style="color: rgb(0, 0, 0);">
+            <br style="color: rgb(0, 0, 0);">
+            <span style="color: rgb(0, 0, 0);">IRC
+and VNC can be accessed via Java applets. To test your browsers
+compatibility with these applets, log in below...<br>
+            <br>
+            <hr> </span></td>
+          </tr>
+          <tr>
+            <td style="height: 107px;" colspan="2" rowspan="1">
+            <form method="post" action="javascript:launchTest()"
+ name="launcher">
+              <table
+ style="text-align: left; margin-left: auto; margin-right: auto; width: 363px; height: 102px;">
+                <tbody>
+                  <tr>
+                    <td
+ style="height: 25px; color: rgb(0, 0, 0); width: 143px;">IRC
+Nickname</td>
+                    <td
+ style="height: 25px; width: 204px; color: rgb(0, 0, 0);"><input
+ name="username" size="30" style="color: rgb(0, 0, 0);"></td>
+                  </tr>
+                  <tr>
+                    <td
+ style="height: 24px; color: rgb(0, 0, 0); width: 143px;">Full
+Name</td>
+                    <td style="height: 24px; width: 204px;"><input
+ name="fullname" size="30" style="color: rgb(0, 0, 0);"></td>
+                  </tr>
+                  <tr>
+                    <td style="height: 49px; width: 204px;" colspan="2"
+ rowspan="1" align="center"><input value="Submit" name="submitbutton"
+ style="color: rgb(0, 0, 0);" type="submit"></td>
+                  </tr>
+                </tbody>
+              </table>
+            </form>
+            </td>
+          </tr>
+        </tbody>
+      </table>
+      <br>
+      <span style="color: rgb(0, 0, 0);"><span
+ style="color: rgb(0, 0, 0);"><br>
+      </span></span></td>
+    </tr>
+  </tbody>
+</table>
+</body>
+</html>

Added: phenote/trunk/doc/phenote-website/irc_chat/french.lng
===================================================================
--- phenote/trunk/doc/phenote-website/irc_chat/french.lng	                        (rev 0)
+++ phenote/trunk/doc/phenote-website/irc_chat/french.lng	2007-04-30 21:34:47 UTC (rev 520)
@@ -0,0 +1,93 @@
+#
+#         This java file is a part of the
+#
+#          -  Plouf's Java IRC Client  -
+#
+#      Copyright (C) 2004 Philippe Detournay
+#
+#   This file is licensed under the GPL license
+#
+#        All contacts : the...@ya...
+#
+#
+#  Syntax :
+#    Comments begin with the # character. This character must be the first character of the line.
+#    A data line has three parts : the data id, the data id description, the data string.
+#      - Data id : An hexadecimal figure identifying the string.
+#      - Data description : Begins by [ and ends by ]. The description is not parsed and
+#                           can contains any string.
+#      - Data string : The string itself. Parameters are specified using the %i syntax.
+#
+#  Trailing spaces can be added using the \s escape character.
+
+0001 [INTERPRETOR_NOT_ON_CHANNEL] Pas sur un canal
+0002 [INTERPRETOR_UNKNOWN_DCC] %1 : sous-commande dcc inconnue
+0003 [INTERPRETOR_INSUFFICIENT_PARAMETERS] %1 : param\xE8tres insuffisants
+0004 [INTERPRETOR_BAD_CONTEXT] Impossible d'effectuer %1 ici
+0005 [INTERPRETOR_CANNOT_CTCP_IN_DCCCHAT] Impossible d'envoyer des codes CTCP dans un DCC Chat
+0006 [INTERPRETOR_UNKNOWN_CONFIG] %1 : sous-commande de configuration inconnue
+0007 [INTERPRETOR_TIMESTAMP_ON] Horodateur activ\xE9
+0008 [INTERPRETOR_TIMESTAMP_OFF] Horodateur d\xE9sactiv\xE9
+0009 [INTERPRETOR_SMILEYS_ON] Emoticons activ\xE9s
+000a [INTERPRETOR_SMILEYS_OFF] Emoticons d\xE9sactiv\xE9s
+000b [INTERPRETOR_IGNORE_ON] Ignore \xE0 pr\xE9sent %1
+000c [INTERPRETOR_IGNORE_OFF] N'ignore plus %1
+000d [INTERPRETOR_MULTISERVER_DISABLED] Le support multiserveur est d\xE9sactiv\xE9
+  
+0101 [DCC_WAITING_INCOMING] Attente de connexion...
+0102 [DCC_UNABLE_TO_OPEN_CONNECTION] Impssible d'ouvrir la connexion : %1
+0103 [DCC_CONNECTION_ESTABLISHED] "Connexion DCC \xE9tablie
+0104 [DCC_CONNECTION_CLOSED] Connexion ferm\xE9e
+0105 [DCC_ERROR] Erreur : %1
+0106 [DCC_UNABLE_TO_SEND_TO] %1 : impossible d'envoyer \xE0 %2
+0107 [DCC_BAD_CONTEXT] Impossible d'ex\xE9cuter la commande dans le contexte actuel
+0108 [DCC_NOT_CONNECTED] Non connect\xE9
+0109 [DCC_UNABLE_PASSIVE_MODE] Impossible d'initialiser le mode passif
+010a [CTCP_PING_REPLY] [%1 PING reply] : %2 secondes
+010b [DCC_STREAM_CLOSED] Stream ferm\xE9
+      
+0201 [IDENT_FAILED_LAUNCH] Impossible de lancer le serveur IDENT : %1
+0202 [IDENT_REQUEST] Requ\xEAte ident de %1
+0203 [IDENT_ERROR] Erreur survenue
+0204 [IDENT_REPLIED] R\xE9pondu %1
+0205 [IDENT_DEFAULT_USER] utilisateur par d\xE9faut
+0206 [IDENT_NO_USER] Aucun utilisateur pour la req\xFBete
+0207 [IDENT_RUNNING_ON_PORT] Le serveur Ident s'ex\xE9cute sur le port %1
+0208 [IDENT_LEAVING] Le serveur Ident se termine : %1
+0209 [IDENT_NONE] aucun
+020a [IDENT_UNKNOWN] inconnu
+020b [IDENT_UNDEFINED] R\xE9sultat ind\xE9termin\xE9
+      
+0301 [FILE_SAVEAS] Sauver le fichier sous
+      
+0401 [ABOUT_ABOUT] A propos
+0402 [ABOUT_PROGRAMMING] Programmation
+0403 [ABOUT_DESIGN] Design
+0404 [ABOUT_THANKS] Remerciements
+0405 [ABOUT_SUPPORT] pour leur support, leurs id\xE9es et les tests
+0406 [ABOUT_GPL] Ce programme est sous license GPL
+      
+0501 [SERVER_UNABLE_TO_CONNECT] Impossible de se connecter : %1
+0502 [SERVER_UNABLE_TO_CONNECT_STILL] Impossible de se connecter \xE0 %1, d\xE9j\xE0 en train d'essayer de se connecter \xE0 %2
+0503 [SERVER_DISCONNECTING] D\xE9connexion de %1
+0504 [SERVER_CONNECTING] Connexion...
+0505 [SERVER_NOT_CONNECTED] Non connect\xE9
+0506 [SERVER_LOGIN] Enregistrement...
+0507 [SERVER_DISCONNECTED] D\xE9connect\xE9 de %1
+0508 [SERVER_ERROR] Erreur : %1
+0509 [SERVER_AUTOREJOIN_ATTEMPT] Tentative de retour sur le canal %1...
+050a [SERVER_AUTOREJOIN_FAILED] Impossible de rejoindre le canal %1
+      
+071a [GUI_CHANGE_NICK] Modifier le nick
+071b [GUI_COPY_WINDOW] Copier le texte
+071c [GUI_DCC_CHAT_WARNING_TITLE] Attention
+071d [GUI_DCC_CHAT_WARNING_TEXT] Voulez-vous accepter une connection DCC-chat en provenance de %1?
+
+0801 [ASL_MALE] Gar\xE7on, %1 ans, %2
+0802 [ASL_FEMALE] Fille, %1 ans, %2
+0803 [ASL_UNKNOWN] %1 ans de %2
+
+0901 [REPLY_IDLE] %1 est inactif depuis %2
+0902 [REPLY_SIGNON] %1 s'est connect\xE9(e) le %2
+
+ffff [ERROR_NOT_DEFINED] Texte non d\xE9fini

Added: phenote/trunk/doc/phenote-website/irc_chat/gizmo.html
===================================================================
--- phenote/trunk/doc/phenote-website/irc_chat/gizmo.html	                        (rev 0)
+++ phenote/trunk/doc/phenote-website/irc_chat/gizmo.html	2007-04-30 21:34:47 UTC (rev 520)
@@ -0,0 +1,90 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html>
+<head>
+  <meta http-equiv="content-type"
+ content="text/html; charset=ISO-8859-1">
+  <title>OBO-Edit Webinar Technologies: The Gizmo Project</title>
+  <link type="text/css" href="style.css" rel="stylesheet">
+</head>
+<body>
+<br>
+<table style="width: 780px; height: 619px;" cellpadding="10"
+ cellspacing="0">
+  <tbody>
+    <tr>
+      <td
+ style="width: 200px; height: 149px; background-color: rgb(109, 150, 202); direction: ltr;"><img
+ style="width: 200px; height: 138px;" alt="OBO-Edit Logo"
+ src="images/splash.jpg"></td>
+      <td
+ style="text-align: center; width: 568px; height: 149px; background-color: rgb(109, 150, 202); font-family: Helvetica,Arial,sans-serif;">
+      <font color="white">
+      <h1>OBO-Edit
+Webinar</h1>
+      <h2>The Gizmo Project<br>
+      </h2>
+      </font> </td>
+    </tr>
+    <tr>
+      <td
+ style="vertical-align: top; background-color: rgb(109, 150, 202); height: 454px;">
+      <ul>
+        <li><a href="index.html">Overview</a></li>
+        <li><a href="technologies.html">Technologies</a><br>
+        </li>
+        <ul>
+          <li><a href="vnc.html">VNC</a></li>
+          <li><a href="irc.html">IRC</a></li>
+          <li style="color: rgb(255, 255, 255);">The Gizmo Project</li>
+          <li><a href="oboedit.html">OBO-Edit</a></li>
+        </ul>
+        <li><a href="etiquette.html">Etiquette</a></li>
+        <li><a href="contact.html">Contact</a></li>
+      </ul>
+      </td>
+      <td
+ style="background-color: rgb(198, 203, 228); width: 568px; vertical-align: top; height: 454px;">
+      <br>
+      <span style="color: rgb(0, 0, 0);"><span
+ style="color: rgb(0, 0, 0);">The OBO-Edit webinar
+will use <a href="gizmo.html">The
+Gizmo Project</a> to handle Voice
+over IP communications.<br>
+      <br>
+      </span></span><span style="color: rgb(0, 0, 0);"><span
+ style="color: rgb(0, 0, 0);"><a
+ href="file:///home/jrichter/oboedit_webinar/gizmo.html">The
+Gizmo Project</a> is an open source
+program similar to Skype. Users can communicate using their computer
+speakers and microphone. </span></span><span
+ style="color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0);"><a
+ href="file:///home/jrichter/oboedit_webinar/gizmo.html">The
+Gizmo Project</a> allows several
+dozen users to teleconference at once, which is why this technology has
+been chosen.<br>
+      <br>
+Download and install your copy from </span></span><span
+ style="color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0);">h<a
+ href="http://www.gizmoproject.com">ttp://www.gizmoproject.com</a></span></span><br>
+      <span style="color: rgb(0, 0, 0);"><span
+ style="color: rgb(0, 0, 0);"> <br>
+Once the software is installed, you will to complete some initial setup
+tasks, such as creating a user id and password, etc. <br>
+      <br>
+To join the conference call, dial <b>1-222-626-3348</b>
+in the phone number field near the top of the screen. If you are the
+first to join, you'll hear strange demo music and a message saying you
+are the first to call.<br>
+      <br>
+      <b>IMPORTANT: MUTE YOUR
+GIZMO PHONE IF YOU AREN'T TALKING!!!</b> <br>
+There is a mute button near the top right corner of the Gizmo window
+once you are connected. The Gizmo conference call system degrades
+quickly as more people talk, so the only way this will work is if only
+one or two people have their mikes unmuted at once.<br>
+      </span></span></td>
+    </tr>
+  </tbody>
+</table>
+</body>
+</html>

Added: phenote/trunk/doc/phenote-website/irc_chat/images/splash.jpg
===================================================================
(Binary files differ)


Property changes on: phenote/trunk/doc/phenote-website/irc_chat/images/splash.jpg
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Added: phenote/trunk/doc/phenote-website/irc_chat/index.html
===================================================================
--- phenote/trunk/doc/phenote-website/irc_chat/index.html	                        (rev 0)
+++ phenote/trunk/doc/phenote-website/irc_chat/index.html	2007-04-30 21:34:47 UTC (rev 520)
@@ -0,0 +1,133 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html>
+<head>
+  <meta content="text/html; charset=ISO-8859-1"
+ http-equiv="content-type">
+  <title>OBO-Edit Webinar Overview</title>
+  <link rel="stylesheet" href="style.css" type="text/css">
+  <script language="JavaScript" src="script.js"><!-- --></script>
+</head>
+<body>
+<br>
+<table style="width: 776px; height: 617px;" cellpadding="10"
+ cellspacing="0">
+  <tbody>
+    <tr>
+      <td
+ style="width: 200px; height: 149px; background-color: rgb(109, 150, 202); direction: ltr;"><img
+ style="width: 200px; height: 138px;" alt="OBO-Edit Logo"
+ src="images/splash.jpg"></td>
+      <td
+ style="text-align: center; width: 568px; height: 149px; background-color: rgb(109, 150, 202); font-family: Helvetica,Arial,sans-serif;">
+      <font color="white">
+      <h1>OBO-Edit
+Webinar</h1>
+      <h2>Overview</h2>
+      </font> </td>
+    </tr>
+    <tr>
+      <td
+ style="vertical-align: top; background-color: rgb(109, 150, 202); height: 454px;">
+      <ul>
+        <li style="color: rgb(255, 255, 255);">Overview</li>
+        <li><a href="technologies.html">Technologies</a></li>
+        <ul>
+          <li><a href="vnc.html">VNC</a></li>
+          <li><a href="irc.html">IRC</a></li>
+          <li><a href="gizmo.html">The Gizmo Project</a></li>
+          <li><a href="oboedit.html">OBO-Edit</a></li>
+        </ul>
+        <li><a href="etiquette.html">Etiquette</a></li>
+        <li><a href="contact.html">Contact</a></li>
+      </ul>
+      </td>
+      <td
+ style="background-color: rgb(198, 203, 228); width: 568px; vertical-align: top; height: 454px;">
+      <table height="361" width="491">
+        <tbody>
+          <tr>
+            <td style="vertical-align: top;"><span
+ style="color: rgb(0, 0, 0); font-weight: bold;">What:</span></td>
+            <td style="color: rgb(0, 0, 0); vertical-align: top;">OBO-Edit
+Tutorial</td>
+          </tr>
+          <tr>
+            <td style="width: 67px; vertical-align: top;"><span
+ style="color: rgb(0, 0, 0); font-weight: bold;">When:</span></td>
+            <td
+ style="color: rgb(0, 0, 0); width: 411px; vertical-align: top;"><span
+ style="color: rgb(0, 0, 0);">February 6th - <i>9:00AM - 9:30AM PST</i>
+- Technology test<br>
+February 7th - </span><span
+ style="font-style: italic; color: rgb(0, 0, 0);">9:00AM
+- 3:00PM PST</span><br style="color: rgb(0, 0, 0);">
+            <span style="color: rgb(0, 0, 0);">February 8th - </span><span
+ style="font-style: italic; color: rgb(0, 0, 0);">1:00PM
+- 3:00PM PST (revised time!)</span></td>
+          </tr>
+          <tr>
+            <td style="width: 67px; vertical-align: top;"><span
+ style="font-weight: bold; color: rgb(0, 0, 0);">Where:</span></td>
+            <td style="width: 411px; vertical-align: top;"><span
+ style="color: rgb(0, 0, 0);">The Internet</span></td>
+          </tr>
+          <tr>
+            <td style="vertical-align: top;"><span
+ style="font-weight: bold; color: rgb(0, 0, 0);">Signups:</span></td>
+            <td style="vertical-align: top;"><span
+ style="color: rgb(0, 0, 0);">Participation
+is
+currently limited to GO Consortium members only</span></td>
+          </tr>
+          <tr>
+            <td style="height: 132px;" colspan="2" rowspan="1">
+            <hr><span style="color: rgb(0, 0, 0);"><br>
+Participants
+should visit the Technologies section to learn how to download and
+install the programs you'll need to join the webinar. All of these
+technologies can be tested immediately; you do not need to wait until
+the webinar begins.</span><br style="color: rgb(0, 0, 0);">
+            <br style="color: rgb(0, 0, 0);">
+            <span style="color: rgb(0, 0, 0);">Voice chat can be
+accessed via The Gizmo Project using phone number <b>1-222-626-3348</b>
+(1-222-OBO-EDIT). Don't try to call from a regular phone; it won't work.<br>
+            <br>
+IRC
+and VNC can be accessed via Java applets. The VNC password is <b>oboedit_vnc</b>.<br>
+            <br>
+            </span>
+            <form method="post" name="launcher">
+              <table
+ style="text-align: left; margin-left: auto; margin-right: auto; width: 524px; height: 84px;"
+ width="100%">
+                <tbody>
+                  <tr>
+                    <td colspan="1" rowspan="1" width="156">IRC
+Nickname</td>
+                    <td style="width: 327px;"><input size="40"
+ name="username"></td>
+                  </tr>
+                  <tr>
+                    <td colspan="2" rowspan="1"
+ style="height: 25px; color: rgb(0, 0, 0); text-align: center; width: 327px;"><input
+ name="appletbutton" value="Start Applets" style="color: rgb(0, 0, 0);"
+ onclick="startApplets()" type="button"><br>
+                    </td>
+                  </tr>
+                </tbody>
+              </table>
+            </form>
+            <span style="color: rgb(0, 0, 0);">
+            <hr> </span></td>
+          </tr>
+        </tbody>
+      </table>
+      <br>
+      <span style="color: rgb(0, 0, 0);"><span
+ style="color: rgb(0, 0, 0);"><br>
+      </span></span></td>
+    </tr>
+  </tbody>
+</table>
+</body>
+</html>

Added: phenote/trunk/doc/phenote-website/irc_chat/irc-unsigned.jar
===================================================================
(Binary files differ)


Property changes on: phenote/trunk/doc/phenote-website/irc_chat/irc-unsigned.jar
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Added: phenote/trunk/doc/phenote-website/irc_chat/irc.cab
===================================================================
(Binary files differ)


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___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Added: phenote/trunk/doc/phenote-website/irc_chat/irc.html
===================================================================
--- phenote/trunk/doc/phenote-website/irc_chat/irc.html	                        (rev 0)
+++ phenote/trunk/doc/phenote-website/irc_chat/irc.html	2007-04-30 21:34:47 UTC (rev 520)
@@ -0,0 +1,96 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html>
+<head>
+  <meta http-equiv="content-type"
+ content="text/html; charset=ISO-8859-1">
+  <title>OBO-Edit Webinar Technologies: IRC</title>
+  <link type="text/css" href="style.css" rel="stylesheet">
+</head>
+<body>
+<br>
+<table style="width: 780px; height: 619px;" cellpadding="10"
+ cellspacing="0">
+  <tbody>
+    <tr>
+      <td
+ style="width: 200px; height: 149px; background-color: rgb(109, 150, 202); direction: ltr;"><img
+ style="width: 200px; height: 138px;" alt="OBO-Edit Logo"
+ src="images/splash.jpg"></td>
+      <td
+ style="text-align: center; width: 568px; height: 149px; background-color: rgb(109, 150, 202); font-family: Helvetica,Arial,sans-serif;">
+      <font color="white">
+      <h1>OBO-Edit
+Webinar</h1>
+      <h2>IRC</h2>
+      </font> </td>
+    </tr>
+    <tr>
+      <td
+ style="vertical-align: top; background-color: rgb(109, 150, 202); height: 454px;">
+      <ul>
+        <li><a href="index.html">Overview</a></li>
+        <li><a href="technologies.html">Technologies</a><br>
+        </li>
+        <ul>
+          <li><a href="vnc.html">VNC</a></li>
+          <li style="color: rgb(255, 255, 255);">IRC</li>
+          <li><a href="gizmo.html">The Gizmo Project</a></li>
+          <li><a href="oboedit.html">OBO-Edit</a></li>
+        </ul>
+        <li><a href="etiquette.html">Etiquette</a></li>
+        <li><a href="contact.html">Contact</a></li>
+      </ul>
+      </td>
+      <td
+ style="background-color: rgb(198, 203, 228); width: 568px; vertical-align: top; height: 454px;">
+      <br>
+      <span style="color: rgb(0, 0, 0);"><span
+ style="color: rgb(0, 0, 0);">The OBO-Edit webinar
+will handle live chat over IRC (Internet Relay Chat).<br>
+      <br>
+The best way to connect to the OBO-Edit IRC chat is to use the applet
+on the <a href="index.html">front
+page</a>. If you decide you'd like
+to use your own IRC applet, connect to <b>irc.sf.net</b>
+and join the <b>#oboedit</b>
+channel.<br>
+      <br>
+There are many, many IRC clients available for every computer platform.
+If you'd like to download your own client, consider:<br>
+      <br>
+      <br>
+      <table border="1" height="40" width="500">
+        <tbody>
+          <tr>
+            <td align="center" width="159"><b>Mac</b></td>
+            <td align="center" width="159"><b>Windows</b></td>
+            <td align="center" width="160"><b>Linux</b></td>
+          </tr>
+          <tr>
+            <td align="center" width="159"><a
+ href="http://homepage.mac.com/philrobin/conversation/">Conversation</a><br>
+            <a href="http://www.snak.com/Snak.html">Snak</a><br>
+            <a href="http://www.ircle.com/">ircle</a></td>
+            <td align="center" width="159"><a
+ href="http://www.mirc.com/">mIRC</a><br>
+            <a href="http://www.xircon.com/">Xircon</a><br>
+            <span style="color: rgb(0, 0, 0);"><span
+ style="color: rgb(0, 0, 0);"><a href="http://www.xchat.org/">xchat</a></span></span></td>
+            <td align="center" width="160"><a
+ href="http://konversation.kde.org/">Konversation</a><br>
+            <a href="http://www.xchat.org/">xchat</a><br>
+            <a href="http://www.bitchx.org/">BitchX</a></td>
+          </tr>
+        </tbody>
+      </table>
+      <br>
+Although we won't be using most IRC features during the webinar, there
+are dozens and dozens of commands and special IRC features. If you want
+to read up, take a look at the IRC primer at <a
+ href="http://www.irchelp.org/irchelp/ircprimer.html">http://www.irchelp.org/irchelp/ircprimer.html</a><br>
+      </span></span></td>
+    </tr>
+  </tbody>
+</table>
+</body>
+</html>

Added: phenote/trunk/doc/phenote-website/irc_chat/irc.jar
===================================================================
(Binary files differ)


Property changes on: phenote/trunk/doc/phenote-website/irc_chat/irc.jar
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Added: phenote/trunk/doc/phenote-website/irc_chat/irc_chat.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/irc_chat/irc_chat.shtml	                        (rev 0)
+++ phenote/trunk/doc/phenote-website/irc_chat/irc_chat.shtml	2007-04-30 21:34:47 UTC (rev 520)
@@ -0,0 +1,36 @@
+<!--#include virtual="/ssi/header.html" -->
+  <script language="JavaScript" src="/irc_script.js"><!-- --></script>
+<div id="page_body">
+
+<!--#include virtual="/ssi/navi_home.html" -->
+
+<div id="main_content">
+<h2>Phenote Working Group IRC Chat</h2>
+
+When: First Tuesday of every month; 8:30am <br/>
+
+<p>You will need an IRC client to visit our chats.  You can download any number of free clients to do this.  You'll need to connect to the <b>irc.sf.net</b> and join the <b>#phenote</b> channel. </p>
+
+<p>Alternatively, you can connect to the Phenote IRC chat using the applet at the bottom of this page. </p>
+
+  <form method="post" name="launcher">
+ <table style="text-align: left; margin-left: auto; margin-right: auto; width: 524px; height: 84px;" width="100%">
+<tbody>
+  <tr>
+    <td colspan="1" rowspan="1" width="156">IRC Nickname</td>
+    <td style="width: 327px;"><input size="40" name="username"></td>
+  </tr>
+  <tr>
+    <td colspan="2" rowspan="1" style="height: 25px; color: rgb(0, 0, 0); text-align: center; width: 327px;"><input name="appletbutton" value="Start Applets" style="color: rgb(0, 0, 0); "onclick="startApplets()" type="button"><br>
+    </td>
+  </tr>
+
+</tbody>
+</table>
+</form>
+
+</div>
+</div>
+
+<!--#include virtual="/ssi/footer.shtml" -->
+

Added: phenote/trunk/doc/phenote-website/irc_chat/irc_script.js
===================================================================
--- phenote/trunk/doc/phenote-website/irc_chat/irc_script.js	                        (rev 0)
+++ phenote/trunk/doc/phenote-website/irc_chat/irc_script.js	2007-04-30 21:34:47 UTC (rev 520)
@@ -0,0 +1,37 @@
+var ircwindow = null;
+var vncwindow = null;
+
+function startApplets() {
+
+   if (ircwindow != null) {
+     ircwindow.close();
+     ircwindow = null;
+   }
+
+   if (vncwindow != null) {
+     vncwindow.close();
+     vncwindow = null;
+   }
+
+   vcnwindow = window.open("http://frizzled.lbl.gov:5801", "VNC", "status=no,width=1100,height=800");
+   ircwindow = window.open("about:blank", "My window", "scrollbars=no,status=no,width=510,height=430");
+
+   var html = "";
+
+   html += "<html><body>\n";
+   html += "<applet code=\"IRCApplet.class\" archive=\"irc.jar,pixx.jar\" width=475 height=400>\n";
+   html += "<param name=\"CABINETS\" value=\"irc.cab,securedirc.cab,pixx.cab\">\n";
+   html += "<param name=\"nick\" value='"+document.forms["launcher"].username.value+"'>\n";
+   html += "<param name=\"fullname\" value='"+document.forms["launcher"].username.value+"'>\n";
+
+   html += "<param name=\"alternatenick\" value=\"Anon???\">\n";
+   html += "<param name=\"host\" value=\"irc.sf.net\">\n";
+   html += "<param name=\"command1\" value=\"/join #phenote\">\n";
+   html += "<param name=\"gui\" value=\"pixx\">\n";
+   html += "</applet>\n";
+   html += "</body></html>";
+
+//   alert(html);
+   ircwindow.document.writeln(html);
+   ircwindow.document.close();
+}

Added: phenote/trunk/doc/phenote-website/irc_chat/junk.html
===================================================================
--- phenote/trunk/doc/phenote-website/irc_chat/junk.html	                        (rev 0)
+++ phenote/trunk/doc/phenote-website/irc_chat/junk.html	2007-04-30 21:34:47 UTC (rev 520)
@@ -0,0 +1,15 @@
+<html>
+<head>
+</head>
+<body>
+<applet code="IRCApplet.class" archive="irc.jar,pixx.jar" width=300 height=300>
+ <param name="CABINETS" value="irc.cab,securedirc.cab,pixx.cab">
+ <param name="nick" value="jrichter">
+ <param name="alternatenick" value="Anon???">
+ <param name="fullname" value="John Day-Richter">
+ <param name="host" value="irc.diboo.net">
+ <param name="command1" value="/join #oboedit">
+ <param name="gui" value="pixx">
+</applet>
+</body>
+</html>
\ No newline at end of file

Added: phenote/trunk/doc/phenote-website/irc_chat/pbtn3.2.zip
===================================================================
(Binary files differ)


Property changes on: phenote/trunk/doc/phenote-website/irc_chat/pbtn3.2.zip
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Added: phenote/trunk/doc/phenote-website/irc_chat/pixx-english.lng
===================================================================
--- phenote/trunk/doc/phenote-website/irc_chat/pixx-english.lng	                        (rev 0)
+++ phenote/trunk/doc/phenote-website/irc_chat/pixx-english.lng	2007-04-30 21:34:47 UTC (rev 520)
@@ -0,0 +1,75 @@
+#
+#         This java file is a part of the
+#
+#          -  Plouf's Java IRC Client  -
+#
+#      Copyright (C) 2004 Philippe Detournay
+#
+#   This file is licensed under the GPL license
+#
+#        All contacts : the...@ya...
+#
+#
+#  Syntax :
+#    Comments begin with the # character. This character must be the first character of the line.
+#    A data line has three parts : the data id, the data id description, the data string.
+#      - Data id : An hexadecimal figure identifying the string.
+#      - Data description : Begins by [ and ends by ]. The description is not parsed and
+#                           can be any string.
+#      - Data string : The string itself. Parameters are specified using the %i syntax.
+#
+#  Trailing spaces can be added using the \s escape character.
+
+8601 [SOURCE_YOU_KICKED] You've been kicked out of %1...
 
[truncated message content]

[Obo-svn-commit] SF.net SVN: obo: [519] phenote/trunk/doc/phenote-website

From: <nl...@us...> - 2007-04-30 21:13:19

Revision: 519
          http://svn.sourceforge.net/obo/?rev=519&view=rev
Author:   nlw
Date:     2007-04-30 14:13:21 -0700 (Mon, 30 Apr 2007)

Log Message:
-----------
adding the other files for irc chat

Added Paths:
-----------
    phenote/trunk/doc/phenote-website/irc-unsigned.jar
    phenote/trunk/doc/phenote-website/irc.cab
    phenote/trunk/doc/phenote-website/irc.jar
    phenote/trunk/doc/phenote-website/securedirc-unsigned.cab
    phenote/trunk/doc/phenote-website/securedirc.cab

Added: phenote/trunk/doc/phenote-website/irc-unsigned.jar
===================================================================
(Binary files differ)


Property changes on: phenote/trunk/doc/phenote-website/irc-unsigned.jar
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Added: phenote/trunk/doc/phenote-website/irc.cab
===================================================================
(Binary files differ)


Property changes on: phenote/trunk/doc/phenote-website/irc.cab
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Added: phenote/trunk/doc/phenote-website/irc.jar
===================================================================
(Binary files differ)


Property changes on: phenote/trunk/doc/phenote-website/irc.jar
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Added: phenote/trunk/doc/phenote-website/securedirc-unsigned.cab
===================================================================
(Binary files differ)


Property changes on: phenote/trunk/doc/phenote-website/securedirc-unsigned.cab
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Added: phenote/trunk/doc/phenote-website/securedirc.cab
===================================================================
(Binary files differ)


Property changes on: phenote/trunk/doc/phenote-website/securedirc.cab
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream


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