Menu
▾
▴
[Obo-svn-commit] SF.net SVN: obo: [654] phenote/trunk
|
From: <nl...@us...> - 2007-05-30 19:59:50
|
Revision: 654
http://svn.sourceforge.net/obo/?rev=654&view=rev
Author: nlw
Date: 2007-05-30 12:59:45 -0700 (Wed, 30 May 2007)
Log Message:
-----------
*Adding in the help docs to work *inside* of phenote. its not smart yet to detect what you might be needing help on, but it'll at least bring up the help. search works.
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/help/toc.html
phenote/trunk/doc/phenote-website/help/toc_generator.xsl
phenote/trunk/src/java/phenote/gui/HelpMenu.java
Added Paths:
-----------
phenote/trunk/src/java/phenote/main/HelpManager.java
Modified: phenote/trunk/doc/phenote-website/help/toc.html
===================================================================
--- phenote/trunk/doc/phenote-website/help/toc.html 2007-05-30 19:49:19 UTC (rev 653)
+++ phenote/trunk/doc/phenote-website/help/toc.html 2007-05-30 19:59:45 UTC (rev 654)
@@ -1,351 +1,362 @@
<html>
<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<META http-equiv="Content-Type" content="text/html; charset=UTF-8">
<title>Table of Contents</title>
</head>
-<body><small><font face="Arial"><p><center><strong>Contents</strong></center></p>
+<body>
+<small><font face="Arial">
+<p>
+<center>
+<strong>Contents</strong>
+</center>
+</p>
-<table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Phenote User's Guide
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">What is Phenote?</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Advantages to Annotation with Ontolgies</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Bugs and Troubleshooting</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Licensing Information</font></td>
-</tr></table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Phenote User's Guide
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">What is Phenote?</font></td>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Advantages to Annotation with Ontolgies</font></td>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Bugs and Troubleshooting</font></td>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Licensing Information</font></td>
+</tr>
+</table>
+
</font></td>
-</tr></table>
-<table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Getting Started
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Phenote Webstart</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Phenote from the Command Line</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Ontologies included with Phenote</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Running Phenote for the First Time</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Exiting Phenote</font></td>
-</tr></table>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Getting Started
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Phenote Webstart</font></td>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Phenote from the Command Line</font></td>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Ontologies included with Phenote</font></td>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Running Phenote for the First Time</font></td>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Exiting Phenote</font></td>
+</tr>
+</table>
+
</font></td>
-</tr></table>
-<table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The Phenote Interface
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Menu Bars</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Data Entry</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Term Info</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Annotation Spreadsheet</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Changing your Configuration</font></td>
-</tr></table>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">The Phenote Interface
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Menu Bars</font></td>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Data Entry</font></td>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Term Info</font></td>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Annotation Spreadsheet</font></td>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Changing your Configuration</font></td>
+</tr>
+</table>
+
</font></td>
-</tr></table>
-<table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Loading/Saving Annotations
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Introduction to Data Adapters</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Loading & Saving</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The PhenoXML adapter</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The PhenoSyntax Adapter</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The Tag-Value Adapter</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The Tab-Delimited Adapter</font></td>
-</tr></table>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Loading/Saving Annotations
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Introduction to Data Adapters</font></td>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Loading & Saving</font></td>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">The PhenoXML adapter</font></td>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">The PhenoSyntax Adapter</font></td>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">The Tag-Value Adapter</font></td>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">The Tab-Delimited Adapter</font></td>
+</tr>
+</table>
+
</font></td>
-</tr></table>
-<table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Creating Annotations
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Editing Functions</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Entering data into Free-Text fields</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Entering data into Ontology Fields</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Term Composition/Refinement</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Changing your Autocompletion Settings</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Sample Annotations</font></td>
-</tr></table>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Creating Annotations
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Editing Functions</font></td>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Entering data into Free-Text fields</font></td>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Entering data into Ontology Fields</font></td>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Term Composition/Refinement</font></td>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Changing your Autocompletion Settings</font></td>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Sample Annotations</font></td>
+</tr>
+</table>
+
</font></td>
-</tr></table>
-<table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Information for Developers
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Writing a Data Adapter</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Connecting to a Database</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Adding configurability</font></td>
-</tr></table>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Information for Developers
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Writing a Data Adapter</font></td>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Connecting to a Database</font></td>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Adding configurability</font></td>
+</tr>
+</table>
+
</font></td>
-</tr></table>
-<table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">What to do after Phenote
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">I've entered my data, now what?</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Other Uses for Phenote</font></td>
-</tr></table>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">What to do after Phenote
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">I've entered my data, now what?</font></td>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Other Uses for Phenote</font></td>
+</tr>
+</table>
+
</font></td>
-</tr></table>
-<table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Customizing Phenote
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">What is a Configuration?</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">How To Edit a Configuration File</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Sample Configuration 1</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Sample Configuration 2</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">XML skeleton</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The <phenote-configuration> Tag</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The <tab> Tag</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The <dataadapter> Tag</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The <master-to-local-config> Tag</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The <field> Tag</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The <ontology> Tag</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The <auto-update-ontologies> Tag</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The <update-timer> Tag</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The <term-history> Tag</font></td>
-</tr></table>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Customizing Phenote
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">What is a Configuration?</font></td>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">How To Edit a Configuration File</font></td>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Sample Configuration 1</font></td>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Sample Configuration 2</font></td>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">XML skeleton</font></td>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">The <phenote-configuration> Tag</font></td>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">The <tab> Tag</font></td>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">The <dataadapter> Tag</font></td>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">The <master-to-local-config> Tag</font></td>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">The <field> Tag</font></td>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">The <ontology> Tag</font></td>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">The <auto-update-ontologies> Tag</font></td>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">The <update-timer> Tag</font></td>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">The <term-history> Tag</font></td>
+</tr>
+</table>
+
</font></td>
-</tr></table>
-<table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Appendix
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">An Introduction to OBO Ontologies</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Basic Concepts and Vocabulary</font></td>
-</tr></table>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Appendix
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">An Introduction to OBO Ontologies</font></td>
+</tr>
+</table>
+
+<table border="0" cellpadding="0" cellspacing="0" width="100%">
+<tr>
+<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td><td valign="top" width="100%"><font face="Arial" size="2">Basic Concepts and Vocabulary</font></td>
+</tr>
+</table>
+
</font></td>
-</tr></table>
-<table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">from OBOedit
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Working with Data Adapters
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The Basic Flat File Interface</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The OBO Adapter</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The GO Flat File Adapter</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The Serial Adapter</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Custom Data Adapters</font></td>
-</tr></table>
- </font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Customizing the Interface
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Working with XML Layouts</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Common Parameters</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The <glue> Tag</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The <spacer> Tag</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The <label> Tag</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The <box> Tag</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The <grid> Tag</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The <panel> Tag</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The <compactgrid> Tag</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The <divider> Tag</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The <tabs> Tag</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The <window> Tag</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The <if> Tag</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The <component> Tag</font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Example Layouts
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The Default Layout</font></td>
-</tr></table>
- </font></td>
-</tr></table>
- </font></td>
-</tr></table>
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">Customizing OBO-Edit
- <table border="0" cellpadding="0" cellspacing="0" width="100%"><tr>
-<td valign="baseline" width="15"><img src="page.gif" width="11" height="11" hspace="3"></td>
-<td valign="top" width="100%"><font face="Arial" size="2">The Configuration Plugin</font></td>
-</tr></table>
- </font></td>
-</tr></table>
-</font></td>
-</tr></table>
-</font></small></body>
+</tr>
+</table>
+
+</font></small>
+</body>
</html>
Modified: phenote/trunk/doc/phenote-website/help/toc_generator.xsl
===================================================================
--- phenote/trunk/doc/phenote-website/help/toc_generator.xsl 2007-05-30 19:49:19 UTC (rev 653)
+++ phenote/trunk/doc/phenote-website/help/toc_generator.xsl 2007-05-30 19:59:45 UTC (rev 654)
@@ -1,6 +1,6 @@
<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform">
-<xsl:param name="mapfile" select='/phenote/doc/phenote-website/help/Phenote.jhm'/>
+<xsl:param name="mapfile" select='Phenote.jhm'/>
<xsl:template match="toc">
<html>
Modified: phenote/trunk/src/java/phenote/gui/HelpMenu.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/HelpMenu.java 2007-05-30 19:49:19 UTC (rev 653)
+++ phenote/trunk/src/java/phenote/gui/HelpMenu.java 2007-05-30 19:59:45 UTC (rev 654)
@@ -8,6 +8,7 @@
import javax.swing.JMenuItem;
import javax.swing.JOptionPane;
import javax.swing.ImageIcon;
+import javax.help.CSH;
import phenote.dataadapter.CharacterListManager;
import phenote.dataadapter.DataAdapterI;
@@ -18,6 +19,7 @@
//import phenote.gui.prefswindow.PrefsWindowController; ???
import phenote.gui.SplashScreen;
import phenote.main.PhenoteVersion;
+import phenote.main.HelpManager;
class HelpMenu extends JMenu {
@@ -38,7 +40,9 @@
help = new JMenuItem("Phenote Help");
help.setEnabled(Config.inst().hasDataAdapters());
help.setActionCommand("help");
- help.addActionListener(actionListener);
+ help.addActionListener(new CSH.DisplayHelpFromSource(HelpManager
+ .getHelpBroker()));
+// help.addActionListener(actionListener);
add(help);
JMenuItem about = new JMenuItem("About");
@@ -57,7 +61,7 @@
JOptionPane.showMessageDialog(null, m, "Phenote Help",
JOptionPane.INFORMATION_MESSAGE);
System.out.println("help selected");
- }
+ }
else if (e.getActionCommand().equals("about")) {
//throw up splash screen here. make sure to make different pic.
// String m = "This is Phenote v (version here)....[more to come]";
Added: phenote/trunk/src/java/phenote/main/HelpManager.java
===================================================================
--- phenote/trunk/src/java/phenote/main/HelpManager.java (rev 0)
+++ phenote/trunk/src/java/phenote/main/HelpManager.java 2007-05-30 19:59:45 UTC (rev 654)
@@ -0,0 +1,29 @@
+package phenote.main;
+
+import java.io.File;
+
+import javax.help.HelpBroker;
+import javax.help.HelpSet;
+
+public class HelpManager {
+ protected static HelpBroker helpBroker;
+ protected static String helpsetPath = "doc/phenote-website/help/Phenote.hs";
+
+ public static HelpBroker getHelpBroker() {
+ if (helpBroker == null) {
+ HelpSet hs;
+ File docsDir = new File(helpsetPath);
+
+ try {
+ hs = new HelpSet(null, docsDir.toURL());
+ } catch (Exception ee) {
+ System.out.println("HelpSet " + ee.getMessage());
+ System.out.println("HelpSet " + docsDir + " not found");
+ return null;
+ }
+ helpBroker = hs.createHelpBroker();
+ }
+
+ return helpBroker;
+ }
+}
\ No newline at end of file
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|