[MOBY-guts] biomoby commit

[Paul Gordon]

gordonp
Wed Oct 25 21:40:43 EDT 2006
Update of /home/repository/moby/moby-live/Java/docs
In directory dev.open-bio.org:/tmp/cvs-serv15388

Modified Files:
	Seahawk.html 
Log Message:
Updated docs to reflect fact that Seahawk is now completely in the jMOBY CVS
moby-live/Java/docs Seahawk.html,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/Seahawk.html,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/docs/Seahawk.html	2006/08/01 16:00:49	1.2
+++ /home/repository/moby/moby-live/Java/docs/Seahawk.html	2006/10/26 01:40:43	1.3
@@ -50,7 +50,7 @@
   <a name="launch"></a>
     <h2>How do I launch it?</h2>
 
-    <p>The applet can be launched from the following Web site: <a href="http://moby.ucalgary.ca/seahawk/">http://moby.ucalgary.ca/seahawk/</a></p>
+    <p>The applet can be launched from the following Web site: <a href="http://moby.ucalgary.ca/seahawk/">http://moby.ucalgary.ca/seahawk/</a>.  If you are a programmer, you can run it with a checked out version of the jMOBY CVS: <tt>./build.sh seahawk/tt></p>
 
 
   <a name="classes"></a>
@@ -69,7 +69,7 @@
 
     <p>The jar (Java archive) file containing all of the required classes (including those from 
        Axis, Jena, Xalan, Xerces, etc.) is available 
-       <a href="http://bluejay.ucalgary.ca/java/seahawk/seahawk.jar">here</a>.  Note that this JAR
+       <a href="http://moby.ucalgary.ca/java/seahawk/seahawk.jar">here</a>.  Note that this JAR
        is signed by the University of Calgary Bioinformatics Lab.  This jar file 
        can be used as an application with the command:
 <blockquote><code><pre>java -jar seahawk.jar</pre></code></blockquote>
@@ -79,8 +79,8 @@
 <p>
 Or it can be launched from within another Java application with the following code (and assuming seahawk.jar is in the classpath):
 <blockquote><code><pre>
-import ca.ucalgary.bluejay.util.MobyUtils;
-import ca.ucalgary.bluejay.gui.MobyContentGUI;
+import ca.ucalgary.seahawk.util.MobyUtils;
+import ca.ucalgary.seahawk.gui.MobyContentGUI;
 
 // the rest of your application code goes here...
 
@@ -108,7 +108,7 @@
   There are 4 main mechanisms for creating Moby Data Instances in Seahawk:
 <ol>
   <li>When a Moby XML file is loaded, the <a href="seahawkXSLT.html">resulting (customizable) HTML</a> display contains XPointer-based hyperlinks to parts of the original XML file.</li>
-  <li>Highlighted text is automatically turned into a Moby String Object by <code>ca.ucalgary.bluejay.gui.MobyContentGUI</code>, and
+  <li>Highlighted text is automatically turned into a Moby String Object by <code>ca.ucalgary.seahawk.gui.MobyContentGUI</code>, and
       this same class will create a MOBY DNASequence, RNASequence or AASequence if 95% of the characters are valid for that sequence type.</li>
   <li>Highlighted text is tested against a set of regular expression rules</li>
   <li>Programmatically selected XML document nodes (e.g. when genes are clicked in <a href="http://bluejay.ucalgary.ca">Bluejay</a>) are tested against a set of XPath rules</li>