[MOBY-guts] biomoby commit

[Paul Gordon]

gordonp
Fri Jun  8 10:04:27 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources
In directory dev.open-bio.org:/tmp/cvs-serv28675/src/main/ca/ucalgary/seahawk/resources

Modified Files:
	MobyContentGUIHelp.html mobyBuilderRules.xml startup.html 
Log Message:
Commit of Seahawk 1.0 updates and associated core updates
moby-live/Java/src/main/ca/ucalgary/seahawk/resources MobyContentGUIHelp.html,1.1,1.2 mobyBuilderRules.xml,1.4,1.5 startup.html,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/MobyContentGUIHelp.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/MobyContentGUIHelp.html	2006/10/25 02:33:22	1.1
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/MobyContentGUIHelp.html	2007/06/08 14:04:27	1.2
@@ -49,6 +49,12 @@
     <a name="create"></a>
     <h2>How do I create data?</h2>
 
+    <h3>Drag and Drop / Cut and Paste</h3>
+    <p>
+      The easiest way to create data is to simply drag a file, text selection, or Web link
+      onto the Seahawk interface. Seahawk will try to display the data you drop.
+    </p>
+
     <h3>Loading documents</h3>
     <p>
       Click the <b>folder/Web icon</b> on the bottom toolbar will give you the option of
@@ -64,14 +70,13 @@
       With the mouse, you can highlight arbitrary sections of text in the Seahawk display.  
       <b>Clicking within selected text</b> will raise a popup menu showing MOBY service
       options.  Seahawk will try to determine the type of data highlighted are 
-      potentially show services for the selection as a:
+      potentially show services for the selection as a, among other things:
       <ul>
 	<li>String</li>
         <li>Search Keyword</li>
         <li>Database Identifier</li>
         <li>Protein Sequence</li>
-        <li>DNA/RNA Sequence <b>(note that highlighting sequence right-to-left 
-	  will create the reverse complement)</b></li>
+        <li>DNA/RNA Sequence</b></li>
       </ul>
     </p>
 

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/mobyBuilderRules.xml,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/mobyBuilderRules.xml	2007/04/26 15:30:01	1.4
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/mobyBuilderRules.xml	2007/06/08 14:04:27	1.5
@@ -4,15 +4,26 @@
 <prefix value="tigr">http://www.bioxml.info/dtd/tigrxml.dtd</prefix>
 <prefix value="bioseq">http://www.bioxml.info/dtd/Bioseq.dtd</prefix>
 
-<!-- Creates a DNASequence, \N is IUPAC nucleotide shorthand -->
+<!-- Creates a DNASequence, \N is IUPAC nucleotide shorthand --> 
 <object>
-  <regex>(\N+(?:\x20|\r|\t|\n)?)+</regex>
+  <regex>(\N*\s*(\N{10,}(?:\x20|\r|\t|\n)?)+\N*)</regex>
   <datatype value="DNASequence"/>
   <namespace>
-    <ns value="unknown">unknown</ns>
+    <ns value="unknown">''</ns>
+  </namespace>
+  <member value="SequenceString" whitespace="strip">$1</member>
+  <member value="Length" whitespace="strip">string-length('$1')</member>
+</object>
+
+<!-- Creates an AminoAcidSequence, \P is IUPAC amino acid residue shorthand -->
+<object>
+  <regex>(\P*\s*(\P{10,}(?:\x20|\r|\t|\n)?)+\P*)</regex>
+  <datatype value="AminoAcidSequence"/>
+  <namespace>
+    <ns value="unknown">''</ns>
   </namespace>
-  <member value="SequenceString" whitespace="strip">$2</member>
-  <member value="Length" whitespace="strip">string-length('$2')</member>
+  <member value="SequenceString" whitespace="strip">$1</member>
+  <member value="Length" whitespace="strip">string-length('$1')</member>
 </object>
 
 <!-- ABI sequence trace's magic signature at start of file -->

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/startup.html,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/startup.html	2007/04/26 15:31:00	1.3
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/startup.html	2007/06/08 14:04:27	1.4
@@ -14,6 +14,8 @@
 
 <i>For example data, and more help on using Seahawk to automatically <b>discover and run Web-based analysis</b> services,
 please click the help icon at the bottom of this window.</i>
-
+<p>
+Please help us improve Seahawk by <a href="http://www.surveymonkey.com/s.aspx?sm=EZTTJXKwQEG82WGWaVBkPg_3d_3d">completing a user survey</a>!
+</p>
   </body>
 </html>