[MOBY-guts] biomoby commit

Thu Aug 4 02:50:31 UTC 2005

gordonp
Wed Aug  3 22:50:31 EDT 2005
Update of /home/repository/moby/moby-live/Java/docs
In directory pub.open-bio.org:/tmp/cvs-serv5995

Modified Files:
	SimpleClient.html 
Log Message:
Incremental update

moby-live/Java/docs SimpleClient.html,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/SimpleClient.html,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4

--- /home/repository/moby/moby-live/Java/docs/SimpleClient.html	2005/07/22 05:00:58	1.3
+++ /home/repository/moby/moby-live/Java/docs/SimpleClient.html	2005/08/04 02:50:31	1.4
@@ -151,12 +151,13 @@
   <h3>Creating a "primitive" data object</h3>
 <p>
 The following data are considered irreducible, atomic, or "primitive" in MOBY:
+<a name="primitives"/>
 <table border="1">
 <thead>
 <tr><th><a href="http://www.biomoby.org/twiki/bin//view/Moby/MobySAPI#The_MOBY_Data_Class_Ontology">MOBY Specification</a></th><th>jMOBY class in <code>org.biomoby.shared.data</code></th><th>underlying Java implementation</th><th>Can be instantiated using any one of</th></tr>
 </thead>
 <tbody>
-  <tr><td><em>Object</em></td><td><code>MobyDataObject</code></td><td>implements <code><a href="http://www.javadocs.org/Comparable">Comparable</a></code></td><td><ul><li>"namespace", "id"</li><li>MOBYDataObject (cloning)</li></ul></tr>
+  <tr><td><em>Object</em></td><td><code>MobyDataObject</code></td><td><code>Object</code></td><td><ul><li>"namespace", "id"</li><li>MOBYDataObject (cloning)</li></ul></tr>
   <tr><td><em>String</em></td><td><code>MobyDataString</code></td><td><code><a href="http://www.javadocs.org/StringBuffer">java.lang.StringBuffer</a></code></td><td><ul><li><a href="http://www.javadocs.org/CharSequence/">java.lang.CharSequence</a> (i.e. CharBuffer, String, StringBuffer, StringBuilder)</li></ul></td></tr>
   <tr><td><em>Integer</em></td><td><code>MobyDataInt</code></td><td><code><a href="http://www.javadocs.org/BigInteger">java.math.BigInteger</a></code></td><td><ul><li>int</li><li><a href="http://www.javadocs.org/Number">java.lang.Number</a> (i.e. Byte, Double, Float, Integer, Long, Short, BigInteger, BigDecimal)</li><li>Strings like "2005"</li></ul></tr>
   <tr><td><em>Float</em></td><td><code>MobyDataFloat</code></td><td><code><a href="http://www.javadocs.org/BigDecimal">java.math.BigDecimal</a></code></td><td><ul><li>double</li><li>java.lang.Number</li><li>Strings like "2.0-e4" or "0.0002"</li></ul></tr>
@@ -169,7 +170,7 @@
 <blockquote><code>MobyDataString sequenceString = new MobyDataString("MPGGFILAIDEGTTSARAIIYNQDLEVLGIGQYDFPQHYPSPGYVEHNPDEIWNAQMLAI");</code></blockquote>
 <blockquote><code>MobyDataInt sequenceLength = new MobyDataInt(60);</code></blockquote>
 <blockquote><code>MobyDataFloat sequence<a href="http://www.expasy.org/tools/pi_tool-doc.html">PI</a> = new MobyDataFloat(3.67);</code></blockquote>
-<blockquote><code>MobyDataFloat sequence<a href="http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/information3.html"><acronym title="Blasic LocalAlignment Search Tool">Blast</acronym></a><a href="http://www.ncbi.nlm.nih.gov/BLAST/tutorial/Altschul-1.html#head2">EValue</a> = new MobyDataFloat("1e-29");</code></blockquote>
+<blockquote><code>MobyDataFloat sequence<a href="http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/information3.html"><acronym title="Blasic Local Alignment Search Tool">Blast</acronym></a><a href="http://www.ncbi.nlm.nih.gov/BLAST/tutorial/Altschul-1.html#head2">EValue</a> = new MobyDataFloat("1e-29");</code></blockquote>
 <blockquote><code>MobyDataDateTime <a href="ftp://ftp.ncbi.nih.gov/blast/db/blastdb.txt">blastDB</a>Updated = new MobyDataDateTime("2005-03-24");</code></blockquote>
 <blockquote><code></code></blockquote>
 </p>
@@ -193,11 +194,26 @@
 <a name="manipulatingjMOBYData"/>
 <h2>Manipulating jMOBY data</h2>
 <p>
-Coming soon.
+One does not only want to create data objects, but also retrieve information from them and edit them.  
+As a client, one may need to display or filter service response data. As a service provider, one needs to extract 
+information from submitted queries.  The jMOBY data instance API endeavours to make these data easily extractable and mutable.
 </p>
 
 <h3>Dissecting queries and responses</h3>
+
 <h3>Changing data objects</h3>
+<p>The <code>getObject</code> method allows the user to retrieve the underlying internal 
+representation of the MOBY data in any <code>MobyDataInstance</code>.  The returned <code>Object</code> can be safely
+cast as listed <a href="#primitives">in the primitives table above</a>, <code>MobyDataComposite</code> 
+uses a <code>HashMap</code>, <code>MobyDataObjectSet</code> uses a <code>Vector</code>.  Modifying mutable returned 
+object modifies the MobyDataObject from which it came.  For example:
+
+<blockquote><code><pre>
+
+</pre></code></blockquote>
+
+</p>
+
     <hr/>
     <a name="creatingMOBYXML"/>
     <h2>Creating MOBY XML (responses and queries)</h2>
@@ -257,7 +273,7 @@
     <address><a href="mailto:gordonp at ucalgary.ca">Paul Gordon</a></address>
 <!-- Created: Wed Jul 20 11:44:30 MDT 2005 -->
 <!-- hhmts start -->
-Last modified: Thu Jul 21 23:45:59 MDT 2005
+Last modified: Fri Jul 22 22:13:34 MDT 2005
 <!-- hhmts end -->
   </body>
 </html>


