[MOBY-guts] biomoby commit

[Paul Gordon]

gordonp
Thu Aug  4 10:12:48 EDT 2005
Update of /home/repository/moby/moby-live/Java/docs
In directory pub.open-bio.org:/tmp/cvs-serv8341

Modified Files:
	SimpleClient.html 
Log Message:
Made HTML anchors compliant to non-XML browsers, and added Boolean as a primitive

moby-live/Java/docs SimpleClient.html,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/SimpleClient.html,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Java/docs/SimpleClient.html	2005/08/04 04:13:31	1.5
+++ /home/repository/moby/moby-live/Java/docs/SimpleClient.html	2005/08/04 14:12:48	1.6
@@ -48,7 +48,7 @@
 
     <hr/>
 
-  <a name="APIAnatomy"/>
+  <a name="APIAnatomy"></a>
     <h2>Basic Anatomy of the Java API</h2>
     <p>
     Three main classes form the core of the API: 
@@ -79,7 +79,7 @@
     </p>
 
     <hr/>
-    <a name="helloWorld"/>
+    <a name="helloWorld"></a>
     <h2>Hello World (or its bioinformatics equivalent)</h2>
 
       <p>
@@ -112,7 +112,7 @@
 	A version of this code with comments and error checking is available in the 
 	<a href="http://www.biomoby.org/GettingTheCode.html">MOBY CVS</a> as Java/src/Clients/TestRequest.java
 <hr/>
-<a name="creatingjMOBYData"/>
+<a name="creatingjMOBYData"></a>
   <h2>Creating jMOBY Data</h2>
   <p>
     The Java API is designed so that all of the MOBY-S XML concepts can be "get" or "set" using Java primitives 
@@ -151,7 +151,7 @@
   <h3>Creating a "primitive" data object</h3>
 <p>
 The following data are considered irreducible, atomic, or "primitive" in MOBY:
-<a name="primitives"/>
+<a name="primitives"></a>
 <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>
@@ -161,6 +161,7 @@
   <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>
+  <tr><td><em>Boolean</em></td><td><code>MobyDataBoolean</code></td><td><code><a href="http://www.javadocs.org/Boolean">java.lang.Boolean</a></code></td><td><ul><li>Boolean</li><li>boolean</li><li>Strings "true" or "false"</li></ul></tr>
   <tr><td><em>DateTime</em></td><td><code>MobyDataDateTime</code></td><td><code><a href="http://www.javadocs.org/GregorianCalendar">java.util.GregorianCalendar</a></code></td><td><ul><li>java.util.GregorianCalendar</li><li>Strings like "2005-07-21" (a <a href="http://www.w3.org/TR/NOTE-datetime">W3C profile version of an ISO 8601 date-time string</a>)</a></ul></tr>
 </tbody>
 </table>
@@ -191,7 +192,7 @@
 </p>
 <hr/>
 
-<a name="manipulatingjMOBYData"/>
+<a name="manipulatingjMOBYData"></a>
 <h2>Manipulating jMOBY data</h2>
 <p>
 One does not only want to create data objects, but also retrieve information from them and edit them.  
@@ -234,7 +235,7 @@
 </p>
 
     <hr/>
-    <a name="creatingMOBYXML"/>
+    <a name="creatingMOBYXML"></a>
     <h2>Creating MOBY XML (responses and queries)</h2>
       <p>
       It may at times be necessary to explicitly create a 
@@ -277,7 +278,7 @@
 MobyDataUtils.toXMLDocument(System.out, queries);
 </pre></code></blockquote>
 <hr/>
-<a name="parsingMOBYXML"/>
+<a name="parsingMOBYXML"></a>
 <h2>Parsing MOBY XML</h2>
 
 <p>As a counterpart to the utility above, jMOBY provides a method to deserialize a response/request envelope, useful if you are rolling your own server:
@@ -293,7 +294,7 @@
     <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: Wed Aug  3 23:08:06 MDT 2005
+Last modified: Thu Aug  4 09:04:40 MDT 2005
 <!-- hhmts end -->
   </body>
 </html>