[MOBY-guts] biomoby commit

[Paul Gordon]

gordonp
Thu Feb  8 11:59:58 EST 2007
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test
In directory dev.open-bio.org:/tmp/cvs-serv27169/main/org/biomoby/service/test

Modified Files:
	ConvertAAtoFASTA_AA.java FromFastaToDNASequence.java 
Log Message:
Documentation updates
moby-live/Java/src/main/org/biomoby/service/test ConvertAAtoFASTA_AA.java,1.1,1.2 FromFastaToDNASequence.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test/ConvertAAtoFASTA_AA.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test/ConvertAAtoFASTA_AA.java	2006/12/06 16:07:10	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test/ConvertAAtoFASTA_AA.java	2007/02/08 16:59:58	1.2
@@ -1,13 +1,13 @@
-/**
- * Simple service used for exemplary and testing purposes.
- */
-
 package org.biomoby.service.test;
 
 import org.biomoby.shared.MobyDataType;
 import org.biomoby.shared.data.*;
 import org.biomoby.service.*;
 
+/**
+ * Simple service used for exemplary and testing purposes.
+ */
+
 @mobyService(name="ConvertAAtoFASTA_AA",
              type="FormatConversion", 
 	     provider="moby.ucalgary.ca", 
@@ -19,6 +19,10 @@
 
 public class ConvertAAtoFASTA_AA extends MobyServlet{
 
+    /**
+     * Builds a FastA record from a MOBY AminoAcidSequence object.  Demonstrates
+     * how to access fields of a MOBY object, and how to build a new object.
+     */
     public void processRequest(MobyDataJob request, MobyDataJob result) throws Exception{
          // The input parameter for this method is registered as "inseq"
          MobyDataComposite aaSeqObject = (MobyDataComposite) request.get("inseq");

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test/FromFastaToDNASequence.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test/FromFastaToDNASequence.java	2006/12/06 16:07:10	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test/FromFastaToDNASequence.java	2007/02/08 16:59:58	1.2
@@ -13,8 +13,19 @@
 	     description={"Converts FastA formatted records into DNASequences, ", 
 			  "primarily to increase inter-service compatibility"})
 
+/**
+ * Simple service used for testing and as an example for users of how to use exceptions 
+ * and warnings in MOBY services.
+ */
+
 public class FromFastaToDNASequence extends MobyServlet{
 
+    /**
+     * Parses a FastA string into its header component and sequence, constructing
+     * a MOBY DNASequence object (or subclass thereof), which can be used in more services.
+     * An exception will be thrown if the data doesn't appear to be FastA, or a warning
+     * will be added to the results if the sequence doesn't appear to be DNA.  
+     */
     public void processRequest(MobyDataJob request, MobyDataJob result) throws Exception{
          // The input parameter for this method is registered as "inseq"
          MobyDataComposite fastaObject = (MobyDataComposite) request.get("inseq");