[MOBY-guts] biomoby commit

[Paul Gordon]

gordonp
Wed Apr 18 11:28:07 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/resources
In directory dev.open-bio.org:/tmp/cvs-serv12088/src/main/ca/ucalgary/services/resources

Modified Files:
	mobyRules.xsl 
Log Message:
Added rules for ABI traces, and DNA sequence-to-plain string
moby-live/Java/src/main/ca/ucalgary/services/resources mobyRules.xsl,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/resources/mobyRules.xsl,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/services/resources/mobyRules.xsl	2007/03/12 14:33:38	1.1
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/resources/mobyRules.xsl	2007/04/18 15:28:07	1.2
@@ -52,11 +52,14 @@
       because XSLT does not handle variables in the mode attribute.  Therefore for each target
       text data type included in this stylesheet, you must include an if condition here.  See
       http://www.dpawson.co.uk/xsl/sect2/nono.html#d1905e383
-	-->      
+	 -->
     <xsl:choose>
       <xsl:when test="$selectedACDTypeTarget = 'seqall'">
 	<xsl:apply-templates select="*" mode="seqall"/>
       </xsl:when>
+      <xsl:when test="$selectedACDTypeTarget = 'nucleotide-sequence'">
+	<xsl:apply-templates select="*" mode="nucleotide-sequence"/>
+      </xsl:when>
       <xsl:otherwise>
 	<xsl:apply-templates select="*"/>
       </xsl:otherwise>
@@ -68,6 +71,11 @@
   <!-- * Specific MOBY -> text rules start below!           * -->
   <!-- ****************************************************** -->
 
+  <!-- Turn any sequence into a plain-old string -->
+  <xsl:template match="moby:NucleotideSequence | NucleotideSequence" name="NucleotideSequence.1" mode="nucleotide-sequence">
+    <xsl:value-of select="*[@articleName='SequenceString'] | *[@moby:articleName='SequenceString']"/>
+  </xsl:template>
+
   <!-- Turn any sequence into a FastA -->
   <!-- The name of the template is "MobyDataType#uniqueid", so we can parse this
        easily, rather than try to figure out what the arbitrarily complex match attribute 
@@ -91,4 +99,14 @@
 
   </xsl:template>
 
+
+  <!-- ****************************************************** -->
+  <!-- * Below here are binary equivalencies of formats,    * -->
+  <!-- * which don't actually do any transformation, but    * -->
+  <!-- * which are kept for TextClient to note and pass the * -->
+  <!-- * base64 decoded Moby data as-is.                    * -->
+  <!-- ****************************************************** -->
+
+  <xsl:template match="/binarydata" name="ABISequenceChromatogram.1" mode="abi-trace"/>
+
 </xsl:stylesheet>