[MOBY-guts] biomoby commit

[Paul Gordon]

gordonp
Tue May  4 12:20:45 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources
In directory dev.open-bio.org:/tmp/cvs-serv6311/src/main/ca/ucalgary/seahawk/resources

Modified Files:
	mobyRules.xsl 
Log Message:
LSIDified more rules, renamed to general, not EMBOSS specific names
moby-live/Java/src/main/ca/ucalgary/seahawk/resources mobyRules.xsl,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/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/seahawk/resources/mobyRules.xsl	2010/04/23 05:21:42	1.1
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/mobyRules.xsl	2010/05/04 16:20:45	1.2
@@ -58,11 +58,8 @@
       <xsl:when test="$selectedACDTypeTarget = 'FASTA'">
 	<xsl:apply-templates select="*" mode="FASTA"/>
       </xsl:when>
-      <xsl:when test="$selectedACDTypeTarget = 'sequence'">
-	<xsl:apply-templates select="*" mode="sequence"/>
-      </xsl:when>
-      <xsl:when test="$selectedACDTypeTarget = 'nucleotide-sequence'">
-	<xsl:apply-templates select="*" mode="nucleotide-sequence"/>
+      <xsl:when test="$selectedACDTypeTarget = 'plain_sequence'">
+	<xsl:apply-templates select="*" mode="plain_sequence"/>
       </xsl:when>
       <xsl:otherwise>
 	<xsl:apply-templates select="*"/>
@@ -76,19 +73,11 @@
   <!-- ****************************************************** -->
 
   <!-- Turn any sequence into a plain-old string -->
-  <xsl:template match="moby:NucleotideSequence | NucleotideSequence" name="NucleotideSequence.1" mode="nucleotide-sequence">
+  <xsl:template match="moby:GenericSequence | GenericSequence" name="GenericSequence.3" mode="plain_sequence">
+    <dc:source>urn:lsid:bioxml.info:mobyLoweringSchemaMapping:GenericSequence2plain_sequence</dc:source>
     <xsl:value-of select="*[@articleName='SequenceString'] | *[@moby:articleName='SequenceString']"/>
   </xsl:template>
 
-  <xsl:template match="moby:Collection/moby:Simple[./moby:GenericSequence] | Collection/Simple[./GenericSequence]" 
-                 name="Collection-GenericSequence.1" mode="seqall">
-    <xsl:apply-templates select="moby:GenericSequence | GenericSequence" mode="seqall"/>
-  </xsl:template>
-
-  <xsl:template match="moby:GenericSequence | GenericSequence" name="GenericSequence.2" mode="sequence">
-    <xsl:apply-templates select="." mode="seqall"/>
-  </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