[Gmod-apollo-cmts] CVS: apollo/src/java/apollo/config ApolloNameAdapterI.java,1.22,1.23 DefaultNameAdapter.java,1.36,1.37

[Mark G. <mg...@us...>]

Update of /cvsroot/gmod/apollo/src/java/apollo/config
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv23420/src/java/apollo/config

Modified Files:
	ApolloNameAdapterI.java DefaultNameAdapter.java 
Log Message:
per request from david waring - annotation editor was setting exon ids in 
a gmod specific fashion - gene:start-end - moved this to name adapter with
generate exon id - so now david can change this behavior in his name adapter



Index: ApolloNameAdapterI.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/config/ApolloNameAdapterI.java,v
retrieving revision 1.22
retrieving revision 1.23
diff -C2 -d -r1.22 -r1.23
*** ApolloNameAdapterI.java	15 Sep 2005 00:07:01 -0000	1.22
--- ApolloNameAdapterI.java	16 Dec 2005 23:05:00 -0000	1.23
***************
*** 34,37 ****
--- 34,39 ----
                             SeqFeatureI feature);
  
+   public String generateExonId(SeqFeatureI exon, String geneId);
+ 
    //ADDED by TAIR
    public String getSuffixDelimiter();

Index: DefaultNameAdapter.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/config/DefaultNameAdapter.java,v
retrieving revision 1.36
retrieving revision 1.37
diff -C2 -d -r1.36 -r1.37
*** DefaultNameAdapter.java	20 Sep 2005 15:09:30 -0000	1.36
--- DefaultNameAdapter.java	16 Dec 2005 23:05:00 -0000	1.37
***************
*** 85,107 ****
    public String generateId(StrandedFeatureSetI annots,
                             String curation_name, SeqFeatureI feature) {
!     if (feature instanceof AnnotatedFeature) {
!       return getId (annots, curation_name,
!                     AnnotatedFeature.class,
!                     nextAnnotNumber(annots, AnnotatedFeature.class),
!                     "GN", "");
!     } else if (feature instanceof Transcript) {
        return getId(annots, curation_name,
                     Transcript.class, 
                     nextAnnotNumber(annots, Transcript.class),
                     "XS", "");
!     } else if (feature instanceof ExonI) {
        return getId(annots, curation_name,
                     ExonI.class,
                     nextAnnotNumber(annots, ExonI.class),
                     "EX", "");
      } else
        return "???";
    }
  
    /** Makes name update transaction, edits model w it, & returns it */
    protected UpdateTransaction setName(AnnotatedFeatureI annFeat, String newName) {
--- 85,111 ----
    public String generateId(StrandedFeatureSetI annots,
                             String curation_name, SeqFeatureI feature) {
!     if (feature.isTranscript()) {
        return getId(annots, curation_name,
                     Transcript.class, 
                     nextAnnotNumber(annots, Transcript.class),
                     "XS", "");
!     } else if (feature.isExon()) {
        return getId(annots, curation_name,
                     ExonI.class,
                     nextAnnotNumber(annots, ExonI.class),
                     "EX", "");
+     } else if (feature.hasAnnotatedFeature()) {
+       return getId (annots, curation_name,
+                     AnnotatedFeature.class,
+                     nextAnnotNumber(annots, AnnotatedFeature.class),
+                     "GN", "");
      } else
        return "???";
    }
  
+   public String generateExonId(SeqFeatureI exon, String geneId) {
+     return geneId + ":" + exon.getStart() + "-" + exon.getEnd();
+   }
+ 
    /** Makes name update transaction, edits model w it, & returns it */
    protected UpdateTransaction setName(AnnotatedFeatureI annFeat, String newName) {