[Gmod-apollo-cmts] SF.net SVN: gmod:[24784] apollo/trunk/src/java/apollo/dataadapter/gff3

[<gk...@us...>]

Revision: 24784
          http://gmod.svn.sourceforge.net/gmod/?rev=24784&view=rev
Author:   gk_fan
Date:     2011-04-06 19:16:27 +0000 (Wed, 06 Apr 2011)

Log Message:
-----------
Added phase to CDS features in GFF3 (as required).

Modified Paths:
--------------
    apollo/trunk/src/java/apollo/dataadapter/gff3/GFF3Adapter.java
    apollo/trunk/src/java/apollo/dataadapter/gff3/GFF3Entry.java

Modified: apollo/trunk/src/java/apollo/dataadapter/gff3/GFF3Adapter.java
===================================================================
--- apollo/trunk/src/java/apollo/dataadapter/gff3/GFF3Adapter.java	2011-04-06 16:00:48 UTC (rev 24783)
+++ apollo/trunk/src/java/apollo/dataadapter/gff3/GFF3Adapter.java	2011-04-06 19:16:27 UTC (rev 24784)
@@ -299,6 +299,7 @@
           tStart = tEnd;
           tEnd = tmp;
         }
+        int currentLength = 0;
         for (Object o : feat.getFeatures()) {
           SeqFeatureI child = (SeqFeatureI)o;
           SeqFeatureI cds = null;
@@ -322,6 +323,8 @@
             cds.setFeatureType("CDS");
             cds.setId(cds.getId() + "-cds");
             cds.setName(cds.getName() + "-cds");
+            cds.setPhase(currentLength % 3);
+            currentLength += cds.length();
             children.add(cds);
           }
         }

Modified: apollo/trunk/src/java/apollo/dataadapter/gff3/GFF3Entry.java
===================================================================
--- apollo/trunk/src/java/apollo/dataadapter/gff3/GFF3Entry.java	2011-04-06 16:00:48 UTC (rev 24783)
+++ apollo/trunk/src/java/apollo/dataadapter/gff3/GFF3Entry.java	2011-04-06 19:16:27 UTC (rev 24784)
@@ -568,7 +568,10 @@
         end = feat.getHigh();
         score = feat.getScore();
         strand = feat.getStrand();
-        phase = feat.getPhase();
+        // phase only applies to CDS
+        if (type.equals("CDS")) {
+          setPhase(feat.getPhase());
+        }
         id = feat.getId();
         name = feat.getName();
         //populate dbxrefs


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