[Gmod-apollo-cmts] SF.net SVN: gmod:[23189] apollo/trunk/src/java/apollo/dataadapter/gff3/ GFF3Adapter.java

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

Revision: 23189
          http://gmod.svn.sourceforge.net/gmod/?rev=23189&view=rev
Author:   gk_fan
Date:     2010-05-12 21:21:51 +0000 (Wed, 12 May 2010)

Log Message:
-----------
GFF3Adapter now skip CDS features that lack a "Parent" attribute (rather than crashing).

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

Modified: apollo/trunk/src/java/apollo/dataadapter/gff3/GFF3Adapter.java
===================================================================
--- apollo/trunk/src/java/apollo/dataadapter/gff3/GFF3Adapter.java	2010-05-12 21:19:09 UTC (rev 23188)
+++ apollo/trunk/src/java/apollo/dataadapter/gff3/GFF3Adapter.java	2010-05-12 21:21:51 UTC (rev 23189)
@@ -896,7 +896,12 @@
 
   private void processCds(GFF3Entry entry, Map<String, int[]> cdsCoords)
   {
-    for (String pid : entry.getAttributeValues("Parent")) {
+    List<String> parents = entry.getAttributeValues("Parent");
+    if (parents == null) {
+      logger.warn("No Parent attribute for CDS " + entry.getId());
+      return;
+    }
+    for (String pid : parents) {
       int []coords = cdsCoords.get(pid);
       if (coords == null) {
         coords = new int[] {entry.getStart(), entry.getEnd()};


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