JAL-1705 derive transcript sequences from gene sequence/GFF; handle CDS

[jalview.git] / src / jalview / io / gff / GffHelperBase.java

diff --git a/src/jalview/io/gff/GffHelperBase.java b/src/jalview/io/gff/GffHelperBase.java
index 6d9327b..499fa7b 100644 (file)
--- a/src/jalview/io/gff/GffHelperBase.java
+++ b/src/jalview/io/gff/GffHelperBase.java
@@ -335,6 +335,8 @@ public abstract class GffHelperBase implements GffHelperI
 
       sf.setStrand(gff[STRAND_COL]);
 
+      sf.setPhase(gff[PHASE_COL]);
+
       if (attributes != null)
       {
         /*
@@ -349,7 +351,7 @@ public abstract class GffHelperBase implements GffHelperI
         for (Entry<String, List<String>> attr : attributes.entrySet())
         {
           String values = StringUtils.listToDelimitedString(
-                  attr.getValue(), "; ");
+                  attr.getValue(), ",");
           sf.setValue(attr.getKey(), values);
           if (NOTE.equals(attr.getKey()))
           {