X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fgff%2FGffHelperBase.java;h=feeec1d2a60c7a87c5e678f87b8acbecb7956793;hb=4eb1ed22600411fe5b6e9ac93084b45429ccfad6;hp=fbde9d99c5e6887b0cedc62a71cf563bb6ccb151;hpb=8f920d337154e092f5f9056ffde3cdf2735eca43;p=jalview.git

diff --git a/src/jalview/io/gff/GffHelperBase.java b/src/jalview/io/gff/GffHelperBase.java
index fbde9d9..feeec1d 100644
--- a/src/jalview/io/gff/GffHelperBase.java
+++ b/src/jalview/io/gff/GffHelperBase.java
@@ -321,18 +321,27 @@ public abstract class GffHelperBase implements GffHelperI
     {
       int start = Integer.parseInt(gff[START_COL]);
       int end = Integer.parseInt(gff[END_COL]);
-      float score = Float.NaN;
+
+      /*
+       * default 'score' is 0 rather than Float.NaN as the latter currently
+       * disables the 'graduated colour => colour by label' option
+       */
+      float score = 0f;
       try
       {
         score = Float.parseFloat(gff[SCORE_COL]);
       } catch (NumberFormatException nfe)
       {
-        // e.g. '.' - leave as NaN to indicate no score
+        // e.g. '.' - leave as zero
       }
 
       SequenceFeature sf = new SequenceFeature(gff[TYPE_COL],
               gff[SOURCE_COL], start, end, score, gff[SOURCE_COL]);
 
+      sf.setStrand(gff[STRAND_COL]);
+
+      sf.setPhase(gff[PHASE_COL]);
+
       if (attributes != null)
       {
         /*
@@ -347,7 +356,7 @@ 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()))
           {