X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fgff%2FGff3Helper.java;h=28bcf4422d3258886dd72452644ca09492968ebe;hb=2ea1fb1e8751ac7272c421820000449525664f02;hp=594040ac88449f1da5b327e4080559f54d8459b8;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git

diff --git a/src/jalview/io/gff/Gff3Helper.java b/src/jalview/io/gff/Gff3Helper.java
index 594040a..28bcf44 100644
--- a/src/jalview/io/gff/Gff3Helper.java
+++ b/src/jalview/io/gff/Gff3Helper.java
@@ -39,6 +39,8 @@ import java.util.Map;
  */
 public class Gff3Helper extends GffHelperBase
 {
+  public static final String ALLELES = "alleles";
+
   protected static final String TARGET = "Target";
 
   protected static final String ID = "ID";
@@ -89,7 +91,7 @@ public class Gff3Helper extends GffHelperBase
       String atts = gff[ATTRIBUTES_COL];
       Map<String, List<String>> attributes = parseNameValuePairs(atts);
 
-      SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+      SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology();
       if (so.isA(soTerm, SequenceOntologyI.PROTEIN_MATCH))
       {
         sf = processProteinMatch(attributes, seq, gff, align, newseqs,
@@ -311,10 +313,9 @@ public class Gff3Helper extends GffHelperBase
          * give the mapped sequence a copy of the sequence feature, with 
          * start/end range adjusted 
          */
-        SequenceFeature sf2 = new SequenceFeature(sf);
-        sf2.setBegin(1);
         int sequenceFeatureLength = 1 + sf.getEnd() - sf.getBegin();
-        sf2.setEnd(sequenceFeatureLength);
+        SequenceFeature sf2 = new SequenceFeature(sf, 1,
+                sequenceFeatureLength, sf.getFeatureGroup(), sf.getScore());
         mappedSequence.addSequenceFeature(sf2);
 
         /*
@@ -363,9 +364,11 @@ public class Gff3Helper extends GffHelperBase
    */
   @Override
   protected SequenceFeature buildSequenceFeature(String[] gff,
+          int typeColumn, String group,
           Map<String, List<String>> attributes)
   {
-    SequenceFeature sf = super.buildSequenceFeature(gff, attributes);
+    SequenceFeature sf = super.buildSequenceFeature(gff, typeColumn, group,
+            attributes);
     String desc = getDescription(sf, attributes);
     if (desc != null)
     {
@@ -391,14 +394,14 @@ public class Gff3Helper extends GffHelperBase
       desc = target.split(" ")[0];
     }
 
-    SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+    SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology();
     String type = sf.getType();
     if (so.isA(type, SequenceOntologyI.SEQUENCE_VARIANT))
     {
       /*
        * Ensembl returns dna variants as 'alleles'
        */
-      desc = StringUtils.listToDelimitedString(attributes.get("alleles"),
+      desc = StringUtils.listToDelimitedString(attributes.get(ALLELES),
               ",");
     }