X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fgff%2FGff3Helper.java;h=a25a0141482317eae632b79764ac7996c4c49cc6;hb=1beac3545a78d4c5c3274dbb53296708d693efe0;hp=8af39332f1e05256c6e8a93acdc8fabfd9fb3963;hpb=51160e18fc93c618169ac9a4e5fda2a6a4486ec5;p=jalview.git

diff --git a/src/jalview/io/gff/Gff3Helper.java b/src/jalview/io/gff/Gff3Helper.java
index 8af3933..a25a014 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";
@@ -152,8 +154,8 @@ public class Gff3Helper extends GffHelperBase
      */
     if ("-".equals(strand))
     {
-      System.err
-              .println("Skipping mapping from reverse complement as not yet supported");
+      System.err.println(
+              "Skipping mapping from reverse complement as not yet supported");
       return null;
     }
 
@@ -244,7 +246,8 @@ public class Gff3Helper extends GffHelperBase
    * @return
    */
   @SuppressWarnings("unused")
-  protected String findTargetId(String target, Map<String, List<String>> set)
+  protected String findTargetId(String target,
+          Map<String, List<String>> set)
   {
     return target;
   }
@@ -275,8 +278,8 @@ public class Gff3Helper extends GffHelperBase
    * @throws IOException
    */
   protected SequenceFeature processProteinMatch(
-          Map<String, List<String>> set, SequenceI seq,
-          String[] gffColumns, AlignmentI align, List<SequenceI> newseqs,
+          Map<String, List<String>> set, SequenceI seq, String[] gffColumns,
+          AlignmentI align, List<SequenceI> newseqs,
           boolean relaxedIdMatching)
   {
     // This is currently tailored to InterProScan GFF output:
@@ -312,7 +315,7 @@ public class Gff3Helper extends GffHelperBase
          */
         int sequenceFeatureLength = 1 + sf.getEnd() - sf.getBegin();
         SequenceFeature sf2 = new SequenceFeature(sf, 1,
-                sequenceFeatureLength, sf.getFeatureGroup());
+                sequenceFeatureLength, sf.getFeatureGroup(), sf.getScore());
         mappedSequence.addSequenceFeature(sf2);
 
         /*
@@ -320,8 +323,8 @@ public class Gff3Helper extends GffHelperBase
          * renamed with its qualified accession id; renaming has to wait until
          * all sequence reference resolution is complete
          */
-        String accessionId = StringUtils.listToDelimitedString(
-                set.get(NAME), ",");
+        String accessionId = StringUtils
+                .listToDelimitedString(set.get(NAME), ",");
         if (accessionId.length() > 0)
         {
           String database = sf.getType(); // TODO InterProScan only??
@@ -398,7 +401,7 @@ public class Gff3Helper extends GffHelperBase
       /*
        * Ensembl returns dna variants as 'alleles'
        */
-      desc = StringUtils.listToDelimitedString(attributes.get("alleles"),
+      desc = StringUtils.listToDelimitedString(attributes.get(ALLELES),
               ",");
     }