X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentUtils.java;h=209020711cfd36ccbc159bd5c9bce0d11283d466;hb=d8084ce0043bb2454cfc48fe9c87f9aef12c0cf8;hp=42a1201e8bb0754ce382c92724d76edb3c78d62a;hpb=2facc9ee2fdb025b5cc79b005e7eb5bd915cd9ba;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 42a1201..2090207 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -1529,6 +1529,8 @@ public class AlignmentUtils
   public static int transferFeatures(SequenceI fromSeq, SequenceI toSeq,
           MapList mapping, String select, String... omitting)
   {
+    Map<String, Integer> featureCounts = new HashMap<String, Integer>();
+
     SequenceI copyTo = toSeq;
     while (copyTo.getDatasetSequence() != null)
     {
@@ -1601,6 +1603,11 @@ public class AlignmentUtils
           copy.setBegin(Math.min(mappedTo[0], mappedTo[1]));
           copy.setEnd(Math.max(mappedTo[0], mappedTo[1]));
           copyTo.addSequenceFeature(copy);
+          int featureNumber = featureCounts.containsKey(type) ? featureCounts
+                  .get(type) : -1;
+          featureNumber++;
+          featureCounts.put(type, featureNumber);
+          copy.setFeatureNumber(featureNumber);
           count++;
         }
       }