X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FHtmlFile.java;h=3cb7c3fc612c7af895aa948d02e0c7d7780c8587;hb=36c3d72e0344f1aaa2137dca8eba829e7395f05a;hp=77da038733aef32b0496680a29725974fed91cf2;hpb=cffabc9d0dce26594ab974db993ce919a9e63b8d;p=jalview.git

diff --git a/src/jalview/io/HtmlFile.java b/src/jalview/io/HtmlFile.java
index 77da038..3cb7c3f 100644
--- a/src/jalview/io/HtmlFile.java
+++ b/src/jalview/io/HtmlFile.java
@@ -70,10 +70,13 @@ public class HtmlFile extends AlignFile
         JSONObject sequence = sequenceIter.next();
         String sequcenceString = sequence.get("seq").toString();
         Sequence seq = new Sequence(sequence.get("name").toString(),
-                sequcenceString, 0, sequcenceString.length());
+                sequcenceString, Integer.valueOf(sequence.get("start")
+                        .toString()), Integer.valueOf(sequence.get("end")
+                        .toString()));
 
         JSONArray jsonSeqArray = (JSONArray) sequence.get("features");
-        SequenceFeature[] retrievedSeqFeatures = getJalviewSequenceFeatures(jsonSeqArray);
+        SequenceFeature[] retrievedSeqFeatures = getJalviewSequenceFeatures(
+                jsonSeqArray, seq);
         if (retrievedSeqFeatures != null)
         {
           seq.setSequenceFeatures(retrievedSeqFeatures);
@@ -88,7 +91,7 @@ public class HtmlFile extends AlignFile
   }
 
   public SequenceFeature[] getJalviewSequenceFeatures(
-          JSONArray jsonSeqFeatures)
+          JSONArray jsonSeqFeatures, Sequence seq)
   {
     SequenceFeature[] seqFeatures = null;
     int count = 0;
@@ -105,11 +108,10 @@ public class HtmlFile extends AlignFile
         Long begin = (Long) jsonFeature.get("xStart");
         Long end = (Long) jsonFeature.get("xEnd");
         String type = (String) jsonFeature.get("text");
-
         // String color = (String) jsonFeature.get("fillColor");
 
-        sequenceFeature.setBegin(begin.intValue());
-        sequenceFeature.setEnd(end.intValue());
+        sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
+        sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
         sequenceFeature.setType(type);
         seqFeatures[count++] = sequenceFeature;
       }