JAL-1925 update source version in license

[jalview.git] / src / jalview / ws / DBRefFetcher.java

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index 7693142..a2526a9 100644 (file)
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
  * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -125,9 +125,13 @@ public class DBRefFetcher implements Runnable
     {
       alseqs[i] = seqs[i];
       if (seqs[i].getDatasetSequence() != null)
+      {
         ds[i] = seqs[i].getDatasetSequence();
+      }
       else
+      {
         ds[i] = seqs[i];
+      }
     }
     this.dataset = ds;
     // TODO Jalview 2.5 lots of this code should be in the gui package!
@@ -596,9 +600,9 @@ public class DBRefFetcher implements Runnable
                 sequence.getSequenceAsString()).toUpperCase();
 
         int absStart = entrySeq.indexOf(nonGapped);
-        int mapStart = entry.getStart();
-        jalview.datamodel.Mapping mp;
+        Mapping mp;
 
+        final int sequenceStart = sequence.getStart();
         if (absStart == -1)
         {
           // Is local sequence contained in dataset sequence?
@@ -618,11 +622,10 @@ public class DBRefFetcher implements Runnable
           // absStart = 0;
           // create valid mapping between matching region of local sequence and
           // the mapped sequence
-          mp = new Mapping(null, new int[] {
-              sequence.getStart() + absStart,
-              sequence.getStart() + absStart + entrySeq.length() - 1 },
-                  new int[] { entry.getStart(),
-                      entry.getStart() + entrySeq.length() - 1 }, 1, 1);
+          mp = new Mapping(null, new int[] { sequenceStart + absStart,
+              sequenceStart + absStart + entrySeq.length() - 1 }, new int[]
+          { entry.getStart(), entry.getStart() + entrySeq.length() - 1 },
+                  1, 1);
           updateRefFrame = false; // mapping is based on current start/end so
           // don't modify start and end
         }
@@ -645,7 +648,7 @@ public class DBRefFetcher implements Runnable
             if (sequence.getSequenceFeatures() != null)
             {
               SequenceFeature[] sf = sequence.getSequenceFeatures();
-              int start = sequence.getStart();
+              int start = sequenceStart;
               int end = sequence.getEnd();
               int startShift = 1 - absStart - start; // how much the features
                                                      // are
@@ -667,8 +670,8 @@ public class DBRefFetcher implements Runnable
                 + " from " + dbSource + " sequence : " + entry.getName());
         sequence.transferAnnotation(entry, mp);
         // unknownSequences.remove(sequence);
-        int absEnd = absStart + nonGapped.length();
-        absStart += 1;
+        absStart += entry.getStart();
+        int absEnd = absStart + nonGapped.length() - 1;
         if (!trimDatasetSeqs)
         {
           // insert full length sequence from record