X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FDBRefFetcher.java;h=d531fea96622ee408002129bd8d4cc163749069d;hb=51f05d7903402a5dec8e915fbe5e49ce913d069a;hp=f5789ea5ee265f7ebe7d0c5e364527f101593a33;hpb=aced09c4feeaf3406269442c14e54abeeb4cad81;p=jalview.git

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index f5789ea..d531fea 100644
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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!
@@ -283,11 +287,14 @@ public class DBRefFetcher implements Runnable
   {
     if (dbSources == null)
     {
-      throw new Error(MessageManager.getString("error.implementation_error_must_init_dbsources"));
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_must_init_dbsources"));
     }
     running = true;
     long startTime = System.currentTimeMillis();
-    af.setProgressBar(MessageManager.getString("status.fetching_db_refs"), startTime);
+    af.setProgressBar(MessageManager.getString("status.fetching_db_refs"),
+            startTime);
     try
     {
       if (Cache.getDefault("DBREFFETCH_USEPICR", false))
@@ -393,8 +400,8 @@ public class DBRefFetcher implements Runnable
             {
               SequenceI sequence = dataset[seqIndex];
               DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(
-                      sequence.getDBRef(), new String[]
-                      { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT
+                      sequence.getDBRef(),
+                      new String[] { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT
               // });
               // check for existing dbrefs to use
               if (uprefs != null && uprefs.length > 0)
@@ -517,8 +524,7 @@ public class DBRefFetcher implements Runnable
       Vector sequenceMatches = new Vector();
       // look for corresponding accession ids
       DBRefEntry[] entryRefs = jalview.util.DBRefUtils.selectRefs(
-              entry.getDBRef(), new String[]
-              { dbSource });
+              entry.getDBRef(), new String[] { dbSource });
       if (entryRefs == null)
       {
         System.err
@@ -594,9 +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?
@@ -616,12 +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
         }
@@ -644,7 +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
@@ -666,8 +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