JAL-1942 JAL-1479 refactored SequenceI.getDBRef/SequenceI.setDBRef to SequenceI.getDB...

[jalview.git] / src / jalview / datamodel / SequenceGroup.java

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index feb714a..0e8fa17 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -76,8 +76,10 @@ public class SequenceGroup implements AnnotatedCollectionI
    */
   public ColourSchemeI cs;
 
+  // start column (base 0)
   int startRes = 0;
 
+  // end column (base 0)
   int endRes = 0;
 
   public Color outlineColour = Color.black;
@@ -207,7 +209,7 @@ public class SequenceGroup implements AnnotatedCollectionI
       if (seqs[ipos] != null)
       {
         seqs[ipos].setDescription(seq.getDescription());
-        seqs[ipos].setDBRef(seq.getDBRef());
+        seqs[ipos].setDBRefs(seq.getDBRefs());
         seqs[ipos].setSequenceFeatures(seq.getSequenceFeatures());
         if (seq.getDatasetSequence() != null)
         {
@@ -611,13 +613,13 @@ public class SequenceGroup implements AnnotatedCollectionI
   {
     synchronized (sequences)
     {
-    if (sequences.contains(s))
-    {
-      deleteSequence(s, recalc);
-    }
-    else
-    {
-      addSequence(s, recalc);
+      if (sequences.contains(s))
+      {
+        deleteSequence(s, recalc);
+      }
+      else
+      {
+        addSequence(s, recalc);
       }
     }
   }
@@ -773,8 +775,9 @@ public class SequenceGroup implements AnnotatedCollectionI
     synchronized (sequences)
     {
       // MC This needs to get reset when characters are inserted and deleted
-      boolean first=true;
-      for (SequenceI seq:sequences) {
+      boolean first = true;
+      for (SequenceI seq : sequences)
+      {
         if (first || seq.getLength() > width)
         {
           width = seq.getLength();