Sequence colour moved to viewport

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

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 4237db8..71e76af 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -269,15 +269,6 @@ public class Alignment implements AlignmentI
     public void deleteAllGroups()
     {
         groups.removeAllElements();
-
-        int i = 0;
-
-        while (i < sequences.size())
-        {
-            SequenceI s = getSequenceAt(i);
-            s.setColor(java.awt.Color.white);
-            i++;
-        }
     }
 
     /**    */
@@ -566,22 +557,25 @@ public class Alignment implements AlignmentI
         // Can only be done once, if dataset is not null
         // This will not be performed
         Sequence[] seqs = new Sequence[getHeight()];
+        SequenceI currentSeq;
         for (int i = 0; i < getHeight(); i++)
         {
-          if(getSequenceAt(i).getDatasetSequence()!=null)
+          currentSeq = getSequenceAt(i);
+          if(currentSeq.getDatasetSequence()!=null)
           {
-            seqs[i] = (Sequence)getSequenceAt(i).getDatasetSequence();
+            seqs[i] = (Sequence)currentSeq.getDatasetSequence();
           }
           else
           {
-            seqs[i] = new Sequence(getSequenceAt(i).getName(),
+            seqs[i] = new Sequence(currentSeq.getName(),
                                    AlignSeq.extractGaps(
                                        jalview.util.Comparison.GapChars,
-                                       getSequenceAt(i).getSequence()
+                                       currentSeq.getSequence()
                                    ),
-                                   getSequenceAt(i).getStart(),
-                                   getSequenceAt(i).getEnd());
-            seqs[i].sequenceFeatures = getSequenceAt(i).getSequenceFeatures();
+                                   currentSeq.getStart(),
+                                   currentSeq.getEnd());
+            seqs[i].sequenceFeatures = currentSeq.getSequenceFeatures();
+            seqs[i].setDescription(currentSeq.getDescription());
             getSequenceAt(i).setSequenceFeatures(null);
             getSequenceAt(i).setDatasetSequence(seqs[i]);
           }