X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=71e76aff2f6835cc26c329b4a32c23c2cae4fa1c;hb=e760a92aa57282a2ea3892656e12f03d45e60cf6;hp=4485c4641fa93d6baf2f4ee8c628edc45935c20a;hpb=1772466d28ffeef4aa4e1a4d5a640fd6a987df8c;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 4485c46..71e76af 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -131,7 +131,6 @@ public class Alignment implements AlignmentI
       {
         if(snew.getDatasetSequence()!=null)
         {
-          System.out.println(snew.getName());
           getDataset().addSequence(snew.getDatasetSequence());
         }
         else
@@ -191,7 +190,7 @@ public class Alignment implements AlignmentI
      */
     public void deleteSequence(int i)
     {
-      if(i>0 && i<getHeight())
+      if(i>-1 && i<getHeight())
       {
         sequences.removeElementAt(i);
         hiddenSequences.adjustHeightSequenceDeleted(i);
@@ -270,15 +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++;
-        }
     }
 
     /**    */
@@ -443,6 +433,9 @@ public class Alignment implements AlignmentI
             aSize = annotations.length;
         }
 
+        if(aSize<1)
+          return;
+
         AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize - 1];
 
         int tIndex = 0;
@@ -564,22 +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]);
           }
@@ -598,7 +594,8 @@ public class Alignment implements AlignmentI
       return dataset;
     }
 
-    public boolean padGaps() {
+    public boolean padGaps()
+    {
       boolean modified=false;
 
       //Remove excess gaps from the end of alignment
@@ -621,14 +618,17 @@ public class Alignment implements AlignmentI
 
       maxLength++;
 
+      int cLength;
       for (int i = 0; i < sequences.size();
            i++)
       {
         current = getSequenceAt(i);
+        cLength = current.getLength();
 
-        if (current.getLength() < maxLength)
+        if (cLength < maxLength)
         {
-          current.insertCharAt(maxLength - 1, gapCharacter);
+          current.insertCharAt(cLength,
+                              maxLength-cLength, gapCharacter);
           modified=true;
         }
         else if(current.getLength() > maxLength)