From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 25 Jul 2006 09:33:56 +0000 (+0000)
Subject: If seq has a dataset, dont clear it
X-Git-Tag: Release_2_1~230
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=f5f5806de6923a8a62906c5a62c6276ba56ae0da;p=jalview.git

If seq has a dataset, dont clear it
---

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 76d9f72..90d6740 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -108,13 +108,23 @@ public class Alignment implements AlignmentI
     {
       if(dataset!=null)
       {
-        Sequence ds = new Sequence(snew.getName(),
-                                   AlignSeq.extractGaps("-. ", snew.getSequence()),
-                                   snew.getStart(),
-                                   snew.getEnd());
-
-        snew.setDatasetSequence(ds);
-        getDataset().addSequence(ds);
+        if(snew.getDatasetSequence()!=null)
+        {
+          System.out.println(snew.getName());
+          getDataset().addSequence(snew.getDatasetSequence());
+        }
+        else
+        {
+          System.out.println("CLEARED HERE");
+          Sequence ds = new Sequence(snew.getName(),
+                                     AlignSeq.extractGaps("-. ",
+              snew.getSequence()),
+                                     snew.getStart(),
+                                     snew.getEnd());
+
+          snew.setDatasetSequence(ds);
+          getDataset().addSequence(ds);
+        }
       }
 
       sequences.addElement(snew);
@@ -657,16 +667,22 @@ public class Alignment implements AlignmentI
         Sequence[] seqs = new Sequence[getHeight()];
         for (int i = 0; i < getHeight(); i++)
         {
-
-          seqs[i] = new Sequence(getSequenceAt(i).getName(),
-                                 AlignSeq.extractGaps(
-                                     jalview.util.Comparison.GapChars,
-                                     getSequenceAt(i).getSequence()
-                                 ),
-                                 getSequenceAt(i).getStart(),
-                                 getSequenceAt(i).getEnd());
-
-          getSequenceAt(i).setDatasetSequence(seqs[i]);
+          if(getSequenceAt(i).getDatasetSequence()!=null)
+          {
+            seqs[i] = (Sequence)getSequenceAt(i).getDatasetSequence();
+          }
+          else
+          {
+            seqs[i] = new Sequence(getSequenceAt(i).getName(),
+                                   AlignSeq.extractGaps(
+                                       jalview.util.Comparison.GapChars,
+                                       getSequenceAt(i).getSequence()
+                                   ),
+                                   getSequenceAt(i).getStart(),
+                                   getSequenceAt(i).getEnd());
+
+            getSequenceAt(i).setDatasetSequence(seqs[i]);
+          }
         }
 
         dataset = new Alignment(seqs);