X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=3689433aefcdcba248a8c16fdb0d005f187a436f;hb=e1c9c652059a67ee96f9fc5f6617fd5d604cbdbb;hp=ba65fd796566b6be25324a2ead43af927325d2af;hpb=e5edd3d9da88468dc7143f7e46cf2ebbe4e3393c;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index ba65fd7..3689433 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -336,11 +336,25 @@ public class Alignment
   /**    */
   public SequenceI findName(String name)
   {
-    int i = 0;
+    return findName(name,false);
+  }
 
+  /* (non-Javadoc)
+   * @see jalview.datamodel.AlignmentI#findName(java.lang.String, boolean)
+   */
+  public SequenceI findName(String token, boolean b)
+  {
+
+    int i = 0;
+    SequenceI sq=null;
+    String sqname=null;
     while (i < sequences.size())
     {
-      if (getSequenceAt(i).getName().equals(name))
+      sq = getSequenceAt(i);
+      sqname = sq.getName();
+      if (sqname.equals(token) // exact match
+          || (b && // allow imperfect matches - case varies 
+              (sqname.equalsIgnoreCase(token))))
       {
         return getSequenceAt(i);
       }
@@ -350,7 +364,6 @@ public class Alignment
 
     return null;
   }
-
   public SequenceI[] findSequenceMatch(String name)
   {
     Vector matches = new Vector();
@@ -617,7 +630,7 @@ public class Alignment
       // Create a new dataset for this alignment.
       // Can only be done once, if dataset is not null
       // This will not be performed
-      Sequence[] seqs = new Sequence[getHeight()];
+      SequenceI[] seqs = new SequenceI[getHeight()];
       SequenceI currentSeq;
       for (int i = 0; i < getHeight(); i++)
       {
@@ -628,17 +641,7 @@ public class Alignment
         }
         else
         {
-          seqs[i] = new Sequence(currentSeq.getName(),
-                                 AlignSeq.extractGaps(
-                                     jalview.util.Comparison.GapChars,
-                                     currentSeq.getSequenceAsString()
-                                 ),
-                                 currentSeq.getStart(),
-                                 currentSeq.getEnd());
-          seqs[i].sequenceFeatures = currentSeq.getSequenceFeatures();
-          seqs[i].setDescription(currentSeq.getDescription());
-          getSequenceAt(i).setSequenceFeatures(null);
-          getSequenceAt(i).setDatasetSequence(seqs[i]);
+          seqs[i] = currentSeq.createDatasetSequence();
         }
       }