X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=161c0108823e6ce78bf184be77e32d031a55083a;hb=d6e1bbede5adc04f34c969213ac6a4c6d9e5d34a;hp=ecdf2bce7313e603b86fdd444d8cbb0ce542a978;hpb=df9b85c1cf39894039018499fe802406cc37f209;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index ecdf2bc..161c010 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -113,6 +113,62 @@ public class SequenceGroup
         endRes = end;
     }
 
+    public SequenceI [] getSelectionAsNewSequences(AlignmentI align)
+    {
+      int iSize = sequences.size();
+      SequenceI [] seqs = new SequenceI[iSize];
+      SequenceI [] inorder = getSequencesInOrder(align);
+
+    char ch;
+    int sres, eres;
+
+    for (int i = 0; i < iSize; i++)
+    {
+      SequenceI seq = inorder[i];
+
+      //FIND START RES
+      //Returns residue following index if gap
+      sres = seq.findPosition(startRes);
+
+      //FIND END RES
+      //Need to find the residue preceeding index if gap
+      eres = 0;
+
+      for (int j = 0; j < endRes + 1 && j < seq.getLength(); j++)
+      {
+        ch = seq.getCharAt(j);
+        if (!jalview.util.Comparison.isGap( (ch)))
+        {
+          eres++;
+        }
+      }
+
+      if (eres > 0)
+      {
+        eres += seq.getStart() - 1;
+      }
+
+      seqs[i] = new Sequence(seq.getName(),
+                             seq.getSequence(startRes, endRes + 1),
+                             sres,
+                             eres);
+      seqs[i].setDescription(seq.getDescription());
+      seqs[i].setDBRef(seq.getDBRef());
+      seqs[i].setSequenceFeatures(seq.getSequenceFeatures());
+      if (seq.getDatasetSequence() != null)
+        seqs[i].setDatasetSequence(seq.getDatasetSequence());
+
+      if(seq.getAnnotation()!=null)
+      {
+        for(int a=0; a<seq.getAnnotation().length; a++)
+          seqs[i].addAlignmentAnnotation(seq.getAnnotation()[a]);
+      }
+    }
+
+    return seqs;
+
+    }
+
     public Vector getSequences(boolean includeHidden)
     {
       if(!includeHidden)