From cb7652a58feba83df46110a571785ce99be6da99 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Sun, 17 Jun 2007 12:43:25 +0000
Subject: [PATCH] correct construction of new dataset sequence when residues
 are deleted

---
 src/jalview/datamodel/Sequence.java |   62 +++++++++++++++++++++++------------
 1 file changed, 41 insertions(+), 21 deletions(-)

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 7d6ba27..16ba407 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -615,14 +615,12 @@ public class Sequence
     return map;
   }
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @param i DOCUMENT ME!
-   * @param j DOCUMENT ME!
+  /* (non-Javadoc)
+   * @see jalview.datamodel.SequenceI#deleteChars(int, int)
    */
   public void deleteChars(int i, int j)
   {
+    int newstart=start,newend=end;
     if (i >= sequence.length)
     {
       return;
@@ -641,29 +639,50 @@ public class Sequence
       System.arraycopy(sequence,0,tmp,0,i);
       System.arraycopy(sequence,j,tmp,i,sequence.length-j);
     }
-
-    if (this.datasetSequence != null)
+    boolean createNewDs=false;
+    for (int s = i; s < j; s++)
     {
-      for (int s = i; s < j; s++)
+      if (jalview.schemes.ResidueProperties.aaIndex[sequence[s]] != 23)
       {
-        if (jalview.schemes.ResidueProperties.aaIndex[sequence[s]] != 23)
+        if (createNewDs)
         {
-
-          Sequence ds = new Sequence(name,
-                                     AlignSeq.extractGaps(
-                                         jalview.util.Comparison.GapChars,
-                                         this.getSequenceAsString()
-                                     ),
-                                     start,
-                                     end);
-          ds.setDescription(description);
+          newend--;
+        } else {
+          int sindex = findIndex(start)-1;
+          if (sindex==s)
+        {
+          // delete characters including start of sequence
+          newstart = findPosition(j);
+          break; // don't need to search for any more residue characters.
+        } else {
+          // delete characters after start.
+          int eindex = findIndex(end)-1;
+          if (eindex<j)
+          {
+            // delete characters at end of sequence
+            newend = findPosition(i-1);
+            break; // don't need to search for any more residue characters.
+          } else {
+            createNewDs=true;
+            newend--; // decrease end position by one for the deleted residue and search further
+          }
+        }
         }
-        break;
       }
     }
-
+    // deletion occured in the middle of the sequence
+    if (createNewDs && this.datasetSequence != null)
+    {
+      // construct a new sequence
+      Sequence ds = new Sequence(datasetSequence);
+      // TODO: remove any non-inheritable properties ?
+      // TODO: create a sequence mapping (since there is a relation here ?)
+      ds.deleteChars(i, j);
+      datasetSequence = ds;
+    }
+    start = newstart;
+    end = newend;
     sequence = tmp;
-
   }
 
 
@@ -843,6 +862,7 @@ public class Sequence
         SequenceI ds = seq;
         ds.setSequence(AlignSeq.extractGaps(jalview.util.Comparison.GapChars, new String(sequence)));
         setDatasetSequence(ds);
+        ds.setSequenceFeatures(getSequenceFeatures());
         seq = this; // and return this sequence as the derived sequence.
       }
     }
-- 
1.7.10.2