From 70d8cbb3e0f3e4986c09d9e5e42a7997d77cf9d5 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 12 Oct 2006 16:14:23 +0000
Subject: [PATCH] Convenient function findEndRes

---
 src/jalview/datamodel/SequenceGroup.java |   58 ++++++++++++++++--------------
 1 file changed, 31 insertions(+), 27 deletions(-)

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 2eed50c..679997e 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -119,39 +119,15 @@ public class SequenceGroup
       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);
+                             seq.findPosition(startRes),
+                             findEndRes(seq));
+
       seqs[i].setDescription(seq.getDescription());
       seqs[i].setDBRef(seq.getDBRef());
       seqs[i].setSequenceFeatures(seq.getSequenceFeatures());
@@ -169,6 +145,34 @@ public class SequenceGroup
 
     }
 
+    /**
+     * If sequence ends in gaps, the end residue can
+     * be correctly calculated here
+     * @param seq SequenceI
+     * @return int
+     */
+    public int findEndRes(SequenceI seq)
+    {
+      int eres = 0;
+      char ch;
+
+      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;
+      }
+
+      return eres;
+    }
+
     public Vector getSequences(boolean includeHidden)
     {
       if(!includeHidden)
-- 
1.7.10.2