Convenient function findEndRes

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 2eed50c..679997e 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -119,39 +119,15 @@ public class SequenceGroup
       SequenceI [] seqs = new SequenceI[iSize];\r
       SequenceI [] inorder = getSequencesInOrder(align);\r
 \r
-    char ch;\r
-    int sres, eres;\r
-\r
     for (int i = 0; i < iSize; i++)\r
     {\r
       SequenceI seq = inorder[i];\r
 \r
-      //FIND START RES\r
-      //Returns residue following index if gap\r
-      sres = seq.findPosition(startRes);\r
-\r
-      //FIND END RES\r
-      //Need to find the residue preceeding index if gap\r
-      eres = 0;\r
-\r
-      for (int j = 0; j < endRes + 1 && j < seq.getLength(); j++)\r
-      {\r
-        ch = seq.getCharAt(j);\r
-        if (!jalview.util.Comparison.isGap( (ch)))\r
-        {\r
-          eres++;\r
-        }\r
-      }\r
-\r
-      if (eres > 0)\r
-      {\r
-        eres += seq.getStart() - 1;\r
-      }\r
-\r
       seqs[i] = new Sequence(seq.getName(),\r
                              seq.getSequence(startRes, endRes + 1),\r
-                             sres,\r
-                             eres);\r
+                             seq.findPosition(startRes),\r
+                             findEndRes(seq));\r
+\r
       seqs[i].setDescription(seq.getDescription());\r
       seqs[i].setDBRef(seq.getDBRef());\r
       seqs[i].setSequenceFeatures(seq.getSequenceFeatures());\r
@@ -169,6 +145,34 @@ public class SequenceGroup
 \r
     }\r
 \r
+    /**\r
+     * If sequence ends in gaps, the end residue can\r
+     * be correctly calculated here\r
+     * @param seq SequenceI\r
+     * @return int\r
+     */\r
+    public int findEndRes(SequenceI seq)\r
+    {\r
+      int eres = 0;\r
+      char ch;\r
+\r
+      for (int j = 0; j < endRes + 1 && j < seq.getLength(); j++)\r
+      {\r
+        ch = seq.getCharAt(j);\r
+        if (!jalview.util.Comparison.isGap( (ch)))\r
+        {\r
+          eres++;\r
+        }\r
+      }\r
+\r
+      if (eres > 0)\r
+      {\r
+        eres += seq.getStart() - 1;\r
+      }\r
+\r
+      return eres;\r
+    }\r
+\r
     public Vector getSequences(boolean includeHidden)\r
     {\r
       if(!includeHidden)\r