From 25e277834e02c37996caf1eb76c7728dbe8e0394 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 9 Aug 2006 16:21:36 +0000
Subject: [PATCH] new SequenceI method for making a sub sequence from a range
 on the current sequence.

---
 src/jalview/datamodel/Sequence.java  |   20 +++++++++++++++++++-
 src/jalview/datamodel/SequenceI.java |    8 +++++++-
 2 files changed, 26 insertions(+), 2 deletions(-)

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 562440f..b5d5199 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -338,7 +338,25 @@ public class Sequence implements SequenceI
 
         return this.sequence.substring(start, end);
     }
-
+    /**
+     * make a new Sequence object from start to end (including gaps) over this seqeunce
+     * @param start int
+     * @param end int
+     * @return SequenceI
+     */
+    public SequenceI getSubSequence(int start, int end) {
+      if (start<0)
+        start = 0;
+      String seq = getSequence(start, end);
+      if (seq=="")
+        return null;
+      start = findPosition(start);
+      end=findPosition(end);
+      // JBPNote - this is an incomplete copy.
+      SequenceI nseq = new Sequence(this.getName(), seq, start, end);
+      nseq.setDatasetSequence(getDatasetSequence());
+      return nseq;
+    }
     /**
      * DOCUMENT ME!
      *
diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index f822fe6..d711788 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -111,7 +111,13 @@ public interface SequenceI
      * @return DOCUMENT ME!
      */
     public String getSequence(int start, int end);
-
+    /**
+     * create a new sequence object from start to end of this sequence
+     * @param start int
+     * @param end int
+     * @return SequenceI
+     */
+    public SequenceI getSubSequence(int start, int end);
     /**
      * DOCUMENT ME!
      *
-- 
1.7.10.2