new SequenceI method for making a sub sequence from a range on the

current sequence.

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

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index f822fe6..d711788 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -111,7 +111,13 @@ public interface SequenceI
      * @return DOCUMENT ME!\r
      */\r
     public String getSequence(int start, int end);\r
-\r
+    /**\r
+     * create a new sequence object from start to end of this sequence\r
+     * @param start int\r
+     * @param end int\r
+     * @return SequenceI\r
+     */\r
+    public SequenceI getSubSequence(int start, int end);\r
     /**\r
      * DOCUMENT ME!\r
      *\r