From 4608f763ad15fdb8b093d205985fb3b4d7077471 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Fri, 11 Oct 2013 11:44:03 +0100
Subject: [PATCH] JAL-1114 promote start/end attributes to gettable fields of
 annotatable collections

---
 src/jalview/datamodel/Alignment.java           |    9 +++++++++
 src/jalview/datamodel/SequenceCollectionI.java |   12 ++++++++++++
 2 files changed, 21 insertions(+)

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 7b545c4..70663aa 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1488,4 +1488,13 @@ public class Alignment implements AlignmentI
      hasRNAStructure = true;
    }
  }
+ @Override
+public int getEndRes()
+{
+  return getWidth()-1;
+}@Override
+public int getStartRes()
+{
+  return 0;
+}
 }
diff --git a/src/jalview/datamodel/SequenceCollectionI.java b/src/jalview/datamodel/SequenceCollectionI.java
index c5cee01..f0d7284 100644
--- a/src/jalview/datamodel/SequenceCollectionI.java
+++ b/src/jalview/datamodel/SequenceCollectionI.java
@@ -29,4 +29,16 @@ public interface SequenceCollectionI
 
   int getWidth();
 
+  /** 
+  * @return the first column included in this collection. Runs from 0<=i<N_cols
+  */
+  int getStartRes();
+  
+
+  /**
+   * 
+   * @return the last column in this collection. Runs from 0<=i<N_cols
+   */
+  int getEndRes();
+
 }
-- 
1.7.10.2