From: Jim Procter <jprocter@dundee.ac.uk>
Date: Wed, 12 Nov 2014 12:40:43 +0000 (+0000)
Subject: javadoc
X-Git-Tag: Release_2_8_2b1^2~36^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=03496bf88fc1bec3ce628ac79ce69440ce244007;p=jalview.git

javadoc
---

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 68bf8f2..69d6da2 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -514,16 +514,7 @@ public class Sequence implements SequenceI
     return reply;
   }
 
-  /**
-   * make a new Sequence object from start to end (including gaps) over this
-   * seqeunce
-   * 
-   * @param start
-   *          int
-   * @param end
-   *          int
-   * @return SequenceI
-   */
+  @Override
   public SequenceI getSubSequence(int start, int end)
   {
     if (start < 0)
@@ -623,14 +614,7 @@ public class Sequence implements SequenceI
     }
   }
 
-  /**
-   * Returns the sequence position for an alignment position
-   * 
-   * @param i
-   *          column index in alignment (from 1)
-   * 
-   * @return residue number for residue (left of and) nearest ith column
-   */
+  @Override
   public int findPosition(int i)
   {
     int j = 0;
diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 876db03..8376047 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -137,10 +137,12 @@ public interface SequenceI
    * create a new sequence object from start to end of this sequence
    * 
    * @param start
-   *          int
+   *          int index for start position
    * @param end
-   *          int
+   *          int index for end position
+   * 
    * @return SequenceI
+   * @note implementations may use getSequence to get the sequence data
    */
   public SequenceI getSubSequence(int start, int end);
 
@@ -189,7 +191,7 @@ public interface SequenceI
    * Returns the sequence position for an alignment position
    * 
    * @param i
-   *          column index in alignment (from 1)
+   *          column index in alignment (from 0..<length)
    * 
    * @return residue number for residue (left of and) nearest ith column
    */