Merge branch 'develop' into menard

[jalview.git] / src / jalview / datamodel / SequenceI.java

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 194f144..57d2569 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
@@ -167,14 +167,17 @@ public interface SequenceI
   public String getDescription();
 
   /**
-   * Return the alignment column for a sequence position
-   *    * Return the alignment position for a sequence position
+   * Return the alignment column for a sequence position * Return the alignment
+   * position for a sequence position
    * 
    * @param pos
    *          lying from start to end
    * 
-   * @return aligned column for residue (0 if residue is upstream from alignment, -1 if residue is downstream from alignment)
-   * note. Sequence object returns sequence.getEnd() for positions upstream currently. TODO: change sequence for assert(findIndex(seq.getEnd()+1)==-1) and fix incremental bugs
+   * @return aligned column for residue (0 if residue is upstream from
+   *         alignment, -1 if residue is downstream from alignment) note.
+   *         Sequence object returns sequence.getEnd() for positions upstream
+   *         currently. TODO: change sequence for
+   *         assert(findIndex(seq.getEnd()+1)==-1) and fix incremental bugs
    * 
    */
   public int findIndex(int pos);
@@ -354,12 +357,13 @@ public interface SequenceI
    *          null or mapping from entry's numbering to local start/end
    */
   public void transferAnnotation(SequenceI entry, Mapping mp);
-  
+
   /**
-   * @param index The sequence index in the MSA 
+   * @param index
+   *          The sequence index in the MSA
    */
   public void setIndex(int index);
-  
+
   /**
    * @return The index of the sequence in the alignment
    */