Merge branch 'docs/2_8_1_Release' into Release_2_8_2_Branch

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

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 186156d..d8f75a4 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -1,24 +1,28 @@
 /*
- * 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 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * 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 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.datamodel;
 
+
 import java.util.Vector;
 
+import fr.orsay.lri.varna.models.rna.RNA;
+
 /**
  * DOCUMENT ME!
  * 
@@ -97,21 +101,21 @@ public interface SequenceI
   public String getSequenceAsString();
 
   /**
-   * get a range on the seuqence as a string
+   * get a range on the sequence as a string
    * 
    * @param start
-   *          DOCUMENT ME!
+   *          position relative to start of sequence including gaps (from 0)
    * @param end
-   *          DOCUMENT ME!
+   *          position relative to start of sequence including gaps (from 0)
    * 
-   * @return DOCUMENT ME!
+   * @return String containing all gap and symbols in specified range
    */
   public String getSequenceAsString(int start, int end);
 
   /**
-   * DOCUMENT ME!
+   * Get the sequence as a character array
    * 
-   * @return DOCUMENT ME!
+   * @return seqeunce and any gaps
    */
   public char[] getSequence();
 
@@ -164,14 +168,17 @@ 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);
@@ -351,15 +358,28 @@ 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
    */
   public int getIndex();
+  
+  /**
+   * @return The RNA of the sequence in the alignment
+   */
+  
+  public RNA getRNA();
+ 
+  /**
+   * @param rna The RNA.
+   */
+  public void setRNA(RNA rna);
+  
 
 }