X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=c31dd3e4fa89160501a0aae175ed8be9535117dd;hb=8d2724b83aca38ef75d68787cc5939d950467e63;hp=aa27d253865423139a53bc403553c6952561bb1e;hpb=a7f8fa9c06d82efbbdbc6a0bf1054bb21610b353;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index aa27d25..c31dd3e 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1,19 +1,20 @@
 /*
- * 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 2.8.0b1)
+ * 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;
 
@@ -22,6 +23,8 @@ import jalview.analysis.AlignSeq;
 import java.util.Enumeration;
 import java.util.Vector;
 
+import fr.orsay.lri.varna.models.rna.RNA;
+
 /**
  * 
  * Implements the SequenceI interface for a char[] based sequence object.
@@ -48,15 +51,17 @@ public class Sequence implements SequenceI
   String vamsasId;
 
   DBRefEntry[] dbrefs;
+  
+  RNA rna;
 
   /**
    * This annotation is displayed below the alignment but the positions are tied
    * to the residues of this sequence
    */
   Vector annotation;
-  
+
   /**
-   * The index of the sequence in a MSA 
+   * The index of the sequence in a MSA
    */
   int index = -1;
 
@@ -122,7 +127,8 @@ public class Sequence implements SequenceI
 
   void checkValidRange()
   {
-    // Note: JAL-774 : http://issues.jalview.org/browse/JAL-774?focusedCommentId=11239&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-11239
+    // Note: JAL-774 :
+    // http://issues.jalview.org/browse/JAL-774?focusedCommentId=11239&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-11239
     {
       int endRes = 0;
       for (int j = 0; j < sequence.length; j++)
@@ -137,7 +143,8 @@ public class Sequence implements SequenceI
         endRes += start - 1;
       }
 
-      if (end<endRes) { 
+      if (end < endRes)
+      {
         end = endRes;
       }
     }
@@ -577,13 +584,10 @@ public class Sequence implements SequenceI
     return this.description;
   }
 
-  /**
-   * Return the alignment position for a sequence position
-   * 
-   * @param pos
-   *          lying from start to end
+  /*
+   * (non-Javadoc)
    * 
-   * @return aligned position of residue pos
+   * @see jalview.datamodel.SequenceI#findIndex(int)
    */
   public int findIndex(int pos)
   {
@@ -708,6 +712,7 @@ public class Sequence implements SequenceI
     {
       tmp = new char[i];
       System.arraycopy(sequence, 0, tmp, 0, i);
+      j=sequence.length;
     }
     else
     {
@@ -716,6 +721,9 @@ public class Sequence implements SequenceI
       System.arraycopy(sequence, j, tmp, i, sequence.length - j);
     }
     boolean createNewDs = false;
+    // TODO: take a look at the new dataset creation validation method below -
+    // this could become time comsuming for large sequences - consider making it
+    // more efficient
     for (int s = i; s < j; s++)
     {
       if (jalview.schemes.ResidueProperties.aaIndex[sequence[s]] != 23)
@@ -1181,16 +1189,29 @@ public class Sequence implements SequenceI
   }
 
   /**
-   * @return The index (zero-based) on this sequence in the MSA. 
-   * It returns {@code -1} if this information is not available.
+   * @return The index (zero-based) on this sequence in the MSA. It returns
+   *         {@code -1} if this information is not available.
    */
-  public int getIndex() { return index; }
-  
+  public int getIndex()
+  {
+    return index;
+  }
+
   /**
-   * Defines the position of this sequence in the MSA. 
-   * Use the value {@code -1} if this information is undefined.
+   * Defines the position of this sequence in the MSA. Use the value {@code -1}
+   * if this information is undefined.
    * 
-   * @param The position for this sequence. This value is zero-based (zero for this first sequence)
+   * @param The
+   *          position for this sequence. This value is zero-based (zero for
+   *          this first sequence)
    */
-  public void setIndex(int value) { index = value; }
+  public void setIndex(int value)
+  {
+    index = value;
+  }
+  
+  public void setRNA(RNA r){rna=r;}
+  
+  public RNA getRNA() { return rna; }
+  
 }