JAL-1517 update copyright to version 2.8.2

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 13f928c..24c409a 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1,25 +1,29 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * 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.*;
+import jalview.analysis.AlignSeq;
+
+import java.util.Enumeration;
+import java.util.Vector;
 
-import jalview.analysis.*;
+import fr.orsay.lri.varna.models.rna.RNA;
 
 /**
  * 
@@ -47,6 +51,8 @@ public class Sequence implements SequenceI
   String vamsasId;
 
   DBRefEntry[] dbrefs;
+  
+  RNA rna;
 
   /**
    * This annotation is displayed below the alignment but the positions are tied
@@ -54,7 +60,12 @@ public class Sequence implements SequenceI
    */
   Vector annotation;
 
-  /** array of seuqence features - may not be null for a valid sequence object */
+  /**
+   * The index of the sequence in a MSA
+   */
+  int index = -1;
+
+  /** array of sequence features - may not be null for a valid sequence object */
   public SequenceFeature[] sequenceFeatures;
 
   /**
@@ -116,7 +127,8 @@ public class Sequence implements SequenceI
 
   void checkValidRange()
   {
-    if (end < 1)
+    // 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++)
@@ -131,7 +143,10 @@ public class Sequence implements SequenceI
         endRes += start - 1;
       }
 
-      this.end = endRes;
+      if (end < endRes)
+      {
+        end = endRes;
+      }
     }
 
   }
@@ -569,20 +584,17 @@ 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)
   {
     // returns the alignment position for a residue
     int j = start;
     int i = 0;
-
+    // Rely on end being at least as long as the length of the sequence.
     while ((i < sequence.length) && (j <= end) && (j <= pos))
     {
       if (!jalview.util.Comparison.isGap(sequence[i]))
@@ -700,6 +712,7 @@ public class Sequence implements SequenceI
     {
       tmp = new char[i];
       System.arraycopy(sequence, 0, tmp, 0, i);
+      j=sequence.length;
     }
     else
     {
@@ -708,6 +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)
@@ -893,8 +909,10 @@ public class Sequence implements SequenceI
     {
       this.annotation = new Vector();
     }
-
-    this.annotation.addElement(annotation);
+    if (!this.annotation.contains(annotation))
+    {
+      this.annotation.addElement(annotation);
+    }
     annotation.setSequenceRef(this);
   }
 
@@ -983,6 +1001,18 @@ public class Sequence implements SequenceI
       datasetSequence.setPDBId(getPDBId());
       setPDBId(null);
       datasetSequence.updatePDBIds();
+      if (annotation != null)
+      {
+        Vector<AlignmentAnnotation> _annot = annotation;
+        annotation = null;
+        for (AlignmentAnnotation aa : _annot)
+        {
+          aa.sequenceRef = datasetSequence;
+          aa.adjustForAlignment(); // uses annotation's own record of
+                                   // sequence-column mapping
+          datasetSequence.addAlignmentAnnotation(aa);
+        }
+      }
     }
     return datasetSequence;
   }
@@ -1170,4 +1200,30 @@ 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.
+   */
+  public int getIndex()
+  {
+    return index;
+  }
+
+  /**
+   * 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)
+   */
+  public void setIndex(int value)
+  {
+    index = value;
+  }
+  
+  public void setRNA(RNA r){rna=r;}
+  
+  public RNA getRNA() { return rna; }
+  
 }