Add support RNAML format

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 13f928c..aa27d25 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1,6 +1,6 @@
 /*
- * 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 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -17,9 +17,10 @@
  */
 package jalview.datamodel;
 
-import java.util.*;
+import jalview.analysis.AlignSeq;
 
-import jalview.analysis.*;
+import java.util.Enumeration;
+import java.util.Vector;
 
 /**
  * 
@@ -53,8 +54,13 @@ public class Sequence implements SequenceI
    * to the residues of this sequence
    */
   Vector annotation;
+  
+  /**
+   * The index of the sequence in a MSA 
+   */
+  int index = -1;
 
-  /** array of seuqence features - may not be null for a valid sequence object */
+  /** array of sequence features - may not be null for a valid sequence object */
   public SequenceFeature[] sequenceFeatures;
 
   /**
@@ -116,7 +122,7 @@ 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 +137,9 @@ public class Sequence implements SequenceI
         endRes += start - 1;
       }
 
-      this.end = endRes;
+      if (end<endRes) { 
+        end = endRes;
+      }
     }
 
   }
@@ -582,7 +590,7 @@ public class Sequence implements SequenceI
     // 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]))
@@ -893,8 +901,10 @@ 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);
   }
 
@@ -1170,4 +1180,17 @@ 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; }
 }