X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=21b877d4083609affa599393782ab5f92ad741a6;hb=e33b171845992fd21094ba754498f9ab3d29f110;hp=3240f843b243b378d17bfc056bee572d3cc8517d;hpb=e1c9c652059a67ee96f9fc5f6617fd5d604cbdbb;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 3240f84..21b877d 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1,26 +1,26 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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.
+ * 
+ * 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/>.
  */
 package jalview.datamodel;
 
-import java.util.*;
+import jalview.analysis.AlignSeq;
 
-import jalview.analysis.*;
+import java.util.Enumeration;
+import java.util.Vector;
 
 /**
  * 
@@ -54,6 +54,11 @@ 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 */
   public SequenceFeature[] sequenceFeatures;
@@ -62,14 +67,14 @@ public class Sequence implements SequenceI
    * Creates a new Sequence object.
    * 
    * @param name
-   *                display name string
+   *          display name string
    * @param sequence
-   *                string to form a possibly gapped sequence out of
+   *          string to form a possibly gapped sequence out of
    * @param start
-   *                first position of non-gap residue in the sequence
+   *          first position of non-gap residue in the sequence
    * @param end
-   *                last position of ungapped residues (nearly always only used
-   *                for display purposes)
+   *          last position of ungapped residues (nearly always only used for
+   *          display purposes)
    */
   public Sequence(String name, String sequence, int start, int end)
   {
@@ -117,7 +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++)
@@ -132,7 +137,9 @@ public class Sequence implements SequenceI
         endRes += start - 1;
       }
 
-      this.end = endRes;
+      if (end<endRes) { 
+        end = endRes;
+      }
     }
 
   }
@@ -141,9 +148,9 @@ public class Sequence implements SequenceI
    * Creates a new Sequence object.
    * 
    * @param name
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param sequence
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public Sequence(String name, String sequence)
   {
@@ -156,7 +163,7 @@ public class Sequence implements SequenceI
    * reference.
    * 
    * @param seq
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public Sequence(SequenceI seq)
   {
@@ -169,9 +176,9 @@ public class Sequence implements SequenceI
    * annotation that is present in the given annotation array.
    * 
    * @param seq
-   *                the sequence to be copied
+   *          the sequence to be copied
    * @param alAnnotation
-   *                an array of annotation including some associated with seq
+   *          an array of annotation including some associated with seq
    */
   public Sequence(SequenceI seq, AlignmentAnnotation[] alAnnotation)
   {
@@ -185,15 +192,16 @@ public class Sequence implements SequenceI
         addSequenceFeature(new SequenceFeature(sf[i]));
       }
     }
-    if (seq.getDBRef() != null)
+    setDatasetSequence(seq.getDatasetSequence());
+    if (datasetSequence == null && seq.getDBRef() != null)
     {
+      // only copy DBRefs if we really are a dataset sequence
       DBRefEntry[] dbr = seq.getDBRef();
       for (int i = 0; i < dbr.length; i++)
       {
         addDBRef(new DBRefEntry(dbr[i]));
       }
     }
-    setDatasetSequence(seq.getDatasetSequence());
     if (seq.getAnnotation() != null)
     {
       AlignmentAnnotation[] sqann = seq.getAnnotation();
@@ -234,7 +242,7 @@ public class Sequence implements SequenceI
    * DOCUMENT ME!
    * 
    * @param v
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setSequenceFeatures(SequenceFeature[] features)
   {
@@ -330,7 +338,7 @@ public class Sequence implements SequenceI
    * DOCUMENT ME!
    * 
    * @param id
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setPDBId(Vector id)
   {
@@ -367,7 +375,7 @@ public class Sequence implements SequenceI
    * DOCUMENT ME!
    * 
    * @param name
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setName(String name)
   {
@@ -389,7 +397,7 @@ public class Sequence implements SequenceI
    * DOCUMENT ME!
    * 
    * @param start
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setStart(int start)
   {
@@ -410,7 +418,7 @@ public class Sequence implements SequenceI
    * DOCUMENT ME!
    * 
    * @param end
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setEnd(int end)
   {
@@ -441,7 +449,7 @@ public class Sequence implements SequenceI
    * DOCUMENT ME!
    * 
    * @param seq
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setSequence(String seq)
   {
@@ -496,9 +504,9 @@ public class Sequence implements SequenceI
    * seqeunce
    * 
    * @param start
-   *                int
+   *          int
    * @param end
-   *                int
+   *          int
    * @return SequenceI
    */
   public SequenceI getSubSequence(int start, int end)
@@ -532,7 +540,7 @@ public class Sequence implements SequenceI
    * DOCUMENT ME!
    * 
    * @param i
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -552,7 +560,7 @@ public class Sequence implements SequenceI
    * DOCUMENT ME!
    * 
    * @param desc
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setDescription(String desc)
   {
@@ -569,20 +577,16 @@ public class Sequence implements SequenceI
     return this.description;
   }
 
-  /**
-   * Return the alignment position for a sequence position
-   * 
-   * @param pos
-   *                lying from start to end
-   * 
-   * @return aligned position of residue pos
+  
+  /* (non-Javadoc)
+   * @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]))
@@ -607,7 +611,7 @@ public class Sequence implements SequenceI
    * Returns the sequence position for an alignment position
    * 
    * @param i
-   *                column index in alignment (from 1)
+   *          column index in alignment (from 1)
    * 
    * @return residue number for residue (left of and) nearest ith column
    */
@@ -656,6 +660,7 @@ public class Sequence implements SequenceI
 
     return map;
   }
+
   /*
    * (non-Javadoc)
    * 
@@ -679,6 +684,7 @@ public class Sequence implements SequenceI
     }
     return map;
   }
+
   /*
    * (non-Javadoc)
    * 
@@ -737,7 +743,7 @@ public class Sequence implements SequenceI
             {
               createNewDs = true;
               newend--; // decrease end position by one for the deleted residue
-                        // and search further
+              // and search further
             }
           }
         }
@@ -762,11 +768,11 @@ public class Sequence implements SequenceI
    * DOCUMENT ME!
    * 
    * @param i
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param c
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param chop
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void insertCharAt(int i, int length, char c)
   {
@@ -819,6 +825,11 @@ public class Sequence implements SequenceI
 
   public DBRefEntry[] getDBRef()
   {
+    if (dbrefs == null && datasetSequence != null
+            && this != datasetSequence)
+    {
+      return datasetSequence.getDBRef();
+    }
     return dbrefs;
   }
 
@@ -886,8 +897,10 @@ 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);
   }
 
@@ -983,8 +996,9 @@ public class Sequence implements SequenceI
   /*
    * (non-Javadoc)
    * 
-   * @see jalview.datamodel.SequenceI#setAlignmentAnnotation(AlignmmentAnnotation[]
-   *      annotations)
+   * @see
+   * jalview.datamodel.SequenceI#setAlignmentAnnotation(AlignmmentAnnotation[]
+   * annotations)
    */
   public void setAlignmentAnnotation(AlignmentAnnotation[] annotations)
   {
@@ -1095,8 +1109,9 @@ public class Sequence implements SequenceI
   /*
    * (non-Javadoc)
    * 
-   * @see jalview.datamodel.SequenceI#transferAnnotation(jalview.datamodel.SequenceI,
-   *      jalview.datamodel.Mapping)
+   * @see
+   * jalview.datamodel.SequenceI#transferAnnotation(jalview.datamodel.SequenceI,
+   * jalview.datamodel.Mapping)
    */
   public void transferAnnotation(SequenceI entry, Mapping mp)
   {
@@ -1161,4 +1176,17 @@ 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; }
 }