Merge branch 'develop' into bug/JAL-2541cutRelocateFeatures

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index e851a29..f555855 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -43,10 +43,7 @@ import fr.orsay.lri.varna.models.rna.RNA;
 
 /**
  * 
- * Implements the SequenceI interface for a char[] based sequence object.
- * 
- * @author $author$
- * @version $Revision$
+ * Implements the SequenceI interface for a char[] based sequence object
  */
 public class Sequence extends ASequence implements SequenceI
 {
@@ -658,10 +655,10 @@ public class Sequence extends ASequence implements SequenceI
   }
 
   /**
-   * DOCUMENT ME!
+   * Sets the sequence description, and also parses out any special formats of
+   * interest
    * 
    * @param desc
-   *          DOCUMENT ME!
    */
   @Override
   public void setDescription(String desc)
@@ -669,10 +666,67 @@ public class Sequence extends ASequence implements SequenceI
     this.description = desc;
   }
 
+  @Override
+  public void setGeneLoci(String speciesId, String assemblyId,
+          String chromosomeId, MapList map)
+  {
+    addDBRef(new DBRefEntry(speciesId, assemblyId, DBRefEntry.CHROMOSOME
+            + ":" + chromosomeId, new Mapping(map)));
+  }
+
   /**
-   * DOCUMENT ME!
+   * Returns the gene loci mapping for the sequence (may be null)
    * 
-   * @return DOCUMENT ME!
+   * @return
+   */
+  @Override
+  public GeneLociI getGeneLoci()
+  {
+    DBRefEntry[] refs = getDBRefs();
+    if (refs != null)
+    {
+      for (final DBRefEntry ref : refs)
+      {
+        if (ref.isChromosome())
+        {
+          return new GeneLociI()
+          {
+            @Override
+            public String getSpeciesId()
+            {
+              return ref.getSource();
+            }
+
+            @Override
+            public String getAssemblyId()
+            {
+              return ref.getVersion();
+            }
+
+            @Override
+            public String getChromosomeId()
+            {
+              // strip off "chromosome:" prefix to chrId
+              return ref.getAccessionId().substring(
+                      DBRefEntry.CHROMOSOME.length() + 1);
+            }
+
+            @Override
+            public MapList getMap()
+            {
+              return ref.getMap().getMap();
+            }
+          };
+        }
+      }
+    }
+    return null;
+  }
+
+  /**
+   * Answers the description
+   * 
+   * @return
    */
   @Override
   public String getDescription()
@@ -740,6 +794,7 @@ public class Sequence extends ASequence implements SequenceI
      * preserve end residue column provided cursor was valid
      */
     int endColumn = isValidCursor(cursor) ? cursor.lastColumnPosition : 0;
+
     if (residuePos == this.end)
     {
       endColumn = column;
@@ -758,7 +813,7 @@ public class Sequence extends ASequence implements SequenceI
    * @param curs
    * @return
    */
-  protected int findIndex(int pos, SequenceCursor curs)
+  protected int findIndex(final int pos, SequenceCursor curs)
   {
     if (!isValidCursor(curs))
     {
@@ -776,16 +831,20 @@ public class Sequence extends ASequence implements SequenceI
     /*
      * move left or right to find pos from hint.position
      */
-    int col = curs.columnPosition - 1; // convert from base 1 to 0-based array
-                                       // index
+    int col = curs.columnPosition - 1; // convert from base 1 to base 0
     int newPos = curs.residuePosition;
     int delta = newPos > pos ? -1 : 1;
 
     while (newPos != pos)
     {
       col += delta; // shift one column left or right
-      if (col < 0 || col == sequence.length)
+      if (col < 0)
+      {
+        break;
+      }
+      if (col == sequence.length)
       {
+        col--; // return last column if we failed to reach pos
         break;
       }
       if (!Comparison.isGap(sequence[col]))
@@ -795,7 +854,14 @@ public class Sequence extends ASequence implements SequenceI
     }
 
     col++; // convert back to base 1
-    updateCursor(pos, col, curs.firstColumnPosition);
+
+    /*
+     * only update cursor if we found the target position
+     */
+    if (newPos == pos)
+    {
+      updateCursor(pos, col, curs.firstColumnPosition);
+    }
 
     return col;
   }
@@ -1194,12 +1260,13 @@ public class Sequence extends ASequence implements SequenceI
     boolean createNewDs = false;
     // TODO: take a (second look) at the dataset creation validation method for
     // the very large sequence case
+
     int startIndex = findIndex(start) - 1;
     int endIndex = findIndex(end) - 1;
     int startDeleteColumn = -1; // for dataset sequence deletions
     int deleteCount = 0;
 
-    for (int s = i; s < j; s++)
+    for (int s = i; s < j && s < sequence.length; s++)
     {
       if (Comparison.isGap(sequence[s]))
       {
@@ -1844,6 +1911,15 @@ public class Sequence extends ASequence implements SequenceI
 
     List<SequenceFeature> result = getFeatures().findFeatures(startPos,
             endPos, types);
+    if (datasetSequence != null)
+    {
+      result = datasetSequence.getFeatures().findFeatures(startPos, endPos,
+              types);
+    }
+    else
+    {
+      result = sequenceFeatureStore.findFeatures(startPos, endPos, types);
+    }
 
     /*
      * if end column is gapped, endPos may be to the right,