X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=5008a3e7a32ecc09b62d158e59ac2234cf02e657;hb=bb5fc546aeefa10a30ae93e01446161372d1e36b;hp=9464c7430ea9b6f002391bb92eda14c3efd3a363;hpb=37f0332f53a8564ba7a9d55b993f8bfd2f368c80;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 9464c74..5008a3e 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -44,10 +44,7 @@ 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
 {
@@ -459,18 +456,19 @@ public class Sequence extends ASequence implements SequenceI
   }
 
   /**
-   * DOCUMENT ME!
+   * Answers the sequence name, with '/start-end' appended if jvsuffix is true
    * 
-   * @return DOCUMENT ME!
+   * @return
    */
   @Override
   public String getDisplayId(boolean jvsuffix)
   {
-    StringBuffer result = new StringBuffer(name);
-    if (jvsuffix)
+    if (!jvsuffix)
     {
-      result.append("/" + start + "-" + end);
+      return name;
     }
+    StringBuilder result = new StringBuilder(name);
+    result.append("/").append(start).append("-").append(end);
 
     return result.toString();
   }
@@ -683,8 +681,8 @@ public class Sequence extends ASequence implements SequenceI
   public void setGeneLoci(String speciesId, String assemblyId,
           String chromosomeId, MapList map)
   {
-    addDBRef(new DBRefEntry(speciesId, assemblyId, DBRefEntry.CHROMOSOME
-            + ":" + chromosomeId, new Mapping(map)));
+    addDBRef(new GeneLocus(speciesId, assemblyId, chromosomeId,
+            new Mapping(map)));
   }
 
   /**
@@ -700,36 +698,9 @@ public class Sequence extends ASequence implements SequenceI
     {
       for (final DBRefEntry ref : refs)
       {
-        if (ref.isChromosome())
+        if (ref instanceof GeneLociI)
         {
-          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 (GeneLociI) ref;
         }
       }
     }
@@ -807,6 +778,7 @@ 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;
@@ -825,7 +797,7 @@ 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))
     {
@@ -843,16 +815,20 @@ 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]))
@@ -862,7 +838,14 @@ 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;
   }
@@ -1067,9 +1050,10 @@ public class Sequence extends ASequence implements SequenceI
    * {@inheritDoc}
    */
   @Override
-  public Range findPositions(int fromColumn, int toColumn)
+  public ContiguousI findPositions(int fromColumn, int toColumn)
   {
-    if (toColumn < fromColumn || fromColumn < 1)
+    fromColumn = Math.max(fromColumn, 1);
+    if (toColumn < fromColumn)
     {
       return null;
     }
@@ -1261,12 +1245,13 @@ 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]))
       {
@@ -1940,6 +1925,15 @@ 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,