JAL-2526 Sequence.findPositions to get residue positions for column

range

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index d7ac7a7..dd7c24a 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -662,7 +662,7 @@ public class Sequence extends ASequence implements SequenceI
     // 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]))
+      if (!Comparison.isGap(sequence[i]))
       {
         j++;
       }
@@ -688,7 +688,7 @@ public class Sequence extends ASequence implements SequenceI
     int seqlen = sequence.length;
     while ((j < i) && (j < seqlen))
     {
-      if (!jalview.util.Comparison.isGap(sequence[j]))
+      if (!Comparison.isGap(sequence[j]))
       {
         pos++;
       }
@@ -700,6 +700,68 @@ public class Sequence extends ASequence implements SequenceI
   }
 
   /**
+   * {@inheritDoc}
+   */
+  @Override
+  public Range findPositions(int fromCol, int toCol)
+  {
+    /*
+     * count residues before fromCol
+     */
+    int j = 0;
+    int count = 0;
+    int seqlen = sequence.length;
+    while (j < fromCol && j < seqlen)
+    {
+      if (!Comparison.isGap(sequence[j]))
+      {
+        count++;
+      }
+      j++;
+    }
+
+    /*
+     * find first and last residues between fromCol and toCol
+     */
+    int firstPos = 0;
+    int lastPos = 0;
+    int firstPosCol = 0;
+    boolean foundFirst = false;
+    
+    while (j <= toCol && j < seqlen)
+    {
+      if (!Comparison.isGap(sequence[j]))
+      {
+        count++;
+        if (!foundFirst)
+        {
+          firstPos = count;
+          firstPosCol = j;
+          foundFirst = true;
+        }
+        lastPos = count;
+      }
+      j++;
+    }
+
+    if (firstPos == 0)
+    {
+      /*
+       * no residues in this range
+       */
+      return null;
+    }
+
+    /*
+     * adjust for sequence start coordinate
+     */
+    firstPos += start - 1;
+    lastPos += start - 1;
+
+    return new Range(firstPos, lastPos);
+  }
+
+  /**
    * Returns an int array where indices correspond to each residue in the
    * sequence and the element value gives its position in the alignment
    * 

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index e4be5ee..163a4a0 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -176,7 +176,7 @@ public interface SequenceI extends ASequenceI
   public String getDescription();
 
   /**
-   * Return the alignment column for a sequence position
+   * Return the alignment column (from 1..) for a sequence position
    * 
    * @param pos
    *          lying from start to end
@@ -201,6 +201,30 @@ public interface SequenceI extends ASequenceI
   public int findPosition(int i);
 
   /**
+   * Returns the range of sequence positions included in the given alignment
+   * position range. If no positions are included (the range is entirely gaps),
+   * then returns null.
+   * 
+   * <pre>
+   * Example: 
+   * >Seq/8-13
+   * ABC--DE-F
+   * findPositions(1, 4) returns Range(9, 9) // B only
+   * findPositions(3, 4) returns null // all gaps
+   * findPositions(2, 6) returns Range(10, 12) // CDE
+   * findPositions(3, 7) returns Range(11,12) // DE
+   * </pre>
+   * 
+   * @param fromCol
+   *          first aligned column position (base 0, inclusive)
+   * @param toCol
+   *          last aligned column position (base 0, inclusive)
+   * 
+   * @return
+   */
+  public Range findPositions(int fromCol, int toCol);
+
+  /**
    * Returns an int array where indices correspond to each residue in the
    * sequence and the element value gives its position in the alignment
    * 

diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
index d6be4c2..5dce2b8 100644 (file)
--- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java
+++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
@@ -21,6 +21,7 @@
 package jalview.renderer.seqfeatures;
 
 import jalview.api.AlignViewportI;
+import jalview.datamodel.Range;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.util.Comparison;
@@ -277,8 +278,14 @@ public class FeatureRenderer extends FeatureRendererModel
               transparency));
     }
 
-    int startPos = seq.findPosition(start);
-    int endPos = seq.findPosition(end);// todo a performant overload of this!
+    /*
+     * get range of sequence positions within column range
+     */
+    Range seqRange = seq.findPositions(start, end);
+    if (seqRange == null)
+    {
+      return null;
+    }
 
     Color drawnColour = null;
 
@@ -293,8 +300,8 @@ public class FeatureRenderer extends FeatureRendererModel
         continue;
       }
 
-      List<SequenceFeature> overlaps = seq.findFeatures(startPos, endPos,
-              type);
+      List<SequenceFeature> overlaps = seq.findFeatures(seqRange.start,
+              seqRange.end, type);
       for (SequenceFeature sequenceFeature : overlaps)
       {
         /*
@@ -309,15 +316,18 @@ public class FeatureRenderer extends FeatureRendererModel
         Color featureColour = getColour(sequenceFeature);
         boolean isContactFeature = sequenceFeature.isContactFeature();
 
+        // todo overload findIndex using Location data
+        int featureStartCol = seq.findIndex(sequenceFeature.begin);
+        int featureEndCol = seq.findIndex(sequenceFeature.end);
         if (isContactFeature)
         {
           boolean drawn = renderFeature(g, seq,
-                  seq.findIndex(sequenceFeature.begin) - 1,
-                  seq.findIndex(sequenceFeature.begin) - 1, featureColour,
+                  featureStartCol - 1,
+                  featureStartCol - 1, featureColour,
                   start, end, y1, colourOnly);
           drawn |= renderFeature(g, seq,
-                  seq.findIndex(sequenceFeature.end) - 1,
-                  seq.findIndex(sequenceFeature.end) - 1, featureColour,
+                  featureEndCol - 1,
+                  featureEndCol - 1, featureColour,
                   start, end, y1, colourOnly);
           if (drawn)
           {
@@ -347,8 +357,8 @@ public class FeatureRenderer extends FeatureRendererModel
           {
           */
             boolean drawn = renderFeature(g, seq,
-                    seq.findIndex(sequenceFeature.begin) - 1,
-                    seq.findIndex(sequenceFeature.end) - 1, featureColour,
+                    featureStartCol - 1,
+                    featureEndCol - 1, featureColour,
                     start, end, y1, colourOnly);
             if (drawn)
             {

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index 7eeac12..4da11eb 100644 (file)
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -231,10 +231,10 @@ public class SequenceTest
     assertEquals(6, sq.findIndex(6));
     assertEquals(6, sq.findIndex(9));
 
-    sq = new Sequence("test", "-A--B-C-D-E-F--");
-    assertEquals(2, sq.findIndex(1));
-    assertEquals(5, sq.findIndex(2));
-    assertEquals(7, sq.findIndex(3));
+    sq = new Sequence("test/8-13", "-A--B-C-D-E-F--");
+    assertEquals(2, sq.findIndex(8));
+    assertEquals(5, sq.findIndex(9));
+    assertEquals(7, sq.findIndex(10));
 
     // before start returns 0
     assertEquals(0, sq.findIndex(0));
@@ -1161,4 +1161,24 @@ public class SequenceTest
     seq2.createDatasetSequence();
     seq.setDatasetSequence(seq2);
   }
+
+  @Test
+  public void testFindPositions()
+  {
+    SequenceI sq = new Sequence("Seq", "ABC--DE-F", 8, 13);
+
+    Range range = sq.findPositions(1, 4); // BC
+    assertEquals(new Range(9, 10), range);
+
+    range = sq.findPositions(2, 4); // C
+    assertEquals(new Range(10, 10), range);
+
+    assertNull(sq.findPositions(3, 4)); // all gaps
+
+    range = sq.findPositions(2, 6); // CDE
+    assertEquals(new Range(10, 12), range);
+
+    range = sq.findPositions(3, 7); // DE
+    assertEquals(new Range(11, 12), range);
+  }
 }