JAL-2754 Sequence.findFeatures(fromCol, toCol)

[jalview.git] / src / jalview / renderer / seqfeatures / FeatureRenderer.java

diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
index d6be4c2..5e071f9 100644 (file)
--- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java
+++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
@@ -226,7 +226,7 @@ public class FeatureRenderer extends FeatureRendererModel
       /*
        * simple case - just find the topmost rendered visible feature colour
        */
-      renderedColour = findFeatureColour(seq, seq.findPosition(column));
+      renderedColour = findFeatureColour(seq, column);
     }
     else
     {
@@ -277,9 +277,6 @@ public class FeatureRenderer extends FeatureRendererModel
               transparency));
     }
 
-    int startPos = seq.findPosition(start);
-    int endPos = seq.findPosition(end);// todo a performant overload of this!
-
     Color drawnColour = null;
 
     /*
@@ -293,38 +290,39 @@ public class FeatureRenderer extends FeatureRendererModel
         continue;
       }
 
-      List<SequenceFeature> overlaps = seq.findFeatures(startPos, endPos,
+      List<SequenceFeature> overlaps = seq.findFeatures(start + 1, end + 1,
               type);
-      for (SequenceFeature sequenceFeature : overlaps)
+      for (SequenceFeature sf : overlaps)
       {
         /*
          * a feature type may be flagged as shown but the group 
          * an instance of it belongs to may be hidden
          */
-        if (featureGroupNotShown(sequenceFeature))
+        if (featureGroupNotShown(sf))
         {
           continue;
         }
 
-        Color featureColour = getColour(sequenceFeature);
-        boolean isContactFeature = sequenceFeature.isContactFeature();
+        Color featureColour = getColour(sf);
+        boolean isContactFeature = sf.isContactFeature();
 
+        int featureStartCol = seq.findIndex(sf.begin);
+        int featureEndCol = sf.begin == sf.end ? featureStartCol : seq
+                .findIndex(sf.end);
         if (isContactFeature)
         {
-          boolean drawn = renderFeature(g, seq,
-                  seq.findIndex(sequenceFeature.begin) - 1,
-                  seq.findIndex(sequenceFeature.begin) - 1, featureColour,
-                  start, end, y1, colourOnly);
-          drawn |= renderFeature(g, seq,
-                  seq.findIndex(sequenceFeature.end) - 1,
-                  seq.findIndex(sequenceFeature.end) - 1, featureColour,
-                  start, end, y1, colourOnly);
+          boolean drawn = renderFeature(g, seq, featureStartCol - 1,
+                  featureStartCol - 1, featureColour, start, end, y1,
+                  colourOnly);
+          drawn |= renderFeature(g, seq, featureEndCol - 1,
+                  featureEndCol - 1, featureColour, start, end, y1,
+                  colourOnly);
           if (drawn)
           {
             drawnColour = featureColour;
           }
         }
-        else if (showFeature(sequenceFeature))
+        else if (showFeature(sf))
         {
           /*
            * showing feature score by height of colour
@@ -347,8 +345,8 @@ 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)
             {
@@ -383,16 +381,21 @@ public class FeatureRenderer extends FeatureRendererModel
   }
 
   /**
-   * Returns the sequence feature colour rendered at the given sequence
-   * position, or null if none found. The feature of highest render order (i.e.
-   * on top) is found, subject to both feature type and feature group being
-   * visible, and its colour returned.
+   * Returns the sequence feature colour rendered at the given column position,
+   * or null if none found. The feature of highest render order (i.e. on top) is
+   * found, subject to both feature type and feature group being visible, and
+   * its colour returned.
+   * <p>
+   * Note this method does not check for a gap in the column so would return the
+   * colour for features enclosing a gapped column. Check for gap before calling
+   * if different behaviour is wanted.
    * 
    * @param seq
-   * @param pos
+   * @param column
+   *          (1..)
    * @return
    */
-  Color findFeatureColour(SequenceI seq, int pos)
+  Color findFeatureColour(SequenceI seq, int column)
   {
     /*
      * check for new feature added while processing
@@ -411,7 +414,8 @@ public class FeatureRenderer extends FeatureRendererModel
         continue;
       }
 
-      List<SequenceFeature> overlaps = seq.findFeatures(pos, pos, type);
+      List<SequenceFeature> overlaps = seq.findFeatures(column, column,
+              type);
       for (SequenceFeature sequenceFeature : overlaps)
       {
         if (!featureGroupNotShown(sequenceFeature))