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 705ea12..5e071f9 100644 (file)
--- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java
+++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
@@ -215,13 +215,6 @@ public class FeatureRenderer extends FeatureRendererModel
       return null;
     }
 
-    SequenceFeature[] sequenceFeatures = seq.getSequenceFeatures();
-
-    if (sequenceFeatures == null || sequenceFeatures.length == 0)
-    {
-      return null;
-    }
-
     if (Comparison.isGap(seq.getCharAt(column)))
     {
       return Color.white;
@@ -233,7 +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
     {
@@ -270,8 +263,7 @@ public class FeatureRenderer extends FeatureRendererModel
           final SequenceI seq, int start, int end, int y1,
           boolean colourOnly)
   {
-    SequenceFeature[] sequenceFeatures = seq.getSequenceFeatures();
-    if (sequenceFeatures == null || sequenceFeatures.length == 0)
+    if (!seq.getFeatures().hasFeatures())
     {
       return null;
     }
@@ -285,9 +277,6 @@ public class FeatureRenderer extends FeatureRendererModel
               transparency));
     }
 
-    int startPos = seq.findPosition(start);
-    int endPos = seq.findPosition(end);
-
     Color drawnColour = null;
 
     /*
@@ -301,37 +290,39 @@ public class FeatureRenderer extends FeatureRendererModel
         continue;
       }
 
-      List<SequenceFeature> overlaps = seq.findFeatures(type, startPos, endPos);
-      for (SequenceFeature sequenceFeature : overlaps)
+      List<SequenceFeature> overlaps = seq.findFeatures(start + 1, end + 1,
+              type);
+      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
@@ -354,8 +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)
             {
@@ -379,24 +370,6 @@ public class FeatureRenderer extends FeatureRendererModel
   }
 
   /**
-   * Answers true if the feature belongs to a feature group which is not
-   * currently displayed, else false
-   * 
-   * @param sequenceFeature
-   * @return
-   */
-  protected boolean featureGroupNotShown(
-          final SequenceFeature sequenceFeature)
-  {
-    return featureGroups != null
-            && sequenceFeature.featureGroup != null
-            && sequenceFeature.featureGroup.length() != 0
-            && featureGroups.containsKey(sequenceFeature.featureGroup)
-            && !featureGroups.get(sequenceFeature.featureGroup)
-                    .booleanValue();
-  }
-
-  /**
    * Called when alignment in associated view has new/modified features to
    * discover and display.
    * 
@@ -408,23 +381,22 @@ 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)
   {
-    SequenceFeature[] sequenceFeatures = seq.getSequenceFeatures();
-    if (sequenceFeatures == null || sequenceFeatures.length == 0)
-    {
-      return null;
-    }
-  
     /*
      * check for new feature added while processing
      */
@@ -442,31 +414,11 @@ public class FeatureRenderer extends FeatureRendererModel
         continue;
       }
 
-      for (int sfindex = 0; sfindex < sequenceFeatures.length; sfindex++)
+      List<SequenceFeature> overlaps = seq.findFeatures(column, column,
+              type);
+      for (SequenceFeature sequenceFeature : overlaps)
       {
-        SequenceFeature sequenceFeature = sequenceFeatures[sfindex];
-        if (!sequenceFeature.type.equals(type))
-        {
-          continue;
-        }
-
-        if (featureGroupNotShown(sequenceFeature))
-        {
-          continue;
-        }
-
-        /*
-         * check the column position is within the feature range
-         * (or is one of the two contact positions for a contact feature)
-         */
-        boolean featureIsAtPosition = sequenceFeature.begin <= pos
-                && sequenceFeature.end >= pos;
-        if (sequenceFeature.isContactFeature())
-        {
-          featureIsAtPosition = sequenceFeature.begin == pos
-                  || sequenceFeature.end == pos;
-        }
-        if (featureIsAtPosition)
+        if (!featureGroupNotShown(sequenceFeature))
         {
           return getColour(sequenceFeature);
         }