JAL-2490 lookup features at each column position

[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 72ac2c8..d6be4c2 100644 (file)
--- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java
+++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
@@ -31,6 +31,7 @@ import java.awt.Color;
 import java.awt.FontMetrics;
 import java.awt.Graphics;
 import java.awt.Graphics2D;
+import java.util.List;
 
 public class FeatureRenderer extends FeatureRendererModel
 {
@@ -214,13 +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;
@@ -269,8 +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 +278,8 @@ public class FeatureRenderer extends FeatureRendererModel
     }
 
     int startPos = seq.findPosition(start);
-    int endPos = seq.findPosition(end);
+    int endPos = seq.findPosition(end);// todo a performant overload of this!
 
-    int sfSize = sequenceFeatures.length;
     Color drawnColour = null;
 
     /*
@@ -301,16 +293,10 @@ public class FeatureRenderer extends FeatureRendererModel
         continue;
       }
 
-      // loop through all features in sequence to find
-      // current feature to render
-      for (int sfindex = 0; sfindex < sfSize; sfindex++)
+      List<SequenceFeature> overlaps = seq.findFeatures(startPos, endPos,
+              type);
+      for (SequenceFeature sequenceFeature : overlaps)
       {
-        final SequenceFeature sequenceFeature = sequenceFeatures[sfindex];
-        if (!sequenceFeature.type.equals(type))
-        {
-          continue;
-        }
-
         /*
          * a feature type may be flagged as shown but the group 
          * an instance of it belongs to may be hidden
@@ -320,16 +306,6 @@ public class FeatureRenderer extends FeatureRendererModel
           continue;
         }
 
-        /*
-         * check feature overlaps the target range
-         * TODO: efficient retrieval of features overlapping a range
-         */
-        if (sequenceFeature.getBegin() > endPos
-                || sequenceFeature.getEnd() < startPos)
-        {
-          continue;
-        }
-
         Color featureColour = getColour(sequenceFeature);
         boolean isContactFeature = sequenceFeature.isContactFeature();
 
@@ -350,6 +326,10 @@ public class FeatureRenderer extends FeatureRendererModel
         }
         else if (showFeature(sequenceFeature))
         {
+          /*
+           * showing feature score by height of colour
+           * is not implemented as a selectable option 
+           *
           if (av.isShowSequenceFeaturesHeight()
                   && !Float.isNaN(sequenceFeature.score))
           {
@@ -365,6 +345,7 @@ public class FeatureRenderer extends FeatureRendererModel
           }
           else
           {
+          */
             boolean drawn = renderFeature(g, seq,
                     seq.findIndex(sequenceFeature.begin) - 1,
                     seq.findIndex(sequenceFeature.end) - 1, featureColour,
@@ -373,7 +354,7 @@ public class FeatureRenderer extends FeatureRendererModel
             {
               drawnColour = featureColour;
             }
-          }
+          /*}*/
         }
       }
     }
@@ -391,24 +372,6 @@ 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.
    * 
@@ -431,12 +394,6 @@ public class FeatureRenderer extends FeatureRendererModel
    */
   Color findFeatureColour(SequenceI seq, int pos)
   {
-    SequenceFeature[] sequenceFeatures = seq.getSequenceFeatures();
-    if (sequenceFeatures == null || sequenceFeatures.length == 0)
-    {
-      return null;
-    }
-  
     /*
      * check for new feature added while processing
      */
@@ -454,31 +411,10 @@ public class FeatureRenderer extends FeatureRendererModel
         continue;
       }
 
-      for (int sfindex = 0; sfindex < sequenceFeatures.length; sfindex++)
+      List<SequenceFeature> overlaps = seq.findFeatures(pos, pos, 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);
         }