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 705ea12..d6be4c2 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;
@@ -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;
     }
@@ -286,7 +278,7 @@ 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!
 
     Color drawnColour = null;
 
@@ -301,7 +293,8 @@ public class FeatureRenderer extends FeatureRendererModel
         continue;
       }
 
-      List<SequenceFeature> overlaps = seq.findFeatures(type, startPos, endPos);
+      List<SequenceFeature> overlaps = seq.findFeatures(startPos, endPos,
+              type);
       for (SequenceFeature sequenceFeature : overlaps)
       {
         /*
@@ -379,24 +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.
    * 
@@ -419,12 +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
      */
@@ -442,31 +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);
         }