Merge branch 'develop' into features/JAL-2446NCList

[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..705ea12 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
 {
@@ -287,7 +288,6 @@ public class FeatureRenderer extends FeatureRendererModel
     int startPos = seq.findPosition(start);
     int endPos = seq.findPosition(end);
 
-    int sfSize = sequenceFeatures.length;
     Color drawnColour = null;
 
     /*
@@ -301,16 +301,9 @@ 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(type, startPos, endPos);
+      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 +313,6 @@ 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 +333,10 @@ 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 +352,7 @@ public class FeatureRenderer extends FeatureRendererModel
           }
           else
           {
+          */
             boolean drawn = renderFeature(g, seq,
                     seq.findIndex(sequenceFeature.begin) - 1,
                     seq.findIndex(sequenceFeature.end) - 1, featureColour,
@@ -373,7 +361,7 @@ public class FeatureRenderer extends FeatureRendererModel
             {
               drawnColour = featureColour;
             }
-          }
+          /*}*/
         }
       }
     }