JAL-2480 efficient test for features present on sequence

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index bf0ab70..da026b5 100755 (executable)
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -1006,15 +1006,11 @@ public class SequenceFetcher extends JPanel implements Runnable
         {
           for (SequenceI sq : alsqs)
           {
         {
           for (SequenceI sq : alsqs)
           {

-            if ((sfs = sq.getSequenceFeatures()) != null)
+            if (sq.getFeatures().hasFeatures())

             {
             {

-              if (sfs.length > 0)
-              {
-                af.setShowSeqFeatures(true);
-                break;
-              }
+              af.setShowSeqFeatures(true);
+              break;

             }
             }

-

           }
         }
 
           }
         }
 

diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
index f4648c4..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;
     }
 
       return null;
     }
 

-    SequenceFeature[] sequenceFeatures = seq.getSequenceFeatures();
-
-    if (sequenceFeatures == null || sequenceFeatures.length == 0)
-    {
-      return null;
-    }
-

     if (Comparison.isGap(seq.getCharAt(column)))
     {
       return Color.white;
     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)
   {
           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;
     }
     {
       return null;
     }

@@ -286,7 +278,7 @@ public class FeatureRenderer extends FeatureRendererModel
     }
 
     int startPos = seq.findPosition(start);
     }
 
     int startPos = seq.findPosition(start);

-    int endPos = seq.findPosition(end);
+    int endPos = seq.findPosition(end);// todo a performant overload of this!

 
     Color drawnColour = null;
 
 
     Color drawnColour = null;