Merge branch 'develop' into trialMerge

[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 d580f2c..a1980c7 100644 (file)
--- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java
+++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
@@ -22,8 +22,8 @@ package jalview.renderer.seqfeatures;
 
 import jalview.api.AlignViewportI;
 import jalview.api.FeatureColourI;
+import jalview.datamodel.ContiguousI;
 import jalview.datamodel.MappedFeatures;
-import jalview.datamodel.Range;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
@@ -276,9 +276,9 @@ public class FeatureRenderer extends FeatureRendererModel
     /*
      * if columns are all gapped, or sequence has no features, nothing to do
      */
-    Range visiblePositions = seq.findPositions(start+1, end+1);
-    if (visiblePositions == null || (!seq.getFeatures().hasFeatures()
-            && !av.isShowComplementFeatures()))
+    ContiguousI visiblePositions = seq.findPositions(start + 1, end + 1);
+    if (visiblePositions == null || !seq.getFeatures().hasFeatures()
+            && !av.isShowComplementFeatures())
     {
       return null;
     }
@@ -447,12 +447,16 @@ public class FeatureRenderer extends FeatureRendererModel
    */
   Color drawComplementFeatures(final Graphics g, final SequenceI seq,
           int start, int end, int y1, boolean colourOnly,
-          Range visiblePositions, Color drawnColour)
+          ContiguousI visiblePositions, Color drawnColour)
   {
     AlignViewportI comp = av.getCodingComplement();
     FeatureRenderer fr2 = Desktop.getAlignFrameFor(comp)
             .getFeatureRenderer();
-    for (int pos = visiblePositions.start; pos <= visiblePositions.end; pos++)
+
+    final int visibleStart = visiblePositions.getBegin();
+    final int visibleEnd = visiblePositions.getEnd();
+
+    for (int pos = visibleStart; pos <= visibleEnd; pos++)
     {
       int column = seq.findIndex(pos);
       MappedFeatures mf = fr2