X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2Fseqfeatures%2FFeatureRenderer.java;h=13885b45370b005378ac348fdbf7edca256bc3a2;hb=a4d55cd869348dbadf0a73950a838504cc32cecc;hp=8feee1fb621f18de177beb3450a61e9301626f3c;hpb=ef7ded229ddd70a406c37a7aac160b832736eb76;p=jalview.git

diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
index 8feee1f..13885b4 100644
--- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java
+++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
@@ -22,7 +22,7 @@ package jalview.renderer.seqfeatures;
 
 import jalview.api.AlignViewportI;
 import jalview.api.FeatureColourI;
-import jalview.datamodel.Range;
+import jalview.datamodel.ContiguousI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.util.Comparison;
@@ -101,8 +101,7 @@ public class FeatureRenderer extends FeatureRendererModel
 
       g.setColor(featureColour);
 
-      g.fillRect((i - start) * charWidth, y1, charWidth,
-              charHeight);
+      g.fillRect((i - start) * charWidth, y1, charWidth, charHeight);
 
       if (colourOnly || !validCharWidth)
       {
@@ -111,8 +110,8 @@ public class FeatureRenderer extends FeatureRendererModel
 
       g.setColor(Color.white);
       int charOffset = (charWidth - fm.charWidth(s)) / 2;
-      g.drawString(String.valueOf(s), charOffset
-              + (charWidth * (i - start)), pady);
+      g.drawString(String.valueOf(s),
+              charOffset + (charWidth * (i - start)), pady);
     }
     return true;
   }
@@ -200,8 +199,8 @@ public class FeatureRenderer extends FeatureRendererModel
 
       g.setColor(Color.black);
       int charOffset = (charWidth - fm.charWidth(s)) / 2;
-      g.drawString(String.valueOf(s), charOffset
-              + (charWidth * (i - start)), pady);
+      g.drawString(String.valueOf(s),
+              charOffset + (charWidth * (i - start)), pady);
     }
     return true;
   }
@@ -217,7 +216,8 @@ public class FeatureRenderer extends FeatureRendererModel
       return null;
     }
 
-    if (Comparison.isGap(seq.getCharAt(column)))
+    // column is 'base 1' but getCharAt is an array index (ie from 0)
+    if (Comparison.isGap(seq.getCharAt(column - 1)))
     {
       /*
        * returning null allows the colour scheme to provide gap colour
@@ -272,7 +272,7 @@ 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);
+    ContiguousI visiblePositions = seq.findPositions(start + 1, end + 1);
     if (visiblePositions == null || !seq.getFeatures().hasFeatures())
     {
       return null;
@@ -304,14 +304,19 @@ public class FeatureRenderer extends FeatureRendererModel
       List<SequenceFeature> overlaps = seq.getFeatures().findFeatures(
               visiblePositions.getBegin(), visiblePositions.getEnd(), type);
 
-      filterFeaturesForDisplay(overlaps, fc);
+      if (fc.isSimpleColour())
+      {
+        filterFeaturesForDisplay(overlaps);
+      }
 
       for (SequenceFeature sf : overlaps)
       {
-        Color featureColour = fc.getColor(sf);
+        Color featureColour = getColor(sf, fc);
         if (featureColour == null)
         {
-          // score feature outwith threshold for colouring
+          /*
+           * feature excluded by visibility settings, filters, or colour threshold
+           */
           continue;
         }
 
@@ -439,7 +444,8 @@ public class FeatureRenderer extends FeatureRendererModel
      * inspect features in reverse renderOrder (the last in the array is 
      * displayed on top) until we find one that is rendered at the position
      */
-    for (int renderIndex = renderOrder.length - 1; renderIndex >= 0; renderIndex--)
+    for (int renderIndex = renderOrder.length
+            - 1; renderIndex >= 0; renderIndex--)
     {
       String type = renderOrder[renderIndex];
       if (!showFeatureOfType(type))
@@ -461,7 +467,7 @@ public class FeatureRenderer extends FeatureRendererModel
         }
       }
     }
-  
+
     /*
      * no displayed feature found at position
      */