X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2Fseqfeatures%2FFeatureRenderer.java;h=1f47da3421c039c2f9f15950421709927a2004bc;hb=d943fcd0dc04fd4974344eddd13902c89fb595b2;hp=d6619150a01ac2812b054f332425b0bf5f69dc33;hpb=fb2d7072a283815141262d70d5f11a5e966d500b;p=jalview.git

diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
index d661915..1f47da3 100644
--- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java
+++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
@@ -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
@@ -416,7 +416,8 @@ public class FeatureRenderer extends FeatureRendererModel
    * Returns the sequence feature colour rendered at the given column position,
    * or null if none found. The feature of highest render order (i.e. on top) is
    * found, subject to both feature type and feature group being visible, and
-   * its colour returned.
+   * its colour returned. This method is suitable when no feature transparency
+   * applied (only the topmost visible feature colour is rendered).
    * <p>
    * Note this method does not check for a gap in the column so would return the
    * colour for features enclosing a gapped column. Check for gap before calling
@@ -438,7 +439,8 @@ 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))
@@ -460,7 +462,7 @@ public class FeatureRenderer extends FeatureRendererModel
         }
       }
     }
-  
+
     /*
      * no displayed feature found at position
      */