JAL-2388 Tidies

[jalview.git] / src / jalview / gui / OverviewRenderer.java

diff --git a/src/jalview/gui/OverviewRenderer.java b/src/jalview/gui/OverviewRenderer.java
index 566846a..62b8601 100644 (file)
--- a/src/jalview/gui/OverviewRenderer.java
+++ b/src/jalview/gui/OverviewRenderer.java
@@ -119,13 +119,13 @@ public class OverviewRenderer
    * Find the colour of a sequence at a specified column position
    */
   private int getColumnColourFromSequence(jalview.datamodel.SequenceI seq,
-          boolean isHidden, int lastcol, FeatureColourFinder finder)
+          boolean isHidden, int lastcol, FeatureColourFinder fcfinder)
   {
     Color color = Color.white;
 
     if ((seq != null) && (seq.getLength() > lastcol))
     {
-      color = sr.getResidueColour(seq, lastcol, finder);
+      color = sr.getResidueColour(seq, lastcol, fcfinder);
     }
 
     if (isHidden)
@@ -136,45 +136,64 @@ public class OverviewRenderer
     return color.getRGB();
   }
 
-  public void drawGraph(Graphics g, AlignmentAnnotation _aa, int charWidth,
+  /**
+   * Draw the alignment annotation in the overview panel
+   * 
+   * @param g
+   *          the graphics object to draw on
+   * @param anno
+   *          alignment annotation information
+   * @param charWidth
+   *          alignment character width value
+   * @param y
+   *          y-position for the annotation graph
+   * @param cols
+   *          the collection of columns used in the overview panel
+   */
+  public void drawGraph(Graphics g, AlignmentAnnotation anno, int charWidth,
           int y, AlignmentColsCollectionI cols)
   {
-    Annotation[] aa_annotations = _aa.annotations;
+    Annotation[] annotations = anno.annotations;
     g.setColor(Color.white);
     g.fillRect(0, 0, miniMe.getWidth(), y);
-    // g.setColor(new Color(0, 0, 180));
 
     int height;
-
     int colIndex = 0;
     int pixelCol = 0;
     for (int alignmentCol : cols)
     {
-      int endCol = Math.min(Math.round((colIndex + 1) * pixelsPerCol) - 1,
-              miniMe.getWidth() - 1);
-
-      if (alignmentCol < aa_annotations.length
-              && aa_annotations[alignmentCol] != null)
+      if (alignmentCol >= annotations.length)
       {
-        if (aa_annotations[alignmentCol].colour == null)
-        {
-          g.setColor(Color.black);
-        }
-        else
-        {
-          g.setColor(aa_annotations[alignmentCol].colour);
-        }
+        break; // no more annotations to draw here
+      }
+      else
+      {
+        int endCol = Math.min(
+                Math.round((colIndex + 1) * pixelsPerCol) - 1,
+                miniMe.getWidth() - 1);
 
-        height = (int) ((aa_annotations[alignmentCol].value / _aa.graphMax) * y);
-        if (height > y)
+        if (annotations[alignmentCol] != null)
         {
-          height = y;
-        }
+          if (annotations[alignmentCol].colour == null)
+          {
+            g.setColor(Color.black);
+          }
+          else
+          {
+            g.setColor(annotations[alignmentCol].colour);
+          }
 
-        g.fillRect(pixelCol, y - height, endCol - pixelCol + 1, height);
+          height = (int) ((annotations[alignmentCol].value / anno.graphMax) * y);
+          if (height > y)
+          {
+            height = y;
+          }
+
+          g.fillRect(pixelCol, y - height, endCol - pixelCol + 1, height);
+        }
+        pixelCol = endCol + 1;
+        colIndex++;
       }
-      pixelCol = endCol + 1;
-      colIndex++;
     }
   }
 }