JAL-3032 just the changes pulled already

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

diff --git a/src/jalview/renderer/OverviewRenderer.java b/src/jalview/renderer/OverviewRenderer.java
index 73f66f0..c9096e2 100644 (file)
--- a/src/jalview/renderer/OverviewRenderer.java
+++ b/src/jalview/renderer/OverviewRenderer.java
@@ -44,8 +44,6 @@ public class OverviewRenderer
   // transparency of hidden cols/seqs overlay
   private final float TRANSPARENCY = 0.5f;
 
-  private final Color HIDDEN_COLOUR = Color.DARK_GRAY.darker();
-
   public static final String UPDATE = "OverviewUpdate";
 
   private static final int MAX_PROGRESS = 100;
@@ -113,6 +111,7 @@ public class OverviewRenderer
     int totalPixels = miniMe.getWidth() * alignmentHeight;
 
     int lastRowUpdate = 0;
+    int lastUpdate = 0;
     changeSupport.firePropertyChange(UPDATE, -1, 0);
 
     for (int alignmentRow : rows)
@@ -151,7 +150,7 @@ public class OverviewRenderer
         if (pixelCol <= endCol)
         {
           rgbcolor = getColumnColourFromSequence(allGroups, seq,
-                  alignmentCol, finder);
+                  alignmentCol);
     
           // fill in the appropriate number of pixels
           for (int row = pixelRow; row <= endRow; ++row)
@@ -162,8 +161,10 @@ public class OverviewRenderer
             }
           }
 
-          sendProgressUpdate((pixelCol + 1) * (endRow - pixelRow),
-                  totalPixels, lastRowUpdate);
+          // store last update value
+          lastUpdate = sendProgressUpdate(
+                  (pixelCol + 1) * (endRow - pixelRow), totalPixels,
+                  lastRowUpdate, lastUpdate);
 
           pixelCol = endCol + 1;
         }
@@ -172,7 +173,10 @@ public class OverviewRenderer
 
       if (pixelRow != endRow + 1)
       {
-        lastRowUpdate = sendProgressUpdate(endRow + 1, alignmentHeight, 0);
+        // store row offset and last update value
+        lastRowUpdate = sendProgressUpdate(endRow + 1, alignmentHeight, 0,
+                lastUpdate);
+        lastUpdate = lastRowUpdate;
         pixelRow = endRow + 1;
       }
       seqIndex++;
@@ -182,52 +186,51 @@ public class OverviewRenderer
     // final update to progress bar if present
     if (redraw)
     {
-      sendProgressUpdate(pixelRow - 1, alignmentHeight, 0);
+      sendProgressUpdate(pixelRow - 1, alignmentHeight, 0, 0);
     }
     else
     {
-      sendProgressUpdate(alignmentHeight, miniMe.getHeight(), 0);
+      sendProgressUpdate(alignmentHeight, miniMe.getHeight(), 0, 0);
     }
     return miniMe;
   }
 
   /*
    * Calculate progress update value and fire event
+   * @param rowOffset number of rows to offset calculation by
+   * @return new rowOffset - return value only to be used when at end of a row
    */
-  private int sendProgressUpdate(int position, int maximum, int offset)
+  private int sendProgressUpdate(int position, int maximum, int rowOffset,
+          int lastUpdate)
   {
-    int newUpdate = offset
+    int newUpdate = rowOffset
             + Math.round(MAX_PROGRESS * ((float) position / maximum));
-    if (newUpdate > offset)
+    if (newUpdate > lastUpdate)
     {
-      changeSupport.firePropertyChange(UPDATE, offset, newUpdate);
+      changeSupport.firePropertyChange(UPDATE, rowOffset, newUpdate);
       return newUpdate;
     }
-    return offset;
+    return newUpdate;
   }
 
   /*
-   * Find the colour of a sequence at a specified column position
+   * Find the RGB value of the colour of a sequence at a specified column position
    * 
    * @param seq
    *          sequence to get colour for
    * @param lastcol
    *          column position to get colour for
-   * @param fcfinder
-   *          FeatureColourFinder to use
    * @return colour of sequence at this position, as RGB
    */
-  private int getColumnColourFromSequence(SequenceGroup[] allGroups,
-          jalview.datamodel.SequenceI seq,
-          int lastcol, FeatureColourFinder fcfinder)
+  int getColumnColourFromSequence(SequenceGroup[] allGroups,
+          SequenceI seq, int lastcol)
   {
-    Color color = Color.white;
+    Color color = resColFinder.GAP_COLOUR;
 
     if ((seq != null) && (seq.getLength() > lastcol))
     {
       color = resColFinder.getResidueColour(true, shader, allGroups, seq,
-              lastcol,
-              fcfinder);
+              lastcol, finder);
     }
 
     return color.getRGB();
@@ -285,8 +288,8 @@ public class OverviewRenderer
     Graphics2D g2d = (Graphics2D) hiddenImage.getGraphics();
 
     // set background to transparent
-    g2d.setComposite(AlphaComposite.Clear);
-    g2d.fillRect(0, 0, width, height);
+    // g2d.setComposite(AlphaComposite.Clear);
+    // g2d.fillRect(0, 0, width, height);
 
     // set next colour to opaque
     g2d.setComposite(AlphaComposite.Src);
@@ -350,15 +353,13 @@ public class OverviewRenderer
    *          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)
+  public void drawGraph(Graphics g, AlignmentAnnotation anno, int y,
+          AlignmentColsCollectionI cols)
   {
     Annotation[] annotations = anno.annotations;
     g.setColor(Color.white);