X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FOverviewRenderer.java;h=c9096e290e5a417d8ee813168744477ce6e02ee5;hb=26501f76ef450657c530de489b8404356a98aca3;hp=56dba82efb9846c665f9e79360c0159f769c5a9d;hpb=a435323c67f5dd67ab887bb0c71cf493d04c9272;p=jalview.git

diff --git a/src/jalview/renderer/OverviewRenderer.java b/src/jalview/renderer/OverviewRenderer.java
index 56dba82..c9096e2 100644
--- a/src/jalview/renderer/OverviewRenderer.java
+++ b/src/jalview/renderer/OverviewRenderer.java
@@ -22,6 +22,7 @@ package jalview.renderer;
 
 import jalview.api.AlignmentColsCollectionI;
 import jalview.api.AlignmentRowsCollectionI;
+import jalview.api.RendererListenerI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
@@ -36,12 +37,20 @@ import java.awt.Color;
 import java.awt.Graphics;
 import java.awt.Graphics2D;
 import java.awt.image.BufferedImage;
+import java.beans.PropertyChangeSupport;
 
 public class OverviewRenderer
 {
   // transparency of hidden cols/seqs overlay
   private final float TRANSPARENCY = 0.5f;
 
+  public static final String UPDATE = "OverviewUpdate";
+
+  private static final int MAX_PROGRESS = 100;
+
+  private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
+          this);
+
   private FeatureColourFinder finder;
 
   // image to render on
@@ -53,6 +62,9 @@ public class OverviewRenderer
   // raw number of pixels to allocate to each row
   private float pixelsPerSeq;
 
+  // height in pixels of graph
+  private int graphHeight;
+
   // flag to indicate whether to halt drawing
   private volatile boolean redraw = false;
 
@@ -61,20 +73,21 @@ public class OverviewRenderer
 
   private ResidueShaderI shader;
 
-  private ResidueColourFinder resColFinder;
+  private OverviewResColourFinder resColFinder;
 
   public OverviewRenderer(FeatureRenderer fr, OverviewDimensions od,
           AlignmentI alignment,
-          ResidueShaderI resshader)
+          ResidueShaderI resshader, OverviewResColourFinder colFinder)
   {
     finder = new FeatureColourFinder(fr);
-    resColFinder = new OverviewResColourFinder();
+    resColFinder = colFinder;
 
     al = alignment;
     shader = resshader;
 
     pixelsPerCol = od.getPixelsPerCol();
     pixelsPerSeq = od.getPixelsPerSeq();
+    graphHeight = od.getGraphHeight();
     miniMe = new BufferedImage(od.getWidth(), od.getHeight(),
             BufferedImage.TYPE_INT_RGB);
   }
@@ -94,6 +107,12 @@ public class OverviewRenderer
     int rgbcolor = Color.white.getRGB();
     int seqIndex = 0;
     int pixelRow = 0;
+    int alignmentHeight = miniMe.getHeight() - graphHeight;
+    int totalPixels = miniMe.getWidth() * alignmentHeight;
+
+    int lastRowUpdate = 0;
+    int lastUpdate = 0;
+    changeSupport.firePropertyChange(UPDATE, -1, 0);
 
     for (int alignmentRow : rows)
     {
@@ -131,7 +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)
@@ -141,41 +160,77 @@ public class OverviewRenderer
               miniMe.setRGB(col, row, rgbcolor);
             }
           }
-    
+
+          // store last update value
+          lastUpdate = sendProgressUpdate(
+                  (pixelCol + 1) * (endRow - pixelRow), totalPixels,
+                  lastRowUpdate, lastUpdate);
+
           pixelCol = endCol + 1;
         }
         colIndex++;
       }
-      pixelRow = endRow + 1;
+
+      if (pixelRow != endRow + 1)
+      {
+        // store row offset and last update value
+        lastRowUpdate = sendProgressUpdate(endRow + 1, alignmentHeight, 0,
+                lastUpdate);
+        lastUpdate = lastRowUpdate;
+        pixelRow = endRow + 1;
+      }
       seqIndex++;
     }
 
     overlayHiddenRegions(rows, cols);
+    // final update to progress bar if present
+    if (redraw)
+    {
+      sendProgressUpdate(pixelRow - 1, alignmentHeight, 0, 0);
+    }
+    else
+    {
+      sendProgressUpdate(alignmentHeight, miniMe.getHeight(), 0, 0);
+    }
     return miniMe;
   }
 
-  /**
-   * Find the colour of a sequence at a specified column position
+  /*
+   * 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 rowOffset,
+          int lastUpdate)
+  {
+    int newUpdate = rowOffset
+            + Math.round(MAX_PROGRESS * ((float) position / maximum));
+    if (newUpdate > lastUpdate)
+    {
+      changeSupport.firePropertyChange(UPDATE, rowOffset, newUpdate);
+      return newUpdate;
+    }
+    return newUpdate;
+  }
+
+  /*
+   * 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();
@@ -228,13 +283,13 @@ public class OverviewRenderer
     int colIndex = 0;
     int pixelCol = 0;
 
-    Color hidden = Color.DARK_GRAY.darker();
+    Color hidden = resColFinder.getHiddenColour();
 
     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);
@@ -298,15 +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);
@@ -319,8 +372,10 @@ public class OverviewRenderer
     {
       if (redraw)
       {
+        changeSupport.firePropertyChange(UPDATE, MAX_PROGRESS - 1, 0);
         break;
       }
+
       if (alignmentCol >= annotations.length)
       {
         break; // no more annotations to draw here
@@ -350,10 +405,13 @@ public class OverviewRenderer
 
           g.fillRect(pixelCol, y - height, endCol - pixelCol + 1, height);
         }
+
         pixelCol = endCol + 1;
         colIndex++;
       }
     }
+    changeSupport.firePropertyChange(UPDATE, MAX_PROGRESS - 1,
+            MAX_PROGRESS);
   }
 
   /**
@@ -370,4 +428,14 @@ public class OverviewRenderer
       redraw = b;
     }
   }
+
+  public void addPropertyChangeListener(RendererListenerI listener)
+  {
+    changeSupport.addPropertyChangeListener(listener);
+  }
+
+  public void removePropertyChangeListener(RendererListenerI listener)
+  {
+    changeSupport.removePropertyChangeListener(listener);
+  }
 }