X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FOverviewRenderer.java;h=0f8cda6a1e78463a7abcaae559cb20e8cfd0de40;hb=b02e2d7bed980ad4c50112575f4253494b993ee2;hp=75b81987f11790c41297788a4347ef5111ec9509;hpb=af00f89579328012da26b151996997b1735265b4;p=jalview.git

diff --git a/src/jalview/renderer/OverviewRenderer.java b/src/jalview/renderer/OverviewRenderer.java
index 75b8198..0f8cda6 100644
--- a/src/jalview/renderer/OverviewRenderer.java
+++ b/src/jalview/renderer/OverviewRenderer.java
@@ -26,6 +26,7 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.SequenceI;
 import jalview.renderer.seqfeatures.FeatureColourFinder;
+import jalview.renderer.seqfeatures.FeatureRenderer;
 import jalview.viewmodel.OverviewDimensions;
 
 import java.awt.Color;
@@ -47,11 +48,14 @@ public class OverviewRenderer
   // raw number of pixels to allocate to each row
   private float pixelsPerSeq;
 
+  // flag to indicate whether to halt drawing
+  private volatile boolean redraw = false;
+
   public OverviewRenderer(jalview.api.SequenceRenderer seqRenderer,
-          FeatureColourFinder colfinder, OverviewDimensions od)
+          FeatureRenderer fr, OverviewDimensions od)
   {
     sr = seqRenderer;
-    finder = colfinder;
+    finder = new FeatureColourFinder(fr);
 
     pixelsPerCol = od.getPixelsPerCol();
     pixelsPerSeq = od.getPixelsPerSeq();
@@ -74,8 +78,14 @@ public class OverviewRenderer
     int rgbcolor = Color.white.getRGB();
     int seqIndex = 0;
     int pixelRow = 0;
+
     for (int alignmentRow : rows)
     {
+      if (redraw)
+      {
+        break;
+      }
+
       // get details of this alignment row
       boolean hidden = rows.isHidden(alignmentRow);
       SequenceI seq = rows.getSequence(alignmentRow);
@@ -88,25 +98,36 @@ public class OverviewRenderer
       int pixelCol = 0;
       for (int alignmentCol : cols)
       {
+        if (redraw)
+        {
+          break;
+        }
+
         // calculate where this column extends to in pixels
-        int endCol = Math.min(
-                Math.round((colIndex + 1) * pixelsPerCol) - 1,
+        int endCol = Math.min(Math.round((colIndex + 1) * pixelsPerCol) - 1,
                 miniMe.getWidth() - 1);
 
-        // determine the colour based on the sequence and column position
-        rgbcolor = getColumnColourFromSequence(seq,
-                hidden || cols.isHidden(alignmentCol), alignmentCol, finder);
-
-        // fill in the appropriate number of pixels
-        for (int row = pixelRow; row <= endRow; ++row)
+        // don't do expensive colour determination if we're not going to use it
+        // NB this is important to avoid performance issues in the overview
+        // panel
+        if (pixelCol <= endCol)
         {
-          for (int col = pixelCol; col <= endCol; ++col)
+          // determine the colour based on the sequence and column position
+          rgbcolor = getColumnColourFromSequence(seq,
+                  hidden || cols.isHidden(alignmentCol), alignmentCol,
+                  finder);
+
+          // fill in the appropriate number of pixels
+          for (int row = pixelRow; row <= endRow; ++row)
           {
-            miniMe.setRGB(col, row, rgbcolor);
+            for (int col = pixelCol; col <= endCol; ++col)
+            {
+              miniMe.setRGB(col, row, rgbcolor);
+            }
           }
-        }
 
-        pixelCol = endCol + 1;
+          pixelCol = endCol + 1;
+        }
         colIndex++;
       }
       pixelRow = endRow + 1;
@@ -162,14 +183,17 @@ public class OverviewRenderer
     int pixelCol = 0;
     for (int alignmentCol : cols)
     {
+      if (redraw)
+      {
+        break;
+      }
       if (alignmentCol >= annotations.length)
       {
         break; // no more annotations to draw here
       }
       else
       {
-        int endCol = Math.min(
-                Math.round((colIndex + 1) * pixelsPerCol) - 1,
+        int endCol = Math.min(Math.round((colIndex + 1) * pixelsPerCol) - 1,
                 miniMe.getWidth() - 1);
 
         if (annotations[alignmentCol] != null)
@@ -183,7 +207,8 @@ public class OverviewRenderer
             g.setColor(annotations[alignmentCol].colour);
           }
 
-          height = (int) ((annotations[alignmentCol].value / anno.graphMax) * y);
+          height = (int) ((annotations[alignmentCol].value / anno.graphMax)
+                  * y);
           if (height > y)
           {
             height = y;
@@ -196,4 +221,12 @@ public class OverviewRenderer
       }
     }
   }
+
+  public void setRedraw(boolean b)
+  {
+    synchronized (this)
+    {
+      redraw = b;
+    }
+  }
 }