JAL-2443 push getResidueBoxColour inside getResidueColour

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

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 609e010..4097c40 100755 (executable)
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -21,6 +21,7 @@
 package jalview.gui;
 
 import jalview.renderer.AnnotationRenderer;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
 
 import java.awt.Color;
 import java.awt.Dimension;
@@ -92,7 +93,7 @@ public class OverviewPanel extends JPanel implements Runnable
     sr.renderGaps = false;
     sr.forOverview = true;
     fr = new FeatureRenderer(ap);
-    
+
     // scale the initial size of overviewpanel to shape of alignment
     float initialScale = (float) av.getAlignment().getWidth()
             / (float) av.getAlignment().getHeight();
@@ -289,20 +290,34 @@ public class OverviewPanel extends JPanel implements Runnable
     float sampleRow = (float) alheight / (float) sequencesHeight;
 
     int lastcol = -1, lastrow = -1;
-    int color = Color.white.getRGB();
+    Color color = Color.white;
     int row, col;
     jalview.datamodel.SequenceI seq;
     final boolean hasHiddenRows = av.hasHiddenRows(), hasHiddenCols = av
             .hasHiddenColumns();
     boolean hiddenRow = false;
+    // get hidden row and hidden column map once at beginning.
+    // clone featureRenderer settings to avoid race conditions... if state is
+    // updated just need to refresh again
+
+    FeatureColourFinder finder = new FeatureColourFinder(fr);
+
     for (row = 0; row < sequencesHeight; row++)
     {
+      if (resizeAgain)
+      {
+        break;
+      }
       if ((int) (row * sampleRow) == lastrow)
       {
         // No need to recalculate the colours,
         // Just copy from the row above
         for (col = 0; col < width; col++)
         {
+          if (resizeAgain)
+          {
+            break;
+          }
           miniMe.setRGB(col, row, miniMe.getRGB(col, row - 1));
         }
         continue;
@@ -340,10 +355,14 @@ public class OverviewPanel extends JPanel implements Runnable
 
       for (col = 0; col < width; col++)
       {
+        if (resizeAgain)
+        {
+          break;
+        }
         if ((int) (col * sampleCol) == lastcol
                 && (int) (row * sampleRow) == lastrow)
         {
-          miniMe.setRGB(col, row, color);
+          miniMe.setRGB(col, row, color.getRGB());
           continue;
         }
 
@@ -351,26 +370,21 @@ public class OverviewPanel extends JPanel implements Runnable
 
         if (seq.getLength() > lastcol)
         {
-          color = sr.getResidueBoxColour(seq, lastcol).getRGB();
-
-          if (av.isShowSequenceFeatures())
-          {
-            color = fr.findFeatureColour(color, seq, lastcol);
-          }
+          color = sr.getResidueColour(seq, lastcol, finder);
         }
         else
         {
-          color = -1; // White
+          color = Color.WHITE;
         }
 
         if (hiddenRow
-                || (hasHiddenCols && !av.getColumnSelection()
-                        .isVisible(lastcol)))
+                || (hasHiddenCols && !av.getColumnSelection().isVisible(
+                        lastcol)))
         {
-          color = new Color(color).darker().darker().getRGB();
+          color = color.darker().darker();
         }
 
-        miniMe.setRGB(col, row, color);
+        miniMe.setRGB(col, row, color.getRGB());
 
       }
     }
@@ -380,6 +394,10 @@ public class OverviewPanel extends JPanel implements Runnable
       renderer.updateFromAlignViewport(av);
       for (col = 0; col < width; col++)
       {
+        if (resizeAgain)
+        {
+          break;
+        }
         lastcol = (int) (col * sampleCol);
         {
           mg.translate(col, sequencesHeight);
@@ -395,13 +413,17 @@ public class OverviewPanel extends JPanel implements Runnable
 
     resizing = false;
 
-    setBoxPosition();
-
     if (resizeAgain)
     {
       resizeAgain = false;
       updateOverviewImage();
     }
+    else
+    {
+      lastMiniMe = miniMe;
+    }
+
+    setBoxPosition();
   }
 
   /**
@@ -456,6 +478,8 @@ public class OverviewPanel extends JPanel implements Runnable
     repaint();
   }
 
+  private BufferedImage lastMiniMe = null;
+
   /**
    * DOCUMENT ME!
    * 
@@ -465,19 +489,32 @@ public class OverviewPanel extends JPanel implements Runnable
   @Override
   public void paintComponent(Graphics g)
   {
-    if (resizing)
+    if (resizing || resizeAgain)
     {
-      g.setColor(Color.white);
+      if (lastMiniMe == null)
+      {
+        g.setColor(Color.white);
+        g.fillRect(0, 0, getWidth(), getHeight());
+      }
+      else
+      {
+        g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
+      }
+      g.setColor(new Color(100, 100, 100, 25));
       g.fillRect(0, 0, getWidth(), getHeight());
     }
-    else if (miniMe != null)
+    else if (lastMiniMe != null)
     {
-      g.drawImage(miniMe, 0, 0, this);
+      g.drawImage(lastMiniMe, 0, 0, this);
+      if (lastMiniMe != miniMe)
+      {
+        g.setColor(new Color(100, 100, 100, 25));
+        g.fillRect(0, 0, getWidth(), getHeight());
+      }
     }
-
+    // TODO: render selected regions
     g.setColor(Color.red);
     g.drawRect(boxX, boxY, boxWidth, boxHeight);
     g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
-
   }
 }