X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FOverviewPanel.java;h=36a4575e784cf274252c1fdc274561943f99e7e2;hb=51728d3951398f9c12d7017c776953f17322cc68;hp=b4c2923d60083c0185231c620c9f0a4d6a03f2bc;hpb=eb244ec04ea14b024ec6b20ecf7a9e636ca57134;p=jalview.git

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index b4c2923..36a4575 100755
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -22,10 +22,17 @@ package jalview.gui;
 
 import jalview.renderer.AnnotationRenderer;
 
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.image.*;
-import javax.swing.*;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Graphics;
+import java.awt.event.ComponentAdapter;
+import java.awt.event.ComponentEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseMotionAdapter;
+import java.awt.image.BufferedImage;
+
+import javax.swing.JPanel;
 
 /**
  * DOCUMENT ME!
@@ -85,7 +92,7 @@ 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();
@@ -135,7 +142,7 @@ public class OverviewPanel extends JPanel implements Runnable
       @Override
       public void mouseDragged(MouseEvent evt)
       {
-        if (!av.wrapAlignment)
+        if (!av.getWrapAlignment())
         {
           // TODO: feature: jv2.5 detect shift drag and update selection from
           // it.
@@ -151,7 +158,7 @@ public class OverviewPanel extends JPanel implements Runnable
       @Override
       public void mousePressed(MouseEvent evt)
       {
-        if (!av.wrapAlignment)
+        if (!av.getWrapAlignment())
         {
           boxX = evt.getX();
           boxY = evt.getY();
@@ -256,7 +263,7 @@ public class OverviewPanel extends JPanel implements Runnable
 
     if (av.isShowSequenceFeatures())
     {
-      fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
+      fr.transferSettings(ap.getSeqPanel().seqCanvas.getFeatureRenderer());
     }
 
     int alwidth = av.getAlignment().getWidth();
@@ -285,15 +292,28 @@ public class OverviewPanel extends JPanel implements Runnable
     int color = Color.white.getRGB();
     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
     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;
@@ -302,7 +322,7 @@ public class OverviewPanel extends JPanel implements Runnable
       lastrow = (int) (row * sampleRow);
 
       hiddenRow = false;
-      if (av.hasHiddenRows())
+      if (hasHiddenRows)
       {
         seq = av.getAlignment().getHiddenSequences()
                 .getHiddenSequence(lastrow);
@@ -329,8 +349,13 @@ public class OverviewPanel extends JPanel implements Runnable
         continue;
       }
 
+      // long start = System.currentTimeMillis();
       for (col = 0; col < width; col++)
       {
+        if (resizeAgain)
+        {
+          break;
+        }
         if ((int) (col * sampleCol) == lastcol
                 && (int) (row * sampleRow) == lastrow)
         {
@@ -355,8 +380,8 @@ public class OverviewPanel extends JPanel implements Runnable
         }
 
         if (hiddenRow
-                || (av.hasHiddenColumns() && !av.getColumnSelection()
-                        .isVisible(lastcol)))
+                || (hasHiddenCols && !av.getColumnSelection().isVisible(
+                        lastcol)))
         {
           color = new Color(color).darker().darker().getRGB();
         }
@@ -364,6 +389,8 @@ public class OverviewPanel extends JPanel implements Runnable
         miniMe.setRGB(col, row, color);
 
       }
+      // System.out.println(String.format("Row %d with width %d took %dms",
+      // row, width, System.currentTimeMillis() - start));
     }
 
     if (av.getAlignmentConservationAnnotation() != null)
@@ -371,6 +398,10 @@ 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);
@@ -386,13 +417,17 @@ public class OverviewPanel extends JPanel implements Runnable
 
     resizing = false;
 
-    setBoxPosition();
-
     if (resizeAgain)
     {
       resizeAgain = false;
       updateOverviewImage();
     }
+    else
+    {
+      lastMiniMe = miniMe;
+    }
+
+    setBoxPosition();
   }
 
   /**
@@ -447,6 +482,8 @@ public class OverviewPanel extends JPanel implements Runnable
     repaint();
   }
 
+  private BufferedImage lastMiniMe = null;
+
   /**
    * DOCUMENT ME!
    * 
@@ -456,19 +493,32 @@ 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);
-
   }
 }