Merge remote-tracking branch 'origin/develop' into feature/JAL-2587

diff --git a/src/jalview/gui/OverviewCanvas.java b/src/jalview/gui/OverviewCanvas.java
index 27f9c3f..8f8cff7 100644 (file)
--- a/src/jalview/gui/OverviewCanvas.java
+++ b/src/jalview/gui/OverviewCanvas.java
@@ -24,15 +24,21 @@ import jalview.api.AlignViewportI;
 import jalview.renderer.OverviewRenderer;
 import jalview.viewmodel.OverviewDimensions;
 
+import java.awt.AlphaComposite;
 import java.awt.Color;
 import java.awt.Dimension;
 import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
 import java.awt.image.BufferedImage;
 
 import javax.swing.JComponent;
+import javax.swing.Timer;
 
 public class OverviewCanvas extends JComponent
 {
+  public static final long RUNNING_TIME = 2000;
   private static final Color TRANS_GREY = new Color(100, 100, 100, 25);
 
   // This is set true if the alignment view changes whilst
@@ -45,6 +51,8 @@ public class OverviewCanvas extends JComponent
 
   private BufferedImage lastMiniMe = null;
 
+  private BufferedImage veryLastMiniMe = null;
+
   // Can set different properties in this seqCanvas than
   // main visible SeqCanvas
   private SequenceRenderer sr;
@@ -57,6 +65,14 @@ public class OverviewCanvas extends JComponent
 
   private AlignViewportI av;
 
+  private boolean resize = false;
+
+  private float alpha = 0f;
+
+  private long startTime = -1;
+
+  private final Timer timer;
+
   public OverviewCanvas(OverviewDimensions overviewDims,
           AlignViewportI alignvp)
   {
@@ -67,6 +83,36 @@ public class OverviewCanvas extends JComponent
     sr.renderGaps = false;
     sr.forOverview = true;
     fr = new jalview.renderer.seqfeatures.FeatureRenderer(av);
+
+    timer = new Timer(40, new ActionListener()
+    {
+
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        if (startTime < 0)
+        {
+          startTime = System.currentTimeMillis();
+        }
+        else
+        {
+
+          long time = System.currentTimeMillis();
+          long duration = time - startTime;
+          if (duration >= RUNNING_TIME)
+          {
+            startTime = -1;
+            ((Timer) e.getSource()).stop();
+            alpha = 0f;
+          }
+          else
+          {
+            alpha = 1f - ((float) duration / (float) RUNNING_TIME);
+          }
+          repaint();
+        }
+      }
+    });
   }
 
   /**
@@ -118,6 +164,7 @@ public class OverviewCanvas extends JComponent
           FeatureRenderer transferRenderer)
   {
     miniMe = null;
+    veryLastMiniMe = lastMiniMe;
 
     if (showSequenceFeatures)
     {
@@ -151,12 +198,15 @@ public class OverviewCanvas extends JComponent
     {
       updaterunning = false;
       lastMiniMe = miniMe;
+      alpha = 1f;
+      timer.start();
     }
   }
 
   @Override
   public void paintComponent(Graphics g)
   {
+
     if (restart)
     {
       if (lastMiniMe == null)
@@ -173,16 +223,83 @@ public class OverviewCanvas extends JComponent
     }
     else if (lastMiniMe != null)
     {
-      g.drawImage(lastMiniMe, 0, 0, this);
-      if (lastMiniMe != miniMe)
+      if ((getWidth() > 0) && (getHeight() > 0)
+              && ((getWidth() != od.getWidth())
+                      || (getHeight() != od.getHeight())))
       {
-        g.setColor(TRANS_GREY);
-        g.fillRect(0, 0, getWidth(), getHeight());
+        // scale the alignment and annotation separately *** if there is
+        // annotation ***
+        if (od.getGraphHeight() > 0)
+        {
+          BufferedImage topImage = lastMiniMe.getSubimage(0, 0,
+                  od.getWidth(), od.getSequencesHeight());
+          BufferedImage bottomImage = lastMiniMe.getSubimage(0,
+                  od.getSequencesHeight(), od.getWidth(),
+                  od.getGraphHeight());
+
+          // must be done at this point as we rely on using old width/height
+          // above, and new width/height below
+          od.setWidth(getWidth());
+          od.setHeight(getHeight());
+
+          // stick the images back together so lastMiniMe is consistent in the
+          // event of a repaint - BUT probably not thread safe
+          lastMiniMe = new BufferedImage(od.getWidth(), od.getHeight(),
+                  BufferedImage.TYPE_INT_RGB);
+          Graphics lg = lastMiniMe.getGraphics();
+          lg.drawImage(topImage, 0, 0, od.getWidth(),
+                  od.getSequencesHeight(), null);
+          lg.drawImage(bottomImage, 0, od.getSequencesHeight(),
+                  od.getWidth(), od.getGraphHeight(), this);
+          lg.dispose();
+        }
+        else
+        {
+          od.setWidth(getWidth());
+          od.setHeight(getHeight());
+        }
+
+        // scale lastMiniMe to the new size
+        g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
+
+        // make sure the box is in the right place
+        od.setBoxPosition(av.getAlignment().getHiddenSequences(),
+                av.getAlignment().getHiddenColumns());
+      }
+      else
+      {
+        if (alpha != 0) // this is a timer triggered dissolve
+        {
+          Graphics2D g2d = (Graphics2D) g.create();
+          
+          // draw the original image
+          g2d.drawImage(veryLastMiniMe, 0, 0, getWidth(), getHeight(),
+                  this);
+
+          // draw the new image on top with varying degrees of transparency
+          g2d.setComposite(AlphaComposite.SrcOver.derive(1f - alpha));
+          g2d.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
+
+          g2d.dispose();
+        }
+        else if (lastMiniMe != miniMe)
+        {
+          g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
+          g.setColor(TRANS_GREY);
+          g.fillRect(0, 0, getWidth(), getHeight());
+        }
+        else
+        {
+          // fall back to normal behaviour
+          g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
+        }
+
       }
+
     }
 
+    // draw the box
     g.setColor(Color.red);
     od.drawBox(g);
   }
-
 }

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index c81ac2f..0b33b3b 100755 (executable)
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -96,12 +96,7 @@ public class OverviewPanel extends JPanel implements Runnable,
       @Override
       public void componentResized(ComponentEvent evt)
       {
-        if ((getWidth() != od.getWidth())
-                || (getHeight() != (od.getHeight())))
-        {
-          updateOverviewImage();
-          setBoxPosition();
-        }
+        updateOverviewImage();
       }
     });