Merge branch 'bug/JAL-2864nullOverviewCanvas' into develop

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

diff --git a/src/jalview/gui/OverviewCanvas.java b/src/jalview/gui/OverviewCanvas.java
index 63075dc..89088b8 100644 (file)
--- a/src/jalview/gui/OverviewCanvas.java
+++ b/src/jalview/gui/OverviewCanvas.java
@@ -21,7 +21,9 @@
 package jalview.gui;
 
 import jalview.api.AlignViewportI;
+import jalview.bin.Cache;
 import jalview.renderer.OverviewRenderer;
+import jalview.renderer.OverviewResColourFinder;
 import jalview.viewmodel.OverviewDimensions;
 
 import java.awt.Color;
@@ -41,6 +43,8 @@ public class OverviewCanvas extends JComponent
 
   private volatile boolean updaterunning = false;
 
+  private boolean dispose = false;
+
   private BufferedImage miniMe;
 
   private BufferedImage lastMiniMe = null;
@@ -57,16 +61,29 @@ public class OverviewCanvas extends JComponent
 
   private AlignViewportI av;
 
+  private OverviewResColourFinder cf;
+
+  private ProgressPanel progressPanel;
+
   public OverviewCanvas(OverviewDimensions overviewDims,
-          AlignViewportI alignvp)
+          AlignViewportI alignvp, ProgressPanel pp)
   {
     od = overviewDims;
     av = alignvp;
+    progressPanel = pp;
 
     sr = new SequenceRenderer(av);
     sr.renderGaps = false;
-    sr.forOverview = true;
     fr = new jalview.renderer.seqfeatures.FeatureRenderer(av);
+
+    boolean useLegacy = Cache.getDefault(Preferences.USE_LEGACY_GAP, false);
+    Color gapCol = Cache.getDefaultColour(Preferences.GAP_COLOUR,
+            jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
+    Color hiddenCol = Cache.getDefaultColour(Preferences.HIDDEN_COLOUR,
+            jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
+    cf = new OverviewResColourFinder(useLegacy, gapCol, hiddenCol);
+
+    setSize(od.getWidth(), od.getHeight());
   }
 
   /**
@@ -119,29 +136,20 @@ public class OverviewCanvas extends JComponent
   {
     miniMe = null;
 
-    if (!av.getShowBoxes())
+    if (showSequenceFeatures)
     {
-      // boxes are not shown on main viewport
-      or = new OverviewRenderer(sr, fr, od);
-      miniMe = new BufferedImage(od.getWidth(), od.getHeight(),
-              BufferedImage.TYPE_INT_RGB);
-      miniMe.getGraphics().setColor(Color.WHITE);
-      miniMe.getGraphics().fillRect(0, 0, od.getWidth(),
-              od.getSequencesHeight());
+      fr.transferSettings(transferRenderer);
     }
-    else
-    {
-      if (showSequenceFeatures)
-      {
-        fr.transferSettings(transferRenderer);
-      }
 
-      setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
+    setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
 
-      or = new OverviewRenderer(sr, fr, od);
-      miniMe = or.draw(od.getRows(av.getAlignment()),
-              od.getColumns(av.getAlignment()));
-    }
+    or = new OverviewRenderer(fr, od, av.getAlignment(),
+            av.getResidueShading(), cf);
+
+    or.addPropertyChangeListener(progressPanel);
+
+    miniMe = or.draw(od.getRows(av.getAlignment()),
+            od.getColumns(av.getAlignment()));
 
     Graphics mg = miniMe.getGraphics();
 
@@ -149,16 +157,19 @@ public class OverviewCanvas extends JComponent
     {
       mg.translate(0, od.getSequencesHeight());
       or.drawGraph(mg, av.getAlignmentConservationAnnotation(),
-              av.getCharWidth(), od.getGraphHeight(),
-              od.getColumns(av.getAlignment()));
+              od.getGraphHeight(), od.getColumns(av.getAlignment()));
       mg.translate(0, -od.getSequencesHeight());
     }
-    System.gc();
 
+    or.removePropertyChangeListener(progressPanel);
+    or = null;
     if (restart)
     {
       restart = false;
-      draw(showSequenceFeatures, showAnnotation, transferRenderer);
+      if (!dispose)
+      {
+        draw(showSequenceFeatures, showAnnotation, transferRenderer);
+      }
     }
     else
     {
@@ -170,6 +181,8 @@ public class OverviewCanvas extends JComponent
   @Override
   public void paintComponent(Graphics g)
   {
+    super.paintComponent(g);
+
     if (restart)
     {
       if (lastMiniMe == null)
@@ -186,16 +199,72 @@ public class OverviewCanvas extends JComponent
     }
     else if (lastMiniMe != null)
     {
-      g.drawImage(lastMiniMe, 0, 0, this);
-      if (lastMiniMe != miniMe)
+      // is this a resize?
+      if ((getWidth() > 0) && (getHeight() > 0)
+              && ((getWidth() != od.getWidth())
+                      || (getHeight() != od.getHeight())))
       {
-        g.setColor(TRANS_GREY);
-        g.fillRect(0, 0, getWidth(), getHeight());
+        // if there is annotation, scale the alignment and annotation
+        // separately
+        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());
+        }
+
+        // make sure the box is in the right place
+        od.setBoxPosition(av.getAlignment().getHiddenSequences(),
+                av.getAlignment().getHiddenColumns());
       }
+      // fall back to normal behaviour
+      g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
     }
-
+    else
+    {
+      g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
+    }
+    
+    // draw the box
     g.setColor(Color.red);
     od.drawBox(g);
   }
 
+
+  public void dispose()
+  {
+    dispose = true;
+    od = null;
+    synchronized (this)
+    {
+      restart = true;
+      if (or != null)
+      {
+        or.setRedraw(true);
+      }
+    }
+  }
 }