X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FOverviewPanel.java;fp=src%2Fjalview%2Fgui%2FOverviewPanel.java;h=a5441a25cb0788125240fa8ff2a4068df1e05ea3;hb=c2e5d3d1ebe3b283bdde15637c590721cd6c5637;hp=095a57385c9d8c45aad35620737e64de975d34af;hpb=557859a3ea9a1e86899ef2033de90eadb6d87118;p=jalview.git

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 095a573..a5441a2 100755
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -20,24 +20,28 @@
  */
 package jalview.gui;
 
-import jalview.datamodel.SequenceI;
-import jalview.renderer.AnnotationRenderer;
-import jalview.renderer.seqfeatures.FeatureColourFinder;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
 import jalview.viewmodel.OverviewDimensions;
+import jalview.viewmodel.OverviewDimensionsHideHidden;
+import jalview.viewmodel.OverviewDimensionsShowHidden;
 import jalview.viewmodel.ViewportListenerI;
 
-import java.awt.Color;
+import java.awt.BorderLayout;
 import java.awt.Dimension;
-import java.awt.Graphics;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
 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 java.beans.PropertyChangeEvent;
 
+import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
+import javax.swing.SwingUtilities;
 
 /**
  * Panel displaying an overview of the full alignment, with an interactive box
@@ -49,32 +53,17 @@ import javax.swing.JPanel;
 public class OverviewPanel extends JPanel implements Runnable,
         ViewportListenerI
 {
-  private static final Color TRANS_GREY = new Color(100, 100, 100, 25);
-
-  private final AnnotationRenderer renderer = new AnnotationRenderer();
-
   private OverviewDimensions od;
 
-  private BufferedImage miniMe;
-
-  private BufferedImage lastMiniMe = null;
+  private OverviewCanvas oviewCanvas;
 
   private AlignViewport av;
 
   private AlignmentPanel ap;
 
-  //
-  private boolean resizing = false;
-
-  // This is set true if the user resizes whilst
-  // the overview is being calculated
-  private boolean resizeAgain = false;
+  private JCheckBoxMenuItem displayToggle;
 
-  // Can set different properties in this seqCanvas than
-  // main visible SeqCanvas
-  private SequenceRenderer sr;
-
-  jalview.renderer.seqfeatures.FeatureRenderer fr;
+  private boolean showHidden = true;
 
   /**
    * Creates a new OverviewPanel object.
@@ -86,17 +75,15 @@ public class OverviewPanel extends JPanel implements Runnable,
   {
     this.av = alPanel.av;
     this.ap = alPanel;
-    setLayout(null);
-
-    sr = new SequenceRenderer(av);
-    sr.renderGaps = false;
-    sr.forOverview = true;
-    fr = new FeatureRenderer(ap);
 
-    od = new OverviewDimensions(av.getRanges(),
+    od = new OverviewDimensionsShowHidden(av.getRanges(),
             (av.isShowAnnotation() && av
                     .getAlignmentConservationAnnotation() != null));
 
+    oviewCanvas = new OverviewCanvas(od, av);
+    setLayout(new BorderLayout());
+    add(oviewCanvas, BorderLayout.CENTER);
+
     av.getRanges().addPropertyChangeListener(this);
 
     addComponentListener(new ComponentAdapter()
@@ -118,13 +105,13 @@ public class OverviewPanel extends JPanel implements Runnable,
       @Override
       public void mouseDragged(MouseEvent evt)
       {
-        if (!av.getWrapAlignment())
+        if (!SwingUtilities.isRightMouseButton(evt)
+                && !av.getWrapAlignment())
         {
           od.updateViewportFromMouse(evt.getX(), evt.getY(), av
-                  .getAlignment().getHiddenSequences(), av
-                  .getColumnSelection(), av.getRanges());
-          // TODO set via ViewportRanges in overview dimensions once JAL-2388 is
-          // merged
+                  .getAlignment().getHiddenSequences(), av.getAlignment()
+                  .getHiddenColumns());
+
         }
       }
     });
@@ -134,193 +121,116 @@ public class OverviewPanel extends JPanel implements Runnable,
       @Override
       public void mousePressed(MouseEvent evt)
       {
-        if (!av.getWrapAlignment())
+        if (SwingUtilities.isRightMouseButton(evt))
+        {
+          if (!Platform.isAMac())
+          {
+            showPopupMenu(evt);
+          }
+        }
+        else if (!av.getWrapAlignment())
         {
           od.updateViewportFromMouse(evt.getX(), evt.getY(), av
-                  .getAlignment().getHiddenSequences(), av
-                  .getColumnSelection(), av.getRanges());
-          // TODO set via ViewportRanges in overview dimensions once JAL-2388 is
-          // merged
+                  .getAlignment().getHiddenSequences(), av.getAlignment()
+                  .getHiddenColumns());
+        }
+      }
+
+      @Override
+      public void mouseClicked(MouseEvent evt)
+      {
+        if (SwingUtilities.isRightMouseButton(evt))
+        {
+          showPopupMenu(evt);
         }
       }
     });
 
+
     updateOverviewImage();
-    setBoxPosition();
   }
 
-  /**
-   * Updates the overview image when the related alignment panel is updated
+  /*
+   * Displays the popup menu and acts on user input
    */
-  public void updateOverviewImage()
+  private void showPopupMenu(MouseEvent e)
   {
-    if (resizing)
+    JPopupMenu popup = new JPopupMenu();
+    ActionListener menuListener = new ActionListener()
     {
-      resizeAgain = true;
-      return;
-    }
-
-    resizing = true;
-
-    if ((getWidth() > 0) && (getHeight() > 0))
-    {
-      od.setWidth(getWidth());
-      od.setHeight(getHeight());
-    }
-
-    setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
-
-    Thread thread = new Thread(this);
-    thread.start();
-    repaint();
-  }
-
-  @Override
-  public void run()
-  {
-    miniMe = null;
-
-    if (av.isShowSequenceFeatures())
-    {
-      fr.transferSettings(ap.getSeqPanel().seqCanvas.getFeatureRenderer());
-    }
-
-    // why do we need to set preferred size again? was set in
-    // updateOverviewImage
-    setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
-
-    miniMe = new BufferedImage(od.getWidth(), od.getHeight(),
-            BufferedImage.TYPE_INT_RGB);
-
-    Graphics mg = miniMe.getGraphics();
-    mg.setColor(Color.orange);
-    mg.fillRect(0, 0, od.getWidth(), miniMe.getHeight());
-
-    // calculate sampleCol and sampleRow
-    // alignment width is max number of residues/bases
-    // alignment height is number of sequences
-    int alwidth = av.getAlignment().getWidth();
-    int alheight = av.getAlignment().getAbsoluteHeight();
-
-    // sampleCol or sampleRow is the width/height allocated to each residue
-    // in particular, sometimes we may need more than one row/col of the
-    // BufferedImage allocated
-    // sampleCol is how much of a residue to assign to each pixel
-    // sampleRow is how many sequences to assign to each pixel
-    float sampleCol = alwidth / (float) od.getWidth();
-    float sampleRow = alheight / (float) od.getSequencesHeight();
-
-    buildImage(sampleRow, sampleCol);
-
-    // check for conservation annotation to make sure overview works for DNA too
-    if (av.isShowAnnotation()
-            && (av.getAlignmentConservationAnnotation() != null))
-    {
-      renderer.updateFromAlignViewport(av);
-      for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
+      @Override
+      public void actionPerformed(ActionEvent event)
       {
-        mg.translate(col, od.getSequencesHeight());
-        renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(),
-                av.getAlignmentConservationAnnotation().annotations,
-                (int) (sampleCol) + 1, od.getGraphHeight(),
-                (int) (col * sampleCol), (int) (col * sampleCol) + 1);
-        mg.translate(-col, -od.getSequencesHeight());
-
+        // switch on/off the hidden columns view
+        toggleHiddenColumns();
+        displayToggle.setSelected(showHidden);
       }
-    }
-    System.gc();
-
-    resizing = false;
-
-    if (resizeAgain)
-    {
-      resizeAgain = false;
-      updateOverviewImage();
-    }
-    else
-    {
-      lastMiniMe = miniMe;
-    }
-
-    // setBoxPosition();
+    };
+    displayToggle = new JCheckBoxMenuItem(
+            MessageManager.getString("label.togglehidden"));
+    displayToggle.setEnabled(true);
+    displayToggle.setSelected(showHidden);
+    popup.add(displayToggle);
+    displayToggle.addActionListener(menuListener);
+    popup.show(this, e.getX(), e.getY());
   }
 
   /*
-   * Build the overview panel image
+   * Toggle overview display between showing hidden columns and hiding hidden columns
    */
-  private void buildImage(float sampleRow, float sampleCol)
+  private void toggleHiddenColumns()
   {
-    int lastcol = -1;
-    int lastrow = -1;
-    int rgbColour = Color.white.getRGB();
-
-    SequenceI seq = null;
-    FeatureColourFinder finder = new FeatureColourFinder(fr);
-
-    final boolean 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 (int row = 0; row < od.getSequencesHeight() && !resizeAgain; row++)
+    if (showHidden)
     {
-      boolean doCopy = true;
-      int currentrow = (int) (row * sampleRow);
-      if (currentrow != lastrow)
-      {
-        doCopy = false;
-
-        lastrow = currentrow;
-
-        // get the sequence which would be at alignment index 'lastrow' if no
-        // rows were hidden, and determine whether it is hidden or not
-        hiddenRow = av.getAlignment().isHidden(lastrow);
-        seq = av.getAlignment().getSequenceAtAbsoluteIndex(lastrow);
-      }
-
-      for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
-      {
-        if (doCopy)
-        {
-          rgbColour = miniMe.getRGB(col, row - 1);
-        }
-        else if ((int) (col * sampleCol) != lastcol
-                || (int) (row * sampleRow) != lastrow)
-        {
-          lastcol = (int) (col * sampleCol);
-          rgbColour = getColumnColourFromSequence(seq, hiddenRow,
-                  hasHiddenCols, lastcol, finder);
-        }
-        // else we just use the color we already have , so don't need to set it
-
-        miniMe.setRGB(col, row, rgbColour);
-      }
+      showHidden = false;
+      od = new OverviewDimensionsHideHidden(av.getRanges(),
+              (av.isShowAnnotation() && av
+                      .getAlignmentConservationAnnotation() != null));
+    }
+    else
+    {
+      showHidden = true;
+      od = new OverviewDimensionsShowHidden(av.getRanges(),
+              (av.isShowAnnotation() && av
+                      .getAlignmentConservationAnnotation() != null));
     }
+    oviewCanvas.resetOviewDims(od);
+    updateOverviewImage();
+    setBoxPosition();
   }
 
-  /*
-   * Find the colour of a sequence at a specified column position
+  /**
+   * Updates the overview image when the related alignment panel is updated
    */
-  private int getColumnColourFromSequence(
-          jalview.datamodel.SequenceI seq,
-          boolean hiddenRow, boolean hasHiddenCols, int lastcol,
-          FeatureColourFinder finder)
+  public void updateOverviewImage()
   {
-    Color color = Color.white;
-
-    if ((seq != null) && (seq.getLength() > lastcol))
+    if ((getWidth() > 0) && (getHeight() > 0))
     {
-    	color = sr.getResidueColour(seq, lastcol, finder);
+      od.setWidth(getWidth());
+      od.setHeight(getHeight());
     }
+    
+    setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
 
-    if (hiddenRow
-            || (hasHiddenCols && !av.getColumnSelection()
-                    .isVisible(lastcol)))
+    if (oviewCanvas.restartDraw())
     {
-      color = color.darker().darker();
+      return;
     }
 
-    return color.getRGB();
+    Thread thread = new Thread(this);
+    thread.start();
+    repaint();
+
+  }
+
+  @Override
+  public void run()
+  {
+    oviewCanvas.draw(av.isShowSequenceFeatures(),
+            (av.isShowAnnotation() && av
+                    .getAlignmentConservationAnnotation() != null), ap
+                    .getSeqPanel().seqCanvas.getFeatureRenderer());
+    setBoxPosition();
   }
 
   /**
@@ -330,43 +240,11 @@ public class OverviewPanel extends JPanel implements Runnable,
    */
   private void setBoxPosition()
   {
-    od.setBoxPosition(av.getAlignment()
-            .getHiddenSequences(), av.getColumnSelection(), av.getRanges());
+    od.setBoxPosition(av.getAlignment().getHiddenSequences(), av
+            .getAlignment().getHiddenColumns());
     repaint();
   }
 
-
-  @Override
-  public void paintComponent(Graphics g)
-  {
-    if (resizing || resizeAgain)
-    {
-      if (lastMiniMe == null)
-      {
-        g.setColor(Color.white);
-        g.fillRect(0, 0, getWidth(), getHeight());
-      }
-      else
-      {
-        g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
-      }
-      g.setColor(TRANS_GREY);
-      g.fillRect(0, 0, getWidth(), getHeight());
-    }
-    else if (lastMiniMe != null)
-    {
-      g.drawImage(lastMiniMe, 0, 0, this);
-      if (lastMiniMe != miniMe)
-      {
-        g.setColor(TRANS_GREY);
-        g.fillRect(0, 0, getWidth(), getHeight());
-      }
-    }
-
-    g.setColor(Color.red);
-    od.drawBox(g);
-  }
-
   @Override
   public void propertyChange(PropertyChangeEvent evt)
   {