X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FOverviewPanel.java;h=b3c4a37ffb7e0eea6fbee6ebf4848d0b77e0b166;hb=52298f6987c5807b9f672e33f416dee9e14e1952;hp=0d3f05843153687745eb48b37c67c8f6f9638f54;hpb=d559b47886de6427219011e6e355320a0babd757;p=jalview.git

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 0d3f058..b3c4a37 100755
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -20,64 +20,60 @@
  */
 package jalview.appletgui;
 
+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.CheckboxMenuItem;
 import java.awt.Dimension;
-import java.awt.Frame;
-import java.awt.Graphics;
-import java.awt.Image;
 import java.awt.Panel;
+import java.awt.PopupMenu;
 import java.awt.event.ComponentAdapter;
 import java.awt.event.ComponentEvent;
+import java.awt.event.InputEvent;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
+import java.beans.PropertyChangeEvent;
 
 public class OverviewPanel extends Panel implements Runnable,
-        MouseMotionListener, MouseListener
+        MouseMotionListener, MouseListener, ViewportListenerI
 {
   private OverviewDimensions od;
 
-  private Image miniMe;
-
-  private Image offscreen;
+  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;
-
-  // Can set different properties in this seqCanvas than
-  // main visible SeqCanvas
-  private SequenceRenderer sr;
-
-  private FeatureRenderer fr;
+  private boolean showHidden = true;
 
-  private Frame nullFrame;
+  private boolean updateRunning = false;
 
-  public OverviewPanel(AlignmentPanel ap)
+  public OverviewPanel(AlignmentPanel alPanel)
   {
-    this.av = ap.av;
-    this.ap = ap;
+    this.av = alPanel.av;
+    this.ap = alPanel;
     setLayout(null);
-    nullFrame = new Frame();
-    nullFrame.addNotify();
 
-    sr = new SequenceRenderer(av);
-    sr.graphics = nullFrame.getGraphics();
-    sr.renderGaps = false;
-    sr.forOverview = true;
-    fr = new FeatureRenderer(av);
+    od = new OverviewDimensionsShowHidden(av.getRanges(),
+            (av.isShowAnnotation() && av.getSequenceConsensusHash() != null));
 
-    od = new OverviewDimensions(av);
+    oviewCanvas = new OverviewCanvas(od, av);
+    setLayout(new BorderLayout());
+    add(oviewCanvas, BorderLayout.CENTER);
 
     setSize(new Dimension(od.getWidth(), od.getHeight()));
+
+    av.getRanges().addPropertyChangeListener(this);
+
     addComponentListener(new ComponentAdapter()
     {
 
@@ -113,6 +109,10 @@ public class OverviewPanel extends Panel implements Runnable,
   @Override
   public void mouseClicked(MouseEvent evt)
   {
+    if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+    {
+      showPopupMenu(evt);
+    }
   }
 
   @Override
@@ -123,232 +123,74 @@ public class OverviewPanel extends Panel implements Runnable,
   @Override
   public void mousePressed(MouseEvent evt)
   {
-    od.setBoxPositionByMouse(evt.getX(), evt.getY());
-    ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
-    ap.paintAlignment(false);
+    mouseAction(evt);
   }
 
   @Override
   public void mouseReleased(MouseEvent evt)
   {
-    od.setBoxPositionByMouse(evt.getX(), evt.getY());
-    ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
-    ap.paintAlignment(false);
+    mouseAction(evt);
   }
 
   @Override
   public void mouseDragged(MouseEvent evt)
   {
-    od.setBoxPositionByMouse(evt.getX(), evt.getY());
-    ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
-    ap.paintAlignment(false);
+    mouseAction(evt);
   }
 
-  /**
-   * DOCUMENT ME!
-   */
-  public void updateOverviewImage()
+  private void mouseAction(MouseEvent evt)
   {
-    if (resizing)
+    if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
     {
-      resizeAgain = true;
-      return;
-    }
-
-    if (av.isShowSequenceFeatures())
-    {
-      fr.transferSettings(ap.seqPanel.seqCanvas.fr);
+      if (!Platform.isAMac())
+      {
+        showPopupMenu(evt);
+      }
     }
-
-    resizing = true;
-
-    if ((getWidth() > 0) && (getHeight() > 0))
+    else
     {
-      od.setWidth(getWidth()); // width = getWidth();
-      od.setHeight(getHeight()); // sequencesHeight = getHeight() - graphHeight;
+      od.updateViewportFromMouse(evt.getX(), evt.getY(), av.getAlignment()
+              .getHiddenSequences(), av.getAlignment().getHiddenColumns());
+      ap.paintAlignment(false);
     }
-    setSize(new Dimension(od.getWidth(), od.getHeight()));
-
-    Thread thread = new Thread(this);
-    thread.start();
-    repaint();
   }
 
-  @Override
-  public void run()
+  /**
+   * Updates the overview image when the related alignment panel is updated
+   */
+  public void updateOverviewImage()
   {
-    miniMe = null;
-
-    if (av.isShowSequenceFeatures())
-    {
-      fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
-    }
-
-    if (getSize().width > 0 && getSize().height > 0)
+    if ((getSize().width > 0) && (getSize().height > 0))
     {
       od.setWidth(getSize().width);
-      od.setHeight(getSize().height - od.getGraphHeight());
+      od.setHeight(getSize().height);
     }
-
     setSize(new Dimension(od.getWidth(), od.getHeight()));
 
-    miniMe = nullFrame.createImage(od.getWidth(), od.getHeight());
-    offscreen = nullFrame.createImage(od.getWidth(), od.getHeight());
-
-    Graphics mg = miniMe.getGraphics();
-
-    od.updateScales();
-
-    int alwidth = av.getAlignment().getWidth();
-    int alheight = av.getAlignment().getHeight()
-            + av.getAlignment().getHiddenSequences().getSize();
-    float sampleCol = alwidth / (float) od.getWidth();
-    float sampleRow = alheight / (float) od.getSequencesHeight();
-
-    buildImage(sampleRow, sampleCol, mg);
-
-    if (av.getAlignmentConservationAnnotation() != null)
-    {
-      for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
-      {
-        mg.translate(col, od.getSequencesHeight());
-        ap.annotationPanel.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());
-      }
-    }
-    System.gc();
-
-    resizing = false;
-
-    setBoxPosition();
-
-    if (resizeAgain)
-    {
-      resizeAgain = false;
-      updateOverviewImage();
-    }
-  }
-
-  private void buildImage(float sampleRow, float sampleCol, Graphics mg)
-  {
-    int lastcol = 0;
-    int lastrow = 0;
-    int xstart = 0;
-    int ystart = 0;
-    Color color = Color.yellow;
-    int sameRow = 0;
-    int sameCol = 0;
-
-    jalview.datamodel.SequenceI seq = null;
-    final boolean hasHiddenRows = av.hasHiddenRows();
-    final boolean hasHiddenCols = av.hasHiddenColumns();
-    boolean hiddenRow = false;
-
-    for (int row = 0; row <= od.getSequencesHeight() && !resizeAgain; row++)
+    synchronized (this)
     {
-      if ((int) (row * sampleRow) == lastrow)
+      if (updateRunning)
       {
-        sameRow++;
+        oviewCanvas.restartDraw();
+        return;
       }
-      else
-      {
-        // this should largely be a method in Alignment
-        hiddenRow = false;
-        if (hasHiddenRows)
-        {
-          // look for sequence in hidden rows
-          seq = av.getAlignment().getHiddenSequences()
-                  .getHiddenSequence(lastrow);
-          if (seq == null)
-          {
-            // didn't find in hidden rows, adjust the index and retrieve from
-            // full row set
-            int index = av.getAlignment().getHiddenSequences()
-                    .findIndexWithoutHiddenSeqs(lastrow);
-
-            seq = av.getAlignment().getSequenceAt(index);
-          }
-          else
-          {
-            // found in hidden rows, ergo this row is hidden
-            hiddenRow = true;
-          }
-        }
-        else
-        {
-          seq = av.getAlignment().getSequenceAt(lastrow);
-        }
-        // end of Alignment method
 
-        for (int col = 0; col < od.getWidth(); col++)
-        {
-          if ((int) (col * sampleCol) == lastcol
-                  && (int) (row * sampleRow) == lastrow)
-          {
-            sameCol++;
-          }
-          else
-          {
-            lastcol = (int) (col * sampleCol);
-
-            color = getColumnColourFromSequence(seq, hiddenRow,
-                    hasHiddenCols, lastcol);
-
-            mg.setColor(color);
-            if (sameCol == 1 && sameRow == 1)
-            {
-              mg.drawLine(xstart, ystart, xstart, ystart);
-            }
-            else
-            {
-              mg.fillRect(xstart, ystart, sameCol, sameRow);
-            }
-
-            xstart = col;
-            sameCol = 1;
-          }
-        }
-        lastrow = (int) (row * sampleRow);
-        ystart = row;
-        sameRow = 1;
-      }
+      updateRunning = true;
     }
-
+    Thread thread = new Thread(this);
+    thread.start();
+    repaint();
+    updateRunning = false;
   }
 
-  /*
-   * Find the colour of a sequence at a specified column position
-   */
-  private Color getColumnColourFromSequence(
-          jalview.datamodel.SequenceI seq, boolean hiddenRow,
-          boolean hasHiddenCols, int lastcol)
+  @Override
+  public void run()
   {
-    Color color;
-    if (seq.getLength() > lastcol)
-    {
-      color = sr.getResidueBoxColour(seq, lastcol);
-
-      if (av.isShowSequenceFeatures())
-      {
-        color = fr.findFeatureColour(color, seq, lastcol);
-      }
-    }
-    else
-    {
-      color = Color.white; // White
-    }
-
-    if (hiddenRow
-            || (hasHiddenCols && !av.getColumnSelection()
-                    .isVisible(lastcol)))
-    {
-      color = color.darker().darker();
-    }
-    return color;
+    oviewCanvas.draw(av.isShowSequenceFeatures(),
+            (av.isShowAnnotation() && av
+                    .getAlignmentConservationAnnotation() != null),
+            ap.seqPanel.seqCanvas.getFeatureRenderer());
+    setBoxPosition();
   }
 
   /**
@@ -356,29 +198,63 @@ public class OverviewPanel extends Panel implements Runnable,
    * changed
    * 
    */
-  public void setBoxPosition()
+  private void setBoxPosition()
   {
-    od.setBoxPosition();
+    od.setBoxPosition(av.getAlignment()
+.getHiddenSequences(), av
+            .getAlignment().getHiddenColumns());
     repaint();
   }
 
-  @Override
-  public void update(Graphics g)
+  /*
+   * Displays the popup menu and acts on user input
+   */
+  private void showPopupMenu(MouseEvent e)
   {
-    paint(g);
+    PopupMenu popup = new PopupMenu();
+    ItemListener menuListener = new ItemListener()
+    {
+      @Override
+      public void itemStateChanged(ItemEvent e)
+      {
+        toggleHiddenColumns();
+      }
+    };
+    CheckboxMenuItem item = new CheckboxMenuItem(
+            MessageManager.getString("label.togglehidden"));
+    item.setState(showHidden);
+    popup.add(item);
+    item.addItemListener(menuListener);
+    this.add(popup);
+    popup.show(this, e.getX(), e.getY());
   }
 
   @Override
-  public void paint(Graphics g)
+  public void propertyChange(PropertyChangeEvent evt)
+  {
+    setBoxPosition();
+  }
+
+  /*
+   * Toggle overview display between showing hidden columns and hiding hidden columns
+   */
+  private void toggleHiddenColumns()
   {
-    Graphics og = offscreen.getGraphics();
-    if (miniMe != null)
+    if (showHidden)
+    {
+      showHidden = false;
+      od = new OverviewDimensionsHideHidden(av.getRanges(),
+              (av.isShowAnnotation() && av
+                      .getAlignmentConservationAnnotation() != null));
+    }
+    else
     {
-      og.drawImage(miniMe, 0, 0, this);
-      og.setColor(Color.red);
-      od.drawBox(og);
-      g.drawImage(offscreen, 0, 0, this);
+      showHidden = true;
+      od = new OverviewDimensionsShowHidden(av.getRanges(),
+              (av.isShowAnnotation() && av
+                      .getAlignmentConservationAnnotation() != null));
     }
+    oviewCanvas.resetOviewDims(od);
+    updateOverviewImage();
   }
-
 }