X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FOverviewPanel.java;h=685b8c9688e200c36a7d455fb7a5aa43af1c9aeb;hb=4a3def9f59cefe629c9a33d87483283aee085928;hp=366f5bcb196d9e6a8722230379eade6e2c73e8ff;hpb=5cd5b6e7864fe435ceb3f5c2f339a436ea0aac93;p=jalview.git

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 366f5bc..685b8c9 100755
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -1,441 +1,350 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.appletgui;
-
-import java.awt.*;
-import java.awt.event.*;
-
-public class OverviewPanel
-    extends Panel implements Runnable, MouseMotionListener, MouseListener
-{
-  Image miniMe;
-  AlignViewport av;
-  AlignmentPanel ap;
-  float scalew = 1f;
-  float scaleh = 1f;
-
-  public int width, sequencesHeight;
-  int graphHeight = 20;
-  int boxX = -1, boxY = -1, boxWidth = -1, boxHeight = -1;
-
-  boolean resizing = false;
-
-  // Can set different properties in this seqCanvas than
-  // main visible SeqCanvas
-  SequenceRenderer sr;
-  FeatureRenderer fr;
-
-
-  Frame nullFrame;
-
-  public OverviewPanel(AlignmentPanel ap)
-  {
-    this.av = ap.av;
-    this.ap = ap;
-    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);
-    fr.overview = true;
-
-
-
-    // scale the initial size of overviewpanel to shape of alignment
-    float initialScale = (float) av.alignment.getWidth() /
-        (float) av.alignment.getHeight();
-
-    if(av.vconsensus==null)
-          graphHeight = 0;
-
-    if (av.alignment.getWidth() > av.alignment.getHeight())
-    {
-      // wider
-      width = 400;
-      sequencesHeight = (int) (400f / initialScale);
-      if(sequencesHeight<40)
-              sequencesHeight = 40;
-    }
-    else
-    {
-      // taller
-      width = (int) (400f * initialScale);
-      sequencesHeight = 300;
-      if (width < 120)
-      {
-        width = 120;
-      }
-    }
-
-    setSize(new Dimension(width, sequencesHeight + graphHeight));
-    addComponentListener(new ComponentAdapter()
-    {
-
-      public void componentResized(ComponentEvent evt)
-      {
-        if (getSize().width != width ||
-            getSize().height != sequencesHeight + graphHeight)
-        {
-          updateOverviewImage();
-        }
-      }
-    });
-
-    addMouseMotionListener(this);
-
-    addMouseListener(this);
-
-    updateOverviewImage();
-
-  }
-
-
-  public void mouseEntered(MouseEvent evt)
-  {}
-  public void mouseExited(MouseEvent evt)
-  {}
-  public void mouseClicked(MouseEvent evt)
-  {}
-  public void mouseMoved(MouseEvent evt)
-  {}
-  public void mousePressed(MouseEvent evt)
-  {
-    boxX = evt.getX();
-    boxY = evt.getY();
-    checkValid();
-  }
-
-  public void mouseReleased(MouseEvent evt)
-  {
-    boxX = evt.getX();
-    boxY = evt.getY();
-    checkValid();
-  }
-
-  public void mouseDragged(MouseEvent evt)
-  {
-    boxX = evt.getX();
-    boxY = evt.getY();
-    checkValid();
-    ap.repaint();
-  }
-
-  void checkValid()
-  {
-    if (boxY < 0)
-    {
-        boxY = 0;
-    }
-
-    if (boxY > (sequencesHeight - boxHeight))
-    {
-        boxY = sequencesHeight - boxHeight + 1;
-    }
-
-    if (boxX < 0)
-    {
-        boxX = 0;
-    }
-
-    if (boxX > (width - boxWidth))
-    {
-      if(av.hasHiddenColumns)
-      {
-        //Try smallest possible box
-        boxWidth = (int) ( (av.endRes - av.startRes + 1) *
-                               av.getCharWidth() * scalew);
-      }
-      boxX = width - boxWidth;
-    }
-
-    int col = (int) (boxX / scalew / av.getCharWidth());
-    int row = (int) (boxY / scaleh / av.getCharHeight());
-
-    if (av.hasHiddenColumns)
-    {
-      if (!av.getColumnSelection().isVisible(col))
-      {
-        return;
-      }
-
-      col = av.getColumnSelection().findColumnPosition(col);
-    }
-
-    if( av.hasHiddenRows )
-    {
-      row = av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(row);
-    }
-
-    ap.setScrollValues( col, row );
-
-  }
-
-  /**
-   * DOCUMENT ME!
-   */
-  public void updateOverviewImage()
-  {
-    if (resizing)
-    {
-        resizeAgain = true;
-        return;
-    }
-
-    if (av.showSequenceFeatures)
-   {
-     fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups;
-     fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours;
-   }
-
-    resizing = true;
-
-    if ( (getSize().width > 0) && (getSize().height > 0))
-    {
-      width = getSize().width;
-      sequencesHeight = getSize().height - graphHeight;
-    }
-    setSize(new Dimension(width, sequencesHeight + graphHeight));
-
-    Thread thread = new Thread(this);
-    thread.start();
-    repaint();
-  }
-
-  // This is set true if the user resizes whilst
-  // the overview is being calculated
-    boolean resizeAgain = false;
-
-  public void run()
-  {
-    miniMe = null;
-    int alwidth = av.alignment.getWidth();
-    int alheight = av.alignment.getHeight();
-
-    if (av.showSequenceFeatures)
-    {
-      fr.transferSettings( ap.seqPanel.seqCanvas.getFeatureRenderer() );
-    }
-
-    if (getSize().width > 0 && getSize().height > 0)
-    {
-      width = getSize().width;
-      sequencesHeight = getSize().height - graphHeight;
-    }
-
-    setSize(new Dimension(width, sequencesHeight + graphHeight));
-
-    int fullsizeWidth = alwidth * av.getCharWidth();
-    int fullsizeHeight = alheight * av.getCharHeight();
-
-    scalew = (float) width / (float) fullsizeWidth;
-    scaleh = (float) sequencesHeight / (float) fullsizeHeight;
-
-    miniMe = nullFrame.createImage(width, sequencesHeight + graphHeight);
-
-    Graphics mg = miniMe.getGraphics();
-    float sampleCol = (float) alwidth / (float) width;
-    float sampleRow = (float) alheight / (float) sequencesHeight;
-
-    int lastcol=-1, lastrow=-1;
-    Color color = Color.yellow;
-    int row, col, sameRow = 0, sameCol = 0;
-    jalview.datamodel.SequenceI seq;
-    boolean hiddenRow = false;
-    for (row = 0; row < sequencesHeight; row++)
-    {
-      if((int)(row*sampleRow)==lastrow)
-      {
-        sameRow ++;
-        continue;
-      }
-
-      lastrow = (int)(row*sampleRow);
-
-      hiddenRow = false;
-      if (av.hasHiddenRows)
-      {
-        seq = av.alignment.getHiddenSequences().getHiddenSequence(lastrow);
-        if (seq == null)
-        {
-          int index =
-             av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(lastrow);
-
-         seq = av.alignment.getSequenceAt(index);
-        }
-        else
-        {
-          hiddenRow = true;
-        }
-      }
-      else
-        seq = av.alignment.getSequenceAt(lastrow);
-
-      if(seq==null)
-      {
-        System.out.println(lastrow+" null");
-        continue;
-      }
-
-        for (col = 0; col < width; col++)
-        {
-          if ( (int) (col * sampleCol) == lastcol && (int) (row * sampleRow) == lastrow)
-          {
-            sameCol ++;
-            continue;
-          }
-
-          lastcol = (int) (col * sampleCol);
-
-          if (seq.getLength() > lastcol)
-          {
-            color = sr.getResidueBoxColour(
-                seq, lastcol);
-
-            if (av.showSequenceFeatures)
-              color = fr.findFeatureColour(color, seq, lastcol);
-          }
-          else
-          {
-            color = Color.white; //White
-          }
-
-          if (hiddenRow ||
-              (av.hasHiddenColumns && !av.getColumnSelection().isVisible(lastcol)))
-          {
-            color = color.darker().darker();
-          }
-
-          mg.setColor(color);
-          if (sameCol == 1 && sameRow == 1)
-            mg.drawLine(col, row, col, row);
-          else
-            mg.fillRect(col, row, col+sameCol, col+sameRow);
-
-          sameCol = 1;
-      }
-      sameRow = 1;
-    }
-
-    if (av.conservation != null)
-    {
-      for (col = 0; col < width; col++)
-      {
-        lastcol = (int) (col * sampleCol);
-        {
-          mg.translate(col, sequencesHeight);
-          ap.annotationPanel.drawGraph(mg, av.conservation,
-                                       (int) (sampleCol) + 1,
-                                       graphHeight,
-                                       (int) (col * sampleCol),
-                                       (int) (col * sampleCol) + 1);
-          mg.translate( -col, -sequencesHeight);
-        }
-      }
-    }
-    System.gc();
-
-    resizing = false;
-
-    setBoxPosition();
-
-    if(resizeAgain)
-    {
-      resizeAgain = false;
-      updateOverviewImage();
-    }
-}
-
-  public void setBoxPosition()
-  {
-    int fullsizeWidth = av.alignment.getWidth() * av.getCharWidth();
-    int fullsizeHeight = (av.alignment.getHeight()
-                          + av.alignment.getHiddenSequences().getSize()) *
-        av.getCharHeight();
-
-    int startRes = av.getStartRes();
-    int endRes = av.getEndRes();
-
-    if (av.hasHiddenColumns)
-    {
-      startRes = av.getColumnSelection().adjustForHiddenColumns(startRes);
-      endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);
-    }
-
-    int startSeq = av.startSeq;
-    int endSeq = av.endSeq;
-
-    if (av.hasHiddenRows)
-    {
-      startSeq =
-          av.alignment.getHiddenSequences().adjustForHiddenSeqs(startSeq);
-
-      endSeq =
-          av.alignment.getHiddenSequences().adjustForHiddenSeqs(endSeq);
-
-    }
-
-    scalew = (float) width / (float) fullsizeWidth;
-    scaleh = (float) sequencesHeight / (float) fullsizeHeight;
-
-    boxX = (int) (startRes * av.getCharWidth() * scalew);
-    boxY = (int) (startSeq * av.getCharHeight() * scaleh);
-
-    if (av.hasHiddenColumns)
-      boxWidth = (int) ( (endRes - startRes + 1) * av.getCharWidth() * scalew);
-    else
-      boxWidth = (int) ( (endRes - startRes + 1) * av.getCharWidth() * scalew);
-
-    boxHeight = (int) ( (endSeq - startSeq) * av.getCharHeight() * scaleh);
-
-    repaint();
-  }
-
-  public void update(Graphics g)
-  {
-    paint(g);
-  }
-
-  public void paint(Graphics g)
-  {
-    if (miniMe != null)
-    {
-      g.drawImage(miniMe, 0, 0, this);
-    }
-    else
-    {
-      g.setColor(Color.white);
-      g.fillRect(0, 0, getSize().width, getSize().height);
-      g.setColor(Color.black);
-      g.setFont(new Font("Verdana", Font.BOLD, 15));
-      g.drawString("Recalculating", 5, sequencesHeight / 2);
-      g.drawString("Overview.....", 5, (sequencesHeight / 2) + 20);
-    }
-
-    g.setColor(Color.red);
-    g.drawRect(boxX, boxY, boxWidth, boxHeight);
-    g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+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.BorderLayout;
+import java.awt.CheckboxMenuItem;
+import java.awt.Cursor;
+import java.awt.Dimension;
+import java.awt.Frame;
+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;
+
+import javax.swing.SwingUtilities;
+
+public class OverviewPanel extends Panel implements Runnable,
+        MouseMotionListener, MouseListener, ViewportListenerI
+{
+  private OverviewDimensions od;
+
+  private OverviewCanvas oviewCanvas;
+
+  private AlignViewport av;
+
+  private AlignmentPanel ap;
+
+  private boolean showHidden = true;
+
+  private boolean updateRunning = false;
+
+  private boolean draggingBox = false;
+
+  public OverviewPanel(AlignmentPanel alPanel)
+  {
+    this.av = alPanel.av;
+    this.ap = alPanel;
+    setLayout(null);
+
+    od = new OverviewDimensionsShowHidden(av.getRanges(),
+            (av.isShowAnnotation()
+                    && av.getSequenceConsensusHash() != null));
+
+    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()
+    {
+
+      @Override
+      public void componentResized(ComponentEvent evt)
+      {
+        if ((getWidth() != od.getWidth())
+                || (getHeight() != (od.getHeight())))
+        {
+          updateOverviewImage();
+        }
+      }
+    });
+
+    addMouseMotionListener(this);
+
+    addMouseListener(this);
+
+    updateOverviewImage();
+
+  }
+
+  @Override
+  public void mouseEntered(MouseEvent evt)
+  {
+  }
+
+  @Override
+  public void mouseExited(MouseEvent evt)
+  {
+  }
+
+  @Override
+  public void mouseClicked(MouseEvent evt)
+  {
+    if ((evt.getModifiersEx()
+            & InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK)
+    {
+      showPopupMenu(evt);
+    }
+  }
+
+  @Override
+  public void mouseMoved(MouseEvent evt)
+  {
+    if (od.isPositionInBox(evt.getX(), evt.getY()))
+    {
+      this.getParent()
+              .setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
+    }
+    else
+    {
+      this.getParent().setCursor(
+              Cursor.getPredefinedCursor(Cursor.CROSSHAIR_CURSOR));
+    }
+  }
+
+  @Override
+  public void mousePressed(MouseEvent evt)
+  {
+    if ((evt.getModifiersEx()
+            & InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK)
+    {
+      if (!Platform.isMac()) // BH was excluding JavaScript
+      {
+        showPopupMenu(evt);
+      }
+    }
+    else
+    {
+      // don't do anything if the mouse press is in the overview's box
+      // (wait to see if it's a drag instead)
+      // otherwise update the viewport
+      if (!od.isPositionInBox(evt.getX(), evt.getY()))
+      {
+        draggingBox = false;
+
+        // display drag cursor at mouse position
+        setCursor(Cursor.getPredefinedCursor(Cursor.MOVE_CURSOR));
+
+        od.updateViewportFromMouse(evt.getX(), evt.getY(),
+                av.getAlignment().getHiddenSequences(),
+                av.getAlignment().getHiddenColumns());
+        getParent()
+                .setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
+      }
+      else
+      {
+        draggingBox = true;
+        od.setDragPoint(evt.getX(), evt.getY(),
+                av.getAlignment().getHiddenSequences(),
+                av.getAlignment().getHiddenColumns());
+      }
+    }
+  }
+
+  @Override
+  public void mouseReleased(MouseEvent evt)
+  {
+    draggingBox = false;
+  }
+
+  @Override
+  public void mouseDragged(MouseEvent evt)
+  {
+    if (Platform.isWinRightButton(evt))
+    {
+      showPopupMenu(evt);
+      return;
+    }
+
+    if (SwingUtilities.isRightMouseButton(evt))
+    {
+      return;
+    }
+
+    if (draggingBox)
+    {
+      // set the mouse position as a fixed point in the box
+      // and drag relative to that position
+      od.adjustViewportFromMouse(evt.getX(), evt.getY(),
+              av.getAlignment().getHiddenSequences(),
+              av.getAlignment().getHiddenColumns());
+    }
+    else
+    {
+      od.updateViewportFromMouse(evt.getX(), evt.getY(),
+              av.getAlignment().getHiddenSequences(),
+              av.getAlignment().getHiddenColumns());
+    }
+    ap.paintAlignment(false, false);
+  }
+
+  /**
+   * Updates the overview image when the related alignment panel is updated
+   */
+  public void updateOverviewImage()
+  {
+    if (oviewCanvas == null)
+    {
+      /*
+       * panel has been disposed
+       */
+      return;
+    }
+
+    if ((getSize().width > 0) && (getSize().height > 0))
+    {
+      od.setWidth(getSize().width);
+      od.setHeight(getSize().height);
+    }
+    setSize(new Dimension(od.getWidth(), od.getHeight()));
+
+    synchronized (this)
+    {
+      if (updateRunning)
+      {
+        oviewCanvas.restartDraw();
+        return;
+      }
+
+      updateRunning = true;
+    }
+    Thread thread = new Thread(this, "OverviewUpdate");
+    thread.start();
+    repaint();
+    updateRunning = false;
+  }
+
+  @Override
+  public void run()
+  {
+    oviewCanvas.draw(av.isShowSequenceFeatures(),
+            (av.isShowAnnotation()
+                    && av.getAlignmentConservationAnnotation() != null),
+            ap.seqPanel.seqCanvas.getFeatureRenderer());
+    setBoxPosition();
+  }
+
+  /**
+   * Update the overview panel box when the associated alignment panel is
+   * changed
+   * 
+   */
+  private void setBoxPosition()
+  {
+    od.setBoxPosition(av.getAlignment().getHiddenSequences(),
+            av.getAlignment().getHiddenColumns());
+    repaint();
+  }
+
+  /*
+   * Displays the popup menu and acts on user input
+   */
+  private void showPopupMenu(MouseEvent e)
+  {
+    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 propertyChange(PropertyChangeEvent evt)
+  {
+    setBoxPosition();
+  }
+
+  /*
+   * Toggle overview display between showing hidden columns and hiding hidden columns
+   */
+  private void toggleHiddenColumns()
+  {
+    if (showHidden)
+    {
+      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();
+  }
+
+  /**
+   * Removes this object as a property change listener, and nulls references
+   */
+  protected void dispose()
+  {
+    try
+    {
+      av.getRanges().removePropertyChangeListener(this);
+      Frame parent = (Frame) getParent();
+      parent.dispose();
+      parent.setVisible(false);
+    } finally
+    {
+      av = null;
+      if (oviewCanvas != null)
+      {
+        oviewCanvas.dispose();
+      }
+      oviewCanvas = null;
+      ap = null;
+      od = null;
+    }
+  }
+}