2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.api.AlignViewportI;
24 import jalview.api.AlignmentViewPanel;
25 import jalview.bin.Cache;
26 import jalview.renderer.OverviewRenderer;
27 import jalview.util.MessageManager;
28 import jalview.util.Platform;
29 import jalview.viewmodel.OverviewDimensions;
30 import jalview.viewmodel.OverviewDimensionsHideHidden;
31 import jalview.viewmodel.OverviewDimensionsShowHidden;
32 import jalview.viewmodel.ViewportListenerI;
34 import java.awt.BorderLayout;
35 import java.awt.Cursor;
36 import java.awt.Dimension;
37 import java.awt.event.ActionEvent;
38 import java.awt.event.ActionListener;
39 import java.awt.event.ComponentAdapter;
40 import java.awt.event.ComponentEvent;
41 import java.awt.event.MouseAdapter;
42 import java.awt.event.MouseEvent;
43 import java.awt.event.MouseMotionAdapter;
44 import java.beans.PropertyChangeEvent;
45 import java.beans.PropertyVetoException;
47 import javax.swing.JCheckBoxMenuItem;
48 import javax.swing.JInternalFrame;
49 import javax.swing.JPanel;
50 import javax.swing.JPopupMenu;
51 import javax.swing.SwingUtilities;
54 * Panel displaying an overview of the full alignment, with an interactive box
55 * representing the viewport onto the alignment.
60 @SuppressWarnings("serial")
61 public class OverviewPanel extends JPanel
62 implements Runnable, ViewportListenerI
64 protected OverviewDimensions od;
66 OverviewCanvas canvas;
68 protected AlignViewportI av;
70 AlignmentViewPanel ap;
72 protected JCheckBoxMenuItem displayToggle;
74 protected boolean showHidden = true;
76 protected boolean draggingBox = false;
78 protected ProgressPanel progressPanel;
80 private Dimension dim;
82 private boolean showProgress = !Platform.isJS(); // Jalview.getInstance().getShowStatus()
85 * Creates a new OverviewPanel object.
88 * The alignment panel which is shown in the overview panel
90 public OverviewPanel(AlignmentViewPanel alPanel, Dimension dim)
92 this.av = alPanel.getAlignViewport();
96 showHidden = Cache.getDefault(Preferences.SHOW_OV_HIDDEN_AT_START,
98 createOverviewDimensions();
99 setLayout(new BorderLayout());
100 progressPanel = new ProgressPanel(OverviewRenderer.UPDATE,
101 MessageManager.getString("label.oview_calc"), getWidth());
102 if (showProgress) // BH 2019
104 add(progressPanel, BorderLayout.SOUTH);
106 canvas = new OverviewCanvas(this, od, av,
107 showProgress ? progressPanel : null);
108 canvas.setPreferredSize(canvas.getSize());
109 add(canvas, BorderLayout.CENTER);
111 av.getRanges().addPropertyChangeListener(this);
113 // without this the overview window does not size to fit the overview canvas
114 // BH - no,no! - This does not include the progressPanel!
115 // BH the problem was that OverviewCanvas.setPreferredSize() had not been set.
116 // setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
118 addComponentListener(new ComponentAdapter()
121 public void componentResized(ComponentEvent evt)
128 addMouseMotionListener(new MouseMotionAdapter()
131 public void mouseDragged(MouseEvent evt)
133 if (!SwingUtilities.isRightMouseButton(evt))
137 // set the mouse position as a fixed point in the box
138 // and drag relative to that position
139 od.adjustViewportFromMouse(evt.getX(), evt.getY(),
140 av.getAlignment().getHiddenSequences(),
141 av.getAlignment().getHiddenColumns());
145 od.updateViewportFromMouse(evt.getX(), evt.getY(),
146 av.getAlignment().getHiddenSequences(),
147 av.getAlignment().getHiddenColumns());
153 public void mouseMoved(MouseEvent evt)
155 if (od.isPositionInBox(evt.getX(), evt.getY()))
158 * using HAND_CURSOR rather than DRAG_CURSOR
159 * as the latter is not supported on Mac
161 getParent().setCursor(
162 Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
167 getParent().setCursor(
168 Cursor.getPredefinedCursor(Cursor.CROSSHAIR_CURSOR));
174 addMouseListener(new MouseAdapter()
177 public void mousePressed(MouseEvent evt)
180 if (Platform.isWinRightButton(evt))
185 if (SwingUtilities.isRightMouseButton(evt))
189 // don't do anything if the mouse press is in the overview's box
190 // (wait to see if it's a drag instead)
191 // otherwise update the viewport
192 if (!od.isPositionInBox(evt.getX(), evt.getY()))
196 // display drag cursor at mouse position
197 setCursor(Cursor.getPredefinedCursor(Cursor.MOVE_CURSOR));
199 od.updateViewportFromMouse(evt.getX(), evt.getY(),
200 av.getAlignment().getHiddenSequences(),
201 av.getAlignment().getHiddenColumns());
202 getParent().setCursor(
203 Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
208 od.setDragPoint(evt.getX(), evt.getY(),
209 av.getAlignment().getHiddenSequences(),
210 av.getAlignment().getHiddenColumns());
215 public void mouseClicked(MouseEvent evt)
217 if (SwingUtilities.isRightMouseButton(evt))
224 public void mouseReleased(MouseEvent evt)
232 // * Javascript does not call componentResized on initial display,
233 // * so do the update here
235 // if (Platform.isJS())
237 // updateOverviewImage();
241 protected void resizePanel()
243 int ph = (progressPanel.getParent() == null ? 0
244 : progressPanel.getHeight());
245 // Resize is called on the initial display of the overview.
246 // This code adjusts sizes to account for the progress bar if it has not
247 // already been accounted for, which triggers another resize call for
248 // the correct sizing, at which point the overview image is updated.
249 // (This avoids a double recalculation of the image.)
250 if (getWidth() == od.getWidth() && getHeight() == od.getHeight() + ph)
252 if (canvas.lastMiniMe == null)
254 updateOverviewImage();
261 if ((w > 0) && (h > 0))
265 dim.setSize(w, h - ph);
268 od.setHeight(h - ph);
269 updateOverviewImage();
271 // BH 2019.07.29 this is unnecessary -- it is what layout managers are
273 // setPreferredSize(new Dimension(od.getWidth(), od.getHeight() +
279 * Create the appropriate type of OverViewDimensions, with the desired size.
281 private void createOverviewDimensions()
283 boolean showAnnotation = (av.isShowAnnotation()
284 && av.getAlignmentConservationAnnotation() != null);
287 od = new OverviewDimensionsShowHidden(av.getRanges(), showAnnotation,
292 od = new OverviewDimensionsHideHidden(av.getRanges(), showAnnotation,
299 * Displays the popup menu and acts on user input
301 protected void showPopupMenu(MouseEvent e)
303 JPopupMenu popup = new JPopupMenu();
304 ActionListener menuListener = new ActionListener()
307 public void actionPerformed(ActionEvent event)
309 // switch on/off the hidden columns view
310 toggleHiddenColumns();
311 displayToggle.setSelected(showHidden);
314 displayToggle = new JCheckBoxMenuItem(
315 MessageManager.getString("label.togglehidden"));
316 displayToggle.setEnabled(true);
317 displayToggle.setSelected(showHidden);
318 popup.add(displayToggle);
319 displayToggle.addActionListener(menuListener);
320 popup.show(this, e.getX(), e.getY());
324 * Toggle overview display between showing hidden columns and hiding hidden columns
326 protected void toggleHiddenColumns()
328 showHidden = !showHidden;
329 createOverviewDimensions();
330 canvas.resetOviewDims(od);
331 updateOverviewImage();
336 * Updates the overview image when the related alignment panel is updated.
340 * AlignFrame.setFeatureGroupState
342 * AlignmentPanel.paintAlignment(true,...) (117 references)
344 * OverviewPanel..componentResized() OverviewPanel.toggleHiddenColumns()
346 * PopupMenu for action.reveal_sequences, action.reveal_all
348 * SliderPanel.mouseReleased()
351 public void updateOverviewImage()
356 * panel has been disposed
361 int ph = (progressPanel.getParent() == null ? 0
362 : progressPanel.getHeight());
364 if ((getWidth() > 0) && (getHeight() > 0))
366 od.setWidth(getWidth());
367 od.setHeight(getHeight() - ph);
370 setPreferredSize(new Dimension(od.getWidth(), od.getHeight() + ph));
372 if (canvas.restartDraw())
377 Thread thread = new Thread(this);
387 canvas.draw(av.isShowSequenceFeatures(),
388 (av.isShowAnnotation()
389 && av.getAlignmentConservationAnnotation() != null),
390 ap.getFeatureRenderer());
395 * Update the overview panel box when the associated alignment panel is
399 private void setBoxPositionOnly()
404 int oldX = od.getBoxX();
405 int oldY = od.getBoxY();
406 int oldWidth = od.getBoxWidth();
407 int oldHeight = od.getBoxHeight();
408 od.setBoxPosition(av.getAlignment().getHiddenSequences(),
409 av.getAlignment().getHiddenColumns());
410 repaint(oldX - 1, oldY - 1, oldWidth + 2, oldHeight + 2);
411 repaint(od.getBoxX(), od.getBoxY(), od.getBoxWidth(),
416 private void setBoxPosition()
420 od.setBoxPosition(av.getAlignment().getHiddenSequences(),
421 av.getAlignment().getHiddenColumns());
427 public void propertyChange(PropertyChangeEvent evt)
429 setBoxPositionOnly();
433 * Removes this object as a property change listener, and nulls references
435 protected void dispose()
441 av.getRanges().removePropertyChangeListener(this);
447 * close the parent frame (which also removes it from the
448 * Desktop Windows menu)
450 ((JInternalFrame) SwingUtilities
451 .getAncestorOfClass(JInternalFrame.class, (this)))
453 } catch (PropertyVetoException e)
458 progressPanel = null;