Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
OverviewPanel	49	87	33	0.00%	Show methods

Class OverviewPanel

Class OverviewPanel	Line # 49	Total Statements 87	Complexity 33	TOTAL Coverage 0.00%
componentResized(ComponentEvent) : void   componentResized(ComponentEvent) : void	8787	2.02	3.03	0.0 0.00%
OverviewPanel(AlignmentPanel)   OverviewPanel(AlignmentPanel)	6666	13.013	1.01	0.0 0.00%
mouseEntered(MouseEvent) : void   mouseEntered(MouseEvent) : void	106106	0.00	1.01	-1.0 -1.0 -
mouseExited(MouseEvent) : void   mouseExited(MouseEvent) : void	111111	0.00	1.01	-1.0 -1.0 -
mouseClicked(MouseEvent) : void   mouseClicked(MouseEvent) : void	116116	2.02	2.02	0.0 0.00%
mouseMoved(MouseEvent) : void   mouseMoved(MouseEvent) : void	126126	3.03	2.02	0.0 0.00%
mousePressed(MouseEvent) : void   mousePressed(MouseEvent) : void	141141	10.010	4.04	0.0 0.00%
mouseReleased(MouseEvent) : void   mouseReleased(MouseEvent) : void	180180	1.01	1.01	0.0 0.00%
mouseDragged(MouseEvent) : void   mouseDragged(MouseEvent) : void	186186	9.09	4.04	0.0 0.00%
updateOverviewImage() : void   updateOverviewImage() : void	220220	15.015	5.05	0.0 0.00%
run() : void   run() : void	253253	2.02	1.01	0.0 0.00%
setBoxPosition() : void   setBoxPosition() : void	268268	2.02	1.01	0.0 0.00%
itemStateChanged(ItemEvent) : void   itemStateChanged(ItemEvent) : void	283283	1.01	1.01	0.0 0.00%
showPopupMenu(MouseEvent) : void   showPopupMenu(MouseEvent) : void	278278	8.08	1.01	0.0 0.00%
propertyChange(PropertyChangeEvent) : void   propertyChange(PropertyChangeEvent) : void	298298	1.01	1.01	0.0 0.00%
toggleHiddenColumns() : void   toggleHiddenColumns() : void	307307	7.07	2.02	0.0 0.00%
dispose() : void   dispose() : void	330330	11.011	2.02	0.0 0.00%

 

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1		/*
2		* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3		* Copyright (C) $$Year-Rel$$ The Jalview Authors
4		*
5		* This file is part of Jalview.
6		*
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.
11		*
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.
16		*
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.
20		*/
21		package jalview.appletgui;
22
23		import jalview.util.MessageManager;
24		import jalview.util.Platform;
25		import jalview.viewmodel.OverviewDimensions;
26		import jalview.viewmodel.OverviewDimensionsHideHidden;
27		import jalview.viewmodel.OverviewDimensionsShowHidden;
28		import jalview.viewmodel.ViewportListenerI;
29
30		import java.awt.BorderLayout;
31		import java.awt.CheckboxMenuItem;
32		import java.awt.Cursor;
33		import java.awt.Dimension;
34		import java.awt.Frame;
35		import java.awt.Panel;
36		import java.awt.PopupMenu;
37		import java.awt.event.ComponentAdapter;
38		import java.awt.event.ComponentEvent;
39		import java.awt.event.InputEvent;
40		import java.awt.event.ItemEvent;
41		import java.awt.event.ItemListener;
42		import java.awt.event.MouseEvent;
43		import java.awt.event.MouseListener;
44		import java.awt.event.MouseMotionListener;
45		import java.beans.PropertyChangeEvent;
46
47		import javax.swing.SwingUtilities;
48
		0% Uncovered Elements: 132 (132) Complexity: 33 Complexity Density: 0.38
49		public class OverviewPanel extends Panel implements Runnable,
50		MouseMotionListener, MouseListener, ViewportListenerI
51		{
52		private OverviewDimensions od;
53
54		private OverviewCanvas oviewCanvas;
55
56		private AlignViewport av;
57
58		private AlignmentPanel ap;
59
60		private boolean showHidden = true;
61
62		private boolean updateRunning = false;
63
64		private boolean draggingBox = false;
65
		0% Uncovered Elements: 13 (13) Complexity: 1 Complexity Density: 0.08
66	0	public OverviewPanel(AlignmentPanel alPanel)...
67		{
68	0	this.av = alPanel.av;
69	0	this.ap = alPanel;
70	0	setLayout(null);
71
72	0	od = new OverviewDimensionsShowHidden(av.getRanges(),
73		(av.isShowAnnotation()
74		&& av.getSequenceConsensusHash() != null));
75
76	0	oviewCanvas = new OverviewCanvas(od, av);
77	0	setLayout(new BorderLayout());
78	0	add(oviewCanvas, BorderLayout.CENTER);
79
80	0	setSize(new Dimension(od.getWidth(), od.getHeight()));
81
82	0	av.getRanges().addPropertyChangeListener(this);
83
84	0	addComponentListener(new ComponentAdapter()
85		{
86
		0% Uncovered Elements: 4 (4) Complexity: 3 Complexity Density: 1.5
87	0	@Override...
88		public void componentResized(ComponentEvent evt)
89		{
90	0	if ((getWidth() != od.getWidth())
91		|| (getHeight() != (od.getHeight())))
92		{
93	0	updateOverviewImage();
94		}
95		}
96		});
97
98	0	addMouseMotionListener(this);
99
100	0	addMouseListener(this);
101
102	0	updateOverviewImage();
103
104		}
105
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
106	0	@Override...
107		public void mouseEntered(MouseEvent evt)
108		{
109		}
110
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
111	0	@Override...
112		public void mouseExited(MouseEvent evt)
113		{
114		}
115
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 1
116	0	@Override...
117		public void mouseClicked(MouseEvent evt)
118		{
119	0	if ((evt.getModifiersEx()
120		& InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK)
121		{
122	0	showPopupMenu(evt);
123		}
124		}
125
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
126	0	@Override...
127		public void mouseMoved(MouseEvent evt)
128		{
129	0	if (od.isPositionInBox(evt.getX(), evt.getY()))
130		{
131	0	this.getParent()
132		.setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
133		}
134		else
135		{
136	0	this.getParent().setCursor(
137		Cursor.getPredefinedCursor(Cursor.CROSSHAIR_CURSOR));
138		}
139		}
140
		0% Uncovered Elements: 16 (16) Complexity: 4 Complexity Density: 0.4
141	0	@Override...
142		public void mousePressed(MouseEvent evt)
143		{
144	0	if ((evt.getModifiersEx()
145		& InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK)
146		{
147	0	if (!Platform.isMac()) // BH was excluding JavaScript
148		{
149	0	showPopupMenu(evt);
150		}
151		}
152		else
153		{
154		// don't do anything if the mouse press is in the overview's box
155		// (wait to see if it's a drag instead)
156		// otherwise update the viewport
157	0	if (!od.isPositionInBox(evt.getX(), evt.getY()))
158		{
159	0	draggingBox = false;
160
161		// display drag cursor at mouse position
162	0	setCursor(Cursor.getPredefinedCursor(Cursor.MOVE_CURSOR));
163
164	0	od.updateViewportFromMouse(evt.getX(), evt.getY(),
165		av.getAlignment().getHiddenSequences(),
166		av.getAlignment().getHiddenColumns());
167	0	getParent()
168		.setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
169		}
170		else
171		{
172	0	draggingBox = true;
173	0	od.setDragPoint(evt.getX(), evt.getY(),
174		av.getAlignment().getHiddenSequences(),
175		av.getAlignment().getHiddenColumns());
176		}
177		}
178		}
179
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
180	0	@Override...
181		public void mouseReleased(MouseEvent evt)
182		{
183	0	draggingBox = false;
184		}
185
		0% Uncovered Elements: 15 (15) Complexity: 4 Complexity Density: 0.44
186	0	@Override...
187		public void mouseDragged(MouseEvent evt)
188		{
189	0	if (Platform.isWinRightButton(evt))
190		{
191	0	showPopupMenu(evt);
192	0	return;
193		}
194
195	0	if (SwingUtilities.isRightMouseButton(evt))
196		{
197	0	return;
198		}
199
200	0	if (draggingBox)
201		{
202		// set the mouse position as a fixed point in the box
203		// and drag relative to that position
204	0	od.adjustViewportFromMouse(evt.getX(), evt.getY(),
205		av.getAlignment().getHiddenSequences(),
206		av.getAlignment().getHiddenColumns());
207		}
208		else
209		{
210	0	od.updateViewportFromMouse(evt.getX(), evt.getY(),
211		av.getAlignment().getHiddenSequences(),
212		av.getAlignment().getHiddenColumns());
213		}
214	0	ap.paintAlignment(false, false);
215		}
216
217		/**
218		* Updates the overview image when the related alignment panel is updated
219		*/
		0% Uncovered Elements: 21 (21) Complexity: 5 Complexity Density: 0.33
220	0	public void updateOverviewImage()...
221		{
222	0	if (oviewCanvas == null)
223		{
224		/*
225		* panel has been disposed
226		*/
227	0	return;
228		}
229
230	0	if ((getSize().width > 0) && (getSize().height > 0))
231		{
232	0	od.setWidth(getSize().width);
233	0	od.setHeight(getSize().height);
234		}
235	0	setSize(new Dimension(od.getWidth(), od.getHeight()));
236
237	0	synchronized (this)
238		{
239	0	if (updateRunning)
240		{
241	0	oviewCanvas.restartDraw();
242	0	return;
243		}
244
245	0	updateRunning = true;
246		}
247	0	Thread thread = new Thread(this);
248	0	thread.start();
249	0	repaint();
250	0	updateRunning = false;
251		}
252
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
253	0	@Override...
254		public void run()
255		{
256	0	oviewCanvas.draw(av.isShowSequenceFeatures(),
257		(av.isShowAnnotation()
258		&& av.getAlignmentConservationAnnotation() != null),
259		ap.seqPanel.seqCanvas.getFeatureRenderer());
260	0	setBoxPosition();
261		}
262
263		/**
264		* Update the overview panel box when the associated alignment panel is
265		* changed
266		*
267		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
268	0	private void setBoxPosition()...
269		{
270	0	od.setBoxPosition(av.getAlignment().getHiddenSequences(),
271		av.getAlignment().getHiddenColumns());
272	0	repaint();
273		}
274
275		/*
276		* Displays the popup menu and acts on user input
277		*/
		0% Uncovered Elements: 8 (8) Complexity: 1 Complexity Density: 0.12
278	0	private void showPopupMenu(MouseEvent e)...
279		{
280	0	PopupMenu popup = new PopupMenu();
281	0	ItemListener menuListener = new ItemListener()
282		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
283	0	@Override...
284		public void itemStateChanged(ItemEvent e)
285		{
286	0	toggleHiddenColumns();
287		}
288		};
289	0	CheckboxMenuItem item = new CheckboxMenuItem(
290		MessageManager.getString("label.togglehidden"));
291	0	item.setState(showHidden);
292	0	popup.add(item);
293	0	item.addItemListener(menuListener);
294	0	this.add(popup);
295	0	popup.show(this, e.getX(), e.getY());
296		}
297
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
298	0	@Override...
299		public void propertyChange(PropertyChangeEvent evt)
300		{
301	0	setBoxPosition();
302		}
303
304		/*
305		* Toggle overview display between showing hidden columns and hiding hidden columns
306		*/
		0% Uncovered Elements: 9 (9) Complexity: 2 Complexity Density: 0.29
307	0	private void toggleHiddenColumns()...
308		{
309	0	if (showHidden)
310		{
311	0	showHidden = false;
312	0	od = new OverviewDimensionsHideHidden(av.getRanges(),
313		(av.isShowAnnotation()
314		&& av.getAlignmentConservationAnnotation() != null));
315		}
316		else
317		{
318	0	showHidden = true;
319	0	od = new OverviewDimensionsShowHidden(av.getRanges(),
320		(av.isShowAnnotation()
321		&& av.getAlignmentConservationAnnotation() != null));
322		}
323	0	oviewCanvas.resetOviewDims(od);
324	0	updateOverviewImage();
325		}
326
327		/**
328		* Removes this object as a property change listener, and nulls references
329		*/
		0% Uncovered Elements: 13 (13) Complexity: 2 Complexity Density: 0.18
330	0	protected void dispose()...
331		{
332	0	try
333		{
334	0	av.getRanges().removePropertyChangeListener(this);
335	0	Frame parent = (Frame) getParent();
336	0	parent.dispose();
337	0	parent.setVisible(false);
338		} finally
339		{
340	0	av = null;
341	0	if (oviewCanvas != null)
342		{
343	0	oviewCanvas.dispose();
344		}
345	0	oviewCanvas = null;
346	0	ap = null;
347	0	od = null;
348		}
349		}
350		}