Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
OverviewCanvas	36	71	21	101	0.00%	Show methods

Class OverviewCanvas

Class OverviewCanvas	Line # 36	Total Statements 71	Complexity 21	Uncovered Elements 101	TOTAL Coverage 0.00%
OverviewCanvas(OverviewDimensions,AlignViewportI,ProgressPanel)   OverviewCanvas(OverviewDimensions,AlignViewportI,ProgressPanel)	6868	11.011	1.01	11.011	0.0 0.00%
resetOviewDims(OverviewDimensions) : void   resetOviewDims(OverviewDimensions) : void	9595	1.01	1.01	1.01	0.0 0.00%
restartDraw() : boolean   restartDraw() : boolean	104104	7.07	3.03	11.011	0.0 0.00%
draw(boolean,boolean,FeatureRenderer) : void   draw(boolean,boolean,FeatureRenderer) : void	134134	20.020	5.05	28.028	0.0 0.00%
paintComponent(Graphics) : void   paintComponent(Graphics) : void	181181	27.027	9.09	37.037	0.0 0.00%
dispose() : void   dispose() : void	257257	5.05	2.02	7.07	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.gui;
22
23		import jalview.api.AlignViewportI;
24		import jalview.bin.Cache;
25		import jalview.renderer.OverviewRenderer;
26		import jalview.renderer.OverviewResColourFinder;
27		import jalview.viewmodel.OverviewDimensions;
28
29		import java.awt.Color;
30		import java.awt.Dimension;
31		import java.awt.Graphics;
32		import java.awt.image.BufferedImage;
33
34		import javax.swing.JPanel;
35
		0% Uncovered Elements: 101 (101) Complexity: 21 Complexity Density: 0.3
36		public class OverviewCanvas extends JPanel
37		{
38		private static final Color TRANS_GREY = new Color(100, 100, 100, 25);
39
40		// This is set true if the alignment view changes whilst
41		// the overview is being calculated
42		private volatile boolean restart = false;
43
44		private volatile boolean updaterunning = false;
45
46		private boolean dispose = false;
47
48		private BufferedImage miniMe;
49
50		private BufferedImage lastMiniMe = null;
51
52		// Can set different properties in this seqCanvas than
53		// main visible SeqCanvas
54		private SequenceRenderer sr;
55
56		private jalview.renderer.seqfeatures.FeatureRenderer fr;
57
58		private OverviewDimensions od;
59
60		private OverviewRenderer or = null;
61
62		private AlignViewportI av;
63
64		private OverviewResColourFinder cf;
65
66		private ProgressPanel progressPanel;
67
		0% Uncovered Elements: 11 (11) Complexity: 1 Complexity Density: 0.09
68	0	public OverviewCanvas(OverviewDimensions overviewDims,...
69		AlignViewportI alignvp, ProgressPanel pp)
70		{
71	0	od = overviewDims;
72	0	av = alignvp;
73	0	progressPanel = pp;
74
75	0	sr = new SequenceRenderer(av);
76	0	sr.renderGaps = false;
77	0	fr = new jalview.renderer.seqfeatures.FeatureRenderer(av);
78
79	0	boolean useLegacy = Cache.getDefault(Preferences.USE_LEGACY_GAP, false);
80	0	Color gapCol = Cache.getDefaultColour(Preferences.GAP_COLOUR,
81		jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
82	0	Color hiddenCol = Cache.getDefaultColour(Preferences.HIDDEN_COLOUR,
83		jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
84	0	cf = new OverviewResColourFinder(useLegacy, gapCol, hiddenCol);
85
86	0	setSize(od.getWidth(), od.getHeight());
87		}
88
89		/**
90		* Update the overview dimensions object used by the canvas (e.g. if we change
91		* from showing hidden columns to hiding them or vice versa)
92		*
93		* @param overviewDims
94		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
95	0	public void resetOviewDims(OverviewDimensions overviewDims)...
96		{
97	0	od = overviewDims;
98		}
99
100		/**
101		* Signals to drawing code that the associated alignment viewport has changed
102		* and a redraw will be required
103		*/
		0% Uncovered Elements: 11 (11) Complexity: 3 Complexity Density: 0.43
104	0	public boolean restartDraw()...
105		{
106	0	synchronized (this)
107		{
108	0	if (updaterunning)
109		{
110	0	restart = true;
111	0	if (or != null)
112		{
113	0	or.setRedraw(true);
114		}
115		}
116		else
117		{
118	0	updaterunning = true;
119		}
120	0	return restart;
121		}
122		}
123
124		/**
125		* Draw the overview sequences
126		*
127		* @param showSequenceFeatures
128		* true if sequence features are to be shown
129		* @param showAnnotation
130		* true if the annotation is to be shown
131		* @param transferRenderer
132		* the renderer to transfer feature colouring from
133		*/
		0% Uncovered Elements: 28 (28) Complexity: 5 Complexity Density: 0.25
134	0	public void draw(boolean showSequenceFeatures, boolean showAnnotation,...
135		FeatureRenderer transferRenderer)
136		{
137	0	miniMe = null;
138
139	0	if (showSequenceFeatures)
140		{
141	0	fr.transferSettings(transferRenderer);
142		}
143
144	0	setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
145
146	0	or = new OverviewRenderer(fr, od, av.getAlignment(),
147		av.getResidueShading(), cf);
148
149	0	or.addPropertyChangeListener(progressPanel);
150
151	0	miniMe = or.draw(od.getRows(av.getAlignment()),
152		od.getColumns(av.getAlignment()));
153
154	0	Graphics mg = miniMe.getGraphics();
155
156	0	if (showAnnotation)
157		{
158	0	mg.translate(0, od.getSequencesHeight());
159	0	or.drawGraph(mg, av.getAlignmentConservationAnnotation(),
160		od.getGraphHeight(), od.getColumns(av.getAlignment()));
161	0	mg.translate(0, -od.getSequencesHeight());
162		}
163
164	0	or.removePropertyChangeListener(progressPanel);
165	0	or = null;
166	0	if (restart)
167		{
168	0	restart = false;
169	0	if (!dispose)
170		{
171	0	draw(showSequenceFeatures, showAnnotation, transferRenderer);
172		}
173		}
174		else
175		{
176	0	updaterunning = false;
177	0	lastMiniMe = miniMe;
178		}
179		}
180
		0% Uncovered Elements: 37 (37) Complexity: 9 Complexity Density: 0.33
181	0	@Override...
182		public void paintComponent(Graphics g)
183		{
184	0	super.paintComponent(g);
185
186	0	if (restart)
187		{
188	0	if (lastMiniMe == null)
189		{
190	0	g.setColor(Color.white);
191	0	g.fillRect(0, 0, getWidth(), getHeight());
192		}
193		else
194		{
195	0	g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
196		}
197	0	g.setColor(TRANS_GREY);
198	0	g.fillRect(0, 0, getWidth(), getHeight());
199		}
200	0	else if (lastMiniMe != null)
201		{
202		// is this a resize?
203	0	if ((getWidth() > 0) && (getHeight() > 0)
204		&& ((getWidth() != od.getWidth())
205		|| (getHeight() != od.getHeight())))
206		{
207		// if there is annotation, scale the alignment and annotation
208		// separately
209	0	if (od.getGraphHeight() > 0)
210		{
211	0	BufferedImage topImage = lastMiniMe.getSubimage(0, 0,
212		od.getWidth(), od.getSequencesHeight());
213	0	BufferedImage bottomImage = lastMiniMe.getSubimage(0,
214		od.getSequencesHeight(), od.getWidth(),
215		od.getGraphHeight());
216
217		// must be done at this point as we rely on using old width/height
218		// above, and new width/height below
219	0	od.setWidth(getWidth());
220	0	od.setHeight(getHeight());
221
222		// stick the images back together so lastMiniMe is consistent in the
223		// event of a repaint - BUT probably not thread safe
224	0	lastMiniMe = new BufferedImage(od.getWidth(), od.getHeight(),
225		BufferedImage.TYPE_INT_RGB);
226	0	Graphics lg = lastMiniMe.getGraphics();
227	0	lg.drawImage(topImage, 0, 0, od.getWidth(),
228		od.getSequencesHeight(), null);
229	0	lg.drawImage(bottomImage, 0, od.getSequencesHeight(),
230		od.getWidth(), od.getGraphHeight(), this);
231	0	lg.dispose();
232		}
233		else
234		{
235	0	od.setWidth(getWidth());
236	0	od.setHeight(getHeight());
237		}
238
239		// make sure the box is in the right place
240	0	od.setBoxPosition(av.getAlignment().getHiddenSequences(),
241		av.getAlignment().getHiddenColumns());
242		}
243		// fall back to normal behaviour
244	0	g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
245		}
246		else
247		{
248	0	g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
249		}
250
251		// draw the box
252	0	g.setColor(Color.red);
253	0	od.drawBox(g);
254		}
255
256
		0% Uncovered Elements: 7 (7) Complexity: 2 Complexity Density: 0.4
257	0	public void dispose()...
258		{
259	0	dispose = true;
260	0	synchronized (this)
261		{
262	0	restart = true;
263	0	if (or != null)
264		{
265	0	or.setRedraw(true);
266		}
267		}
268		}
269		}