Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
OverviewCanvas	37	71	22	0.00%	Show methods

Class OverviewCanvas

Class OverviewCanvas	Line # 37	Total Statements 71	Complexity 22	TOTAL Coverage 0.00%
OverviewCanvas(OverviewDimensions,AlignViewportI,ProgressPanel)   OverviewCanvas(OverviewDimensions,AlignViewportI,ProgressPanel)	6969	11.011	1.01	0.0 0.00%
resetOviewDims(OverviewDimensions) : void   resetOviewDims(OverviewDimensions) : void	9696	1.01	1.01	0.0 0.00%
restartDraw() : boolean   restartDraw() : boolean	105105	7.07	3.03	0.0 0.00%
draw(boolean,boolean,FeatureRendererModel) : void   draw(boolean,boolean,FeatureRendererModel) : void	135135	20.020	5.05	0.0 0.00%
paintComponent(Graphics) : void   paintComponent(Graphics) : void	182182	26.026	10.010	0.0 0.00%
dispose() : void   dispose() : void	260260	6.06	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.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		import jalview.viewmodel.seqfeatures.FeatureRendererModel;
29
30		import java.awt.Color;
31		import java.awt.Dimension;
32		import java.awt.Graphics;
33		import java.awt.image.BufferedImage;
34
35		import javax.swing.JPanel;
36
		0% Uncovered Elements: 101 (101) Complexity: 22 Complexity Density: 0.31
37		public class OverviewCanvas extends JPanel
38		{
39		private static final Color TRANS_GREY = new Color(100, 100, 100, 25);
40
41		// This is set true if the alignment view changes whilst
42		// the overview is being calculated
43		private volatile boolean restart = false;
44
45		private volatile boolean updaterunning = false;
46
47		private boolean dispose = false;
48
49		private BufferedImage miniMe;
50
51		private BufferedImage lastMiniMe = null;
52
53		// Can set different properties in this seqCanvas than
54		// main visible SeqCanvas
55		private SequenceRenderer sr;
56
57		private jalview.renderer.seqfeatures.FeatureRenderer fr;
58
59		private OverviewDimensions od;
60
61		private OverviewRenderer or = null;
62
63		private AlignViewportI av;
64
65		private OverviewResColourFinder cf;
66
67		private ProgressPanel progressPanel;
68
		0% Uncovered Elements: 11 (11) Complexity: 1 Complexity Density: 0.09
69	0	public OverviewCanvas(OverviewDimensions overviewDims,...
70		AlignViewportI alignvp, ProgressPanel pp)
71		{
72	0	od = overviewDims;
73	0	av = alignvp;
74	0	progressPanel = pp;
75
76	0	sr = new SequenceRenderer(av);
77	0	sr.renderGaps = false;
78	0	fr = new jalview.renderer.seqfeatures.FeatureRenderer(av);
79
80	0	boolean useLegacy = Cache.getDefault(Preferences.USE_LEGACY_GAP, false);
81	0	Color gapCol = Cache.getDefaultColour(Preferences.GAP_COLOUR,
82		jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
83	0	Color hiddenCol = Cache.getDefaultColour(Preferences.HIDDEN_COLOUR,
84		jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
85	0	cf = new OverviewResColourFinder(useLegacy, gapCol, hiddenCol);
86
87	0	setSize(od.getWidth(), od.getHeight());
88		}
89
90		/**
91		* Update the overview dimensions object used by the canvas (e.g. if we change
92		* from showing hidden columns to hiding them or vice versa)
93		*
94		* @param overviewDims
95		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
96	0	public void resetOviewDims(OverviewDimensions overviewDims)...
97		{
98	0	od = overviewDims;
99		}
100
101		/**
102		* Signals to drawing code that the associated alignment viewport has changed
103		* and a redraw will be required
104		*/
		0% Uncovered Elements: 11 (11) Complexity: 3 Complexity Density: 0.43
105	0	public boolean restartDraw()...
106		{
107	0	synchronized (this)
108		{
109	0	if (updaterunning)
110		{
111	0	restart = true;
112	0	if (or != null)
113		{
114	0	or.setRedraw(true);
115		}
116		}
117		else
118		{
119	0	updaterunning = true;
120		}
121	0	return restart;
122		}
123		}
124
125		/**
126		* Draw the overview sequences
127		*
128		* @param showSequenceFeatures
129		* true if sequence features are to be shown
130		* @param showAnnotation
131		* true if the annotation is to be shown
132		* @param transferRenderer
133		* the renderer to transfer feature colouring from
134		*/
		0% Uncovered Elements: 28 (28) Complexity: 5 Complexity Density: 0.25
135	0	public void draw(boolean showSequenceFeatures, boolean showAnnotation,...
136		FeatureRendererModel transferRenderer)
137		{
138	0	miniMe = null;
139
140	0	if (showSequenceFeatures)
141		{
142	0	fr.transferSettings(transferRenderer);
143		}
144
145	0	setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
146
147	0	or = new OverviewRenderer(fr, od, av.getAlignment(),
148		av.getResidueShading(), cf);
149
150	0	or.addPropertyChangeListener(progressPanel);
151
152	0	miniMe = or.draw(od.getRows(av.getAlignment()),
153		od.getColumns(av.getAlignment()));
154
155	0	Graphics mg = miniMe.getGraphics();
156
157	0	if (showAnnotation)
158		{
159	0	mg.translate(0, od.getSequencesHeight());
160	0	or.drawGraph(mg, av.getAlignmentConservationAnnotation(),
161		od.getGraphHeight(), od.getColumns(av.getAlignment()));
162	0	mg.translate(0, -od.getSequencesHeight());
163		}
164
165	0	or.removePropertyChangeListener(progressPanel);
166	0	or = null;
167	0	if (restart)
168		{
169	0	restart = false;
170	0	if (!dispose)
171		{
172	0	draw(showSequenceFeatures, showAnnotation, transferRenderer);
173		}
174		}
175		else
176		{
177	0	updaterunning = false;
178	0	lastMiniMe = miniMe;
179		}
180		}
181
		0% Uncovered Elements: 36 (36) Complexity: 10 Complexity Density: 0.38
182	0	@Override...
183		public void paintComponent(Graphics g)
184		{
185		//super.paintComponent(g);
186
187	0	if (restart)
188		{
189	0	if (lastMiniMe == null)
190		{
191	0	g.setColor(Color.white);
192	0	g.fillRect(0, 0, getWidth(), getHeight());
193		}
194		else
195		{
196	0	g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
197		}
198	0	g.setColor(TRANS_GREY);
199	0	g.fillRect(0, 0, getWidth(), getHeight());
200		}
201	0	else if (lastMiniMe != null)
202		{
203		// is this a resize?
204	0	if ((getWidth() > 0) && (getHeight() > 0)
205		&& ((getWidth() != od.getWidth())
206		|| (getHeight() != od.getHeight())))
207		{
208		// if there is annotation, scale the alignment and annotation
209		// separately
210	0	if (od.getGraphHeight() > 0
211		&& od.getSequencesHeight() > 0 // BH 2019
212		)
213		{
214	0	BufferedImage topImage = lastMiniMe.getSubimage(0, 0,
215		od.getWidth(), od.getSequencesHeight());
216	0	BufferedImage bottomImage = lastMiniMe.getSubimage(0,
217		od.getSequencesHeight(), od.getWidth(),
218		od.getGraphHeight());
219
220		// must be done at this point as we rely on using old width/height
221		// above, and new width/height below
222	0	od.setWidth(getWidth());
223	0	od.setHeight(getHeight());
224
225		// stick the images back together so lastMiniMe is consistent in the
226		// event of a repaint - BUT probably not thread safe
227	0	lastMiniMe = new BufferedImage(od.getWidth(), od.getHeight(),
228		BufferedImage.TYPE_INT_RGB);
229	0	Graphics lg = lastMiniMe.getGraphics();
230	0	lg.drawImage(topImage, 0, 0, od.getWidth(),
231		od.getSequencesHeight(), null);
232	0	lg.drawImage(bottomImage, 0, od.getSequencesHeight(),
233		od.getWidth(), od.getGraphHeight(), this);
234	0	lg.dispose();
235		}
236		else
237		{
238	0	od.setWidth(getWidth());
239	0	od.setHeight(getHeight());
240		}
241
242		// make sure the box is in the right place
243	0	od.setBoxPosition(av.getAlignment().getHiddenSequences(),
244		av.getAlignment().getHiddenColumns());
245		}
246		// fall back to normal behaviour
247	0	g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
248		}
249		else
250		{
251	0	g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
252		}
253
254		// draw the box
255	0	g.setColor(Color.red);
256	0	od.drawBox(g);
257		}
258
259
		0% Uncovered Elements: 8 (8) Complexity: 2 Complexity Density: 0.33
260	0	public void dispose()...
261		{
262	0	dispose = true;
263	0	od = null;
264	0	synchronized (this)
265		{
266	0	restart = true;
267	0	if (or != null)
268		{
269	0	or.setRedraw(true);
270		}
271		}
272		}
273		}