Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
OverviewCanvas	34	38	13	0.00%	Show methods

Class OverviewCanvas

Class OverviewCanvas	Line # 34	Total Statements 38	Complexity 13	TOTAL Coverage 0.00%
OverviewCanvas(OverviewDimensions,AlignViewport)   OverviewCanvas(OverviewDimensions,AlignViewport)	5656	5.05	1.01	0.0 0.00%
resetOviewDims(OverviewDimensions) : void   resetOviewDims(OverviewDimensions) : void	7474	1.01	1.01	0.0 0.00%
restartDraw() : boolean   restartDraw() : boolean	8383	7.07	3.03	0.0 0.00%
draw(boolean,boolean,FeatureRenderer) : void   draw(boolean,boolean,FeatureRenderer) : void	103103	17.017	4.04	0.0 0.00%
update(Graphics) : void   update(Graphics) : void	146146	1.01	1.01	0.0 0.00%
paint(Graphics) : void   paint(Graphics) : void	152152	6.06	2.02	0.0 0.00%
dispose() : void   dispose() : void	168168	1.01	1.01	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.renderer.OverviewRenderer;
24		import jalview.renderer.OverviewResColourFinder;
25		import jalview.viewmodel.OverviewDimensions;
26
27		import java.awt.Color;
28		import java.awt.Component;
29		import java.awt.Dimension;
30		import java.awt.Frame;
31		import java.awt.Graphics;
32		import java.awt.Image;
33
		0% Uncovered Elements: 57 (57) Complexity: 13 Complexity Density: 0.34
34		public class OverviewCanvas extends Component
35		{
36		// This is set true if the alignment view changes whilst
37		// the overview is being calculated
38		private volatile boolean restart = false;
39
40		private volatile boolean updaterunning = false;
41
42		private OverviewDimensions od;
43
44		private OverviewRenderer or = null;
45
46		private Image miniMe;
47
48		private Image offscreen;
49
50		private AlignViewport av;
51
52		private jalview.renderer.seqfeatures.FeatureRenderer fr;
53
54		private Frame nullFrame;
55
		0% Uncovered Elements: 5 (5) Complexity: 1 Complexity Density: 0.2
56	0	public OverviewCanvas(OverviewDimensions overviewDims,...
57		AlignViewport alignvp)
58		{
59	0	od = overviewDims;
60	0	av = alignvp;
61
62	0	nullFrame = new Frame();
63	0	nullFrame.addNotify();
64
65	0	fr = new jalview.renderer.seqfeatures.FeatureRenderer(av);
66		}
67
68		/**
69		* Update the overview dimensions object used by the canvas (e.g. if we change
70		* from showing hidden columns to hiding them or vice versa)
71		*
72		* @param overviewDims
73		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
74	0	public void resetOviewDims(OverviewDimensions overviewDims)...
75		{
76	0	od = overviewDims;
77		}
78
79		/**
80		* Signals to drawing code that the associated alignment viewport has changed
81		* and a redraw will be required
82		*/
		0% Uncovered Elements: 11 (11) Complexity: 3 Complexity Density: 0.43
83	0	public boolean restartDraw()...
84		{
85	0	synchronized (this)
86		{
87	0	if (updaterunning)
88		{
89	0	restart = true;
90	0	if (or != null)
91		{
92	0	or.setRedraw(true);
93		}
94		}
95		else
96		{
97	0	updaterunning = true;
98		}
99	0	return restart;
100		}
101		}
102
		0% Uncovered Elements: 23 (23) Complexity: 4 Complexity Density: 0.24
103	0	public void draw(boolean showSequenceFeatures, boolean showAnnotation,...
104		FeatureRenderer transferRenderer)
105		{
106	0	miniMe = null;
107
108	0	if (showSequenceFeatures)
109		{
110	0	fr.transferSettings(transferRenderer);
111		}
112
113	0	setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
114
115	0	or = new OverviewRenderer(fr, od, av.getAlignment(),
116		av.getResidueShading(), new OverviewResColourFinder());
117	0	miniMe = nullFrame.createImage(od.getWidth(), od.getHeight());
118	0	offscreen = nullFrame.createImage(od.getWidth(), od.getHeight());
119
120	0	miniMe = or.draw(od.getRows(av.getAlignment()),
121		od.getColumns(av.getAlignment()));
122
123	0	Graphics mg = miniMe.getGraphics();
124
125		// checks for conservation annotation to make sure overview works for DNA
126		// too
127	0	if (showAnnotation)
128		{
129	0	mg.translate(0, od.getSequencesHeight());
130	0	or.drawGraph(mg, av.getAlignmentConservationAnnotation(),
131		od.getGraphHeight(), od.getColumns(av.getAlignment()));
132	0	mg.translate(0, -od.getSequencesHeight());
133		}
134
135	0	if (restart)
136		{
137	0	restart = false;
138	0	draw(showSequenceFeatures, showAnnotation, transferRenderer);
139		}
140		else
141		{
142	0	updaterunning = false;
143		}
144		}
145
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
146	0	@Override...
147		public void update(Graphics g)
148		{
149	0	paint(g);
150		}
151
		0% Uncovered Elements: 8 (8) Complexity: 2 Complexity Density: 0.33
152	0	@Override...
153		public void paint(Graphics g)
154		{
155	0	Graphics og = offscreen.getGraphics();
156	0	if (miniMe != null)
157		{
158	0	og.drawImage(miniMe, 0, 0, this);
159	0	og.setColor(Color.red);
160	0	od.drawBox(og);
161	0	g.drawImage(offscreen, 0, 0, this);
162		}
163		}
164
165		/**
166		* Nulls references to protect against potential memory leaks
167		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
168	0	void dispose()...
169		{
170	0	od = null;
171		}
172
173		}