Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
OverviewCanvas	39	80	29	0.889830589%	Show methods

Class OverviewCanvas

Class OverviewCanvas	Line # 39	Total Statements 80	Complexity 29	TOTAL Coverage 0.889830589%
OverviewCanvas(OverviewDimensions,AlignViewportI,ProgressPanel)   OverviewCanvas(OverviewDimensions,AlignViewportI,ProgressPanel)	8282	12.012	2.02	1.0 1.0100%
resetOviewDims(OverviewDimensions) : void   resetOviewDims(OverviewDimensions) : void	112112	1.01	1.01	0.0 0.00%
restartDraw() : boolean   restartDraw() : boolean	121121	7.07	3.03	1.0 1.0100%
draw(boolean,boolean,FeatureRendererModel) : void   draw(boolean,boolean,FeatureRendererModel) : void	151151	20.020	6.06	0.9 0.990%
paintComponent(Graphics) : void   paintComponent(Graphics) : void	198198	30.030	11.011	0.8 0.880%
dispose() : void   dispose() : void	283283	6.06	2.02	1.0 1.0100%
getGapColour() : Color   getGapColour() : Color	297297	1.01	1.01	1.0 1.0100%
getHiddenColour() : Color   getHiddenColour() : Color	302302	1.01	1.01	1.0 1.0100%
getResidueColour() : Color   getResidueColour() : Color	307307	1.01	1.01	1.0 1.0100%
setColours(Color,Color,Color) : void   setColours(Color,Color,Color) : void	319319	1.01	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.87288135	jalview.project.Jalview2xmlTests.testStoreAndRecoverOverviewjalview.project.Jalview2xmlTests.testStoreAndRecoverOverview	1PASS
	0.65254235	jalview.project.Jalview2xmlTests.testStoreAndRecoverPDBEntryjalview.project.Jalview2xmlTests.testStoreAndRecoverPDBEntry	1PASS
	0.58474576	jalview.project.Jalview2xmlTests.testStoreAndRestoreIDwidthAndAnnotationHeightjalview.project.Jalview2xmlTests.testStoreAndRestoreIDwidthAndAnnotationHeight	1PASS
	0.58474576	jalview.project.Jalview2xmlTests.testStoreAndRecoverReferenceSeqSettingsjalview.project.Jalview2xmlTests.testStoreAndRecoverReferenceSeqSettings	1PASS
	0.5677966	jalview.project.Jalview2xmlTests.testTCoffeeScoresjalview.project.Jalview2xmlTests.testTCoffeeScores	1PASS
	0.4915254	jalview.gui.AlignmentPanelTest.testSetOverviewTitle_automaticOverviewjalview.gui.AlignmentPanelTest.testSetOverviewTitle_automaticOverview	1PASS
	0.48305085	jalview.project.Jalview2xmlTests.testStoreAndRecoverNoOverviewjalview.project.Jalview2xmlTests.testStoreAndRecoverNoOverview	1PASS
	0.45762712	jalview.project.Jalview2xmlTests.viewRefPdbAnnotationjalview.project.Jalview2xmlTests.viewRefPdbAnnotation	1PASS
	0.44067797	jalview.project.Jalview2xmlTests.testAutoShowOverviewForLegacyProjectsjalview.project.Jalview2xmlTests.testAutoShowOverviewForLegacyProjects	1PASS
	0.3983051	jalview.gui.AlignmentPanelTest.testSetOverviewTitlejalview.gui.AlignmentPanelTest.testSetOverviewTitle	1PASS
	0.059322033	jalview.project.Jalview2xmlTests.testMergeDatasetsforManyViewsjalview.project.Jalview2xmlTests.testMergeDatasetsforManyViews	1PASS

 

Source view

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 java.awt.Color;
24		import java.awt.Dimension;
25		import java.awt.Graphics;
26		import java.awt.image.BufferedImage;
27		import java.awt.image.RasterFormatException;
28
29		import javax.swing.JPanel;
30
31		import jalview.api.AlignViewportI;
32		import jalview.bin.Cache;
33		import jalview.bin.Console;
34		import jalview.renderer.OverviewRenderer;
35		import jalview.renderer.OverviewResColourFinder;
36		import jalview.viewmodel.OverviewDimensions;
37		import jalview.viewmodel.seqfeatures.FeatureRendererModel;
38
		89% Uncovered Elements: 13 (118) Complexity: 29 Complexity Density: 0.36
39		public class OverviewCanvas extends JPanel
40		{
41		public static final Color OVERVIEW_DEFAULT_GAP = Color.lightGray;
42
43		public static final Color OVERVIEW_DEFAULT_LEGACY_GAP = Color.white;
44
45		public static final Color OVERVIEW_DEFAULT_RESIDUE = Color.white;
46
47		public static final Color OVERVIEW_DEFAULT_LEGACY_RESIDUE = Color.lightGray;
48
49		public static final Color OVERVIEW_DEFAULT_HIDDEN = Color.darkGray
50		.darker();
51
52		private static final Color TRANS_GREY = new Color(100, 100, 100, 25);
53
54		// This is set true if the alignment view changes whilst
55		// the overview is being calculated
56		private volatile boolean restart = false;
57
58		private volatile boolean updaterunning = false;
59
60		private boolean dispose = false;
61
62		private BufferedImage miniMe;
63
64		private BufferedImage lastMiniMe = null;
65
66		// Can set different properties in this seqCanvas than
67		// main visible SeqCanvas
68		private SequenceRenderer sr;
69
70		private jalview.renderer.seqfeatures.FeatureRenderer fr;
71
72		private OverviewDimensions od;
73
74		private OverviewRenderer or = null;
75
76		private AlignViewportI av;
77
78		private OverviewResColourFinder cf;
79
80		private ProgressPanel progressPanel;
81
		100% Uncovered Elements: 0 (14) Complexity: 2 Complexity Density: 0.17
82	38	public OverviewCanvas(OverviewDimensions overviewDims,...
83		AlignViewportI alignvp, ProgressPanel pp)
84		{
85	38	od = overviewDims;
86	38	av = alignvp;
87	38	progressPanel = pp;
88
89	38	sr = new SequenceRenderer(av);
90	38	sr.renderGaps = false;
91	38	fr = new jalview.renderer.seqfeatures.FeatureRenderer(av);
92
93	38	boolean useLegacy = Cache.getDefault(Preferences.USE_LEGACY_GAP, false);
94	38	Color gapCol = Cache.getDefaultColour(Preferences.GAP_COLOUR,
95		OVERVIEW_DEFAULT_GAP);
96	38	Color hiddenCol = Cache.getDefaultColour(Preferences.HIDDEN_COLOUR,
97		OVERVIEW_DEFAULT_HIDDEN);
98	38	Color residueCol = useLegacy ? OVERVIEW_DEFAULT_LEGACY_RESIDUE
99		: OVERVIEW_DEFAULT_RESIDUE;
100
101	38	cf = new OverviewResColourFinder(gapCol, residueCol, hiddenCol);
102
103	38	setSize(od.getWidth(), od.getHeight());
104		}
105
106		/**
107		* Update the overview dimensions object used by the canvas (e.g. if we change
108		* from showing hidden columns to hiding them or vice versa)
109		*
110		* @param overviewDims
111		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
112	0	public void resetOviewDims(OverviewDimensions overviewDims)...
113		{
114	0	od = overviewDims;
115		}
116
117		/**
118		* Signals to drawing code that the associated alignment viewport has changed
119		* and a redraw will be required
120		*/
		100% Uncovered Elements: 0 (11) Complexity: 3 Complexity Density: 0.43
121	428	public boolean restartDraw()...
122		{
123	428	synchronized (this)
124		{
125	428	if (updaterunning)
126		{
127	332	restart = true;
128	332	if (or != null)
129		{
130	202	or.setRedraw(true);
131		}
132		}
133		else
134		{
135	96	updaterunning = true;
136		}
137	427	return restart;
138		}
139		}
140
141		/**
142		* Draw the overview sequences
143		*
144		* @param showSequenceFeatures
145		* true if sequence features are to be shown
146		* @param showAnnotation
147		* true if the annotation is to be shown
148		* @param transferRenderer
149		* the renderer to transfer feature colouring from
150		*/
		90% Uncovered Elements: 3 (30) Complexity: 6 Complexity Density: 0.3
151	245	public void draw(boolean showSequenceFeatures, boolean showAnnotation,...
152		FeatureRendererModel transferRenderer)
153		{
154	245	miniMe = null;
155
156	245	if (showSequenceFeatures)
157		{
158	35	fr.transferSettings(transferRenderer);
159		}
160
161	245	setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
162
163	245	or = new OverviewRenderer(fr, od, av.getAlignment(),
164		av.getResidueShading(), cf);
165
166	245	or.addPropertyChangeListener(progressPanel);
167
168	245	miniMe = or.draw(od.getRows(av.getAlignment()),
169		od.getColumns(av.getAlignment()));
170
171	245	Graphics mg = miniMe.getGraphics();
172
173	245	if (showAnnotation)
174		{
175	245	mg.translate(0, od.getSequencesHeight());
176	240	or.drawGraph(mg, av.is3di() ? av.getAlignmentQualityAnnot() : av.getAlignmentConservationAnnotation(),
177		od.getGraphHeight(), od.getColumns(av.getAlignment()));
178	236	mg.translate(0, -od.getSequencesHeight());
179		}
180
181	236	or.removePropertyChangeListener(progressPanel);
182	236	or = null;
183	236	if (restart)
184		{
185	146	restart = false;
186	146	if (!dispose)
187		{
188	146	draw(showSequenceFeatures, showAnnotation, transferRenderer);
189		}
190		}
191		else
192		{
193	90	updaterunning = false;
194	90	lastMiniMe = miniMe;
195		}
196		}
197
		80% Uncovered Elements: 8 (40) Complexity: 11 Complexity Density: 0.37
198	21	@Override...
199		public void paintComponent(Graphics g)
200		{
201		// super.paintComponent(g);
202
203	21	if (restart)
204		{
205	1	if (lastMiniMe == null)
206		{
207	1	g.setColor(Color.white);
208	1	g.fillRect(0, 0, getWidth(), getHeight());
209		}
210		else
211		{
212	0	g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
213		}
214	1	g.setColor(TRANS_GREY);
215	1	g.fillRect(0, 0, getWidth(), getHeight());
216		}
217	20	else if (lastMiniMe != null)
218		{
219		// is this a resize?
220	17	if ((getWidth() > 0) && (getHeight() > 0)
221		&& ((getWidth() != od.getWidth())
222		|| (getHeight() != od.getHeight())))
223		{
224		// if there is annotation, scale the alignment and annotation
225		// separately
226	1	if (od.getGraphHeight() > 0 && od.getSequencesHeight() > 0 // BH 2019
227		)
228		{
229	1	try
230		{
231	1	BufferedImage topImage = lastMiniMe.getSubimage(0, 0,
232		od.getWidth(), od.getSequencesHeight());
233	1	BufferedImage bottomImage = lastMiniMe.getSubimage(0,
234		od.getSequencesHeight(), od.getWidth(),
235		od.getGraphHeight());
236
237		// must be done at this point as we rely on using old width/height
238		// above, and new width/height below
239	1	od.setWidth(getWidth());
240	1	od.setHeight(getHeight());
241
242		// stick the images back together so lastMiniMe is consistent in the
243		// event of a repaint - BUT probably not thread safe
244	1	lastMiniMe = new BufferedImage(od.getWidth(), od.getHeight(),
245		BufferedImage.TYPE_INT_RGB);
246	1	Graphics lg = lastMiniMe.getGraphics();
247	1	lg.drawImage(topImage, 0, 0, od.getWidth(),
248		od.getSequencesHeight(), null);
249	1	lg.drawImage(bottomImage, 0, od.getSequencesHeight(),
250		od.getWidth(), od.getGraphHeight(), this);
251	1	lg.dispose();
252		} catch (RasterFormatException e)
253		{
254	0	Console.debug(
255		"Scaling miscalculation resizing Overview window");
256	0	od.setWidth(getWidth());
257	0	od.setHeight(getHeight());
258		}
259		}
260		else
261		{
262	0	od.setWidth(getWidth());
263	0	od.setHeight(getHeight());
264		}
265
266		// make sure the box is in the right place
267	1	od.setBoxPosition(av.getAlignment().getHiddenSequences(),
268		av.getAlignment().getHiddenColumns());
269		}
270		// fall back to normal behaviour
271	17	g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
272		}
273		else
274		{
275	3	g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
276		}
277
278		// draw the box
279	21	g.setColor(Color.red);
280	21	od.drawBox(g);
281		}
282
		100% Uncovered Elements: 0 (8) Complexity: 2 Complexity Density: 0.33
283	35	public void dispose()...
284		{
285	35	dispose = true;
286	35	od = null;
287	35	synchronized (this)
288		{
289	35	restart = true;
290	35	if (or != null)
291		{
292	4	or.setRedraw(true);
293		}
294		}
295		}
296
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
297	14	public Color getGapColour()...
298		{
299	14	return cf.getGapColour();
300		}
301
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
302	14	public Color getHiddenColour()...
303		{
304	14	return cf.getHiddenColour();
305		}
306
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
307	14	public Color getResidueColour()...
308		{
309	14	return cf.getResidueColour();
310		}
311
312		/**
313		* Sets the colours to use for gaps, residues and hidden regions
314		*
315		* @param gaps
316		* @param residues
317		* @param hidden
318		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
319	9	public void setColours(Color gaps, Color residues, Color hidden)...
320		{
321	9	cf = new OverviewResColourFinder(gaps, residues, hidden);
322		}
323		}