Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
IdCanvas	35	154	58	0.00%	Show methods

Class IdCanvas

Class IdCanvas	Line # 35	Total Statements 154	Complexity 58	TOTAL Coverage 0.00%
IdCanvas(AlignViewport)   IdCanvas(AlignViewport)	5555	4.04	1.01	0.0 0.00%
drawIdString(Graphics,boolean,SequenceI,int,int,int) : void   drawIdString(Graphics,boolean,SequenceI,int,int,int) : void	6363	15.015	6.06	0.0 0.00%
fastPaint(int) : void   fastPaint(int) : void	102102	20.020	7.07	0.0 0.00%
update(Graphics) : void   update(Graphics) : void	149149	1.01	1.01	0.0 0.00%
paint(Graphics) : void   paint(Graphics) : void	155155	20.020	7.07	0.0 0.00%
drawIds(int,int) : void   drawIds(int,int) : void	200200	31.031	10.010	0.0 0.00%
drawIdsWrapped(int,boolean,boolean) : void   drawIdsWrapped(int,boolean,boolean) : void	280280	29.029	8.08	0.0 0.00%
setHighlighted(List<SequenceI>) : void   setHighlighted(List<SequenceI>) : void	341341	2.02	1.01	0.0 0.00%
drawMarker(int,int,int) : void   drawMarker(int,int,int) : void	347347	20.020	8.08	0.0 0.00%
setHiddenFont(SequenceI) : boolean   setHiddenFont(SequenceI) : boolean	410410	5.05	3.03	0.0 0.00%
propertyChange(PropertyChangeEvent) : void   propertyChange(PropertyChangeEvent) : void	435435	7.07	6.06	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.datamodel.SequenceI;
24		import jalview.viewmodel.ViewportListenerI;
25		import jalview.viewmodel.ViewportRanges;
26
27		import java.awt.Color;
28		import java.awt.Font;
29		import java.awt.Graphics;
30		import java.awt.Image;
31		import java.awt.Panel;
32		import java.beans.PropertyChangeEvent;
33		import java.util.List;
34
		0% Uncovered Elements: 237 (237) Complexity: 58 Complexity Density: 0.38
35		public class IdCanvas extends Panel implements ViewportListenerI
36		{
37		protected AlignViewport av;
38
39		protected boolean showScores = true;
40
41		protected int maxIdLength = -1;
42
43		protected String maxIdStr = null;
44
45		Image image;
46
47		Graphics gg;
48
49		int imgHeight = 0;
50
51		boolean fastPaint = false;
52
53		List<SequenceI> searchResults;
54
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
55	0	public IdCanvas(AlignViewport av)...
56		{
57	0	setLayout(null);
58	0	this.av = av;
59	0	PaintRefresher.Register(this, av.getSequenceSetId());
60	0	av.getRanges().addPropertyChangeListener(this);
61		}
62
		0% Uncovered Elements: 21 (21) Complexity: 6 Complexity Density: 0.4
63	0	public void drawIdString(Graphics gg, boolean hiddenRows, SequenceI s,...
64		int i, int starty, int ypos)
65		{
66	0	int charHeight = av.getCharHeight();
67
68	0	if (searchResults != null && searchResults.contains(s))
69		{
70	0	gg.setColor(Color.black);
71	0	gg.fillRect(0, ((i - starty) * charHeight) + ypos, getSize().width,
72		charHeight);
73	0	gg.setColor(Color.white);
74		}
75	0	else if (av.getSelectionGroup() != null
76		&& av.getSelectionGroup().getSequences(null).contains(s))
77		{
78	0	gg.setColor(Color.lightGray);
79	0	gg.fillRect(0, ((i - starty) * charHeight) + ypos, getSize().width,
80		charHeight);
81	0	gg.setColor(Color.white);
82		}
83		else
84		{
85	0	gg.setColor(av.getSequenceColour(s));
86	0	gg.fillRect(0, ((i - starty) * charHeight) + ypos, getSize().width,
87		charHeight);
88	0	gg.setColor(Color.black);
89		}
90
91	0	gg.drawString(s.getDisplayId(av.getShowJVSuffix()), 0,
92		((i - starty) * charHeight) + ypos + charHeight
93		- (charHeight / 5));
94
95	0	if (hiddenRows)
96		{
97	0	drawMarker(i, starty, ypos);
98		}
99
100		}
101
		0% Uncovered Elements: 30 (30) Complexity: 7 Complexity Density: 0.35
102	0	public void fastPaint(int vertical)...
103		{
104	0	if (gg == null || av.getWrapAlignment())
105		{
106	0	repaint();
107	0	return;
108		}
109
110	0	ViewportRanges ranges = av.getRanges();
111
112	0	gg.copyArea(0, 0, getSize().width, imgHeight, 0,
113		-vertical * av.getCharHeight());
114
115	0	int ss = ranges.getStartSeq(), es = ranges.getEndSeq(), transY = 0;
116	0	if (vertical > 0) // scroll down
117		{
118	0	ss = es - vertical;
119	0	if (ss < ranges.getStartSeq()) // ie scrolling too fast, more than a page
120		// at a
121		// time
122		{
123	0	ss = ranges.getStartSeq();
124		}
125		else
126		{
127	0	transY = imgHeight - ((vertical + 1) * av.getCharHeight());
128		}
129		}
130	0	else if (vertical < 0)
131		{
132	0	es = ss - vertical;
133	0	if (es > ranges.getEndSeq())
134		{
135	0	es = ranges.getEndSeq();
136		}
137		}
138
139	0	gg.translate(0, transY);
140
141	0	drawIds(ss, es);
142
143	0	gg.translate(0, -transY);
144
145	0	fastPaint = true;
146	0	repaint();
147		}
148
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
149	0	@Override...
150		public void update(Graphics g)
151		{
152	0	paint(g);
153		}
154
		0% Uncovered Elements: 28 (28) Complexity: 7 Complexity Density: 0.35
155	0	@Override...
156		public void paint(Graphics g)
157		{
158	0	if (getSize().height < 0 || getSize().width < 0)
159		{
160	0	return;
161		}
162	0	if (fastPaint)
163		{
164	0	fastPaint = false;
165	0	g.drawImage(image, 0, 0, this);
166	0	return;
167		}
168
169	0	imgHeight = getSize().height;
170	0	imgHeight -= imgHeight % av.getCharHeight();
171
172	0	if (imgHeight < 1)
173		{
174	0	return;
175		}
176
177	0	if (image == null || imgHeight != image.getHeight(this))
178		{
179	0	image = createImage(getSize().width, imgHeight);
180	0	gg = image.getGraphics();
181	0	gg.setFont(av.getFont());
182		}
183
184		// Fill in the background
185	0	gg.setColor(Color.white);
186	0	Font italic = new Font(av.getFont().getName(), Font.ITALIC,
187		av.getFont().getSize());
188	0	gg.setFont(italic);
189
190	0	gg.fillRect(0, 0, getSize().width, getSize().height);
191	0	drawIds(av.getRanges().getStartSeq(), av.getRanges().getEndSeq());
192	0	g.drawImage(image, 0, 0, this);
193		}
194
195		/**
196		* local copy of av.getCharHeight set at top of drawIds
197		*/
198		private int avcharHeight;
199
		0% Uncovered Elements: 45 (45) Complexity: 10 Complexity Density: 0.32
200	0	void drawIds(int starty, int endy)...
201		{
202	0	avcharHeight = av.getCharHeight();
203
204	0	Color currentColor = Color.white;
205	0	Color currentTextColor = Color.black;
206
207	0	final boolean doHiddenCheck = av.isDisplayReferenceSeq()
208		|| av.hasHiddenRows();
209	0	boolean hiddenRows = av.hasHiddenRows() && av.getShowHiddenMarkers();
210
211	0	if (av.getWrapAlignment())
212		{
213	0	drawIdsWrapped(starty, doHiddenCheck, hiddenRows);
214	0	return;
215		}
216
217		// Now draw the id strings
218	0	SequenceI seq;
219	0	for (int i = starty; i <= endy; i++)
220		{
221	0	seq = av.getAlignment().getSequenceAt(i);
222	0	if (seq == null)
223		{
224	0	continue;
225		}
226		// hardwired italic IDs in applet currently
227	0	Font italic = new Font(av.getFont().getName(), Font.ITALIC,
228		av.getFont().getSize());
229	0	gg.setFont(italic);
230		// boolean isrep=false;
231	0	if (doHiddenCheck)
232		{
233		// isrep =
234	0	setHiddenFont(seq);
235		}
236
237		// Selected sequence colours
238	0	if ((searchResults != null) && searchResults.contains(seq))
239		{
240	0	currentColor = Color.black;
241	0	currentTextColor = Color.white;
242		}
243	0	else if ((av.getSelectionGroup() != null)
244		&& av.getSelectionGroup().getSequences(null).contains(seq))
245		{
246	0	currentColor = Color.lightGray;
247	0	currentTextColor = Color.black;
248		}
249		else
250		{
251	0	currentColor = av.getSequenceColour(seq);
252	0	currentTextColor = Color.black;
253		}
254
255	0	gg.setColor(currentColor);
256		// TODO: isrep could be used to highlight the representative in a
257		// different way
258	0	gg.fillRect(0, (i - starty) * avcharHeight, getSize().width,
259		avcharHeight);
260	0	gg.setColor(currentTextColor);
261
262	0	gg.drawString(seq.getDisplayId(av.getShowJVSuffix()), 0,
263		(((i - starty) * avcharHeight) + avcharHeight)
264		- (avcharHeight / 5));
265
266	0	if (hiddenRows)
267		{
268	0	drawMarker(i, starty, 0);
269		}
270		}
271		}
272
273		/**
274		* Draws sequence ids in wrapped mode
275		*
276		* @param starty
277		* @param doHiddenCheck
278		* @param hiddenRows
279		*/
		0% Uncovered Elements: 41 (41) Complexity: 8 Complexity Density: 0.28
280	0	protected void drawIdsWrapped(int starty, final boolean doHiddenCheck,...
281		boolean hiddenRows)
282		{
283	0	int maxwidth = av.getAlignment().getVisibleWidth();
284	0	int alheight = av.getAlignment().getHeight();
285
286	0	int annotationHeight = 0;
287	0	AnnotationLabels labels = null;
288
289	0	if (av.isShowAnnotation())
290		{
291	0	AnnotationPanel ap = new AnnotationPanel(av);
292	0	annotationHeight = ap.adjustPanelHeight();
293	0	labels = new AnnotationLabels(av);
294		}
295	0	int hgap = avcharHeight;
296	0	if (av.getScaleAboveWrapped())
297		{
298	0	hgap += avcharHeight;
299		}
300
301	0	int cHeight = alheight * avcharHeight + hgap + annotationHeight;
302
303	0	int rowSize = av.getRanges().getViewportWidth();
304
305		// hardwired italic IDs in applet currently
306	0	Font italic = new Font(av.getFont().getName(), Font.ITALIC,
307		av.getFont().getSize());
308	0	gg.setFont(italic);
309
310		/*
311		* draw repeating sequence ids until out of sequence data or
312		* out of visible space, whichever comes first
313		*/
314	0	int ypos = hgap;
315	0	int row = av.getRanges().getStartRes();
316	0	while ((ypos <= getHeight()) && (row < maxwidth))
317		{
318	0	for (int i = starty; i < alheight; i++)
319		{
320
321	0	SequenceI s = av.getAlignment().getSequenceAt(i);
322		// gg.setFont(italic);
323	0	if (doHiddenCheck)
324		{
325	0	setHiddenFont(s);
326		}
327	0	drawIdString(gg, hiddenRows, s, i, 0, ypos);
328		}
329
330	0	if (labels != null)
331		{
332	0	gg.translate(0, ypos + (alheight * avcharHeight));
333	0	labels.drawComponent(gg, getSize().width);
334	0	gg.translate(0, -ypos - (alheight * avcharHeight));
335		}
336	0	ypos += cHeight;
337	0	row += rowSize;
338		}
339		}
340
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
341	0	public void setHighlighted(List<SequenceI> list)...
342		{
343	0	searchResults = list;
344	0	repaint();
345		}
346
		0% Uncovered Elements: 34 (34) Complexity: 8 Complexity Density: 0.4
347	0	void drawMarker(int i, int starty, int yoffset)...
348		{
349	0	SequenceI[] hseqs = av.getAlignment()
350		.getHiddenSequences().hiddenSequences;
351		// Use this method here instead of calling hiddenSeq adjust
352		// 3 times.
353	0	int hSize = hseqs.length;
354
355	0	int hiddenIndex = i;
356	0	int lastIndex = i - 1;
357	0	int nextIndex = i + 1;
358
359	0	for (int j = 0; j < hSize; j++)
360		{
361	0	if (hseqs[j] != null)
362		{
363	0	if (j - 1 < hiddenIndex)
364		{
365	0	hiddenIndex++;
366		}
367	0	if (j - 1 < lastIndex)
368		{
369	0	lastIndex++;
370		}
371	0	if (j - 1 < nextIndex)
372		{
373	0	nextIndex++;
374		}
375		}
376		}
377
378	0	boolean below = (hiddenIndex > lastIndex + 1);
379	0	boolean above = (nextIndex > hiddenIndex + 1);
380
381	0	gg.setColor(Color.blue);
382	0	if (below)
383		{
384	0	gg.fillPolygon(
385		new int[]
386		{ getSize().width - avcharHeight,
387		getSize().width - avcharHeight, getSize().width },
388		new int[]
389		{ (i - starty) * avcharHeight + yoffset,
390		(i - starty) * avcharHeight + yoffset + avcharHeight / 4,
391		(i - starty) * avcharHeight + yoffset },
392		3);
393		}
394	0	if (above)
395		{
396	0	gg.fillPolygon(
397		new int[]
398		{ getSize().width - avcharHeight,
399		getSize().width - avcharHeight, getSize().width },
400		new int[]
401		{ (i - starty + 1) * avcharHeight + yoffset,
402		(i - starty + 1) * avcharHeight + yoffset
403		- avcharHeight / 4,
404		(i - starty + 1) * avcharHeight + yoffset },
405		3);
406
407		}
408		}
409
		0% Uncovered Elements: 7 (7) Complexity: 3 Complexity Density: 0.6
410	0	boolean setHiddenFont(SequenceI seq)...
411		{
412	0	Font bold = new Font(av.getFont().getName(), Font.BOLD,
413		av.getFont().getSize());
414
415	0	if (av.isReferenceSeq(seq) || av.isHiddenRepSequence(seq))
416		{
417	0	gg.setFont(bold);
418	0	return true;
419		}
420	0	return false;
421		}
422
423		/**
424		* Respond to viewport range changes (e.g. alignment panel was scrolled). Both
425		* scrolling and resizing change viewport ranges. Scrolling changes both start
426		* and end points, but resize only changes end values. Here we only want to
427		* fastpaint on a scroll, with resize using a normal paint, so scroll events
428		* are identified as changes to the horizontal or vertical start value.
429		* <p>
430		* In unwrapped mode, only responds to a vertical scroll, as horizontal scroll
431		* leaves sequence ids unchanged. In wrapped mode, only vertical scroll is
432		* provided, but it generates a change of "startres" which does require an
433		* update here.
434		*/
		0% Uncovered Elements: 13 (13) Complexity: 6 Complexity Density: 0.86
435	0	@Override...
436		public void propertyChange(PropertyChangeEvent evt)
437		{
438	0	String propertyName = evt.getPropertyName();
439	0	if (propertyName.equals(ViewportRanges.STARTSEQ)
440		|| (av.getWrapAlignment()
441		&& propertyName.equals(ViewportRanges.STARTRES)))
442		{
443	0	fastPaint((int) evt.getNewValue() - (int) evt.getOldValue());
444		}
445	0	else if (propertyName.equals(ViewportRanges.STARTRESANDSEQ))
446		{
447	0	fastPaint(((int[]) evt.getNewValue())[1]
448		- ((int[]) evt.getOldValue())[1]);
449		}
450	0	else if (propertyName.equals(ViewportRanges.MOVE_VIEWPORT))
451		{
452	0	repaint();
453		}
454		}
455		}