Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SequenceRenderer	33	112	54	0.00%	Show methods

Class SequenceRenderer

Class SequenceRenderer	Line # 33	Total Statements 112	Complexity 54	TOTAL Coverage 0.00%
SequenceRenderer(AlignViewport)   SequenceRenderer(AlignViewport)	5151	2.02	1.01	0.0 0.00%
prepare(Graphics,boolean) : void   prepare(Graphics,boolean) : void	6363	3.03	1.01	0.0 0.00%
getResidueColour(SequenceI,int,FeatureColourFinder) : Color   getResidueColour(SequenceI,int,FeatureColourFinder) : Color	8181	1.01	1.01	0.0 0.00%
findSequenceColour(SequenceI,int) : Color   findSequenceColour(SequenceI,int) : Color	9191	3.03	1.01	0.0 0.00%
drawSequence(SequenceI,SequenceGroup[],int,int,int) : void   drawSequence(SequenceI,SequenceGroup[],int,int,int) : void	9898	6.06	3.03	0.0 0.00%
drawBoxes(SequenceI,int,int,int) : void   drawBoxes(SequenceI,int,int,int) : void	116116	25.025	8.08	0.0 0.00%
drawText(SequenceI,int,int,int) : void   drawText(SequenceI,int,int,int) : void	175175	46.046	19.019	0.0 0.00%
getDisplayChar(boolean,int,char,char,SequenceGroup) : char   getDisplayChar(boolean,int,char,char,SequenceGroup) : char	294294	4.04	14.014	0.0 0.00%
drawHighlightedText(SequenceI,int,int,int,int) : void   drawHighlightedText(SequenceI,int,int,int,int) : void	326326	13.013	4.04	0.0 0.00%
drawCursor(Graphics,char,int,int) : void   drawCursor(Graphics,char,int,int) : void	356356	9.09	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.appletgui;
22
23		import jalview.datamodel.SequenceGroup;
24		import jalview.datamodel.SequenceI;
25		import jalview.renderer.ResidueColourFinder;
26		import jalview.renderer.seqfeatures.FeatureColourFinder;
27
28		import java.awt.Color;
29		import java.awt.Font;
30		import java.awt.FontMetrics;
31		import java.awt.Graphics;
32
		0% Uncovered Elements: 190 (190) Complexity: 54 Complexity Density: 0.48
33		public class SequenceRenderer implements jalview.api.SequenceRenderer
34		{
35		final static int CHAR_TO_UPPER = 'A' - 'a';
36
37		AlignViewport av;
38
39		FontMetrics fm;
40
41		boolean renderGaps = true;
42
43		SequenceGroup[] allGroups = null;
44
45		Color resBoxColour;
46
47		Graphics graphics;
48
49		ResidueColourFinder resColourFinder;
50
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
51	0	public SequenceRenderer(AlignViewport av)...
52		{
53	0	this.av = av;
54	0	resColourFinder = new ResidueColourFinder();
55		}
56
57		/**
58		* DOCUMENT ME!
59		*
60		* @param b
61		* DOCUMENT ME!
62		*/
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
63	0	public void prepare(Graphics g, boolean renderGaps)...
64		{
65	0	graphics = g;
66	0	fm = g.getFontMetrics();
67
68	0	this.renderGaps = renderGaps;
69		}
70
71		/**
72		* Get the residue colour at the given sequence position - as determined by
73		* the sequence group colour (if any), else the colour scheme, possibly
74		* overridden by a feature colour.
75		*
76		* @param seq
77		* @param position
78		* @param finder
79		* @return
80		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
81	0	@Override...
82		public Color getResidueColour(final SequenceI seq, int position,
83		FeatureColourFinder finder)
84		{
85		// TODO replace 8 or so code duplications with calls to this method
86		// (refactored as needed)
87	0	return resColourFinder.getResidueColour(av.getShowBoxes(),
88		av.getResidueShading(), allGroups, seq, position, finder);
89		}
90
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
91	0	public Color findSequenceColour(SequenceI seq, int i)...
92		{
93	0	allGroups = av.getAlignment().findAllGroups(seq);
94	0	drawBoxes(seq, i, i, 0);
95	0	return resBoxColour;
96		}
97
		0% Uncovered Elements: 10 (10) Complexity: 3 Complexity Density: 0.5
98	0	public void drawSequence(SequenceI seq, SequenceGroup[] sg, int start,...
99		int end, int y1)
100		{
101	0	if (seq == null)
102		{
103	0	return;
104		}
105
106	0	allGroups = sg;
107
108	0	drawBoxes(seq, start, end, y1);
109
110	0	if (av.validCharWidth)
111		{
112	0	drawText(seq, start, end, y1);
113		}
114		}
115
		0% Uncovered Elements: 39 (39) Complexity: 8 Complexity Density: 0.32
116	0	public void drawBoxes(SequenceI seq, int start, int end, int y1)...
117		{
118	0	int i = start;
119	0	int length = seq.getLength();
120
121	0	int curStart = -1;
122	0	int curWidth = av.getCharWidth(), avCharWidth = av.getCharWidth(),
123		avCharHeight = av.getCharHeight();
124
125	0	Color resBoxColour = Color.white;
126	0	Color tempColour = null;
127	0	while (i <= end)
128		{
129	0	resBoxColour = Color.white;
130	0	if (i < length)
131		{
132	0	SequenceGroup currentSequenceGroup = resColourFinder
133		.getCurrentSequenceGroup(allGroups, i);
134	0	if (currentSequenceGroup != null)
135		{
136	0	if (currentSequenceGroup.getDisplayBoxes())
137		{
138	0	resBoxColour = resColourFinder.getBoxColour(
139		currentSequenceGroup.getGroupColourScheme(), seq, i);
140		}
141		}
142	0	else if (av.getShowBoxes())
143		{
144	0	resBoxColour = resColourFinder
145		.getBoxColour(av.getResidueShading(), seq, i);
146		}
147		}
148
149	0	if (resBoxColour != tempColour)
150		{
151	0	if (tempColour != null)
152		{
153	0	graphics.fillRect(avCharWidth * (curStart - start), y1, curWidth,
154		avCharHeight);
155		}
156	0	graphics.setColor(resBoxColour);
157
158	0	curStart = i;
159	0	curWidth = avCharWidth;
160	0	tempColour = resBoxColour;
161
162		}
163		else
164		{
165	0	curWidth += avCharWidth;
166		}
167
168	0	i++;
169		}
170
171	0	graphics.fillRect(avCharWidth * (curStart - start), y1, curWidth,
172		avCharHeight);
173		}
174
		0% Uncovered Elements: 78 (78) Complexity: 19 Complexity Density: 0.41
175	0	public void drawText(SequenceI seq, int start, int end, int y1)...
176		{
177	0	int avCharWidth = av.getCharWidth(), avCharHeight = av.getCharHeight();
178	0	Font boldFont = null;
179	0	boolean bold = false;
180	0	if (av.isUpperCasebold())
181		{
182	0	boldFont = new Font(av.getFont().getName(), Font.BOLD, avCharHeight);
183
184	0	graphics.setFont(av.getFont());
185		}
186
187	0	y1 += avCharHeight - avCharHeight / 5; // height/5 replaces pady
188
189	0	int charOffset = 0;
190
191		// Need to find the sequence position here.
192	0	if (end + 1 >= seq.getLength())
193		{
194	0	end = seq.getLength() - 1;
195		}
196
197	0	char s = ' ';
198	0	boolean srep = av.isDisplayReferenceSeq();
199	0	for (int i = start; i <= end; i++)
200		{
201	0	graphics.setColor(Color.black);
202
203	0	s = seq.getCharAt(i);
204	0	if (!renderGaps && jalview.util.Comparison.isGap(s))
205		{
206	0	continue;
207		}
208
209	0	SequenceGroup currentSequenceGroup = resColourFinder
210		.getCurrentSequenceGroup(allGroups, i);
211	0	if (currentSequenceGroup != null)
212		{
213	0	if (!currentSequenceGroup.getDisplayText())
214		{
215	0	continue;
216		}
217
218	0	if (currentSequenceGroup.getColourText())
219		{
220	0	resBoxColour = resColourFinder.getBoxColour(
221		currentSequenceGroup.getGroupColourScheme(), seq, i);
222	0	graphics.setColor(resBoxColour.darker());
223		}
224	0	if (currentSequenceGroup.getShowNonconserved())
225		{
226	0	s = getDisplayChar(srep, i, s, '.', currentSequenceGroup);
227		}
228		}
229		else
230		{
231	0	if (!av.getShowText())
232		{
233	0	continue;
234		}
235
236	0	if (av.getColourText())
237		{
238	0	resBoxColour = resColourFinder
239		.getBoxColour(av.getResidueShading(), seq, i);
240	0	if (av.getShowBoxes())
241		{
242	0	graphics.setColor(resBoxColour.darker());
243		}
244		else
245		{
246	0	graphics.setColor(resBoxColour);
247		}
248		}
249	0	if (av.getShowUnconserved())
250		{
251	0	s = getDisplayChar(srep, i, s, '.', null);
252
253		}
254		}
255
256	0	if (av.isUpperCasebold())
257		{
258	0	fm = graphics.getFontMetrics();
259	0	if ('A' <= s && s <= 'Z')
260		{
261	0	if (!bold)
262		{
263
264	0	graphics.setFont(boldFont);
265		}
266	0	bold = true;
267		}
268	0	else if (bold)
269		{
270	0	graphics.setFont(av.font);
271	0	bold = false;
272		}
273
274		}
275
276	0	charOffset = (avCharWidth - fm.charWidth(s)) / 2;
277	0	graphics.drawString(String.valueOf(s),
278		charOffset + avCharWidth * (i - start), y1);
279		}
280
281		}
282
283		/**
284		* Returns 'conservedChar' to represent the given position if the sequence
285		* character at that position is equal to the consensus (ignoring case), else
286		* returns the sequence character
287		*
288		* @param usesrep
289		* @param position
290		* @param sequenceChar
291		* @param conservedChar
292		* @return
293		*/
		0% Uncovered Elements: 14 (14) Complexity: 14 Complexity Density: 3.5
294	0	private char getDisplayChar(final boolean usesrep, int position,...
295		char sequenceChar, char conservedChar, SequenceGroup currentGroup)
296		{
297		// TODO - use currentSequenceGroup rather than alignment
298		// currentSequenceGroup.getConsensus()
299	0	char conschar = (usesrep) ? (currentGroup == null
300		|| position < currentGroup.getStartRes()
301		|| position > currentGroup.getEndRes()
302		? av.getAlignment().getSeqrep().getCharAt(position)
303	0	: (currentGroup.getSeqrep() != null
304		? currentGroup.getSeqrep().getCharAt(position)
305		: av.getAlignment().getSeqrep()
306		.getCharAt(position)))
307	0	: (currentGroup != null && currentGroup.getConsensus() != null
308		&& position >= currentGroup.getStartRes()
309		&& position <= currentGroup.getEndRes()
310		&& currentGroup
311		.getConsensus().annotations.length > position)
312		? currentGroup
313		.getConsensus().annotations[position].displayCharacter
314		.charAt(0)
315		: av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter
316		.charAt(0);
317	0	if (!jalview.util.Comparison.isGap(conschar)
318		&& (sequenceChar == conschar
319		|| sequenceChar + CHAR_TO_UPPER == conschar))
320		{
321	0	sequenceChar = conservedChar;
322		}
323	0	return sequenceChar;
324		}
325
		0% Uncovered Elements: 19 (19) Complexity: 4 Complexity Density: 0.31
326	0	public void drawHighlightedText(SequenceI seq, int start, int end, int x1,...
327		int y1)
328		{
329	0	int avCharWidth = av.getCharWidth(), avCharHeight = av.getCharHeight();
330	0	int pady = avCharHeight / 5;
331	0	int charOffset = 0;
332	0	graphics.setColor(Color.black);
333	0	graphics.fillRect(x1, y1, avCharWidth * (end - start + 1),
334		avCharHeight);
335	0	graphics.setColor(Color.white);
336
337	0	char s = '~';
338		// Need to find the sequence position here.
339	0	if (av.validCharWidth)
340		{
341	0	for (int i = start; i <= end; i++)
342		{
343	0	if (i < seq.getLength())
344		{
345	0	s = seq.getCharAt(i);
346		}
347
348	0	charOffset = (avCharWidth - fm.charWidth(s)) / 2;
349	0	graphics.drawString(String.valueOf(s),
350		charOffset + x1 + avCharWidth * (i - start),
351		y1 + avCharHeight - pady);
352		}
353		}
354		}
355
		0% Uncovered Elements: 11 (11) Complexity: 2 Complexity Density: 0.22
356	0	public void drawCursor(Graphics graphics, char s, int x1, int y1)...
357		{
358	0	int pady = av.getCharHeight() / 5;
359	0	int charOffset = 0;
360	0	graphics.setColor(Color.black);
361	0	graphics.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight());
362	0	graphics.setColor(Color.white);
363
364	0	graphics.setColor(Color.white);
365
366	0	if (av.validCharWidth)
367		{
368
369	0	charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
370	0	graphics.drawString(String.valueOf(s), charOffset + x1,
371		(y1 + av.getCharHeight()) - pady);
372		}
373		}
374
375		}