Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
UserColourScheme	39	100	46	0.487804948.8%	Show methods

Class UserColourScheme

Class UserColourScheme	Line # 39	Total Statements 100	Complexity 46	TOTAL Coverage 0.487804948.8%
UserColourScheme()   UserColourScheme()	4848	1.01	1.01	1.0 1.0100%
UserColourScheme(Color[])   UserColourScheme(Color[])	5353	2.02	1.01	1.0 1.0100%
getInstance(AlignViewportI,AnnotatedCollectionI) : ColourSchemeI   getInstance(AlignViewportI,AnnotatedCollectionI) : ColourSchemeI	5959	1.01	1.01	0.0 0.00%
UserColourScheme(UserColourScheme)   UserColourScheme(UserColourScheme)	7171	5.05	2.02	0.0 0.00%
UserColourScheme(String)   UserColourScheme(String)	9494	10.010	3.03	0.9285714 0.928571492.9%
setAll(Color) : void   setAll(Color) : void	124124	8.08	3.03	0.8333333 0.833333383.3%
getColours() : Color[]   getColours() : Color[]	142142	1.01	1.01	0.0 0.00%
getLowerCaseColours() : Color[]   getLowerCaseColours() : Color[]	147147	1.01	1.01	0.0 0.00%
setName(String) : void   setName(String) : void	152152	1.01	1.01	1.0 1.0100%
getName() : String   getName() : String	157157	1.01	1.01	0.0 0.00%
parseAppletParameter(String) : void   parseAppletParameter(String) : void	177177	28.028	11.011	0.6304348 0.630434863%
setLowerCaseColours(Color[]) : void   setLowerCaseColours(Color[]) : void	243243	1.01	1.01	0.0 0.00%
findColour(char) : Color   findColour(char) : Color	253253	5.05	5.05	1.0 1.0100%
getSchemeName() : String   getSchemeName() : String	271271	3.03	3.03	1.0 1.0100%
toAppletParameter() : String   toAppletParameter() : String	286286	31.031	10.010	0.0 0.00%
hasGapColour() : boolean   hasGapColour() : boolean	355355	1.01	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.39634147	jalview.schemes.ColourSchemePropertyTest.testGetColourSchemejalview.schemes.ColourSchemePropertyTest.testGetColourScheme	1PASS
	0.06097561	jalview.schemes.ColourSchemePropertyTest.testGetColourNamejalview.schemes.ColourSchemePropertyTest.testGetColourName	1PASS
	0.05487805	jalview.renderer.OverviewResColourFinderTest.testGetResidueBoxColour_userdefjalview.renderer.OverviewResColourFinderTest.testGetResidueBoxColour_userdef	1PASS
	0.042682927	jalview.renderer.ResidueColourFinderTest.testGetResidueColour_userdefjalview.renderer.ResidueColourFinderTest.testGetResidueColour_userdef	1PASS
	0.042682927	jalview.renderer.ResidueShaderTest.testFindColour_gapColourjalview.renderer.ResidueShaderTest.testFindColour_gapColour	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.schemes;
22
23		import java.util.Locale;
24
25		import jalview.api.AlignViewportI;
26		import jalview.datamodel.AnnotatedCollectionI;
27		import jalview.util.ColorUtils;
28		import jalview.util.StringUtils;
29
30		import java.awt.Color;
31		import java.util.ArrayList;
32		import java.util.Collections;
33		import java.util.HashMap;
34		import java.util.List;
35		import java.util.Map;
36		import java.util.Map.Entry;
37		import java.util.StringTokenizer;
38
		48.8% Uncovered Elements: 84 (164) Complexity: 46 Complexity Density: 0.46
39		public class UserColourScheme extends ResidueColourScheme
40		{
41		/*
42		* lookup (by symbol index) of lower case colours (if configured)
43		*/
44		Color[] lowerCaseColours;
45
46		protected String schemeName;
47
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
48	1	public UserColourScheme()...
49		{
50	1	super(ResidueProperties.aaIndex);
51		}
52
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
53	7	public UserColourScheme(Color[] newColors)...
54		{
55	7	super(ResidueProperties.aaIndex);
56	7	colors = newColors;
57		}
58
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
59	0	@Override...
60		public ColourSchemeI getInstance(AlignViewportI view,
61		AnnotatedCollectionI sg)
62		{
63	0	return new UserColourScheme(this);
64		}
65
66		/**
67		* Copy constructor
68		*
69		* @return
70		*/
		0% Uncovered Elements: 7 (7) Complexity: 2 Complexity Density: 0.4
71	0	protected UserColourScheme(UserColourScheme from)...
72		{
73	0	this(from.colors);
74	0	schemeName = from.schemeName;
75	0	if (from.lowerCaseColours != null)
76		{
77	0	lowerCaseColours = new Color[from.lowerCaseColours.length];
78	0	System.arraycopy(from.lowerCaseColours, 0, lowerCaseColours, 0,
79		from.lowerCaseColours.length);
80		}
81		}
82
83		/**
84		* Constructor for an animino acid colour scheme. The colour specification may
85		* be one of
86		* <ul>
87		* <li>an AWT colour name e.g. red</li>
88		* <li>an AWT hex rgb colour e.g. ff2288</li>
89		* <li>residue colours list e.g. D,E=red;K,R,H=0022FF;c=yellow</li>
90		* </ul>
91		*
92		* @param colour
93		*/
		92.9% Uncovered Elements: 1 (14) Complexity: 3 Complexity Density: 0.3
94	2	public UserColourScheme(String colour)...
95		{
96	2	super(ResidueProperties.aaIndex);
97
98	2	if (colour.contains("="))
99		{
100		/*
101		* a list of colours per residue(s)
102		*/
103	1	parseAppletParameter(colour);
104	1	return;
105		}
106
107	1	Color col = ColorUtils.parseColourString(colour);
108
109	1	if (col == null)
110		{
111	1	jalview.bin.Console.outPrintln("Making colour from name: " + colour);
112	1	col = ColorUtils.createColourFromName(colour);
113		}
114
115	1	setAll(col);
116	1	schemeName = colour;
117		}
118
119		/**
120		* Sets all symbols to the specified colour
121		*
122		* @param col
123		*/
		83.3% Uncovered Elements: 2 (12) Complexity: 3 Complexity Density: 0.38
124	2	protected void setAll(Color col)...
125		{
126	2	if (symbolIndex == null)
127		{
128	0	return;
129		}
130	2	int max = 0;
131	2	for (int index : symbolIndex)
132		{
133	510	max = Math.max(max, index);
134		}
135	2	colors = new Color[max + 1];
136	50	for (int i = 0; i <= max; i++)
137		{
138	48	colors[i] = col;
139		}
140		}
141
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
142	0	public Color[] getColours()...
143		{
144	0	return colors;
145		}
146
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
147	0	public Color[] getLowerCaseColours()...
148		{
149	0	return lowerCaseColours;
150		}
151
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
152	3	public void setName(String name)...
153		{
154	3	schemeName = name;
155		}
156
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
157	0	public String getName()...
158		{
159	0	return schemeName;
160		}
161
162		/**
163		* Parse and save residue colours specified as (for example)
164		*
165		* <pre>
166		* D,E=red; K,R,H=0022FF; c=100,50,75
167		* </pre>
168		*
169		* This should be a semi-colon separated list of colours, which may be defined
170		* by colour name, hex value or comma-separated RGB triple. Each colour is
171		* defined for a comma-separated list of amino acid single letter codes. (Note
172		* that this also allows a colour scheme to be defined for ACGT, but not for
173		* U.)
174		*
175		* @param paramValue
176		*/
		63% Uncovered Elements: 17 (46) Complexity: 11 Complexity Density: 0.39
177	1	void parseAppletParameter(String paramValue)...
178		{
179	1	setAll(Color.white);
180
181	1	StringTokenizer st = new StringTokenizer(paramValue, ";");
182	1	StringTokenizer st2;
183	1	String token = null, colour, residues;
184	1	try
185		{
186	6	while (st.hasMoreElements())
187		{
188	5	token = st.nextToken().trim();
189	5	residues = token.substring(0, token.indexOf("="));
190	5	colour = token.substring(token.indexOf("=") + 1);
191
192	5	st2 = new StringTokenizer(residues, " ,");
193	12	while (st2.hasMoreTokens())
194		{
195	7	String residue = st2.nextToken();
196
197	7	int colIndex = ResidueProperties.aaIndex[residue.charAt(0)];
198	7	if (colIndex == -1)
199		{
200	0	continue;
201		}
202
203	7	if (residue.equalsIgnoreCase("lowerCase"))
204		{
205	0	if (lowerCaseColours == null)
206		{
207	0	lowerCaseColours = new Color[colors.length];
208		}
209	0	for (int i = 0; i < lowerCaseColours.length; i++)
210		{
211	0	if (lowerCaseColours[i] == null)
212		{
213	0	lowerCaseColours[i] = ColorUtils.parseColourString(colour);
214		}
215		}
216
217	0	continue;
218		}
219
220	7	if (residue.equals(residue.toLowerCase(Locale.ROOT)))
221		{
222	1	if (lowerCaseColours == null)
223		{
224	1	lowerCaseColours = new Color[colors.length];
225		}
226	1	lowerCaseColours[colIndex] = ColorUtils
227		.parseColourString(colour);
228		}
229		else
230		{
231	6	colors[colIndex] = ColorUtils.parseColourString(colour);
232		}
233		}
234		}
235		} catch (Exception ex)
236		{
237	0	jalview.bin.Console.outPrintln(
238		"Error parsing userDefinedColours:\n" + token + "\n" + ex);
239		}
240
241		}
242
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
243	0	public void setLowerCaseColours(Color[] lcolours)...
244		{
245	0	lowerCaseColours = lcolours;
246		}
247
248		/**
249		* Returns the colour for the given residue character. If the residue is
250		* lower-case, and there is a specific colour defined for lower case, that
251		* colour is returned, else the colour for the upper case residue.
252		*/
		100% Uncovered Elements: 0 (9) Complexity: 5 Complexity Density: 1
253	29	@Override...
254		public Color findColour(char c)
255		{
256	29	if ('a' <= c && c <= 'z' && lowerCaseColours != null)
257		{
258	2	Color colour = lowerCaseColours[symbolIndex[c]];
259	2	if (colour != null)
260		{
261	1	return colour;
262		}
263		}
264	28	return super.findColour(c);
265		}
266
267		/**
268		* Answers the customised name of the colour scheme, if it has one, else "User
269		* Defined"
270		*/
		100% Uncovered Elements: 0 (5) Complexity: 3 Complexity Density: 1
271	4	@Override...
272		public String getSchemeName()
273		{
274	4	if (schemeName != null && schemeName.length() > 0)
275		{
276	1	return schemeName;
277		}
278	3	return ResidueColourScheme.USER_DEFINED;
279		}
280
281		/**
282		* Generate an applet colour parameter like A,C,D=12ffe9;Q,W=2393fd;w=9178dd
283		*
284		* @return
285		*/
		0% Uncovered Elements: 45 (45) Complexity: 10 Complexity Density: 0.32
286	0	public String toAppletParameter()...
287		{
288		/*
289		* step 1: build a map from colours to the symbol(s) that have the colour
290		*/
291	0	Map<Color, List<String>> colours = new HashMap<>();
292
293	0	for (char symbol = 'A'; symbol <= 'Z'; symbol++)
294		{
295	0	String residue = String.valueOf(symbol);
296	0	int index = symbolIndex[symbol];
297	0	Color c = colors[index];
298	0	if (c != null && !c.equals(Color.white))
299		{
300	0	if (colours.get(c) == null)
301		{
302	0	colours.put(c, new ArrayList<String>());
303		}
304	0	colours.get(c).add(residue);
305		}
306	0	if (lowerCaseColours != null)
307		{
308	0	c = lowerCaseColours[index];
309	0	if (c != null && !c.equals(Color.white))
310		{
311	0	residue = residue.toLowerCase(Locale.ROOT);
312	0	if (colours.get(c) == null)
313		{
314	0	colours.put(c, new ArrayList<String>());
315		}
316	0	colours.get(c).add(residue);
317		}
318		}
319		}
320
321		/*
322		* step 2: make a list of { A,G,R=12f9d6 } residues/colour specs
323		*/
324	0	List<String> residueColours = new ArrayList<>();
325	0	for (Entry<Color, List<String>> cols : colours.entrySet())
326		{
327	0	boolean first = true;
328	0	StringBuilder sb = new StringBuilder();
329	0	for (String residue : cols.getValue())
330		{
331	0	if (!first)
332		{
333	0	sb.append(",");
334		}
335	0	sb.append(residue);
336	0	first = false;
337		}
338	0	sb.append("=");
339		/*
340		* get color as hex value, dropping the alpha (ff) part
341		*/
342	0	String hexString = Integer.toHexString(cols.getKey().getRGB())
343		.substring(2);
344	0	sb.append(hexString);
345	0	residueColours.add(sb.toString());
346		}
347
348		/*
349		* sort and output
350		*/
351	0	Collections.sort(residueColours);
352	0	return StringUtils.listToDelimitedString(residueColours, ";");
353		}
354
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
355	4	@Override...
356		public boolean hasGapColour()
357		{
358	4	return (findColour(' ') != null);
359		}
360		}