Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ColourSchemes	39	45	26	0.00%	Show methods

Class ColourSchemes

Class ColourSchemes	Line # 39	Total Statements 45	Complexity 26	TOTAL Coverage 0.00%
getInstance() : ColourSchemes   getInstance() : ColourSchemes	4747	1.01	1.01	0.0 0.00%
ColourSchemes()   ColourSchemes()	5252	1.01	1.01	0.0 0.00%
resetRnaHelicesShading() : void   resetRnaHelicesShading() : void	6565	1.01	1.01	0.0 0.00%
initRnaHelicesShading(int) : void   initRnaHelicesShading(int) : void	7070	12.012	5.05	0.0 0.00%
loadColourSchemes() : void   loadColourSchemes() : void	107107	7.07	3.03	0.0 0.00%
registerColourScheme(ColourSchemeI) : void   registerColourScheme(ColourSchemeI) : void	139139	8.08	3.03	0.0 0.00%
getColourSchemeShortName(ColourSchemeI) : String   getColourSchemeShortName(ColourSchemeI) : String	161161	1.01	1.01	0.0 0.00%
getColourSchemeShortName(String) : String   getColourSchemeShortName(String) : String	166166	3.03	2.02	0.0 0.00%
removeColourScheme(String) : void   removeColourScheme(String) : void	179179	2.02	2.02	0.0 0.00%
getColourScheme(String,AlignViewportI,AnnotatedCollectionI,Map<SequenceI, SequenceCollectionI>) : ColourSchemeI   getColourScheme(String,AlignViewportI,AnnotatedCollectionI,Map<SequenceI, SequenceCollectionI>) : ColourSchemeI	201201	4.04	3.03	0.0 0.00%
getColourScheme(String,AnnotatedCollectionI) : ColourSchemeI   getColourScheme(String,AnnotatedCollectionI) : ColourSchemeI	223223	1.01	1.01	0.0 0.00%
getColourSchemes() : Iterable<ColourSchemeI>   getColourSchemes() : Iterable<ColourSchemeI>	235235	1.01	1.01	0.0 0.00%
nameExists(String) : boolean   nameExists(String) : boolean	247247	3.03	2.02	0.0 0.00%

 

Contributing tests

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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.schemes;
22
23		import java.util.LinkedHashMap;
24		import java.util.Locale;
25		import java.util.Map;
26
27		import jalview.api.AlignViewportI;
28		import jalview.bin.ApplicationSingletonProvider;
29		import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
30		import jalview.datamodel.AnnotatedCollectionI;
31		import jalview.datamodel.SequenceCollectionI;
32		import jalview.datamodel.SequenceI;
33		import jalview.util.ColorUtils;
34
35		import java.awt.Color;
36		import java.util.LinkedHashMap;
37		import java.util.Map;
38
		0% Uncovered Elements: 78 (78) Complexity: 26 Complexity Density: 0.58
39		public class ColourSchemes implements ApplicationSingletonI
40		{
41
42		/**
43		* Returns the singleton instance of this class
44		*
45		* @return
46		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
47	0	public static ColourSchemes getInstance()...
48		{
49	0	return ApplicationSingletonProvider.getInstance(ColourSchemes.class);
50		}
51
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
52	0	private ColourSchemes()...
53		{
54	0	loadColourSchemes();
55		}
56
57		/**
58		* ColourSchemeProperty "static"
59		*/
60		public Color[] rnaHelices = null;
61
62		/**
63		* delete the existing cached RNA helices colours
64		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
65	0	public static void resetRnaHelicesShading()...
66		{
67	0	getInstance().rnaHelices = null;
68		}
69
		0% Uncovered Elements: 18 (18) Complexity: 5 Complexity Density: 0.42
70	0	public static void initRnaHelicesShading(int n)...
71		{
72	0	int i = 0;
73	0	ColourSchemes j = getInstance();
74
75	0	if (j.rnaHelices == null)
76		{
77	0	j.rnaHelices = new Color[n + 1];
78		}
79	0	else if (j.rnaHelices != null && j.rnaHelices.length <= n)
80		{
81	0	Color[] t = new Color[n + 1];
82	0	System.arraycopy(j.rnaHelices, 0, t, 0, j.rnaHelices.length);
83	0	i = j.rnaHelices.length;
84	0	j.rnaHelices = t;
85		}
86		else
87		{
88	0	return;
89		}
90		// Generate random colors and store
91	0	for (; i <= n; i++)
92		{
93	0	j.rnaHelices[i] = ColorUtils.generateRandomColor(Color.white);
94		}
95		}
96
97		/**
98		* a map from scheme name (lower-cased) to an instance of it
99		*/
100		private Map<String, ColourSchemeI> schemes;
101
102		/**
103		* Loads an instance of each standard or user-defined colour scheme
104		*
105		* @return
106		*/
		0% Uncovered Elements: 7 (7) Complexity: 3 Complexity Density: 0.43
107	0	void loadColourSchemes()...
108		{
109		/*
110		* store in an order-preserving map, so items can be added to menus
111		* in the order in which they are 'discovered'
112		*/
113	0	schemes = new LinkedHashMap<>();
114
115	0	for (JalviewColourScheme cs : JalviewColourScheme.values())
116		{
117	0	try
118		{
119	0	registerColourScheme(
120		cs.getSchemeClass().getDeclaredConstructor().newInstance());
121		} catch (InstantiationException | IllegalAccessException e)
122		{
123	0	jalview.bin.Console
124		.errPrintln("Error instantiating colour scheme for "
125		+ cs.toString() + " " + e.getMessage());
126	0	e.printStackTrace();
127		} catch (ReflectiveOperationException roe)
128		{
129	0	roe.printStackTrace();
130		}
131		}
132		}
133
134		/**
135		* Registers a colour scheme
136		*
137		* @param cs
138		*/
		0% Uncovered Elements: 12 (12) Complexity: 3 Complexity Density: 0.38
139	0	public void registerColourScheme(ColourSchemeI cs)...
140		{
141	0	String name = cs.getSchemeName();
142	0	if (name == null)
143		{
144	0	jalview.bin.Console.errPrintln("ColourScheme name may not be null");
145	0	return;
146		}
147
148		/*
149		* name is lower-case for non-case-sensitive lookup
150		* (name in the colour keeps its true case)
151		*/
152	0	String lower = getColourSchemeShortName(cs);
153	0	if (schemes.containsKey(lower))
154		{
155	0	System.err
156		.println("Warning: overwriting colour scheme named " + name);
157		}
158	0	schemes.put(lower, cs);
159		}
160
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
161	0	private String getColourSchemeShortName(ColourSchemeI cs)...
162		{
163	0	return getColourSchemeShortName(cs.getSchemeName());
164		}
165
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
166	0	private String getColourSchemeShortName(String name)...
167		{
168	0	if (name == null)
169	0	return null;
170	0	return name.toLowerCase(Locale.ROOT).replaceAll("%", "pc")
171		.replaceAll("[^a-z0-9]", "-").replaceAll("--+", "-");
172		}
173
174		/**
175		* Removes a colour scheme by name
176		*
177		* @param name
178		*/
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 1
179	0	public void removeColourScheme(String name)...
180		{
181	0	if (name != null)
182		{
183	0	schemes.remove(getColourSchemeShortName(name));
184		}
185		}
186
187		/**
188		* Returns an instance of the colour scheme with which the given view may be
189		* coloured
190		*
191		* @param name
192		* name of the colour scheme
193		* @param viewport
194		* @param forData
195		* the data to be coloured
196		* @param optional
197		* map from hidden representative sequences to the sequences they
198		* represent
199		* @return
200		*/
		0% Uncovered Elements: 8 (8) Complexity: 3 Complexity Density: 0.75
201	0	public ColourSchemeI getColourScheme(String name, AlignViewportI viewport,...
202		AnnotatedCollectionI forData,
203		Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
204		{
205	0	if (name == null)
206		{
207	0	return null;
208		}
209	0	ColourSchemeI cs = schemes.get(getColourSchemeShortName(name));
210	0	return cs == null ? null : cs.getInstance(viewport, forData);
211		}
212
213		/**
214		* Returns an instance of the colour scheme with which the given view may be
215		* coloured
216		*
217		* @param name
218		* name of the colour scheme
219		* @param forData
220		* the data to be coloured
221		* @return
222		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
223	0	public ColourSchemeI getColourScheme(String name,...
224		AnnotatedCollectionI forData)
225		{
226	0	return getColourScheme(name, null, forData, null);
227		}
228
229		/**
230		* Returns an iterable set of the colour schemes, in the order in which they
231		* were added
232		*
233		* @return
234		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
235	0	public Iterable<ColourSchemeI> getColourSchemes()...
236		{
237	0	return schemes.values();
238		}
239
240		/**
241		* Answers true if there is a scheme with the given name, else false. The test
242		* is not case-sensitive.
243		*
244		* @param name
245		* @return
246		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
247	0	public boolean nameExists(String name)...
248		{
249	0	if (name == null)
250		{
251	0	return false;
252		}
253	0	return schemes.containsKey(getColourSchemeShortName(name));
254		}
255		}