Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ColourSchemes	32	32	20	0.00%	Show methods

Class ColourSchemes

Class ColourSchemes	Line # 32	Total Statements 32	Complexity 20	TOTAL Coverage 0.00%
getInstance() : ColourSchemes   getInstance() : ColourSchemes	4949	1.01	1.01	0.0 0.00%
ColourSchemes()   ColourSchemes()	5454	1.01	1.01	0.0 0.00%
loadColourSchemes() : void   loadColourSchemes() : void	6464	7.07	3.03	0.0 0.00%
registerColourScheme(ColourSchemeI) : void   registerColourScheme(ColourSchemeI) : void	9696	8.08	3.03	0.0 0.00%
getColourSchemeShortName(ColourSchemeI) : String   getColourSchemeShortName(ColourSchemeI) : String	118118	1.01	1.01	0.0 0.00%
getColourSchemeShortName(String) : String   getColourSchemeShortName(String) : String	123123	3.03	2.02	0.0 0.00%
removeColourScheme(String) : void   removeColourScheme(String) : void	136136	2.02	2.02	0.0 0.00%
getColourScheme(String,AlignViewportI,AnnotatedCollectionI,Map<SequenceI, SequenceCollectionI>) : ColourSchemeI   getColourScheme(String,AlignViewportI,AnnotatedCollectionI,Map<SequenceI, SequenceCollectionI>) : ColourSchemeI	158158	4.04	3.03	0.0 0.00%
getColourScheme(String,AnnotatedCollectionI) : ColourSchemeI   getColourScheme(String,AnnotatedCollectionI) : ColourSchemeI	180180	1.01	1.01	0.0 0.00%
getColourSchemes() : Iterable<ColourSchemeI>   getColourSchemes() : Iterable<ColourSchemeI>	192192	1.01	1.01	0.0 0.00%
nameExists(String) : boolean   nameExists(String) : boolean	204204	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.datamodel.AnnotatedCollectionI;
29		import jalview.datamodel.SequenceCollectionI;
30		import jalview.datamodel.SequenceI;
31
		0% Uncovered Elements: 57 (57) Complexity: 20 Complexity Density: 0.62
32		public class ColourSchemes
33		{
34		/*
35		* singleton instance of this class
36		*/
37		private static ColourSchemes instance = new ColourSchemes();
38
39		/*
40		* a map from scheme name (lower-cased) to an instance of it
41		*/
42		private Map<String, ColourSchemeI> schemes;
43
44		/**
45		* Returns the singleton instance of this class
46		*
47		* @return
48		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
49	0	public static ColourSchemes getInstance()...
50		{
51	0	return instance;
52		}
53
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
54	0	private ColourSchemes()...
55		{
56	0	loadColourSchemes();
57		}
58
59		/**
60		* Loads an instance of each standard or user-defined colour scheme
61		*
62		* @return
63		*/
		0% Uncovered Elements: 7 (7) Complexity: 3 Complexity Density: 0.43
64	0	void loadColourSchemes()...
65		{
66		/*
67		* store in an order-preserving map, so items can be added to menus
68		* in the order in which they are 'discovered'
69		*/
70	0	schemes = new LinkedHashMap<>();
71
72	0	for (JalviewColourScheme cs : JalviewColourScheme.values())
73		{
74	0	try
75		{
76	0	registerColourScheme(
77		cs.getSchemeClass().getDeclaredConstructor().newInstance());
78		} catch (InstantiationException | IllegalAccessException e)
79		{
80	0	jalview.bin.Console
81		.errPrintln("Error instantiating colour scheme for "
82		+ cs.toString() + " " + e.getMessage());
83	0	e.printStackTrace();
84		} catch (ReflectiveOperationException roe)
85		{
86	0	roe.printStackTrace();
87		}
88		}
89		}
90
91		/**
92		* Registers a colour scheme
93		*
94		* @param cs
95		*/
		0% Uncovered Elements: 12 (12) Complexity: 3 Complexity Density: 0.38
96	0	public void registerColourScheme(ColourSchemeI cs)...
97		{
98	0	String name = cs.getSchemeName();
99	0	if (name == null)
100		{
101	0	jalview.bin.Console.errPrintln("ColourScheme name may not be null");
102	0	return;
103		}
104
105		/*
106		* name is lower-case for non-case-sensitive lookup
107		* (name in the colour keeps its true case)
108		*/
109	0	String lower = getColourSchemeShortName(cs);
110	0	if (schemes.containsKey(lower))
111		{
112	0	System.err
113		.println("Warning: overwriting colour scheme named " + name);
114		}
115	0	schemes.put(lower, cs);
116		}
117
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
118	0	private String getColourSchemeShortName(ColourSchemeI cs)...
119		{
120	0	return getColourSchemeShortName(cs.getSchemeName());
121		}
122
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
123	0	private String getColourSchemeShortName(String name)...
124		{
125	0	if (name == null)
126	0	return null;
127	0	return name.toLowerCase(Locale.ROOT).replaceAll("%", "pc")
128		.replaceAll("[^a-z0-9]", "-").replaceAll("--+", "-");
129		}
130
131		/**
132		* Removes a colour scheme by name
133		*
134		* @param name
135		*/
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 1
136	0	public void removeColourScheme(String name)...
137		{
138	0	if (name != null)
139		{
140	0	schemes.remove(getColourSchemeShortName(name));
141		}
142		}
143
144		/**
145		* Returns an instance of the colour scheme with which the given view may be
146		* coloured
147		*
148		* @param name
149		* name of the colour scheme
150		* @param viewport
151		* @param forData
152		* the data to be coloured
153		* @param optional
154		* map from hidden representative sequences to the sequences they
155		* represent
156		* @return
157		*/
		0% Uncovered Elements: 8 (8) Complexity: 3 Complexity Density: 0.75
158	0	public ColourSchemeI getColourScheme(String name, AlignViewportI viewport,...
159		AnnotatedCollectionI forData,
160		Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
161		{
162	0	if (name == null)
163		{
164	0	return null;
165		}
166	0	ColourSchemeI cs = schemes.get(getColourSchemeShortName(name));
167	0	return cs == null ? null : cs.getInstance(viewport, forData);
168		}
169
170		/**
171		* Returns an instance of the colour scheme with which the given view may be
172		* coloured
173		*
174		* @param name
175		* name of the colour scheme
176		* @param forData
177		* the data to be coloured
178		* @return
179		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
180	0	public ColourSchemeI getColourScheme(String name,...
181		AnnotatedCollectionI forData)
182		{
183	0	return getColourScheme(name, null, forData, null);
184		}
185
186		/**
187		* Returns an iterable set of the colour schemes, in the order in which they
188		* were added
189		*
190		* @return
191		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
192	0	public Iterable<ColourSchemeI> getColourSchemes()...
193		{
194	0	return schemes.values();
195		}
196
197		/**
198		* Answers true if there is a scheme with the given name, else false. The test
199		* is not case-sensitive.
200		*
201		* @param name
202		* @return
203		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
204	0	public boolean nameExists(String name)...
205		{
206	0	if (name == null)
207		{
208	0	return false;
209		}
210	0	return schemes.containsKey(getColourSchemeShortName(name));
211		}
212		}