Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
ColourSchemeMapper	41	54	28	43	0.3064516230.6%	Show methods

Class ColourSchemeMapper

Class ColourSchemeMapper	Line # 41	Total Statements 54	Complexity 28	Uncovered Elements 43	TOTAL Coverage 0.3064516230.6%
<clinit>, line 46()   <clinit>, line 46()	4646	12.012	1.01	0.00	1.0 1.0100%
getJalviewColourScheme(String,AnnotatedCollectionI) : ColourSchemeI   getJalviewColourScheme(String,AnnotatedCollectionI) : ColourSchemeI	6262	42.042	27.027	43.043	0.104166664 0.10416666410.4%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.09677419	jalview.io.JSONFileTest.testBioJSONRoundTripWithColourSchemeNonejalview.io.JSONFileTest.testBioJSONRoundTripWithColourSchemeNone	1PASS
	0.06451613	jalview.io.JSONFileTest.testGrpParsed_colourNonejalview.io.JSONFileTest.testGrpParsed_colourNone	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.json.binding.biojson.v1;
22
23		import jalview.datamodel.AnnotatedCollectionI;
24		import jalview.schemes.Blosum62ColourScheme;
25		import jalview.schemes.BuriedColourScheme;
26		import jalview.schemes.ClustalxColourScheme;
27		import jalview.schemes.ColourSchemeI;
28		import jalview.schemes.HelixColourScheme;
29		import jalview.schemes.HydrophobicColourScheme;
30		import jalview.schemes.NucleotideColourScheme;
31		import jalview.schemes.PIDColourScheme;
32		import jalview.schemes.PurinePyrimidineColourScheme;
33		import jalview.schemes.RNAHelicesColour;
34		import jalview.schemes.RNAInteractionColourScheme;
35		import jalview.schemes.StrandColourScheme;
36		import jalview.schemes.TCoffeeColourScheme;
37		import jalview.schemes.TaylorColourScheme;
38		import jalview.schemes.TurnColourScheme;
39		import jalview.schemes.ZappoColourScheme;
40
		30.6% Uncovered Elements: 43 (62) Complexity: 28 Complexity Density: 0.52
41		public class ColourSchemeMapper
42		{
43		private static ColourSchemeI csZappo, csTaylor, csNucleotide, csPurine,
44		csHelix, csTurn, csStrand, csBuried, csHydro,
45		csRNAInteractionType, csPID, csBlosum62 = null;
		100% Uncovered Elements: 0 (12) Complexity: 1 Complexity Density: 0.08
46	1	static...
47		{
48	1	csZappo = new ZappoColourScheme();
49	1	csTaylor = new TaylorColourScheme();
50	1	csNucleotide = new NucleotideColourScheme();
51	1	csPurine = new PurinePyrimidineColourScheme();
52	1	csHelix = new HelixColourScheme();
53	1	csTurn = new TurnColourScheme();
54	1	csStrand = new StrandColourScheme();
55	1	csBuried = new BuriedColourScheme();
56	1	csHydro = new HydrophobicColourScheme();
57	1	csRNAInteractionType = new RNAInteractionColourScheme();
58	1	csPID = new PIDColourScheme();
59	1	csBlosum62 = new Blosum62ColourScheme();
60		}
61
		10.4% Uncovered Elements: 43 (48) Complexity: 27 Complexity Density: 0.64
62	8	public static ColourSchemeI getJalviewColourScheme(...
63		String colourSchemeName, AnnotatedCollectionI annotCol)
64		{
65	8	switch (colourSchemeName.toUpperCase())
66		{
67	6	case "ZAPPO":
68	6	return csZappo;
69	0	case "TAYLOR":
70	0	return csTaylor;
71	0	case "NUCLEOTIDE":
72	0	return csNucleotide;
73	0	case "PURINE":
74	0	case "PURINE/PYRIMIDINE":
75	0	return csPurine;
76	0	case "HELIX":
77	0	case "HELIX PROPENSITY":
78	0	return csHelix;
79	0	case "TURN":
80	0	case "TURN PROPENSITY":
81	0	return csTurn;
82	0	case "STRAND":
83	0	case "STRAND PROPENSITY":
84	0	return csStrand;
85	0	case "BURIED":
86	0	case "BURIED INDEX":
87	0	return csBuried;
88	0	case "HYDRO":
89	0	case "HYDROPHOBIC":
90	0	return csHydro;
91	0	case "RNA INTERACTION TYPE":
92	0	return csRNAInteractionType;
93	0	case "PID":
94	0	case "% IDENTITY":
95	0	return csPID;
96	0	case "BLOSUM62":
97	0	return csBlosum62;
98	0	case "T-COFFEE SCORES":
99	0	return (annotCol != null) ? new TCoffeeColourScheme(annotCol) : null;
100	0	case "RNA HELICES":
101	0	return (annotCol != null) ? new RNAHelicesColour(annotCol) : null;
102	0	case "CLUSTAL":
103	0	return (annotCol != null) ? new ClustalxColourScheme(annotCol, null)
104		: null;
105	0	case "USER DEFINED":
106	0	return null;
107	2	default:
108	2	return null;
109		}
110		}
111		}