Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ColourSchemeMapper	43	54	28	0.00%	Show methods

Class ColourSchemeMapper

Class ColourSchemeMapper	Line # 43	Total Statements 54	Complexity 28	TOTAL Coverage 0.00%
<clinit>, line 48()   <clinit>, line 48()	4848	12.012	1.01	0.0 0.00%
getJalviewColourScheme(String,AnnotatedCollectionI) : ColourSchemeI   getJalviewColourScheme(String,AnnotatedCollectionI) : ColourSchemeI	6464	42.042	27.027	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.json.binding.biojson.v1;
22
23		import java.util.Locale;
24
25		import jalview.datamodel.AnnotatedCollectionI;
26		import jalview.schemes.Blosum62ColourScheme;
27		import jalview.schemes.BuriedColourScheme;
28		import jalview.schemes.ClustalxColourScheme;
29		import jalview.schemes.ColourSchemeI;
30		import jalview.schemes.HelixColourScheme;
31		import jalview.schemes.HydrophobicColourScheme;
32		import jalview.schemes.NucleotideColourScheme;
33		import jalview.schemes.PIDColourScheme;
34		import jalview.schemes.PurinePyrimidineColourScheme;
35		import jalview.schemes.RNAHelicesColour;
36		import jalview.schemes.RNAInteractionColourScheme;
37		import jalview.schemes.StrandColourScheme;
38		import jalview.schemes.TCoffeeColourScheme;
39		import jalview.schemes.TaylorColourScheme;
40		import jalview.schemes.TurnColourScheme;
41		import jalview.schemes.ZappoColourScheme;
42
		0% Uncovered Elements: 62 (62) Complexity: 28 Complexity Density: 0.52
43		public class ColourSchemeMapper
44		{
45		private static ColourSchemeI csZappo, csTaylor, csNucleotide, csPurine,
46		csHelix, csTurn, csStrand, csBuried, csHydro,
47		csRNAInteractionType, csPID, csBlosum62 = null;
		0% Uncovered Elements: 12 (12) Complexity: 1 Complexity Density: 0.08
48	0	static...
49		{
50	0	csZappo = new ZappoColourScheme();
51	0	csTaylor = new TaylorColourScheme();
52	0	csNucleotide = new NucleotideColourScheme();
53	0	csPurine = new PurinePyrimidineColourScheme();
54	0	csHelix = new HelixColourScheme();
55	0	csTurn = new TurnColourScheme();
56	0	csStrand = new StrandColourScheme();
57	0	csBuried = new BuriedColourScheme();
58	0	csHydro = new HydrophobicColourScheme();
59	0	csRNAInteractionType = new RNAInteractionColourScheme();
60	0	csPID = new PIDColourScheme();
61	0	csBlosum62 = new Blosum62ColourScheme();
62		}
63
		0% Uncovered Elements: 48 (48) Complexity: 27 Complexity Density: 0.64
64	0	public static ColourSchemeI getJalviewColourScheme(...
65		String colourSchemeName, AnnotatedCollectionI annotCol)
66		{
67	0	switch (colourSchemeName.toUpperCase(Locale.ROOT))
68		{
69	0	case "ZAPPO":
70	0	return csZappo;
71	0	case "TAYLOR":
72	0	return csTaylor;
73	0	case "NUCLEOTIDE":
74	0	return csNucleotide;
75	0	case "PURINE":
76	0	case "PURINE/PYRIMIDINE":
77	0	return csPurine;
78	0	case "HELIX":
79	0	case "HELIX PROPENSITY":
80	0	return csHelix;
81	0	case "TURN":
82	0	case "TURN PROPENSITY":
83	0	return csTurn;
84	0	case "STRAND":
85	0	case "STRAND PROPENSITY":
86	0	return csStrand;
87	0	case "BURIED":
88	0	case "BURIED INDEX":
89	0	return csBuried;
90	0	case "HYDRO":
91	0	case "HYDROPHOBIC":
92	0	return csHydro;
93	0	case "RNA INTERACTION TYPE":
94	0	return csRNAInteractionType;
95	0	case "PID":
96	0	case "% IDENTITY":
97	0	return csPID;
98	0	case "BLOSUM62":
99	0	return csBlosum62;
100	0	case "T-COFFEE SCORES":
101	0	return (annotCol != null) ? new TCoffeeColourScheme(annotCol) : null;
102	0	case "RNA HELICES":
103	0	return (annotCol != null) ? new RNAHelicesColour(annotCol) : null;
104	0	case "CLUSTAL":
105	0	return (annotCol != null) ? new ClustalxColourScheme(annotCol, null)
106		: null;
107	0	case "USER DEFINED":
108	0	return null;
109	0	default:
110	0	return null;
111		}
112		}
113		}