Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
Constants	30	14	3	1.0100%	Show methods

Class Constants

Class Constants	Line # 30	Total Statements 14	Complexity 3	TOTAL Coverage 1.0100%
<clinit>, line 47()   <clinit>, line 47()	4747	2.02	1.01	1.0 1.0100%
<clinit>, line 68()   <clinit>, line 68()	6868	6.06	1.01	1.0 1.0100%
<clinit>, line 86()   <clinit>, line 86()	8686	6.06	1.01	1.0 1.0100%

 

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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.util;
22
23		import java.awt.Color;
24		import java.util.HashMap;
25		import java.util.Map;
26
27		/**
28		* A class to hold constants relating to Url links used in Jalview
29		*/
		100% Uncovered Elements: 0 (17) Complexity: 3 Complexity Density: 0.21
30		public class Constants
31		{
32
33		// character used to represent secondary structures
34		public static final char HELIX = 'H';
35
36		public static final char SHEET = 'E';
37
38		public static final char COIL = 'C';
39
40		// label in secondary structure annotation data model from 3d structures
41		public static final String SS_ANNOTATION_LABEL = "Secondary Structure";
42
43		// label in secondary structure annotation data model from JPred
44		public static final String SS_ANNOTATION_FROM_JPRED_LABEL = "jnetpred";
45
46		public static final Map<String, String> SECONDARY_STRUCTURE_LABELS = new HashMap<>();
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
47	54	static...
48		{
49	54	SECONDARY_STRUCTURE_LABELS.put(SS_ANNOTATION_LABEL, "3D Structures");
50	54	SECONDARY_STRUCTURE_LABELS.put(SS_ANNOTATION_FROM_JPRED_LABEL, "JPred");
51		// Add other secondary structure labels here if needed
52		}
53
54		public static final String SS_PROVIDER_PROPERTY = "SS_PROVIDER";
55
56		// generic secondary structure provider options
57		public static final String SS_ALL_PROVIDERS = "All";
58
59		public static final String SS_NONE_PROVIDER = "None";
60
61		// Secondary structure consensus label
62		public static final String SECONDARY_STRUCTURE_CONSENSUS_LABEL = "Secondary Structure Consensus";
63
64		// A map that stores abbreviations of structure providers as keys and their
65		// full names as values.
66		public static final Map<String, String> STRUCTURE_PROVIDERS = new HashMap<>();
67
		100% Uncovered Elements: 0 (6) Complexity: 1 Complexity Density: 0.17
68	54	static...
69		{
70	54	STRUCTURE_PROVIDERS.put("None", "No Secondary Structure");
71	54	STRUCTURE_PROVIDERS.put("AF", "AlphaFold DB");
72	54	STRUCTURE_PROVIDERS.put("SM", "SWISS-MODEL");
73	54	STRUCTURE_PROVIDERS.put("PDB", "PDB");
74	54	STRUCTURE_PROVIDERS.put("JP", "JPred");
75	54	STRUCTURE_PROVIDERS.put("AFill", "AlphaFill");
76		}
77
78		public static final Map<String, Color> STRUCTURE_PROVIDERS_COLOR = new HashMap<>();
79
80		public static final String CHAINID = "CHAINID"; // String used to save CHAINID as annot property
81
82		public static final String PDBID = "PDBID"; // String used to save PDBID as annot property
83
84		public static final String PDB = "PDB"; // String used for PDB provider
85
		100% Uncovered Elements: 0 (6) Complexity: 1 Complexity Density: 0.17
86	54	static...
87		{
88	54	STRUCTURE_PROVIDERS_COLOR.put("No Secondary Structure", Color.GRAY);
89	54	STRUCTURE_PROVIDERS_COLOR.put("AlphaFold DB", new Color(255, 0, 0));
90	54	STRUCTURE_PROVIDERS_COLOR.put("SWISS-MODEL", new Color(255, 165, 0));
91	54	STRUCTURE_PROVIDERS_COLOR.put("PDB", new Color(0, 128, 0));
92	54	STRUCTURE_PROVIDERS_COLOR.put("JPred", new Color(0, 0, 255));
93	54	STRUCTURE_PROVIDERS_COLOR.put("AlphaFill", Color.CYAN);
94		}
95		}