Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
Blosum62ColourScheme	32	20	12	0.00%	Show methods

Class Blosum62ColourScheme

Class Blosum62ColourScheme	Line # 32	Total Statements 20	Complexity 12	TOTAL Coverage 0.00%
Blosum62ColourScheme()   Blosum62ColourScheme()	3838	1.01	1.01	0.0 0.00%
getInstance(AlignViewportI,AnnotatedCollectionI) : ColourSchemeI   getInstance(AlignViewportI,AnnotatedCollectionI) : ColourSchemeI	4747	1.01	1.01	0.0 0.00%
findColour(char,int,SequenceI,String,float) : Color   findColour(char,int,SequenceI,String,float) : Color	5454	15.015	7.07	0.0 0.00%
isPeptideSpecific() : boolean   isPeptideSpecific() : boolean	101101	1.01	1.01	0.0 0.00%
getSchemeName() : String   getSchemeName() : String	107107	1.01	1.01	0.0 0.00%
isSimple() : boolean   isSimple() : boolean	113113	1.01	1.01	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.schemes;
22
23		import jalview.analysis.scoremodels.ScoreModels;
24		import jalview.api.AlignViewportI;
25		import jalview.api.analysis.PairwiseScoreModelI;
26		import jalview.datamodel.AnnotatedCollectionI;
27		import jalview.datamodel.SequenceI;
28		import jalview.util.Comparison;
29
30		import java.awt.Color;
31
		0% Uncovered Elements: 34 (34) Complexity: 12 Complexity Density: 0.6
32		public class Blosum62ColourScheme extends ResidueColourScheme
33		{
34		private static final Color LIGHT_BLUE = new Color(204, 204, 255);
35
36		private static final Color DARK_BLUE = new Color(154, 154, 255);
37
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
38	0	public Blosum62ColourScheme()...
39		{
40	0	super();
41		}
42
43		/**
44		* Returns a new instance of this colour scheme with which the given data may
45		* be coloured
46		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
47	0	@Override...
48		public ColourSchemeI getInstance(AlignViewportI view,
49		AnnotatedCollectionI coll)
50		{
51	0	return new Blosum62ColourScheme();
52		}
53
		0% Uncovered Elements: 23 (23) Complexity: 7 Complexity Density: 0.47
54	0	@Override...
55		public Color findColour(char res, int j, SequenceI seq,
56		String consensusResidue, float pid)
57		{
58	0	PairwiseScoreModelI sm = ScoreModels.getInstance().getBlosum62();
59
60		/*
61		* compare as upper case; note consensusResidue is
62		* always computed as uppercase
63		*/
64	0	if ('a' <= res && res <= 'z')
65		{
66	0	res -= ('a' - 'A');
67		}
68
69	0	if (Comparison.isGap(res) || consensusResidue == null)
70		{
71	0	return Color.white;
72		}
73
74	0	Color colour;
75
76	0	if (consensusResidue.indexOf(res) > -1)
77		{
78	0	colour = DARK_BLUE;
79		}
80		else
81		{
82	0	float score = 0;
83
84	0	for (char consensus : consensusResidue.toCharArray())
85		{
86	0	score += sm.getPairwiseScore(consensus, res);
87		}
88
89	0	if (score > 0)
90		{
91	0	colour = LIGHT_BLUE;
92		}
93		else
94		{
95	0	colour = Color.white;
96		}
97		}
98	0	return colour;
99		}
100
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
101	0	@Override...
102		public boolean isPeptideSpecific()
103		{
104	0	return true;
105		}
106
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
107	0	@Override...
108		public String getSchemeName()
109		{
110	0	return JalviewColourScheme.Blosum62.toString();
111		}
112
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
113	0	@Override...
114		public boolean isSimple()
115		{
116	0	return false;
117		}
118		}