Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
PIDColourScheme	31	15	12	0.00%	Show methods

Class PIDColourScheme

Class PIDColourScheme	Line # 31	Total Statements 15	Complexity 12	TOTAL Coverage 0.00%
PIDColourScheme()   PIDColourScheme()	4040	0.00	1.01	-1.0 -1.0 -
findColour(char,int,SequenceI,String,float) : Color   findColour(char,int,SequenceI,String,float) : Color	4444	12.012	8.08	0.0 0.00%
getSchemeName() : String   getSchemeName() : String	8383	1.01	1.01	0.0 0.00%
getInstance(AlignViewportI,AnnotatedCollectionI) : ColourSchemeI   getInstance(AlignViewportI,AnnotatedCollectionI) : ColourSchemeI	9393	1.01	1.01	0.0 0.00%
isSimple() : boolean   isSimple() : boolean	100100	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.api.AlignViewportI;
24		import jalview.datamodel.AnnotatedCollectionI;
25		import jalview.datamodel.SequenceGroup;
26		import jalview.datamodel.SequenceI;
27		import jalview.util.Comparison;
28
29		import java.awt.Color;
30
		0% Uncovered Elements: 30 (30) Complexity: 12 Complexity Density: 0.8
31		public class PIDColourScheme extends ResidueColourScheme
32		{
33		private static final Color[] pidColours = { new Color(100, 100, 255),
34		new Color(153, 153, 255), new Color(204, 204, 255), };
35
36		private static final float[] thresholds = { 80, 60, 40, };
37
38		SequenceGroup group;
39
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
40	0	public PIDColourScheme()...
41		{
42		}
43
		0% Uncovered Elements: 22 (22) Complexity: 8 Complexity Density: 0.67
44	0	@Override...
45		public Color findColour(char c, int j, SequenceI seq,
46		String consensusResidue, float pid)
47		{
48		/*
49		* compare as upper case; note consensusResidue is
50		* always computed as uppercase
51		*/
52	0	if ('a' <= c && c <= 'z')
53		{
54	0	c -= ('a' - 'A');
55		}
56
57	0	if (consensusResidue == null || Comparison.isGap(c))
58		{
59	0	return Color.white;
60		}
61
62	0	Color colour = Color.white;
63
64		/*
65		* test whether this is the consensus (or joint consensus) residue
66		*/
67	0	boolean matchesConsensus = consensusResidue.contains(String.valueOf(c));
68	0	if (matchesConsensus)
69		{
70	0	for (int i = 0; i < thresholds.length; i++)
71		{
72	0	if (pid > thresholds[i])
73		{
74	0	colour = pidColours[i];
75	0	break;
76		}
77		}
78		}
79
80	0	return colour;
81		}
82
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
83	0	@Override...
84		public String getSchemeName()
85		{
86	0	return JalviewColourScheme.PID.toString();
87		}
88
89		/**
90		* Returns a new instance of this colour scheme with which the given data may
91		* be coloured
92		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
93	0	@Override...
94		public ColourSchemeI getInstance(AlignViewportI view,
95		AnnotatedCollectionI coll)
96		{
97	0	return new PIDColourScheme();
98		}
99
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
100	0	@Override...
101		public boolean isSimple()
102		{
103	0	return false;
104		}
105		}