Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ScoreColourScheme	36	19	9	0.00%	Show methods

Class ScoreColourScheme

Class ScoreColourScheme	Line # 36	Total Statements 19	Complexity 9	TOTAL Coverage 0.00%
ScoreColourScheme(int[],double[],double,double)   ScoreColourScheme(int[],double[],double,double)	5454	13.013	4.04	0.0 0.00%
findColour(char,int,SequenceI) : Color   findColour(char,int,SequenceI) : Color	8787	3.03	2.02	0.0 0.00%
makeColour(float) : Color   makeColour(float) : Color	105105	1.01	1.01	0.0 0.00%
getSchemeName() : String   getSchemeName() : String	110110	1.01	1.01	0.0 0.00%
getInstance(AlignViewportI,AnnotatedCollectionI) : ColourSchemeI   getInstance(AlignViewportI,AnnotatedCollectionI) : ColourSchemeI	120120	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.SequenceI;
26		import jalview.util.Comparison;
27
28		import java.awt.Color;
29
30		/**
31		* DOCUMENT ME!
32		*
33		* @author $author$
34		* @version $Revision$
35		*/
		0% Uncovered Elements: 32 (32) Complexity: 9 Complexity Density: 0.47
36		public class ScoreColourScheme extends ResidueColourScheme
37		{
38		public double min;
39
40		public double max;
41
42		public double[] scores;
43
44		/**
45		* Creates a new ScoreColourScheme object.
46		*
47		* @param scores
48		* DOCUMENT ME!
49		* @param min
50		* DOCUMENT ME!
51		* @param max
52		* DOCUMENT ME!
53		*/
		0% Uncovered Elements: 19 (19) Complexity: 4 Complexity Density: 0.31
54	0	public ScoreColourScheme(int symbolIndex[], double[] scores, double min,...
55		double max)
56		{
57	0	super(symbolIndex);
58
59	0	this.scores = scores;
60	0	this.min = min;
61	0	this.max = max;
62
63		// Make colours in constructor
64		// Why wasn't this done earlier?
65	0	int iSize = scores.length;
66	0	colors = new Color[scores.length];
67	0	for (int i = 0; i < iSize; i++)
68		{
69		/*
70		* scale score between min and max to the range 0.0 - 1.0
71		*/
72	0	float score = (float) (scores[i] - (float) min) / (float) (max - min);
73
74	0	if (score > 1.0f)
75		{
76	0	score = 1.0f;
77		}
78
79	0	if (score < 0.0f)
80		{
81	0	score = 0.0f;
82		}
83	0	colors[i] = makeColour(score);
84		}
85		}
86
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
87	0	@Override...
88		public Color findColour(char c, int j, SequenceI seq)
89		{
90	0	if (Comparison.isGap(c))
91		{
92	0	return Color.white;
93		}
94	0	return super.findColour(c);
95		}
96
97		/**
98		* DOCUMENT ME!
99		*
100		* @param c
101		* DOCUMENT ME!
102		*
103		* @return DOCUMENT ME!
104		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
105	0	public Color makeColour(float c)...
106		{
107	0	return new Color(c, (float) 0.0, (float) 1.0 - c);
108		}
109
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
110	0	@Override...
111		public String getSchemeName()
112		{
113	0	return "Score";
114		}
115
116		/**
117		* Returns a new instance of this colour scheme with which the given data may
118		* be coloured
119		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
120	0	@Override...
121		public ColourSchemeI getInstance(AlignViewportI view,
122		AnnotatedCollectionI coll)
123		{
124	0	return new ScoreColourScheme(symbolIndex, scores, min, max);
125		}
126		}