Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
CovariationColourScheme	39	19	11	34	0.00%	Show methods

Class CovariationColourScheme

Class CovariationColourScheme	Line # 39	Total Statements 19	Complexity 11	Uncovered Elements 34	TOTAL Coverage 0.00%
getInstance(AnnotatedCollectionI,Map<SequenceI, SequenceCollectionI>) : ColourSchemeI   getInstance(AnnotatedCollectionI,Map<SequenceI, SequenceCollectionI>) : ColourSchemeI	5353	1.01	1.01	1.01	0.0 0.00%
CovariationColourScheme(AlignmentAnnotation)   CovariationColourScheme(AlignmentAnnotation)	6363	8.08	4.04	14.014	0.0 0.00%
findColour(char) : Color   findColour(char) : Color	105105	1.01	1.01	1.01	0.0 0.00%
findColour(char,int) : Color   findColour(char,int) : Color	124124	6.06	2.02	8.08	0.0 0.00%
isNucleotideSpecific() : boolean   isNucleotideSpecific() : boolean	142142	1.01	1.01	1.01	0.0 0.00%
getSchemeName() : String   getSchemeName() : String	148148	1.01	1.01	1.01	0.0 0.00%
isSimple() : boolean   isSimple() : boolean	154154	1.01	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.datamodel.AlignmentAnnotation;
24		import jalview.datamodel.AnnotatedCollectionI;
25		import jalview.datamodel.SequenceCollectionI;
26		import jalview.datamodel.SequenceI;
27		import jalview.util.ColorUtils;
28
29		import java.awt.Color;
30		import java.util.Hashtable;
31		import java.util.Map;
32
33		/**
34		* Became RNAHelicesColour.java. Placeholder for true covariation color scheme
35		*
36		* @author Lauren Michelle Lui
37		* @version 2.5
38		*/
		0% Uncovered Elements: 34 (34) Complexity: 11 Complexity Density: 0.58
39		public class CovariationColourScheme extends ResidueColourScheme
40		{
41		public Map<String, Color> helixcolorhash = new Hashtable<String, Color>();
42
43		public Map<Integer, String> positionsToHelix = new Hashtable<Integer, String>();
44
45		int numHelix = 0;
46
47		public AlignmentAnnotation annotation;
48
49		/**
50		* Returns a new instance of this colour scheme with which the given data may
51		* be coloured
52		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
53	0	@Override...
54		public ColourSchemeI getInstance(AnnotatedCollectionI coll,
55		Map<SequenceI, SequenceCollectionI> hrs)
56		{
57	0	return new CovariationColourScheme(coll.getAlignmentAnnotation()[0]);
58		}
59
60		/**
61		* Creates a new CovariationColourScheme object.
62		*/
		0% Uncovered Elements: 14 (14) Complexity: 4 Complexity Density: 0.5
63	0	public CovariationColourScheme(AlignmentAnnotation annotation)...
64		{
65	0	this.annotation = annotation;
66
67	0	for (int x = 0; x < this.annotation._rnasecstr.length; x++)
68		{
69		// System.out.println(this.annotation._rnasecstr[x] + " Begin" +
70		// this.annotation._rnasecstr[x].getBegin());
71		// System.out.println(this.annotation._rnasecstr[x].getFeatureGroup());
72		// pairs.put(this.annotation._rnasecstr[x].getBegin(),
73		// this.annotation._rnasecstr[x].getEnd());
74
75	0	positionsToHelix.put(this.annotation._rnasecstr[x].getBegin(),
76		this.annotation._rnasecstr[x].getFeatureGroup());
77	0	positionsToHelix.put(this.annotation._rnasecstr[x].getEnd(),
78		this.annotation._rnasecstr[x].getFeatureGroup());
79
80	0	if (Integer.parseInt(
81		this.annotation._rnasecstr[x].getFeatureGroup()) > numHelix)
82		{
83	0	numHelix = Integer
84		.parseInt(this.annotation._rnasecstr[x].getFeatureGroup());
85		}
86
87		}
88
89	0	for (int j = 0; j <= numHelix; j++)
90		{
91	0	helixcolorhash.put(String.valueOf(j),
92		ColorUtils.generateRandomColor(Color.white));
93		}
94
95		}
96
97		/**
98		* DOCUMENT ME!
99		*
100		* @param n
101		* DOCUMENT ME!
102		*
103		* @return DOCUMENT ME!
104		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
105	0	@Override...
106		public Color findColour(char c)
107		{
108		// System.out.println("called"); log.debug
109		// Generate a random pastel color
110
111	0	return ResidueProperties.purinepyrimidine[ResidueProperties.purinepyrimidineIndex[c]];// jalview.util.ColorUtils.generateRandomColor(Color.white);
112		}
113
114		/**
115		* DOCUMENT ME!
116		*
117		* @param n
118		* DOCUMENT ME!
119		* @param j
120		* DOCUMENT ME!
121		*
122		* @return DOCUMENT ME!
123		*/
		0% Uncovered Elements: 8 (8) Complexity: 2 Complexity Density: 0.33
124	0	public Color findColour(char c, int j)...
125		{
126	0	Color currentColour = Color.white;
127	0	String currentHelix = null;
128		// System.out.println(c + " " + j);
129	0	currentHelix = positionsToHelix.get(j);
130		// System.out.println(positionsToHelix.get(j));
131
132	0	if (currentHelix != null)
133		{
134	0	currentColour = helixcolorhash.get(currentHelix);
135		}
136
137		// System.out.println(c + " " + j + " helix " + currentHelix + " " +
138		// currentColour);
139	0	return currentColour;
140		}
141
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
142	0	@Override...
143		public boolean isNucleotideSpecific()
144		{
145	0	return true;
146		}
147
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
148	0	@Override...
149		public String getSchemeName()
150		{
151	0	return "Covariation";
152		}
153
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
154	0	@Override...
155		public boolean isSimple()
156		{
157	0	return false;
158		}
159		}