Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
CovariationColourScheme	39	22	12	0.00%	Show methods

Class CovariationColourScheme

Class CovariationColourScheme	Line # 39	Total Statements 22	Complexity 12	TOTAL Coverage 0.00%
getInstance(AlignViewportI,AnnotatedCollectionI) : ColourSchemeI   getInstance(AlignViewportI,AnnotatedCollectionI) : ColourSchemeI	5353	1.01	1.01	0.0 0.00%
CovariationColourScheme(AlignmentAnnotation)   CovariationColourScheme(AlignmentAnnotation)	6363	11.011	5.05	0.0 0.00%
findColour(char) : Color   findColour(char) : Color	110110	1.01	1.01	0.0 0.00%
findColour(char,int) : Color   findColour(char,int) : Color	129129	6.06	2.02	0.0 0.00%
isNucleotideSpecific() : boolean   isNucleotideSpecific() : boolean	148148	1.01	1.01	0.0 0.00%
getSchemeName() : String   getSchemeName() : String	154154	1.01	1.01	0.0 0.00%
isSimple() : boolean   isSimple() : boolean	160160	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.AlignmentAnnotation;
25		import jalview.datamodel.AnnotatedCollectionI;
26		import jalview.datamodel.SequenceFeature;
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: 39 (39) Complexity: 12 Complexity Density: 0.55
39		public class CovariationColourScheme extends ResidueColourScheme
40		{
41		public Map<String, Color> helixcolorhash = new Hashtable<>();
42
43		public Map<Integer, String> positionsToHelix = new Hashtable<>();
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(AlignViewportI view,
55		AnnotatedCollectionI coll)
56		{
57	0	return new CovariationColourScheme(coll.getAlignmentAnnotation()[0]);
58		}
59
60		/**
61		* Creates a new CovariationColourScheme object.
62		*/
		0% Uncovered Elements: 19 (19) Complexity: 5 Complexity Density: 0.45
63	0	public CovariationColourScheme(AlignmentAnnotation annotation)...
64		{
65	0	this.annotation = annotation;
66	0	SequenceFeature[] sf = annotation.getRnaSecondaryStructure();
67	0	if (sf==null)
68		{
69	0	return;
70		}
71	0	for (int x = 0; x < sf.length; x++)
72		{
73		// jalview.bin.Console.outPrintln(this.annotation._rnasecstr[x] + " Begin"
74		// +
75		// this.annotation._rnasecstr[x].getBegin());
76		// jalview.bin.Console.outPrintln(this.annotation._rnasecstr[x].getFeatureGroup());
77		// pairs.put(this.annotation._rnasecstr[x].getBegin(),
78		// this.annotation._rnasecstr[x].getEnd());
79
80	0	positionsToHelix.put(sf[x].getBegin(),
81		sf[x].getFeatureGroup());
82	0	positionsToHelix.put(sf[x].getEnd(),
83		sf[x].getFeatureGroup());
84
85	0	if (Integer.parseInt(
86		sf[x].getFeatureGroup()) > numHelix)
87		{
88	0	numHelix = Integer
89		.parseInt(sf[x].getFeatureGroup());
90		}
91
92		}
93
94	0	for (int j = 0; j <= numHelix; j++)
95		{
96	0	helixcolorhash.put(String.valueOf(j),
97		ColorUtils.generateRandomColor(Color.white));
98		}
99
100		}
101
102		/**
103		* DOCUMENT ME!
104		*
105		* @param n
106		* DOCUMENT ME!
107		*
108		* @return DOCUMENT ME!
109		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
110	0	@Override...
111		public Color findColour(char c)
112		{
113		// jalview.bin.Console.outPrintln("called"); log.debug
114		// Generate a random pastel color
115
116	0	return ResidueProperties.purinepyrimidine[ResidueProperties.purinepyrimidineIndex[c]];// jalview.util.ColorUtils.generateRandomColor(Color.white);
117		}
118
119		/**
120		* DOCUMENT ME!
121		*
122		* @param n
123		* DOCUMENT ME!
124		* @param j
125		* DOCUMENT ME!
126		*
127		* @return DOCUMENT ME!
128		*/
		0% Uncovered Elements: 8 (8) Complexity: 2 Complexity Density: 0.33
129	0	public Color findColour(char c, int j)...
130		{
131	0	Color currentColour = Color.white;
132	0	String currentHelix = null;
133		// jalview.bin.Console.outPrintln(c + " " + j);
134	0	currentHelix = positionsToHelix.get(j);
135		// jalview.bin.Console.outPrintln(positionsToHelix.get(j));
136
137	0	if (currentHelix != null)
138		{
139	0	currentColour = helixcolorhash.get(currentHelix);
140		}
141
142		// jalview.bin.Console.outPrintln(c + " " + j + " helix " + currentHelix + "
143		// " +
144		// currentColour);
145	0	return currentColour;
146		}
147
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
148	0	@Override...
149		public boolean isNucleotideSpecific()
150		{
151	0	return true;
152		}
153
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
154	0	@Override...
155		public String getSchemeName()
156		{
157	0	return "Covariation";
158		}
159
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
160	0	@Override...
161		public boolean isSimple()
162		{
163	0	return false;
164		}
165		}