Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
TCoffeeColourScheme	47	33	20	0.00%	Show methods

Class TCoffeeColourScheme

Class TCoffeeColourScheme	Line # 47	Total Statements 33	Complexity 20	TOTAL Coverage 0.00%
TCoffeeColourScheme()   TCoffeeColourScheme()	5454	0.00	1.01	-1.0 -1.0 -
TCoffeeColourScheme(AnnotatedCollectionI)   TCoffeeColourScheme(AnnotatedCollectionI)	6666	1.01	1.01	0.0 0.00%
alignmentChanged(AnnotatedCollectionI,Map<SequenceI, SequenceCollectionI>) : void   alignmentChanged(AnnotatedCollectionI,Map<SequenceI, SequenceCollectionI>) : void	7878	16.016	7.07	0.0 0.00%
findColour(char,int,SequenceI) : Color   findColour(char,int,SequenceI) : Color	124124	8.08	5.05	0.0 0.00%
getInstance(AlignViewportI,AnnotatedCollectionI) : ColourSchemeI   getInstance(AlignViewportI,AnnotatedCollectionI) : ColourSchemeI	146146	1.01	1.01	0.0 0.00%
isApplicableTo(AnnotatedCollectionI) : boolean   isApplicableTo(AnnotatedCollectionI) : boolean	156156	5.05	3.03	0.0 0.00%
getSchemeName() : String   getSchemeName() : String	170170	1.01	1.01	0.0 0.00%
isSimple() : boolean   isSimple() : boolean	176176	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.AlignmentI;
26		import jalview.datamodel.AnnotatedCollectionI;
27		import jalview.datamodel.Annotation;
28		import jalview.datamodel.SequenceCollectionI;
29		import jalview.datamodel.SequenceI;
30		import jalview.io.TCoffeeScoreFile;
31
32		import java.awt.Color;
33		import java.util.ArrayList;
34		import java.util.IdentityHashMap;
35		import java.util.List;
36		import java.util.Map;
37
38		/**
39		* Defines the color score for T-Coffee MSA
40		* <p>
41		* See http://tcoffee.org
42		*
43		*
44		* @author Paolo Di Tommaso
45		*
46		*/
		0% Uncovered Elements: 61 (61) Complexity: 20 Complexity Density: 0.61
47		public class TCoffeeColourScheme extends ResidueColourScheme
48		{
49		IdentityHashMap<SequenceI, Color[]> seqMap;
50
51		/**
52		* Default constructor (required for Class.newInstance())
53		*/
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
54	0	public TCoffeeColourScheme()...
55		{
56
57		}
58
59		/**
60		* the color scheme needs to look at the alignment to get and cache T-COFFEE
61		* scores
62		*
63		* @param alignment
64		* - annotated sequences to be searched
65		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
66	0	public TCoffeeColourScheme(AnnotatedCollectionI alignment)...
67		{
68	0	alignmentChanged(alignment, null);
69		}
70
71		/**
72		* Finds the TCoffeeScore annotation (if any) for each sequence and notes the
73		* annotation colour for each column position. The colours are fixed for
74		* scores 0-9 and are set when annotation is parsed.
75		*
76		* @see TCoffeeScoreFile#annotateAlignment(AlignmentI, boolean)
77		*/
		0% Uncovered Elements: 26 (26) Complexity: 7 Complexity Density: 0.44
78	0	@Override...
79		public void alignmentChanged(AnnotatedCollectionI alignment,
80		Map<SequenceI, SequenceCollectionI> hiddenReps)
81		{
82		// TODO: if sequences have been represented and they have scores, could
83		// compute an average sequence score for the representative
84
85		// assume only one set of TCOFFEE scores - but could have more than one
86		// potentially.
87	0	List<AlignmentAnnotation> annots = new ArrayList<>();
88		// Search alignment to get all tcoffee annotation and pick one set of
89		// annotation to use to colour seqs.
90	0	seqMap = new IdentityHashMap<>();
91	0	AnnotatedCollectionI alcontext = alignment instanceof AlignmentI
92		? alignment
93		: alignment.getContext();
94	0	if (alcontext == null)
95		{
96	0	return;
97		}
98	0	int w = 0;
99	0	for (AlignmentAnnotation al : alcontext
100		.findAnnotation(TCoffeeScoreFile.TCOFFEE_SCORE))
101		{
102	0	if (al.sequenceRef != null && !al.belowAlignment)
103		{
104	0	annots.add(al);
105	0	if (w < al.annotations.length)
106		{
107	0	w = al.annotations.length;
108		}
109	0	Color[] scores = new Color[al.annotations.length];
110	0	int i = 0;
111	0	for (Annotation an : al.annotations)
112		{
113	0	scores[i++] = (an != null) ? an.colour : Color.white;
114		}
115	0	seqMap.put(al.sequenceRef, scores);
116		}
117		}
118		// TODO: compute average colour for each symbol type in each column - gives
119		// a second order colourscheme for colouring a sequence logo derived from
120		// the alignment (colour reflects quality of alignment for each residue
121		// class)
122		}
123
		0% Uncovered Elements: 14 (14) Complexity: 5 Complexity Density: 0.62
124	0	@Override...
125		public Color findColour(char c, int j, SequenceI seq)
126		{
127	0	if (seqMap == null)
128		{
129	0	return Color.WHITE;
130		}
131	0	Color[] cols = seqMap.get(seq);
132	0	if (cols == null)
133		{
134		// see above TODO about computing a colour for each residue in each
135		// column: cc = _rcols[i][indexFor[c]];
136	0	return Color.white;
137		}
138
139	0	if (j < 0 || j >= cols.length)
140		{
141	0	return Color.white;
142		}
143	0	return cols[j];
144		}
145
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
146	0	@Override...
147		public ColourSchemeI getInstance(AlignViewportI view,
148		AnnotatedCollectionI sg)
149		{
150	0	return new TCoffeeColourScheme(sg);
151		}
152
153		/**
154		* Answers true if the data has TCoffee score annotation
155		*/
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6
156	0	@Override...
157		public boolean isApplicableTo(AnnotatedCollectionI ac)
158		{
159	0	AnnotatedCollectionI alcontext = ac instanceof AlignmentI ? ac
160		: ac.getContext();
161	0	if (alcontext == null)
162		{
163	0	return false;
164		}
165	0	Iterable<AlignmentAnnotation> anns = alcontext
166		.findAnnotation(TCoffeeScoreFile.TCOFFEE_SCORE);
167	0	return anns.iterator().hasNext();
168		}
169
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
170	0	@Override...
171		public String getSchemeName()
172		{
173	0	return JalviewColourScheme.TCoffee.toString();
174		}
175
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
176	0	@Override...
177		public boolean isSimple()
178		{
179	0	return false;
180		}
181		}