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  1. Project Clover database Wed Oct 31 2018 15:13:58 GMT
  2. Package jalview.schemes

File TCoffeeColourScheme.java

 

Coverage histogram

../../img/srcFileCovDistChart7.png
28% of files have more coverage

Code metrics

20
33
8
1
180
105
20
0.61
4.12
8
2.5

Classes

Class Line # Actions
TCoffeeColourScheme 46 33 20 20
0.672131167.2%
 

Contributing tests

This file is covered by 80 tests. .

Source view

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.AlignmentI;
25    import jalview.datamodel.AnnotatedCollectionI;
26    import jalview.datamodel.Annotation;
27    import jalview.datamodel.SequenceCollectionI;
28    import jalview.datamodel.SequenceI;
29    import jalview.io.TCoffeeScoreFile;
30   
31    import java.awt.Color;
32    import java.util.ArrayList;
33    import java.util.IdentityHashMap;
34    import java.util.List;
35    import java.util.Map;
36   
37    /**
38    * Defines the color score for T-Coffee MSA
39    * <p>
40    * See http://tcoffee.org
41    *
42    *
43    * @author Paolo Di Tommaso
44    *
45    */
 
46    public class TCoffeeColourScheme extends ResidueColourScheme
47    {
48    IdentityHashMap<SequenceI, Color[]> seqMap;
49   
50    /**
51    * Default constructor (required for Class.newInstance())
52    */
 
53  1 toggle public TCoffeeColourScheme()
54    {
55   
56    }
57   
58    /**
59    * the color scheme needs to look at the alignment to get and cache T-COFFEE
60    * scores
61    *
62    * @param alignment
63    * - annotated sequences to be searched
64    */
 
65  11 toggle public TCoffeeColourScheme(AnnotatedCollectionI alignment)
66    {
67  11 alignmentChanged(alignment, null);
68    }
69   
70    /**
71    * Finds the TCoffeeScore annotation (if any) for each sequence and notes the
72    * annotation colour for each column position. The colours are fixed for
73    * scores 0-9 and are set when annotation is parsed.
74    *
75    * @see TCoffeeScoreFile#annotateAlignment(AlignmentI, boolean)
76    */
 
77  15 toggle @Override
78    public void alignmentChanged(AnnotatedCollectionI alignment,
79    Map<SequenceI, SequenceCollectionI> hiddenReps)
80    {
81    // TODO: if sequences have been represented and they have scores, could
82    // compute an average sequence score for the representative
83   
84    // assume only one set of TCOFFEE scores - but could have more than one
85    // potentially.
86  15 List<AlignmentAnnotation> annots = new ArrayList<AlignmentAnnotation>();
87    // Search alignment to get all tcoffee annotation and pick one set of
88    // annotation to use to colour seqs.
89  15 seqMap = new IdentityHashMap<SequenceI, Color[]>();
90  15 AnnotatedCollectionI alcontext = alignment instanceof AlignmentI
91    ? alignment
92    : alignment.getContext();
93  15 if (alcontext == null)
94    {
95  0 return;
96    }
97  15 int w = 0;
98  15 for (AlignmentAnnotation al : alcontext
99    .findAnnotation(TCoffeeScoreFile.TCOFFEE_SCORE))
100    {
101  114 if (al.sequenceRef != null && !al.belowAlignment)
102    {
103  105 annots.add(al);
104  105 if (w < al.annotations.length)
105    {
106  7 w = al.annotations.length;
107    }
108  105 Color[] scores = new Color[al.annotations.length];
109  105 int i = 0;
110  105 for (Annotation an : al.annotations)
111    {
112  16485 scores[i++] = (an != null) ? an.colour : Color.white;
113    }
114  105 seqMap.put(al.sequenceRef, scores);
115    }
116    }
117    // TODO: compute average colour for each symbol type in each column - gives
118    // a second order colourscheme for colouring a sequence logo derived from
119    // the alignment (colour reflects quality of alignment for each residue
120    // class)
121    }
122   
 
123  0 toggle @Override
124    public Color findColour(char c, int j, SequenceI seq)
125    {
126  0 if (seqMap == null)
127    {
128  0 return Color.WHITE;
129    }
130  0 Color[] cols = seqMap.get(seq);
131  0 if (cols == null)
132    {
133    // see above TODO about computing a colour for each residue in each
134    // column: cc = _rcols[i][indexFor[c]];
135  0 return Color.white;
136    }
137   
138  0 if (j < 0 || j >= cols.length)
139    {
140  0 return Color.white;
141    }
142  0 return cols[j];
143    }
144   
 
145  4 toggle @Override
146    public ColourSchemeI getInstance(AnnotatedCollectionI sg,
147    Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
148    {
149  4 return new TCoffeeColourScheme(sg);
150    }
151   
152    /**
153    * Answers true if the data has TCoffee score annotation
154    */
 
155  202 toggle @Override
156    public boolean isApplicableTo(AnnotatedCollectionI ac)
157    {
158  202 AnnotatedCollectionI alcontext = ac instanceof AlignmentI ? ac
159    : ac.getContext();
160  202 if (alcontext == null)
161    {
162  0 return false;
163    }
164  202 Iterable<AlignmentAnnotation> anns = alcontext
165    .findAnnotation(TCoffeeScoreFile.TCOFFEE_SCORE);
166  202 return anns.iterator().hasNext();
167    }
168   
 
169  208 toggle @Override
170    public String getSchemeName()
171    {
172  208 return JalviewColourScheme.TCoffee.toString();
173    }
174   
 
175  10 toggle @Override
176    public boolean isSimple()
177    {
178  10 return false;
179    }
180    }
  • Report generated by OpenClover v 4.2.1 on Wed Oct 31 2018 15:15:54 GMT using coverage data from Wed Oct 31 2018 15:15:47 GMT.
  • Clover free edition.