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Coverage Report

  1. Project Clover database Fri Nov 15 2024 13:56:46 GMT
  2. Package jalview.schemes

File ResidueColourScheme.java

 

Coverage histogram

../../img/srcFileCovDistChart9.png
12% of files have more coverage

Code metrics

8
22
12
1
227
92
21
0.95
1.83
12
1.75

Classes

Class Line # Actions
ResidueColourScheme 34 22 21
0.8809523688.1%
 

Contributing tests

This file is covered by 221 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.AnnotatedCollectionI;
24    import jalview.datamodel.SequenceCollectionI;
25    import jalview.datamodel.SequenceGroup;
26    import jalview.datamodel.SequenceI;
27   
28    import java.awt.Color;
29    import java.util.Map;
30   
31    /**
32    * Base class for residue-based colour schemes
33    */
 
34    public abstract class ResidueColourScheme implements ColourSchemeI
35    {
36    public static final String NONE = "None";
37   
38    /*
39    * default display name for a user defined colour scheme
40    */
41    public static final String USER_DEFINED = "User Defined";
42   
43    /*
44    * name for (new) "User Defined.." colour scheme menu item
45    */
46    public static final String USER_DEFINED_MENU = "*User Defined*";
47   
48    /*
49    * the canonical name of the annotation colour scheme
50    * (may be used to identify it in menu items)
51    */
52    public static final String ANNOTATION_COLOUR = "Annotation";
53   
54    /*
55    * lookup up by character value e.g. 'G' to the colors array index
56    * e.g. if symbolIndex['K'] = 11 then colors[11] is the colour for K
57    */
58    final int[] symbolIndex;
59   
60    /*
61    * colour for residue characters as indexed by symbolIndex
62    */
63    Color[] colors = null;
64   
65    /* Set when threshold colouring to either pid_gaps or pid_nogaps */
66    protected boolean ignoreGaps = false;
67   
68    /**
69    * Creates a new ResidueColourScheme object.
70    *
71    * @param final
72    * int[] index table into colors (ResidueProperties.naIndex or
73    * ResidueProperties.aaIndex)
74    * @param colors
75    * colours for symbols in sequences
76    */
 
77  2713 toggle public ResidueColourScheme(int[] aaOrnaIndex, Color[] colours)
78    {
79  2713 symbolIndex = aaOrnaIndex;
80  2713 this.colors = colours;
81    }
82   
83    /**
84    * Creates a new ResidueColourScheme object with a lookup table for indexing
85    * the colour map
86    */
 
87  356 toggle public ResidueColourScheme(int[] aaOrNaIndex)
88    {
89  356 symbolIndex = aaOrNaIndex;
90    }
91   
92    /**
93    * Creates a new ResidueColourScheme object - default constructor for
94    * non-sequence dependent colourschemes
95    */
 
96  339 toggle public ResidueColourScheme()
97    {
98  339 symbolIndex = null;
99    }
100   
101    /**
102    * Find a colour without an index in a sequence
103    */
 
104  557967 toggle public Color findColour(char c)
105    {
106  557972 Color colour = Color.white;
107   
108  557977 if (colors != null && symbolIndex != null && c < symbolIndex.length
109    && symbolIndex[c] < colors.length)
110    {
111  557976 colour = colors[symbolIndex[c]];
112    }
113   
114  557986 return colour;
115    }
116   
117    /**
118    * Default is to call the overloaded method that ignores consensus. A colour
119    * scheme that depends on consensus (for example, Blosum62), should override
120    * this method instead.
121    */
 
122  574511 toggle @Override
123    public Color findColour(char c, int j, SequenceI seq,
124    String consensusResidue, float pid)
125    {
126  574517 return findColour(c, j, seq);
127    }
128   
129    /**
130    * Default implementation looks up the residue colour in a fixed scheme, or
131    * returns White if not found. Override this method for a colour scheme that
132    * depends on the column position or sequence.
133    *
134    * @param c
135    * @param j
136    * @param seq
137    * @return
138    */
 
139  539205 toggle protected Color findColour(char c, int j, SequenceI seq)
140    {
141  539206 return findColour(c);
142    }
143   
 
144  324 toggle @Override
145    public void alignmentChanged(AnnotatedCollectionI alignment,
146    Map<SequenceI, SequenceCollectionI> hiddenReps)
147    {
148    }
149   
150    /**
151    * Answers false if the colour scheme is nucleotide or peptide specific, and
152    * the data does not match, else true. Override to modify or extend this test
153    * as required.
154    */
 
155  8854 toggle @Override
156    public boolean isApplicableTo(AnnotatedCollectionI ac)
157    {
158  8854 if (!isPeptideSpecific() && !isNucleotideSpecific())
159    {
160  794 return true;
161    }
162  8060 if (ac == null)
163    {
164  0 return true;
165    }
166    /*
167    * pop-up menu on selection group before group created
168    * (no alignment context)
169    */
170    // TODO: add nucleotide flag to SequenceGroup?
171  8060 if (ac instanceof SequenceGroup && ac.getContext() == null)
172    {
173  0 return true;
174    }
175   
176    /*
177    * inspect the data context (alignment) for residue type
178    */
179  8060 boolean nucleotide = ac.isNucleotide();
180   
181    /*
182    * does data type match colour scheme type?
183    */
184  8060 return (nucleotide && isNucleotideSpecific())
185    || (!nucleotide && isPeptideSpecific());
186    }
187   
188    /**
189    * Answers true if the colour scheme is normally only for peptide data
190    *
191    * @return
192    */
 
193  3602 toggle public boolean isPeptideSpecific()
194    {
195  3602 return false;
196    }
197   
198    /**
199    * Answers true if the colour scheme is normally only for nucleotide data
200    *
201    * @return
202    */
 
203  1882 toggle public boolean isNucleotideSpecific()
204    {
205  1882 return false;
206    }
207   
208    /**
209    * Default method returns true. Override this to return false in colour
210    * schemes that are not determined solely by the sequence symbol.
211    */
 
212  678 toggle @Override
213    public boolean isSimple()
214    {
215  678 return true;
216    }
217   
218    /**
219    * Default method returns false. Override this to return true in colour
220    * schemes that have a colour associated with gap residues.
221    */
 
222  7148 toggle @Override
223    public boolean hasGapColour()
224    {
225  7148 return false;
226    }
227    }
  • Report generated by OpenClover v 4.4.1 on Fri Nov 15 2024 14:04:22 GMT using coverage data from Fri Nov 15 2024 14:04:05 GMT.
  • OpenClover is free and open-source software.