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

File ResidueColourScheme.java

 

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12% of files have more coverage

Code metrics

8
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0.95
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1.75

Classes

Class Line # Actions
ResidueColourScheme 34 22 21 5
0.8809523688.1%
 

Contributing tests

This file is covered by 111 tests. .

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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.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    * lookup up by character value e.g. 'G' to the colors array index
50    * e.g. if symbolIndex['K'] = 11 then colors[11] is the colour for K
51    */
52    final int[] symbolIndex;
53   
54    /*
55    * colour for residue characters as indexed by symbolIndex
56    */
57    Color[] colors = null;
58   
59    /* Set when threshold colouring to either pid_gaps or pid_nogaps */
60    protected boolean ignoreGaps = false;
61   
62    /**
63    * Creates a new ResidueColourScheme object.
64    *
65    * @param final
66    * int[] index table into colors (ResidueProperties.naIndex or
67    * ResidueProperties.aaIndex)
68    * @param colors
69    * colours for symbols in sequences
70    */
 
71  965 toggle public ResidueColourScheme(int[] aaOrnaIndex, Color[] colours)
72    {
73  965 symbolIndex = aaOrnaIndex;
74  965 this.colors = colours;
75    }
76   
77    /**
78    * Creates a new ResidueColourScheme object with a lookup table for indexing
79    * the colour map
80    */
 
81  94 toggle public ResidueColourScheme(int[] aaOrNaIndex)
82    {
83  94 symbolIndex = aaOrNaIndex;
84    }
85   
86    /**
87    * Creates a new ResidueColourScheme object - default constructor for
88    * non-sequence dependent colourschemes
89    */
 
90  76 toggle public ResidueColourScheme()
91    {
92  76 symbolIndex = null;
93    }
94   
95    /**
96    * Find a colour without an index in a sequence
97    */
 
98  339873 toggle public Color findColour(char c)
99    {
100  339873 Color colour = Color.white;
101   
102  339873 if (colors != null && symbolIndex != null && c < symbolIndex.length
103    && symbolIndex[c] < colors.length)
104    {
105  339873 colour = colors[symbolIndex[c]];
106    }
107   
108  339873 return colour;
109    }
110   
111    /**
112    * Default is to call the overloaded method that ignores consensus. A colour
113    * scheme that depends on consensus (for example, Blosum62), should override
114    * this method instead.
115    */
 
116  345770 toggle @Override
117    public Color findColour(char c, int j, SequenceI seq,
118    String consensusResidue, float pid)
119    {
120  345770 return findColour(c, j, seq);
121    }
122   
123    /**
124    * Default implementation looks up the residue colour in a fixed scheme, or
125    * returns White if not found. Override this method for a colour scheme that
126    * depends on the column position or sequence.
127    *
128    * @param c
129    * @param j
130    * @param seq
131    * @return
132    */
 
133  327675 toggle protected Color findColour(char c, int j, SequenceI seq)
134    {
135  327675 return findColour(c);
136    }
137   
 
138  334 toggle @Override
139    public void alignmentChanged(AnnotatedCollectionI alignment,
140    Map<SequenceI, SequenceCollectionI> hiddenReps)
141    {
142    }
143   
144    /**
145    * Answers false if the colour scheme is nucleotide or peptide specific, and
146    * the data does not match, else true. Override to modify or extend this test
147    * as required.
148    */
 
149  2776 toggle @Override
150    public boolean isApplicableTo(AnnotatedCollectionI ac)
151    {
152  2776 if (!isPeptideSpecific() && !isNucleotideSpecific())
153    {
154  484 return true;
155    }
156  2292 if (ac == null)
157    {
158  0 return true;
159    }
160    /*
161    * pop-up menu on selection group before group created
162    * (no alignment context)
163    */
164    // TODO: add nucleotide flag to SequenceGroup?
165  2292 if (ac instanceof SequenceGroup && ac.getContext() == null)
166    {
167  0 return true;
168    }
169   
170    /*
171    * inspect the data context (alignment) for residue type
172    */
173  2292 boolean nucleotide = ac.isNucleotide();
174   
175    /*
176    * does data type match colour scheme type?
177    */
178  2292 return (nucleotide && isNucleotideSpecific())
179    || (!nucleotide && isPeptideSpecific());
180    }
181   
182    /**
183    * Answers true if the colour scheme is normally only for peptide data
184    *
185    * @return
186    */
 
187  1307 toggle public boolean isPeptideSpecific()
188    {
189  1307 return false;
190    }
191   
192    /**
193    * Answers true if the colour scheme is normally only for nucleotide data
194    *
195    * @return
196    */
 
197  574 toggle public boolean isNucleotideSpecific()
198    {
199  574 return false;
200    }
201   
202    /**
203    * Default method returns true. Override this to return false in colour
204    * schemes that are not determined solely by the sequence symbol.
205    */
 
206  106 toggle @Override
207    public boolean isSimple()
208    {
209  106 return true;
210    }
211   
212    /**
213    * Default method returns false. Override this to return true in colour
214    * schemes that have a colour associated with gap residues.
215    */
 
216  2 toggle @Override
217    public boolean hasGapColour()
218    {
219  2 return false;
220    }
221    }
  • 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.