2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
21 package jalview.schemes;
23 import jalview.datamodel.AlignmentI;
24 import jalview.datamodel.AnnotatedCollectionI;
25 import jalview.datamodel.SequenceCollectionI;
26 import jalview.datamodel.SequenceI;
28 import java.awt.Color;
32 * Base class for residue-based colour schemes
34 public abstract class ResidueColourScheme implements ColourSchemeI
36 public static final String NONE = "None";
38 public static final String USER_DEFINED = "User Defined";
41 * lookup up by character value e.g. 'G' to the colors array index
42 * e.g. if symbolIndex['K'] = 11 then colors[11] is the colour for K
44 final int[] symbolIndex;
47 * colour for residue characters as indexed by symbolIndex
49 Color[] colors = null;
51 /* Set when threshold colouring to either pid_gaps or pid_nogaps */
52 protected boolean ignoreGaps = false;
55 * Creates a new ResidueColourScheme object.
57 * @param final int[] index table into colors (ResidueProperties.naIndex or
58 * ResidueProperties.aaIndex)
60 * colours for symbols in sequences
62 public ResidueColourScheme(int[] aaOrnaIndex, Color[] colours)
64 symbolIndex = aaOrnaIndex;
65 this.colors = colours;
69 * Creates a new ResidueColourScheme object with a lookup table for indexing
72 public ResidueColourScheme(int[] aaOrNaIndex)
74 symbolIndex = aaOrNaIndex;
78 * Creates a new ResidueColourScheme object - default constructor for
79 * non-sequence dependent colourschemes
81 public ResidueColourScheme()
87 * Returns the colour for symbol 'A'. Intended for use in a 'fixed colour'
88 * colour scheme (for example a feature colour).
91 public Color findColour()
93 // TODO delete this method in favour of ColorUtils.parseColourString()?
94 return findColour('A');
98 * Find a colour without an index in a sequence
101 public Color findColour(char c)
103 return colors == null ? Color.white : colors[symbolIndex[c]];
107 * Default is to call the overloaded method that ignores consensus. A colour
108 * scheme that depends on consensus (for example, Blosum62), should override
109 * this method instead.
112 public Color findColour(char c, int j, SequenceI seq,
113 String consensusResidue, float pid)
115 return findColour(c, j, seq);
118 protected Color findColour(char c, int j, SequenceI seq)
120 Color colour = Color.white;
122 if (colors != null && symbolIndex != null && c < symbolIndex.length
123 && symbolIndex[c] < colors.length)
125 colour = colors[symbolIndex[c]];
127 // colour = adjustColour(c, j, colour);
133 public void alignmentChanged(AnnotatedCollectionI alignment,
134 Map<SequenceI, SequenceCollectionI> hiddenReps)
139 * Answers false if the colour scheme is nucleotide or peptide specific, and
140 * the data does not match, else true. Override to modify or extend this test
144 public boolean isApplicableTo(AnnotatedCollectionI ac)
146 if (!isPeptideSpecific() && !isNucleotideSpecific())
152 * inspect the data context (alignment) for residue type
154 boolean nucleotide = false;
155 if (ac instanceof AlignmentI)
157 nucleotide = ((AlignmentI) ac).isNucleotide();
161 AnnotatedCollectionI context = ac.getContext();
162 if (context instanceof AlignmentI)
164 nucleotide = ((AlignmentI) context).isNucleotide();
168 // not sure what's going on, play safe
174 * does data type match colour scheme type?
176 return (nucleotide && isNucleotideSpecific())
177 || (!nucleotide && isPeptideSpecific());
181 * Answers true if the colour scheme is normally only for peptide data
185 public boolean isPeptideSpecific()
191 * Answers true if the colour scheme is normally only for nucleotide data
195 public boolean isNucleotideSpecific()
201 * Default method returns true. Override this to return false in colour
202 * schemes that are not determined solely by the sequence symbol.
205 public boolean isSimple()