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.AnnotatedCollectionI;
24 import jalview.datamodel.SequenceCollectionI;
25 import jalview.datamodel.SequenceGroup;
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 * Find a colour without an index in a sequence
89 public Color findColour(char c)
91 Color colour = Color.white;
93 if (colors != null && symbolIndex != null
94 && c < symbolIndex.length
95 && symbolIndex[c] < colors.length)
97 colour = colors[symbolIndex[c]];
104 * Default is to call the overloaded method that ignores consensus. A colour
105 * scheme that depends on consensus (for example, Blosum62), should override
106 * this method instead.
109 public Color findColour(char c, int j, SequenceI seq,
110 String consensusResidue, float pid)
112 return findColour(c, j, seq);
116 * Default implementation looks up the residue colour in a fixed scheme, or
117 * returns White if not found. Override this method for a colour scheme that
118 * depends on the column position or sequence.
125 protected Color findColour(char c, int j, SequenceI seq)
127 return findColour(c);
131 public void alignmentChanged(AnnotatedCollectionI alignment,
132 Map<SequenceI, SequenceCollectionI> hiddenReps)
137 * Answers false if the colour scheme is nucleotide or peptide specific, and
138 * the data does not match, else true. Override to modify or extend this test
142 public boolean isApplicableTo(AnnotatedCollectionI ac)
144 if (!isPeptideSpecific() && !isNucleotideSpecific())
153 * pop-up menu on selection group before group created
154 * (no alignment context)
156 // TODO: add nucleotide flag to SequenceGroup?
157 if (ac instanceof SequenceGroup && ac.getContext() == null)
163 * inspect the data context (alignment) for residue type
165 boolean nucleotide = ac.isNucleotide();
168 * does data type match colour scheme type?
170 return (nucleotide && isNucleotideSpecific())
171 || (!nucleotide && isPeptideSpecific());
175 * Answers true if the colour scheme is normally only for peptide data
179 public boolean isPeptideSpecific()
185 * Answers true if the colour scheme is normally only for nucleotide data
189 public boolean isNucleotideSpecific()
195 * Default method returns true. Override this to return false in colour
196 * schemes that are not determined solely by the sequence symbol.
199 public boolean isSimple()