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.analysis.Conservation;
24 import jalview.datamodel.AnnotatedCollectionI;
25 import jalview.datamodel.ProfilesI;
26 import jalview.datamodel.SequenceCollectionI;
27 import jalview.datamodel.SequenceI;
29 import java.awt.Color;
32 public interface ColourSchemeI
35 * Returns the colour for the given character. For use when the colour depends
41 Color findColour(char c);
44 * Returns the possibly context dependent colour for the given symbol at the
45 * aligned position in the given sequence. For example, the colour may depend
46 * on the symbol's relationship to the consensus residue for the column.
53 Color findColour(char symbol, int position, SequenceI seq);
56 * Assigns the given consensus profile for the colourscheme
58 void setConsensus(ProfilesI hconsensus);
61 * Assigns the given conservation to the colourscheme
65 void setConservation(Conservation c);
68 * Enable or disable conservation shading for this colourscheme
70 * @param conservationApplied
72 void setConservationApplied(boolean conservationApplied);
75 * Answers true if conservation shading is enabled for this colourscheme
79 boolean conservationApplied();
82 * Sets the scale factor for bleaching of colour in unconserved regions
86 void setConservationInc(int i);
89 * Returns the scale factor for bleaching colour in unconserved regions
93 int getConservationInc();
96 * Returns the percentage identity threshold for applying colourscheme
103 * Sets the percentage identity threshold and type of %age identity
104 * calculation for shading
107 * 0..100 percentage identity for applying this colourscheme
109 * when true, calculate PID without including gapped positions
111 void setThreshold(int pct, boolean ignoreGaps);
114 * Recalculate dependent data using the given sequence collection, taking
115 * account of hidden rows
120 void alignmentChanged(AnnotatedCollectionI alignment,
121 Map<SequenceI, SequenceCollectionI> hiddenReps);
124 * Creates and returns a new instance of the colourscheme configured to colour
125 * the given collection. Note that even simple colour schemes should return a
126 * new instance for each call to this method, as different instances may have
127 * differing shading by consensus or percentage identity applied.
130 * @param hiddenRepSequences
131 * @return copy of current scheme with any inherited settings transferred
133 ColourSchemeI getInstance(AnnotatedCollectionI sg,
134 Map<SequenceI, SequenceCollectionI> hiddenRepSequences);
137 * Answers true if the colour scheme is suitable for the given data, else
138 * false. For example, some colour schemes are specific to either peptide or
139 * nucleotide, or only apply if certain kinds of annotation are present.
144 // TODO can make this method static in Java 8
145 boolean isApplicableTo(AnnotatedCollectionI ac);
148 * Answers the 'official' name of the colour scheme (as used, for example, as
149 * a Jalview startup parameter)
153 String getSchemeName();
156 * Answers true if the colour scheme depends only on the sequence symbol, and
157 * not on other information such as alignment consensus or annotation. (Note
158 * that simple colour schemes may have a fading by percentage identity or
159 * conservation overlaid.) Simple colour schemes can be propagated to