1 /* 2 * Jalview - A Sequence Alignment Editor and Viewer (2.11.1.4) 3 * Copyright (C) 2021 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.api.AlignViewportI; 24 import jalview.datamodel.AnnotatedCollectionI; 25 import jalview.datamodel.SequenceCollectionI; 26 import jalview.datamodel.SequenceI; 27 28 import java.awt.Color; 29 import java.util.Map; 30 31 public interface ColourSchemeI 32 { 33 /** 34 * Returns the possibly context dependent colour for the given symbol at the 35 * aligned position in the given sequence. For example, the colour may depend 36 * on the symbol's relationship to the consensus residue for the column. 37 * 38 * @param symbol 39 * @param position 40 * @param seq 41 * @param consensusResidue 42 * the modal symbol (e.g. K) or symbols (e.g. KF) for the column 43 * @param pid 44 * the percentage identity of the column's consensus (if known) 45 * @return 46 */ findColour(char symbol, int position, SequenceI seq, String consensusResidue, float pid)47 Color findColour(char symbol, int position, SequenceI seq, 48 String consensusResidue, float pid); 49 50 /** 51 * Recalculate dependent data using the given sequence collection, taking 52 * account of hidden rows 53 * 54 * @param alignment 55 * @param hiddenReps 56 */ alignmentChanged(AnnotatedCollectionI alignment, Map<SequenceI, SequenceCollectionI> hiddenReps)57 void alignmentChanged(AnnotatedCollectionI alignment, 58 Map<SequenceI, SequenceCollectionI> hiddenReps); 59 60 /** 61 * Creates and returns a new instance of the colourscheme configured to colour 62 * the given collection. Note that even simple colour schemes should return a 63 * new instance for each call to this method, as different instances may have 64 * differing shading by consensus or percentage identity applied. 65 * 66 * @param viewport 67 * - the parent viewport 68 * @param sg 69 * - the collection of sequences to be coloured 70 * @return copy of current scheme with any inherited settings transferred 71 */ getInstance(AlignViewportI viewport, AnnotatedCollectionI sg)72 ColourSchemeI getInstance(AlignViewportI viewport, 73 AnnotatedCollectionI sg); 74 75 /** 76 * Answers true if the colour scheme is suitable for the given data, else 77 * false. For example, some colour schemes are specific to either peptide or 78 * nucleotide, or only apply if certain kinds of annotation are present. 79 * 80 * @param ac 81 * @return 82 */ 83 // TODO can make this method static in Java 8 isApplicableTo(AnnotatedCollectionI ac)84 boolean isApplicableTo(AnnotatedCollectionI ac); 85 86 /** 87 * Answers the 'official' name of the colour scheme (as used, for example, as 88 * a Jalview startup parameter) 89 * 90 * @return 91 */ getSchemeName()92 String getSchemeName(); 93 94 /** 95 * Answers true if the colour scheme depends only on the sequence symbol, and 96 * not on other information such as alignment consensus or annotation. (Note 97 * that simple colour schemes may have a fading by percentage identity or 98 * conservation overlaid.) Simple colour schemes can be propagated to 99 * structure viewers. 100 * 101 * @return 102 */ isSimple()103 boolean isSimple(); 104 105 /** 106 * Answers true if the colour scheme has a colour specified for gaps. 107 * 108 * @return 109 */ hasGapColour()110 boolean hasGapColour(); 111 } 112