Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ColourSchemeI	31	0	0	-1.0 -	Show methods

Class ColourSchemeI

Class ColourSchemeI	Line # 31	Total Statements 0	Complexity 0	TOTAL Coverage -1.0 -

 

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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.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
		- Uncovered Elements: 0 (0) Complexity: 0 Complexity Density: -
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		*/
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		*/
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		*/
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
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		*/
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		*/
103		boolean isSimple();
104
105		/**
106		* Answers true if the colour scheme has a colour specified for gaps.
107		*
108		* @return
109		*/
110		boolean hasGapColour();
111		}