Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ResidueShaderI	33	0	0	-1.0 -	Show methods

Class ResidueShaderI

Class ResidueShaderI	Line # 33	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 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 License for more details.
16		*
17		* You should have received a copy of the GNU General 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.renderer;
22
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;
28		import jalview.schemes.ColourSchemeI;
29
30		import java.awt.Color;
31		import java.util.Map;
32
		- Uncovered Elements: 0 (0) Complexity: 0 Complexity Density: -
33		public interface ResidueShaderI
34		{
35		void setConsensus(ProfilesI cons);
36
37		boolean conservationApplied();
38
39		public abstract void setSSConsensusProfileMap(
40		Map<String, ProfilesI> ssConsensusProfileMap);
41
42		void setConservationApplied(boolean conservationApplied);
43
44		void setConservation(Conservation cons);
45
46		void alignmentChanged(AnnotatedCollectionI alignment,
47		Map<SequenceI, SequenceCollectionI> hiddenReps);
48
49		/**
50		* Sets the percentage consensus threshold value, and whether gaps are ignored
51		* in percentage identity calculation
52		*
53		* @param consensusThreshold
54		* @param ignoreGaps
55		*/
56		void setThreshold(int consensusThreshold,
57		boolean ignoreGaps);
58
59		void setConservationInc(int i);
60
61		int getConservationInc();
62
63		/**
64		* Get the percentage threshold for this colour scheme
65		*
66		* @return Returns the percentage threshold
67		*/
68		int getThreshold();
69
70		/**
71		* Returns the possibly context dependent colour for the given symbol at the
72		* aligned position in the given sequence. For example, the colour may depend
73		* on the symbol's relationship to the consensus residue for the column.
74		*
75		* @param symbol
76		* @param position
77		* @param seq
78		* @return
79		*/
80		Color findColour(char symbol, int position,
81		SequenceI seq);
82
83		ColourSchemeI getColourScheme();
84
85		void setColourScheme(ColourSchemeI cs);
86
87		Color findSSColour(char symbol, int position);
88
89		int getConsensusSecondaryStructureThreshold();
90
91		void setConsensusSecondaryStructureThreshold(int i);
92
93		void setConsensusSecondaryStructureColouring(
94		boolean colourByConsensusSecondaryStructure);
95
96		boolean isConsensusSecondaryStructureColouring();
97		}