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 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.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
36		public abstract void setConsensus(ProfilesI cons);
37
38		public abstract void setSSConsensusProfileMap(
39		Map<String, ProfilesI> ssConsensusProfileMap);
40
41		public abstract boolean conservationApplied();
42
43		public abstract void setConservationApplied(boolean conservationApplied);
44
45		public abstract void setConservation(Conservation cons);
46
47		public abstract void alignmentChanged(AnnotatedCollectionI alignment,
48		Map<SequenceI, SequenceCollectionI> hiddenReps);
49
50		/**
51		* Sets the percentage consensus threshold value, and whether gaps are ignored
52		* in percentage identity calculation
53		*
54		* @param consensusThreshold
55		* @param ignoreGaps
56		*/
57		public abstract void setThreshold(int consensusThreshold,
58		boolean ignoreGaps);
59
60		public abstract void setConservationInc(int i);
61
62		public abstract int getConservationInc();
63
64		/**
65		* Get the percentage threshold for this colour scheme
66		*
67		* @return Returns the percentage threshold
68		*/
69		public abstract int getThreshold();
70
71		/**
72		* Returns the possibly context dependent colour for the given symbol at the
73		* aligned position in the given sequence. For example, the colour may depend
74		* on the symbol's relationship to the consensus residue for the column.
75		*
76		* @param symbol
77		* @param position
78		* @param seq
79		* @return
80		*/
81		public abstract Color findColour(char symbol, int position,
82		SequenceI seq);
83
84		public abstract ColourSchemeI getColourScheme();
85
86		public abstract void setColourScheme(ColourSchemeI cs);
87
88		Color findSSColour(char symbol, int position);
89
90		int getConsensusSecondaryStructureThreshold();
91
92		void setConsensusSecondaryStructureThreshold(int i);
93
94		void setConsensusSecondaryStructureColouring(
95		boolean colourByConsensusSecondaryStructure);
96
97		boolean isConsensusSecondaryStructureColouring();
98
99		}