Classes

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

Class ResidueShaderI

Class ResidueShaderI	Line # 33	Total Statements 0	Complexity 0	Uncovered Elements 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 boolean conservationApplied();
39
40		public abstract void setConservationApplied(boolean conservationApplied);
41
42		public abstract void setConservation(Conservation cons);
43
44		public abstract void alignmentChanged(AnnotatedCollectionI alignment,
45		Map<SequenceI, SequenceCollectionI> hiddenReps);
46
47		/**
48		* Sets the percentage consensus threshold value, and whether gaps are ignored
49		* in percentage identity calculation
50		*
51		* @param consensusThreshold
52		* @param ignoreGaps
53		*/
54		public abstract void setThreshold(int consensusThreshold,
55		boolean ignoreGaps);
56
57		public abstract void setConservationInc(int i);
58
59		public abstract int getConservationInc();
60
61		/**
62		* Get the percentage threshold for this colour scheme
63		*
64		* @return Returns the percentage threshold
65		*/
66		public abstract int getThreshold();
67
68		/**
69		* Returns the possibly context dependent colour for the given symbol at the
70		* aligned position in the given sequence. For example, the colour may depend
71		* on the symbol's relationship to the consensus residue for the column.
72		*
73		* @param symbol
74		* @param position
75		* @param seq
76		* @return
77		*/
78		public abstract Color findColour(char symbol, int position,
79		SequenceI seq);
80
81		public abstract ColourSchemeI getColourScheme();
82
83		public abstract void setColourScheme(ColourSchemeI cs);
84
85		}