Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
FeatureSetCounterI	34	0	0	-1.0 -	Show methods

Class FeatureSetCounterI

Class FeatureSetCounterI	Line # 34	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
22		package jalview.workers;
23
24		import jalview.datamodel.SequenceFeature;
25
26		import java.util.List;
27
28		/**
29		* An interface for a type that returns counts (per computed annotation type) of
30		* any value of interest at a sequence position that can be determined from the
31		* sequence character and any features present at that position
32		*
33		*/
		- Uncovered Elements: 0 (0) Complexity: 0 Complexity Density: -
34		public interface FeatureSetCounterI
35		{
36		/**
37		* Returns counts (per annotation type) of some properties of interest, for
38		* example
39		* <ul>
40		* <li>the number of variant features at the position</li>
41		* <li>the number of Cath features of status 'True Positive'</li>
42		* <li>1 if the residue is hydrophobic, else 0</li>
43		* <li>etc</li>
44		* </ul>
45		*
46		* @param residue
47		* the residue (or gap) at the position
48		* @param a
49		* list of any sequence features which include the position
50		*/
51		int[] count(String residue, List<SequenceFeature> features);
52
53		/**
54		* Returns names for the annotations that this is counting, for use as the
55		* displayed labels
56		*
57		* @return
58		*/
59		String[] getNames();
60
61		/**
62		* Returns descriptions for the annotations, for display as tooltips
63		*
64		* @return
65		*/
66		String[] getDescriptions();
67
68		/**
69		* Returns the colour (as [red, green, blue] values in the range 0-255) to use
70		* for the minimum value on histogram bars. If this is different to
71		* getMaxColour(), then bars will have a graduated colour.
72		*
73		* @return
74		*/
75		int[] getMinColour();
76
77		/**
78		* Returns the colour (as [red, green, blue] values in the range 0-255) to use
79		* for the maximum value on histogram bars. If this is the same as
80		* getMinColour(), then bars will have a single colour (not graduated).
81		*
82		* @return
83		*/
84		int[] getMaxColour();
85		}