Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SimilarityParamsI	27	0	0	-1.0 -	Show methods

Class SimilarityParamsI

Class SimilarityParamsI	Line # 27	Total Statements 0	Complexity 0	TOTAL Coverage -1.0 -

 

Contributing tests

Source view

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.api.analysis;
22
23		/**
24		* A description of options when computing percentage identity of two aligned
25		* sequences
26		*/
		- Uncovered Elements: 0 (0) Complexity: 0 Complexity Density: -
27		public interface SimilarityParamsI
28		{
29		/**
30		* Answers true if gap-gap aligned positions should be included in the
31		* calculation
32		*
33		* @return
34		*/
35		boolean includeGappedColumns();
36
37		/**
38		* Answers true if gap-residue alignment is considered a match
39		*
40		* @return
41		*/
42		// TODO is this specific to a PID score only?
43		// score matrix will compute whatever is configured for gap-residue
44		boolean matchGaps();
45
46		/**
47		* Answers true if gaps are included in the calculation. This may affect the
48		* calculated score, the denominator (normalisation factor) of the score, or
49		* both. Gap-gap positions are included if this and includeGappedColumns both
50		* answer true.
51		*
52		* @return
53		*/
54		boolean includeGaps();
55
56		/**
57		* Answers true if only the shortest sequence length is used to divide the
58		* total score, false if the longest sequence length
59		*
60		* @return
61		*/
62		boolean denominateByShortestLength();
63
64		String getSecondaryStructureSource();
65
66		void setSecondaryStructureSource(String secondaryStructureSource);
67		}