Classes

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

Class SearchResultMatchI

Class SearchResultMatchI	Line # 27	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.datamodel;
22
23		/**
24		* An interface that describes one matched region of an alignment, as one
25		* contiguous portion of a single dataset sequence
26		*/
		- Uncovered Elements: 0 (0) Complexity: 0 Complexity Density: -
27		public interface SearchResultMatchI
28		{
29		/**
30		* Returns the matched sequence
31		*
32		* @return
33		*/
34		SequenceI getSequence();
35
36		/**
37		* Returns the start position of the match in the sequence (base 1)
38		*
39		* @return
40		*/
41		int getStart();
42
43		/**
44		* Returns the end position of the match in the sequence (base 1)
45		*
46		* @return
47		*/
48		int getEnd();
49
50		/**
51		* Answers true if this match is for the given sequence and includes (matches
52		* or encloses) the given start-end range
53		*
54		* @param seq
55		* @param start
56		* @param end
57		* @return
58		*/
59		boolean contains(SequenceI seq, int start, int end);
60
61		/**
62		*
63		* @param seq
64		* @param from
65		* - first position to highlight
66		* @param to
67		* - last position to highlight (assumed higher than from)
68		* @return true iff from-to intersects or marks positions either side of
69		* start/end
70		*/
71		boolean adjacent(SequenceI seq, int from, int to);
72		}