Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SearchResultsI	30	0	0	-1.0 -	Show methods

Class SearchResultsI

Class SearchResultsI	Line # 30	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		import java.util.BitSet;
24		import java.util.List;
25
26		/**
27		* An interface describing the result of a search or other operation which
28		* highlights matched regions of an alignment
29		*/
		- Uncovered Elements: 0 (0) Complexity: 0 Complexity Density: -
30		public interface SearchResultsI
31		{
32
33		/**
34		* Adds one region to the results (unless already added, to avoid duplicates)
35		*
36		* @param seq
37		* @param start
38		* @param end
39		* @return
40		*/
41		SearchResultMatchI addResult(SequenceI seq, int start, int end);
42
43		/**
44		* adds all match results in the argument to this set
45		*
46		* @param toAdd
47		*/
48		void addSearchResults(SearchResultsI toAdd);
49
50		/**
51		* Answers true if the search results include the given sequence (or its
52		* dataset sequence), else false
53		*
54		* @param sequence
55		* @return
56		*/
57		boolean involvesSequence(SequenceI sequence);
58
59		/**
60		* Returns an array of [from, to, from, to..] matched columns (base 0) between
61		* the given start and end columns of the given sequence. Returns null if no
62		* matches overlap the specified region.
63		* <p>
64		* Implementations should provide an optimised method to return locations to
65		* highlight on a visible portion of an alignment.
66		*
67		* @param sequence
68		* @param start
69		* first column of range (base 0, inclusive)
70		* @param end
71		* last column of range base 0, inclusive)
72		* @return int[]
73		*/
74		int[] getResults(SequenceI sequence, int start, int end);
75
76		/**
77		* Returns the number of matches found
78		*
79		* @return
80		*/
81		int getSize();
82
83		/**
84		* Returns true if no search result matches are held.
85		*
86		* @return
87		*/
88		boolean isEmpty();
89
90		/**
91		* Returns the list of matches.
92		*
93		* @return
94		*/
95		List<SearchResultMatchI> getResults();
96
97		/**
98		* Set bits in a bitfield for all columns in the given sequence collection
99		* that are highlighted
100		*
101		* @param sqcol
102		* the set of sequences to search for highlighted regions
103		* @param bs
104		* bitset to set
105		* @return number of bits set
106		*/
107		int markColumns(SequenceCollectionI sqcol, BitSet bs);
108		}