Classes

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

Class SearchResultsI

Class SearchResultsI	Line # 30	Total Statements 0	Complexity 0	Uncovered Elements 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.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
35		*
36		* @param seq
37		* Sequence
38		* @param start
39		* int
40		* @param end
41		* int
42		* @return
43		*/
44		SearchResultMatchI addResult(SequenceI seq, int start, int end);
45
46		/**
47		* adds all match results in the argument to this set
48		*
49		* @param toAdd
50		*/
51		void addSearchResults(SearchResultsI toAdd);
52
53		/**
54		* Answers true if the search results include the given sequence (or its
55		* dataset sequence), else false
56		*
57		* @param sequence
58		* @return
59		*/
60		boolean involvesSequence(SequenceI sequence);
61
62		/**
63		* Returns an array of [from, to, from, to..] matched columns (base 0) between
64		* the given start and end columns of the given sequence. Returns null if no
65		* matches overlap the specified region.
66		* <p>
67		* Implementations should provide an optimised method to return locations to
68		* highlight on a visible portion of an alignment.
69		*
70		* @param sequence
71		* @param start
72		* first column of range (base 0, inclusive)
73		* @param end
74		* last column of range base 0, inclusive)
75		* @return int[]
76		*/
77		int[] getResults(SequenceI sequence, int start, int end);
78
79		/**
80		* Returns the number of matches found
81		*
82		* @return
83		*/
84		int getSize();
85
86		/**
87		* Returns true if no search result matches are held.
88		*
89		* @return
90		*/
91		boolean isEmpty();
92
93		/**
94		* Returns the list of matches.
95		*
96		* @return
97		*/
98		List<SearchResultMatchI> getResults();
99
100		/**
101		* Set bits in a bitfield for all columns in the given sequence collection
102		* that are highlighted
103		*
104		* @param sqcol
105		* the set of sequences to search for highlighted regions
106		* @param bs
107		* bitset to set
108		* @return number of bits set
109		*/
110		int markColumns(SequenceCollectionI sqcol, BitSet bs);
111		}