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 one ore more [start, end] ranges to the results (unless already added
45		* to avoid duplicates). This method only increments the match count by 1.
46		* This is for the case where a match spans ignored hidden residues - it is
47		* formally two or more contiguous matches, but only counted as one match.
48		*
49		* @param seq
50		* @param positions
51		*/
52		void addResult(SequenceI seq, int[] positions);
53
54		/**
55		* Adds the given start/end region to this search result. If sequence already
56		* has a search result and the range is adjacent to already highlighted
57		* positions, they will be merged
58		*
59		* @param sequence
60		* @param start
61		* @param end
62		* @return true if an existing range was updated with this one
63		*/
64		boolean appendResult(SequenceI sequence, int start, int end);
65
66		/**
67		* adds all match results in the argument to this set
68		*
69		* @param toAdd
70		*/
71		void addSearchResults(SearchResultsI toAdd);
72
73		/**
74		* Answers true if the search results include the given sequence (or its
75		* dataset sequence), else false
76		*
77		* @param sequence
78		* @return
79		*/
80		boolean involvesSequence(SequenceI sequence);
81
82		/**
83		* Returns an array of [from, to, from, to..] matched columns (base 0) between
84		* the given start and end columns of the given sequence. Returns null if no
85		* matches overlap the specified region.
86		* <p>
87		* Implementations should provide an optimised method to return locations to
88		* highlight on a visible portion of an alignment.
89		*
90		* @param sequence
91		* @param start
92		* first column of range (base 0, inclusive)
93		* @param end
94		* last column of range base 0, inclusive)
95		* @return int[]
96		*/
97		int[] getResults(SequenceI sequence, int start, int end);
98
99		/**
100		* Returns the number of matches found. Note that if a match straddles ignored
101		* hidden residues, it is counted as one match, although formally recorded as
102		* two (or more) contiguous matched sequence regions
103		*
104		* @return
105		*/
106		int getCount();
107
108		/**
109		* Returns true if no search result matches are held.
110		*
111		* @return
112		*/
113		boolean isEmpty();
114
115		/**
116		* Returns the list of matches.
117		*
118		* @return
119		*/
120		List<SearchResultMatchI> getResults();
121
122		/**
123		* Set bits in a bitfield for all columns in the given sequence collection
124		* that are highlighted
125		*
126		* @param sqcol
127		* the set of sequences to search for highlighted regions
128		* @param bs
129		* bitset to set
130		* @return number of bits set
131		*/
132		int markColumns(SequenceCollectionI sqcol, BitSet bs);
133
134		/**
135		* Return sub-sequences corresponding to distinct contiguous ranges in the
136		* matching set
137		*
138		* @return list of sequence objects
139		*/
140		List<SequenceI> getMatchingSubSequences();
141		}