Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
FinderI	31	0	0	-1.0 -	Show methods

Class FinderI

Class FinderI	Line # 31	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.api;
22
23		import java.util.List;
24
25		import jalview.datamodel.SearchResultsI;
26		import jalview.datamodel.SequenceI;
27
28		/**
29		* An interface for searching for a pattern in an aligment
30		*/
		- Uncovered Elements: 0 (0) Complexity: 0 Complexity Density: -
31		public interface FinderI
32		{
33
34		/**
35		* Performs a find for the given search string (interpreted as a regular
36		* expression). Search may optionally be case-sensitive, and may optionally
37		* including match in sequence description (sequence id is always searched).
38		* If the viewport has an active selection, then the find is restricted to the
39		* selection region. Sequences matched by id or description can be retrieved
40		* by getIdMatches(), and matched residue patterns by getSearchResults().
41		* <p>
42		* If {@code ignoreHidden} is true, then any residues in hidden columns are
43		* ignored (skipped) when matching, so for example pattern {@code KRT} would
44		* match sequence {@code KRqmT} (where {@code qm} are in hidden columns).
45		* <p>
46		* Matches of entirely hidden patterns are not returned. Matches that span
47		* hidden regions on one or both sides may be returned.
48		*
49		* @param theSearchString
50		* @param caseSensitive
51		* @param searchDescription
52		* @param searchFeatureDesc
53		* @param ignoreHidden
54		* @return
55		*/
56		void findAll(String theSearchString, boolean caseSensitive,
57		boolean searchDescription, boolean searchFeatureDesc,
58		boolean ignoreHidden);
59
60		/**
61		* Finds the next match for the given search string (interpreted as a regular
62		* expression), starting from the position after the last match found. Search
63		* may optionally be case-sensitive, and may optionally including match in
64		* sequence description (sequence id is always searched). If the viewport has
65		* an active selection, then the find is restricted to the selection region.
66		* Sequences matched by id or description can be retrieved by getIdMatches(),
67		* and matched residue patterns by getSearchResults().
68		* <p>
69		* If {@code ignoreHidden} is true, any hidden residues are skipped (matches
70		* may span them). If false, they are included for matching purposes. In
71		* either cases, entirely hidden matches are not returned.
72		*
73		* @param theSearchString
74		* @param caseSensitive
75		* @param searchDescription
76		* @param searchFeatureDesc
77		* @param ignoreHidden
78		* @return
79		*/
80		void findNext(String theSearchString, boolean caseSensitive,
81		boolean searchDescription, boolean searchFeatureDesc,
82		boolean ignoreHidden);
83
84		/**
85		* Returns the (possibly empty) list of sequences matched on sequence name or
86		* description
87		*
88		* @return
89		*/
90		List<SequenceI> getIdMatches();
91
92		/**
93		* Answers the search results (possibly empty) from the last search
94		*
95		* @return
96		*/
97		SearchResultsI getSearchResults();
98
99		void setFeatureRenderer(FeatureRenderer featureRenderer);
100
101		}