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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 | */ | |
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 | } |