2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
23 import java.util.List;
25 import jalview.datamodel.SearchResultsI;
26 import jalview.datamodel.SequenceI;
29 * An interface for searching for a pattern in an aligment
31 public interface FinderI
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().
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).
46 * Matches of entirely hidden patterns are not returned. Matches that span
47 * hidden regions on one or both sides may be returned.
49 * @param theSearchString
50 * @param caseSensitive
51 * @param searchDescription
52 * @param searchFeatureDesc
56 void findAll(String theSearchString, boolean caseSensitive,
57 boolean searchDescription, boolean searchFeatureDesc,
58 boolean ignoreHidden);
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().
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.
73 * @param theSearchString
74 * @param caseSensitive
75 * @param searchDescription
76 * @param searchFeatureDesc
80 void findNext(String theSearchString, boolean caseSensitive,
81 boolean searchDescription, boolean searchFeatureDesc,
82 boolean ignoreHidden);
85 * Returns the (possibly empty) list of sequences matched on sequence name or
90 List<SequenceI> getIdMatches();
93 * Answers the search results (possibly empty) from the last search
97 SearchResultsI getSearchResults();
99 void setFeatureRenderer(FeatureRenderer featureRenderer);