3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
24 <style type="text/css">
35 <strong>Search</strong>
37 <p>The search box is displayed by pressing Control and F or
38 selecting "Find..." from the "Search" menu.</p>
39 <img src="search.gif" width="339" height="110">
40 <p>"Find next" will find the next occurence of the
41 specified and adjust the alignment window view to show it, and
42 "Find all" highlights all matches for a pattern. The
43 "New Feature" is a quick way to highlight and group
44 residues matching the specified search pattern throughout the
47 <li>The search uses regular expressions. (understands a mixture
48 of posix and perl style regex - see below for a summary)</li>
49 <li>Gaps are ignored when matching the query to the sequences
50 in the alignment.</li>
51 <li>The search is applied to both sequences and their IDs.</li>
52 <li>If a region is selected, then search will <strong>only</strong>
53 be performed on that region.
55 <li>To quickly clear the current selection, press the
56 "Escape" key.</li>
57 <li>Tick the "Match Case" box to perform a case
58 sensitive search.</li>
61 <strong>Creating Features from Search Results</strong>
63 <p>If "New Feature" is selected, the feature can be
64 given a name from a popup input box. Use the "Feature
65 Settings" under the "View" menu to change the
66 visibility and colour of the new sequence feature.</p>
68 <strong>A quick Regular Expression Guide</strong>
70 <p>A regular expression is not just a simple text query - although
71 it can be used like one, the query is not parsed literally, but
72 interpreted like a series of instructions defining the features of
73 the match. For example, a simple query like "ACDED" would
74 match all occurences of that string, but "ACD+ED" matches
75 both 'ACDDED' and 'ACDDDDDDDDED'. More usefully, the query
76 "[ILGVMA]{;5,}" would find stretches of small, hydrophobic
77 amino acids of at least five residues in length.</p>
79 The table below describes some of the regular expression syntax:<br>
81 <table width="100%" border="1">
83 <td width="24%">Regular Expression Element</td>
84 <td width="76%">Effect</td>
87 <td width="24%">.</td>
88 <td width="76%">Matches any single character</td>
92 <td>Matches any one of the characters in the brackets</td>
96 <td>Matches at the start of an ID or sequence</td>
100 <td>Matches at the end of an ID or sequence</td>
104 <td>Matches if the preceding element matches zero or more
109 <td>Matches if the preceding element matched once or not at
114 <td>Matches if the preceding element matched at least once</td>
118 <td>Matches if the preceding element matches a specified
123 <td>Matches of the preceding element matched at least the
124 specified number of times</td>
128 <td>Matches if the preceding element matches min or at most
129 max number of times</td>