3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
4 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
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 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 along with Jalview. If not, see <http://www.gnu.org/licenses/>.
23 <p><strong>Search</strong></p>
24 <p>The search box is displayed by pressing Control and F or
25 selecting "Find..." from the "Search" menu.</p>
26 <img src="search.gif" width="339" height="110">
27 <p>"Find next" will find the next occurence of the specified and adjust
28 the alignment window view to show it, and "Find all" highlights all
29 matches for a pattern. The "New Feature" is a quick way to highlight
30 and group residues matching the specified search pattern throughout the alignment.
32 <li>The search uses regular expressions. (understands a mixture of posix and
33 perl style regex - see below for a summary)</li>
34 <li>Gaps are ignored when matching the query to the sequences in the alignment.</li>
35 <li>The search is applied to both sequences and their IDs.</li>
36 <li>If a region is selected, then search will <strong>only</strong> be performed
38 <li>To quickly clear the current selection, press the "Escape" key.</li>
39 <li>Tick the "Match Case" box to perform a case sensitive search.</li>
41 <p><strong>Creating Features from Search Results</strong></p>
43 If "New Feature" is selected, the feature can be given a name from
44 a popup input box. Use the "Feature Settings" under the "View"
45 menu to change the visibility and colour of the new sequence feature.</p>
46 <p><strong>A quick Regular Expression Guide</strong></p>
47 <p>A regular expression is not just a simple text query - although it
48 can be used like one, the query is not parsed literally, but
49 interpreted like a series of instructions defining the features of the
50 match. For example, a simple query like "ACDED" would
51 match all occurences of that string, but "ACD+ED" matches
52 both 'ACDDED' and 'ACDDDDDDDDED'. More usefully, the query
53 "[ILGVMA]{;5,}" would find stretches of small,
54 hydrophobic amino acids of at least five residues in length.
57 below describes some of the regular expression syntax:<br></p>
58 <table width="100%" border="1">
60 <td width="24%">Regular Expression Element</td>
61 <td width="76%">Effect</td>
64 <td width="24%">.</td>
65 <td width="76%">Matches any single character</td>
69 <td>Matches any one of the characters in the brackets</td>
73 <td>Matches at the start of an ID or sequence</td>
77 <td>Matches at the end of an ID or sequence</td>
81 <td>Matches if the preceding element matches zero or more times</td>
85 <td>Matches if the preceding element matched once or not at all</td>
89 <td>Matches if the preceding element matched at least once</td>
93 <td>Matches if the preceding element matches a specified number of
99 <td> Matches of the preceding element matched at least the
100 specified number of times</td>
104 <td>Matches if the preceding element matches min or at most max