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.png" width="398" height="124">
40 <p>"Find next" will find the next occurrence 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, and
52 optionally also to the description string (<em>since Jalview
55 <li>If a region is selected, then search will <strong>only</strong>
56 be performed on that region.
58 <li>To quickly clear the current selection, press the
59 "Escape" key.</li>
60 <li>Tick the "Match Case" box to perform a case
61 sensitive search.</li>
62 <li>To access a <a ref="#queryhistory">previously used
63 query</a> press the down arrow or click on the button on the right
67 <strong>Creating Features from Search Results</strong>
69 <p>If "New Feature" is selected, the feature can be
70 given a name from a popup input box. Use the "Feature
71 Settings" under the "View" menu to change the
72 visibility and colour of the new sequence feature.</p>
75 <strong>Selecting regions from Search Results</strong>
78 Press 'B' or use the <em>Select Highlighted Columns</em> option from
79 the alignment window's select menu to add columns containing
80 highlighted search results to the alignment window's column
81 selection. Alt-'B' will add all but the highlighted columns, and
82 Ctrl (or Cmd) -B will toggle the column selection for the
87 <strong>A quick Regular Expression Guide</strong>
89 <p>A regular expression is not just a simple text query - although
90 it can be used like one, the query is not parsed literally, but
91 interpreted like a series of instructions defining the features of
92 the match. For example, a simple query like "ACDED" would
93 match all occurences of that string, but "ACD+ED" matches
94 both 'ACDDED' and 'ACDDDDDDDDED'. More usefully, the query
95 "[GVATC]{;5,}" would find stretches of small, hydrophobic
96 amino acids of at least five residues in length.</p>
98 The table below describes some of the regular expression syntax:<br>
100 <table width="100%" border="1">
102 <td width="24%">Regular Expression Element</td>
103 <td width="76%">Effect</td>
106 <td width="24%">.</td>
107 <td width="76%">Matches any single character</td>
111 <td>Matches any one of the characters in the brackets</td>
115 <td>Matches at the start of an ID or sequence</td>
119 <td>Matches at the end of an ID or sequence</td>
123 <td>Matches if the preceding element matches zero or more
128 <td>Matches if the preceding element matched once or not at
133 <td>Matches if the preceding element matched at least once</td>
137 <td>Matches if the preceding element matches a specified
142 <td>Matches of the preceding element matched at least the
143 specified number of times</td>
147 <td>Matches if the preceding element matches min or at most
148 max number of times</td>
152 <a name="queryhistory" /><strong>Search History</strong>
154 <p>A record of all the recent queries made via the Find dialog are
155 stored along with your Jalview user preferences. To open the search
156 history, click on the button to the right of the query field, or
157 press the down arrow key.</p>
158 <img src="searchhist.png" width="404" height="185" align="left" />
159 <p>The search history keeps up to 99 queries by default. To clear
160 the history, or modify the size of the history, right-click the text
162 <img src="searchclearhist.png" width="402" height="121" align="left" />
164 <strong>Other dialogs that provide a query history</strong>
167 Jalview's <a href="uniprotsequencefetcher.html">Uniprot</a> and <a
168 href="pdbsequencefetcher.html">PDB</a> free text database search
169 dialogs also provide a query history.
171 <em>The query histories were introduced in Jalview 2.10.2</em>