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>
59 <li>To access a <a ref="#queryhistory">previously used query</a> press the down arrow or click on the button on the right of the text field.
62 <strong>Creating Features from Search Results</strong>
64 <p>If "New Feature" is selected, the feature can be
65 given a name from a popup input box. Use the "Feature
66 Settings" under the "View" menu to change the
67 visibility and colour of the new sequence feature.</p>
70 <strong>Selecting regions from Search Results</strong>
73 Press 'B' or use the <em>Select Highlighted Columns</em> option from
74 the alignment window's select menu to add columns containing
75 highlighted search results to the alignment window's column
76 selection. Alt-'B' will add all but the highlighted columns, and
77 Ctrl (or Cmd) -B will toggle the column selection for the
82 <strong>A quick Regular Expression Guide</strong>
84 <p>A regular expression is not just a simple text query - although
85 it can be used like one, the query is not parsed literally, but
86 interpreted like a series of instructions defining the features of
87 the match. For example, a simple query like "ACDED" would
88 match all occurences of that string, but "ACD+ED" matches
89 both 'ACDDED' and 'ACDDDDDDDDED'. More usefully, the query
90 "[GVATC]{;5,}" would find stretches of small, hydrophobic
91 amino acids of at least five residues in length.</p>
93 The table below describes some of the regular expression syntax:<br>
95 <table width="100%" border="1">
97 <td width="24%">Regular Expression Element</td>
98 <td width="76%">Effect</td>
101 <td width="24%">.</td>
102 <td width="76%">Matches any single character</td>
106 <td>Matches any one of the characters in the brackets</td>
110 <td>Matches at the start of an ID or sequence</td>
114 <td>Matches at the end of an ID or sequence</td>
118 <td>Matches if the preceding element matches zero or more
123 <td>Matches if the preceding element matched once or not at
128 <td>Matches if the preceding element matched at least once</td>
132 <td>Matches if the preceding element matches a specified
137 <td>Matches of the preceding element matched at least the
138 specified number of times</td>
142 <td>Matches if the preceding element matches min or at most
143 max number of times</td>
146 <p><a name="queryhistory"/><strong>Search History</strong></p>
147 <p>A record of all the recent queries made via the Find dialog are stored along with your Jalview user preferences. To open the search history, click on the button to the right of the query field, or press the down arrow key.</p>
148 <img src="searchhist.png" width="404" height="185" align="left"/>
149 <p>The search history keeps up to 99 queries by default. To clear the history, or modify the size of the history, right-click the text box.</p>
150 <img src="searchclearhist.png" width="402" height="121" align="left"/>
151 <p><strong>Other dialogs that provide a query history</strong></p>
152 <p>Jalview's <a href="uniprotsequencefetcher.html">Uniprot</a> and <a href="pdbsequencefetcher.html">PDB</a> free text database search dialogs also provide a query history.</p>
153 <em>The query histories were introduced in Jalview 2.10.2</em>