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-<html>
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- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
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- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
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- * of the License, or (at your option) any later version.
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-<head>
-<title>Search</title>
-<style type="text/css">
-<!--
-td {
- text-align: center;
-}
--->
-</style>
-</head>
-
-<body>
- <p>
- <strong>Search</strong>
- </p>
- <p>The search box is displayed by pressing Control and F or
- selecting "Find..." from the "Search" menu.</p>
- <img src="search.png" width="398" height="124">
- <p>"Find next" will find the next occurrence of the
- specified and adjust the alignment window view to show it, and
- "Find all" highlights all matches for a pattern. The
- "New Feature" is a quick way to highlight and group
- residues matching the specified search pattern throughout the
- alignment.
- <ul>
- <li>The search uses regular expressions. (understands a mixture
- of posix and perl style regex - see below for a summary)</li>
- <li>Gaps are ignored when matching the query to the sequences
- in the alignment.</li>
- <li>The search is applied to both sequences and their IDs, and
- optionally also to the description string (<em>since Jalview
- 2.10</em>)
- </li>
- <li>If a region is selected, then search will <strong>only</strong>
- be performed on that region.
- </li>
- <li>To quickly clear the current selection, press the
- "Escape" key.</li>
- <li>Tick the "Match Case" box to perform a case
- sensitive search.</li>
- <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.
- </ul>
- <p>
- <strong>Creating Features from Search Results</strong>
- </p>
- <p>If "New Feature" is selected, the feature can be
- given a name from a popup input box. Use the "Feature
- Settings" under the "View" menu to change the
- visibility and colour of the new sequence feature.</p>
- <p>
- <p>
- <strong>Selecting regions from Search Results</strong>
- </p>
- <p>
- Press 'B' or use the <em>Select Highlighted Columns</em> option from
- the alignment window's select menu to add columns containing
- highlighted search results to the alignment window's column
- selection. Alt-'B' will add all but the highlighted columns, and
- Ctrl (or Cmd) -B will toggle the column selection for the
- highlighted region.
- </p>
- <p>
-
- <strong>A quick Regular Expression Guide</strong>
- </p>
- <p>A regular expression is not just a simple text query - although
- it can be used like one, the query is not parsed literally, but
- interpreted like a series of instructions defining the features of
- the match. For example, a simple query like "ACDED" would
- match all occurences of that string, but "ACD+ED" matches
- both 'ACDDED' and 'ACDDDDDDDDED'. More usefully, the query
- "[GVATC]{;5,}" would find stretches of small, hydrophobic
- amino acids of at least five residues in length.</p>
- <p>
- The table below describes some of the regular expression syntax:<br>
- </p>
- <table width="100%" border="1">
- <tr>
- <td width="24%">Regular Expression Element</td>
- <td width="76%">Effect</td>
- </tr>
- <tr>
- <td width="24%">.</td>
- <td width="76%">Matches any single character</td>
- </tr>
- <tr>
- <td>[]</td>
- <td>Matches any one of the characters in the brackets</td>
- </tr>
- <tr>
- <td>^</td>
- <td>Matches at the start of an ID or sequence</td>
- </tr>
- <tr>
- <td>$</td>
- <td>Matches at the end of an ID or sequence</td>
- </tr>
- <tr>
- <td>*</td>
- <td>Matches if the preceding element matches zero or more
- times</td>
- </tr>
- <tr>
- <td>?</td>
- <td>Matches if the preceding element matched once or not at
- all</td>
- </tr>
- <tr>
- <td>+</td>
- <td>Matches if the preceding element matched at least once</td>
- </tr>
- <tr>
- <td>{count}</td>
- <td>Matches if the preceding element matches a specified
- number of times</td>
- </tr>
- <tr>
- <td>{min,}</td>
- <td>Matches of the preceding element matched at least the
- specified number of times</td>
- </tr>
- <tr>
- <td>{min,max}</td>
- <td>Matches if the preceding element matches min or at most
- max number of times</td>
- </tr>
- </table>
- <p>
- <a name="queryhistory" /><strong>Search History</strong>
- </p>
- <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>
- <img src="searchhist.png" width="404" height="185" align="left" />
- <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>
- <img src="searchclearhist.png" width="402" height="127" align="left" />
- <p>
- <strong>Other dialogs that provide a query history</strong>
- </p>
- <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>
- <em>The query histories were introduced in Jalview 2.10.2</em>
-</body>
-</html>
git://source.jalview.org / jalview.git / blobdiff