<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head><title>Search</title>
+<head>
+<title>Search</title>
<style type="text/css">
<!--
td {
</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.gif" width="339" height="110">
-<p>"Find next" will find the next occurence 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.</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>
-</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><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
-"[ILGVMA]{;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>
+ <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.gif" width="339" height="110">
+ <p>"Find next" will find the next occurence 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.</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>
+ </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>
+ <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
+ "[ILGVMA]{;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>
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff