-<html>\r
-<head><title>Search</title>\r
-<style type="text/css">\r
-<!--\r
-td {\r
- text-align: center;\r
-}\r
--->\r
-</style>\r
-</head>\r
-\r
-<body>\r
-<p><strong>Search</strong></p>\r
-<p>The search box can be displayed by pressing the keys Control and F or selecting\r
- "Search"</p>\r
-Note:\r
-<ul>\r
- <li>The search will be performed on the selected region. If no region is selected,\r
- the search will operate on the full alignment.</li>\r
- <li>To clear any selection, press the "Escape" key.</li>\r
-</ul>\r
-<p>Using the "Create new group" is a quick way to group and highlight\r
- residues with the specified search pattern throughout the alignment.</p>\r
-<p>The search allows regular expression matching. </p>\r
-<p> </p>\r
-<table width="100%" border="1">\r
- <tr>\r
- <td width="24%">.</td>\r
- <td width="76%">Any single character.</td>\r
- </tr>\r
- <tr>\r
- <td>[]</td>\r
- <td>Any one of the characters in the brackets</td>\r
- </tr>\r
- <tr>\r
- <td>^</td>\r
- <td>The start of a line (column 1). </td>\r
- </tr>\r
- <tr>\r
- <td>$</td>\r
- <td>The end of a line </td>\r
- </tr>\r
- <tr>\r
- <td>*</td>\r
- <td> Matches zero or more of the preceding characters or expressions. </td>\r
- </tr>\r
- <tr>\r
- <td>?</td>\r
- <td>Matches zero or one of the preceding characters or expressions. </td>\r
- </tr>\r
- <tr>\r
- <td>+</td>\r
- <td>Matches one or more of the preceding characters or expressions. </td>\r
- </tr>\r
- <tr>\r
- <td>{count}</td>\r
- <td> Matches the specified number of the preceding characters or expressions.\r
- </td>\r
- </tr>\r
- <tr>\r
- <td>{min,}</td>\r
- <td> Matches at least the specified number of the preceding characters or\r
- expressions.</td>\r
- </tr>\r
- <tr>\r
- <td>{min,max} </td>\r
- <td>Matches between min and max of the preceding characters or expressions.</td>\r
- </tr>\r
-</table>\r
-</body>\r
-</html>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<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.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