-<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 is displayed by pressing Control and F or\r
- selecting "Find..." from the "Search" menu.</p>\r
-<img src="search.gif" width="339" height="110">\r
-<p>"Find next" will find the next occurence of the specified and adjust \r
- the alignment window view to show it, and "Find all" highlights all \r
- matches for a pattern. The "New Feature" is a quick way to highlight \r
- and group residues matching the specified search pattern throughout the alignment. \r
-<ul>\r
- <li>The search uses regular expressions. (understands a mixture of posix and \r
- perl style regex - see below for a summary)</li>\r
- <li>Gaps are ignored when matching the query to the sequences in the alignment.</li>\r
- <li>The search is applied to both sequences and their IDs but the "Find \r
- next" and "Find all" buttons only count the sequence matches.</li>\r
- <li>If a region is selected, then search will <strong>only</strong> be performed \r
- on that region. </li>\r
- <li>To quickly clear the current selection, press the "Escape" key.</li>\r
- <li>Tick the "Match Case" box to perform a case sensitive search.</li>\r
-</ul>\r
-<p><strong>Creating Features from Search Results</strong></p>\r
-<p>\r
- If "New Feature" is selected, the feature can be given a name from \r
- a popup input box. Use the "Feature Settings" under the "View" \r
- menu to change the visibility and colour of the new sequence feature.</p> \r
-<p><strong>A quick Regular Expression Guide</strong></p>\r
-<p>A regular expression is not just a simple text query - although it\r
-can be used like one, the query is not parsed literally, but\r
-interpreted like a series of instructions defining the features of the\r
-match. For example, a simple query like "ACDED" would\r
-match all occurences of that string, but "ACD+ED" matches\r
-both 'ACDDED' and 'ACDDDDDDDDED'. More usefully, the query\r
-"[ILGVMA]{;5,}" would find stretches of small,\r
-hydrophobic amino acids of at least five residues in length.\r
-</p>\r
-<p> The table\r
-below describes some of the regular expression syntax:<br></p>\r
-<table width="100%" border="1">\r
- <tr>\r
- <td width="24%">Regular Expression Element</td>\r
- <td width="76%">Effect</td>\r
- </tr>\r
- <tr>\r
- <td width="24%">.</td>\r
- <td width="76%">Matches any single character</td>\r
- </tr>\r
- <tr>\r
- <td>[]</td>\r
- <td>Matches any one of the characters in the brackets</td>\r
- </tr>\r
- <tr>\r
- <td>^</td>\r
- <td>Matches at the start of an ID or sequence</td>\r
- </tr>\r
- <tr>\r
- <td>$</td>\r
- <td>Matches at the end of an ID or sequence</td>\r
- </tr>\r
- <tr>\r
- <td>*</td>\r
- <td>Matches if the preceding element matches zero or more times</td>\r
- </tr>\r
- <tr>\r
- <td>?</td>\r
- <td>Matches if the preceding element matched once or not at all</td>\r
- </tr>\r
- <tr>\r
- <td>+</td>\r
- <td>Matches if the preceding element matched at least once</td>\r
- </tr>\r
- <tr>\r
- <td>{count}</td>\r
- <td>Matches if the preceding element matches a specified number of\r
- times\r
- </td>\r
- </tr>\r
- <tr>\r
- <td>{min,}</td>\r
- <td> Matches of the preceding element matched at least the\r
- specified number of times</td>\r
- </tr>\r
- <tr>\r
- <td>{min,max} </td>\r
- <td>Matches if the preceding element matches min or at most max\r
- number of times</td>\r
- </tr>\r
-</table>\r
-</body>\r
-</html>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.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