<html>\r
-<head>\r
+<head><title>Search</title>\r
<style type="text/css">\r
<!--\r
td {\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
+<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 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
+ <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>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
+<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>.</td>\r
- <td>Any single character.</td>\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>Any one of the characters in the brackets</td>\r
+ <td>Matches 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
+ <td>Matches at the start of an ID or sequence</td>\r
</tr>\r
<tr>\r
<td>$</td>\r
- <td>The end of a line </td>\r
+ <td>Matches at the end of an ID or sequence</td>\r
</tr>\r
<tr>\r
<td>*</td>\r
- <td> Matches zero or more of the preceding characters or expressions. </td>\r
+ <td>Matches if the preceding element matches zero or more times</td>\r
</tr>\r
<tr>\r
<td>?</td>\r
- <td>Matches zero or one of the preceding characters or expressions. </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 one or more of the preceding characters or expressions. </td>\r
+ <td>Matches if the preceding element matched at least once</td>\r
</tr>\r
<tr>\r
<td>{count}</td>\r
- <td> Matches the specified number of the preceding characters or expressions.\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 at least the specified number of the preceding characters or\r
- expressions.</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 between min and max of the preceding characters or expressions.</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
git://source.jalview.org / jalview.git / blobdiff