<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">\r
-<p>"Find next" will find the next occurence of the specified\r
- and adjust the alignment window view to show it, and "Find\r
- all" highlights all matches for a pattern. The "Create new\r
- group" is a quick way to highlight and group residues matching\r
- the specified search pattern throughout the alignment.</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\r
- posix and perl style regex - see below for a summary)</li>\r
-<li>Gaps are ignored when matching the query to the sequences in the\r
- alignment.</li>\r
-<li>The search is applied to both sequences and their IDs but the "Find next"\r
- and "Find all" buttons only count the sequence matches.</li>\r
- <li>If a region is selected, then search will <strong>only</strong>\r
- be performed on that region. </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><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
</tr>\r
<tr>\r
<td>{min,}</td>\r
- <td> Matches at least the specified number of the preceding element.</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 between min and max\r
- number of times.</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