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</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
+ <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
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>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>
"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>
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
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
+ "[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>
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>
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