</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">
+ <img src="search.png" height="152">
<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
+ query and adjust the alignment window view to show it, and
+ "Find all" highlights all matches for a query. 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>If a region is selected, then search will <strong>only</strong>
+ be performed on that region.<br />
+ <em>Tip: to quickly clear the current selection, click the
+ alignment view you wish to search, then press 'Escape'.</em>
+ </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>Hidden columns can optionally be ignored (<em>since Jalview 2.11</em>)</li>
+ <li>The search is applied to both sequences and their IDs. <br />
+ Check boxes also enable searching of:
+ <ul>
+ <li><strong>Sequence description</strong> (<em>since Jalview 2.10</em>)
+ </li>
+ <li><strong>Sequence Feature</strong> type and description for currently displayed features (<em>since Jalview
+ 2.11.3.0</em>)
+ </li>
+ </ul>
+ </li>
<li>Tick the "Match Case" box to perform a case
sensitive search.</li>
- <li>To access a <a ref="#queryhistory">previously used
+ <li>To access a <a href="#queryhistory">previously used
query</a> press the down arrow or click on the button on the right
of the text field.
</ul>
highlighted region.
</p>
<p>
+ <strong>Copying highlighted regions to a new alignment</strong>
+ </p>
+ <p>
+ Press <strong>Copy</strong> button or type Ctrl (Cmd on OSX) + Shift +
+ C to copy highlighted search results to the clipboard, enabling them
+ to be pasted to a new alignment (via Shift+Ctrl (or Cmd) + V).
+ </p>
+ <p>
<strong>A quick Regular Expression Guide</strong>
</p>
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
+ <p><img src="searchhist.png" width="404" height="185" />
+ </p><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>
+ <p><img src="searchclearhist.png" width="402" height="127"/>
+ </p>
+<p width="100%">
<strong>Other dialogs that provide a query history</strong>
</p>
<p>