</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="400" height="152">
+ <img src="search.png" height="152">
<p>"Find next" will find the next occurrence of the
query and adjust the alignment window view to show it, and
"Find all" highlights all matches for a query. The
<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>Hidden columns can optionally be ignored (<em>since Jalview 2.11</em>)</li>
- <li>The search is applied to both sequences and their IDs. It can
- optionally also be applied to the description string (<em>since Jalview
- 2.10</em>), and sequence feature descriptions (<em>since Jalview 2.11.2.5</em>).
- </li>
- <li>If a region is selected, then search will <strong>only</strong>
+ <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>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 href="#queryhistory">previously used
<strong>Copying highlighted regions to a new alignment</strong>
</p>
<p>
- You can copy the currently highlighted matching regions of sequences to the clipboard with alt-Command-C.
+ 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>
+ <p>
<strong>A quick Regular Expression Guide</strong>
</p>
- <!-- JAL-4019 --> Ambiguous Base Colourscheme
- <!-- JAL-4061 --> Find can search sequence features' type and description
- <!-- JAL-4062 --> Hold down Shift + CMD/CTRL C to copy highlighted regions as new sequences
-- <!-- JAL-1556 --> Quickly enable select and/or colour by for displayed annotation row via its popup menu
+- <!-- JAL-1556 --> Quickly enable select and/or colour by for displayed annotation row via annotation panel popup menu
- <!-- JAL-4094 --> Shift+Click+Drag to adjust height of all annotation tracks of same type
- <!-- JAL-4190 --> Pressing escape in tree panel clears any current selection