* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<title>Jalview Command Line Arguments: basic usage</title>
+<title>Command Line: basic usage</title>
<body>
- <h1>Jalview Command Line Arguments: basic usage</h1>
+ <h1>Command Line: basic usage</h1>
<p>
- <a href="clarguments.html">Jalview Command Line Arguments: summary</a>
+ <a href="clarguments.html">Command Line: introduction</a>
<br/>
- <a href="clarguments-intro.html">Jalview Command Line Arguments: introduction</a>
+ Command Line: basic usage
<br/>
- Jalview Command Line Arguments: basic usage
+ <a href="clarguments-advanced.html">Command Line: advanced usage</a>
<br/>
- <a href="clarguments-advanced.html">Jalview Command Line Arguments: advanced usage</a>
+ <a href="clarguments-argfiles.html">Command Line: argument files</a>
<br/>
- <a href="clarguments-argfiles.html">Jalview Command Line Arguments: argfiles</a>
+ <a href="clarguments-reference.html">Command Line: reference</a>
</p>
<hr/>
</pre>
</p>
+ <p>
+ <em>Important!</em> If you use <code>--output</code> or any other argument that outputs a file, then it will be assumed you want to run Jalview in headless mode (as if you had specified <code>--headless</code>). To use Jalview with <code>--output</code> and not assume headless mode, use the <code>--gui</code> argument (the order doesn't matter).
+ </p>
+
<h3><a name="format"></a><code>--format</code></h3>
<p>
<h3><a name="all"></a><code>--all / -noall</code></h3>
<p>
- When using the <code>--all</code> argument, following arguments will apply to all of the previously opened alignment windows. You can turn this behaviour off for following arguments using the <code>--noall</code> argument. The arguments that can apply to all previously opened alignments are:
+ When using the <code>--all</code> argument, following arguments will apply to all of the previously opened alignment windows. You can turn this behaviour off again for following arguments using the <code>--noall</code> argument. The arguments that can apply to all previously opened alignments are:
<br/>
<code>--colour</code>
<br/>
<h2><a name="alloutputwildcard"></a>The all output wildcard: <code>--output "*.ext"</code>, <code>--image "*.ext"</code></h2>
<p>
- Purely as an intuitive syntactic sweetener, you can use the <code>--output</code> wildcard <code>*</code> <em>at the beginning of the output filename</em> as shorthand for <code>--all --output {dirname}/{basename}</code> followed by whatever you put after the <code>*</code>. For example, to achieve the same as the thumbnails example above, you could use
+ Purely as an intuitive syntactic sweetener, you can use the <code>--output</code> wildcard <code>*</code> <em>at the beginning of the output filename</em> as shorthand for <code>--all --output {dirname}/{basename}</code> followed by whatever you put after the '<code>*</code>'. For example, to achieve the same as the thumbnails example above, you could use
<pre>
jalview --open */*.fa --image "*.png" --colour gecos-flower --width 256 --height 256 --close --headless
</pre>
</p>
<p>
- <strong>Important!</strong> Please note that using a bareword <code>*.ext</code> (i.e. without an escape or quotation marks) in a shell command line will potentially be expanded by the shell to a list of all the files in the current directory ending with <code>.ext</code> <em>before</em> this value is passed to Jalview. This will result in the first of these files being overwritten (multiple times)! If you shell-escape the <code>*</code> (usually with a backslash '\') or enclose the value in quotation marks ('"*.ext"') then the shell will not expand the wildcard.
+ <strong>Important!</strong> Please note that using a bareword <code>*.ext</code> (i.e. without an escape or quotation marks) in a shell command line will potentially be expanded by the shell to a list of all the files in the current directory ending with <code>.ext</code> <em>before</em> this value is passed to Jalview. This will result in the first of these files being overwritten (multiple times)! If you shell-escape the <code>*</code> (usually with a backslash '\') or enclose the value in quotation marks (<code>"*.ext"</code> - that's including the quotation marks) then the shell will not expand the wildcard.
</p>
<p>
</p>
<hr/>
- Continue to <a href="clarguments-advanced.html">Jalview Command Line Arguments: advanced usage</a>.
+ Continue to <a href="clarguments-advanced.html">Command Line: advanced usage</a>.
<br/>
- Return to <a href="clarguments.html">Jalview Command Line Arguments: summary</a>.
-
+ <a href="clarguments-reference.html">Command Line: reference</a>
</body>
</html>