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+<title>Summary of Command Line Arguments (version 2.11.3.0 onwards)</title>
+<body>
+
+ <h1>Summary of Command Line Arguments (version 2.11.3.0 onwards)</h1>
+
+ <p>
+ See <a href="clarguments-ng.html">Jalview Command Line Arguments (next generation)</a>
+ for more explanation about using Jalview's command line arguments.
+ </p>
+
+ <table border="1" cellpadding="3">
+ <tr>
+ <td><strong>argument</strong></td>
+ <td><strong>action</strong></td>
+ <td><strong>subval modifiers</strong> (optional)</td>
+ <td align="center"><strong>linked</strong> (optional)</td>
+ </tr>
+
+ <tr>
+ <td><code>--open <em>filename/URL ...</em></code></td>
+ <td>
+ Opens one or more alignment files in new alignment windows.
+ <a href="clarguments-ng.html#open">Examples</a>.
+ </td>
+ <td>
+ <code>
+ colour=<em>colourscheme</em>,
+ title=<em>title</em>,
+ features=<em>featurefile</em>,
+ annotations=<em>annotationfile</em>,
+ tree=<em>treefile</em>,
+ showannotations,
+ ssannotations,
+ sortbytree,
+ wrap
+ </code>
+ </td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr>
+ <td><code>--append <em>filename/URL ...</em></code></td>
+ <td>Appends one or more alignment files to an open alignment window (or opens a new alignment if none already open).</td>
+ <td>
+ <code>
+ colour=<em>colourscheme</em>,
+ title=<em>title</em>,
+ features=<em>featurefile</em>,
+ annotations=<em>annotationfile</em>,
+ tree=<em>treefile</em>,
+ showannotations,
+ ssannotations,
+ sortbytree,
+ wrap
+ </code>.
+ <a href="clarguments-ng.html#append">Examples</a>.
+ </td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr>
+ <td><code>--title <em>"title"</em></code></td>
+ <td>Specifies the title for the open alignment window.</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr>
+ <td><code>--colour <em>colourscheme</em></code></td>
+ <td>Applies the given colour scheme to the open alignment window. Valid values are:
+ <code>clustal</code>,
+ <code>blosum62</code>,
+ <code>pc-identity</code>,
+ <code>zappo</code>,
+ <code>taylor</code>,
+ <code>gecos-flower</code>,
+ <code>gecos-blossom</code>,
+ <code>gecos-sunset</code>,
+ <code>gecos-ocean</code>,
+ <code>hydrophobic</code>,
+ <code>helix-propensity</code>,
+ <code>strand-propensity</code>,
+ <code>turn-propensity</code>,
+ <code>buried-index</code>,
+ <code>nucleotide</code>,
+ <code>nucleotide-ambiguity</code>,
+ <code>purine-pyrimidine</code>,
+ <code>rna-helices</code>,
+ <code>t-coffee-scores</code>,
+ <code>sequence-id</code>.
+ <a href="clarguments-ng.html#colour">Examples</a>.
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr>
+ <td><code>--features <em>filename/URL</em></code></td>
+ <td>Add a feature file to the open alignment.</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+
+
+ <tr>
+ <td><code>--tree <em>filename/URL</em></code></td>
+ <td>Add a tree file to the open alignment.</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr>
+ <td><code>--sortbytree / --nosortbytree</code></td>
+ <td>Enforces sorting (or not sorting) the alignment in the order of an attached phylogenetic tree.</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+
+ <tr>
+ <td><code>--annotations <em>filename/URL</em></code></td>
+ <td>Add an annotations file to the open alignment.</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr>
+ <td><code>--showannotations / --noshowannotations</code></td>
+ <td>Enforces showing (or not showing) alignment annotations.</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+
+ <tr>
+ <td><code>--structure <em>filename/URL</em></code></td>
+ <td>Load a structure file attached to a sequence in the open alignment.</td>
+ <td>
+ <code>
+ seqid=<em>sequenceid</em></code> or <code><em>sequence index</em>,
+ paefile=<em>paefilename</em>,
+ tempfac=<em>temperature factor type</em>,
+ ssannotations,
+ notempfac,
+ structureviewer=<em>structure viewer</em>
+ </code></td>
+ <td align="center">✓</td>
+ </tr>
+
+
+ <tr>
+ <td><code>--paematrix <em>filename</em></code></td>
+ <td>Add a PAE file to the preceding <code>--structure</code></td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+
+ <tr>
+ <td><code>--tempfac <em>temperature factor type</em></code></td>
+ <td>Set the type of temperature factor. Possible values are
+ <code>default</code>,
+ <code>plddt</code>
+ </td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+
+ <tr>
+ <td><code>--structureviewer <em>structure viewer</em></code></td>
+ <td>Set the structure viewer to use to open the 3d structure file specified in previous <code>--structure</code>. Possible values are:
+ <br/>
+ <code>none</code>,
+ <br/>
+ <code>jmol</code>,
+ <br/>
+ <code>chimera</code> <em>- requires installation, might need configuring in Preferences</em>,
+ <br/>
+ <code>chimerax</code> <em>- requires installation, might need configuring in Preferences</em>,
+ <br/>
+ <code>pymol</code> <em>- requires installation, might need configuring in Preferences</em>
+ </td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+
+ <tr>
+ <td><code>--notempfac</code></td>
+ <td>Do not show the temperature factor annotation for the preceding <code>--structure</code></td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+
+ <tr>
+ <td><code>--groovy <em>filename</em></code></td>
+ <td>Process a groovy script in the file for the open alignment.</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+
+ <tr>
+ <td><code>--image <em>new filename</em></code></td>
+ <td>Output an image of the open alignment window. Format is specified by the subval modifier, a following <code>--type</code> argument or guessed from the file extension. Valid formats/extensions are:
+ <code>svg</code>,
+ <code>png</code>,
+ <code>eps</code>,
+ <code>html</code>,
+ <code>biojs</code>
+ </td>
+ <td>
+ <code>type=<em>image format</em>,
+ <code>textrenderer=<em>text format</em>
+ </td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr>
+ <td><code>--type <em>image format</em></code></td>
+ <td>Set the image format for the preceding <code>--image</code>. Valid values are:
+ <code>svg</code>,
+ <code>png</code>,
+ <code>eps</code>,
+ <code>html</code>,
+ <code>biojs</code>
+ </td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr>
+ <td><code>--textrenderer <em>text format</em></code></td>
+ <td>Sets whether text in a vector image format (SVG, HTML, EPS) should be rendered as text or vector line-art. Possible values are:
+ <code>text</code>,
+ <code>lineart</code>
+ </td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr>
+ <td><code>--output <em>outputfilename</em></code></td>
+ <td>Export the open alignment. Format is specified by the subval modifier, a following <code>--format</code> argument or guessed from the file extension. Valid formats/extensions are:
+ <br/>
+ Fasta (<code>fa, fasta</code>),
+ <br/>
+
+ </td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+
+ <tr>
+ <td><code>-- <em></em></code></td>
+ <td></td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+
+ <tr>
+ <td><code>-- <em></em></code></td>
+ <td></td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ <tr>
+ <td><code>-- <em></em></code></td>
+ <td></td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+
+
+ </table>
<h1>Jalview Command Line Arguments (version 2.11.3.0 and later)</h1>
<p>
+ For a summary of Jalview command line arguments see <a href="clarguments-ng-summary.html">Summary
+ of Command Line Arguments</a>.
+ </p>
+
+ <p>
From version 2.11.3.0 Jalview processes a new set of command line arguments
which allow more powerful and flexible combinations of arguments, though can
also be used for very simple use cases too.
in typical use cases you may still want to think of it as doing so.
<br/>
For more advanced use please see
- <a href="advancedclarguments.html">Advanced Command Line Arguments</a>.
+ <!--<a href="advancedclarguments.html">Advanced Command Line Arguments</a>.-->
</p>
<h4 name="opening_files">Opening files (<code>--open</code>, <code>--append</code>, <code>--new</code>)</h4>
<p>
- To simply open one or more alignment files in different frames just put the filenames as the first arguments:
+ To simply open one or more alignment files in different windows just put the filenames as the first arguments:
<pre>
jalview filename1 filename2 ...
</pre>
after the initial filenames.)
</p>
- <h5 name="--open"><code>--open</code></h5>
+ <h5 name="open"><code>--open</code></h5>
<p>
- Use the <code>--open</code> argument to open alignment files each in their own frame.
+ Use the <code>--open</code> argument to open alignment files each in their own window.
</p>
<p>
</pre>
</p>
- <h5 name="--append"><code>--append</code></h5>
+ <h5 name="append"><code>--append</code></h5>
<p>
To append several alignment files together use:
<pre>
jalview --open filename1.fa --append filename2.fa filename3.fa
</pre>
- or, if you haven't previously used <code>--open</code> then you can use --append to open one new frame and keep appending each set of alignments:
+ or, if you haven't previously used <code>--open</code> then you can use --append to open one new window and keep appending each set of alignments:
<pre>
jalview --append these/filename*.fa --append more/filename*.fa
</p>
<p>
- <strong>Note</strong> that whilst you can include a Jalview Project File (<code>.jvp</code>) as an <code>--append</code> value, the items in the file will always open in their original frames and not append to another.
+ <strong>Note</strong> that whilst you can include a Jalview Project File (<code>.jvp</code>) as an <code>--append</code> value, the items in the file will always open in their original windows and not append to another.
</p>
- <h5 name="--new"><code>--new</code></h5>
+ <h5 name="new"><code>--new</code></h5>
<p>
- To append different sets of alignment files in different frames, use <code>--new</code> to move on to a new alignment frame:
+ To append different sets of alignment files in different windows, use <code>--new</code> to move on to a new alignment window:
<pre>
jalview --append these/filename*.fa --new --append other/filename*.fa
</pre>
<h5 name="annotations"><code>--annotations</code></h5>
<p>
- You can specify whether the currently opened alignment frame should show alignment annotations (e.g. Conservation, Quality, Consensus...) or not with either <code>--annotations</code> or <code>--noannotations</code>. If you don't specify then your saved preference will be used.
+ You can specify whether the currently opened alignment window should show alignment annotations (e.g. Conservation, Quality, Consensus...) or not with either <code>--annotations</code> or <code>--noannotations</code>. If you don't specify then your saved preference will be used.
<pre>
jalview --open examples/uniref50.fa --noannotations
</pre>
<h5 name="title"><code>--title</code></h5>
<p>
- If you would like to give the alignment frame a specific title you can do so with the <code>--title</code> option:
+ If you would like to give the alignment window a specific title you can do so with the <code>--title</code> option:
<pre>
jalview --open examples/uniref50.fa --title "My example alignment"
</pre>
<h5 name=""><code>--structure</code></h5>
<p>
- You can add a 3D structure file to a sequence in the current alignment frame with the <code>--structure</code> option:
+ You can add a 3D structure file to a sequence in the current alignment window with the <code>--structure</code> option:
<pre>
jalview --open examples/uniref50.fa --structure examples/AlphaFold/AF-P00221-F1-model_v4.pdb
</pre>
git://source.jalview.org / jalview.git / commitdiff