* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<title>Summary of Command Line Arguments (version 2.11.3.0 onwards)</title>
+<title>Summary of Command Line Arguments (next generation)</title>
<body>
- <h1>Summary of Command Line Arguments (version 2.11.3.0 onwards)</h1>
+ <h1>Summary of Command Line Arguments (next generation)</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>
+
+
+
+
+ <h2>Initialising arguments</h2>
+
<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 <em>filename</em> or URLs <em>URL</em> 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 <em>filename</em> or URLs <em>URL</em> to the open alignment window (or opens a new alignment if none already open).</td>
- <td>
- <code>
- colour=<em>name</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>"string""</em></code></td>
- <td>Specifies the title for the open alignment window as <em>string</em>.</td>
- <td></td>
- <td align="center">✓</td>
- </tr>
-
- <tr>
- <td><code>--colour <em>name</em></code></td>
- <td>Applies the colour scheme <em>name</em> to the open alignment window. Valid values for <em>name</em>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 <em>filename</em> or URL <em>URL</em> to the open alignment.</td>
- <td></td>
- <td align="center">✓</td>
- </tr>
+ <tr valign="top">
+ <td><strong>argument</strong></td>
+ <td><strong>action</strong></td>
+ </tr>
-
-
- <tr>
- <td><code>--tree <em>filename/URL</em></code></td>
- <td>Add a tree file <em>filename</em> or URL <em>URL</em> 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 <em>filename</em> or URL <em>URL</em> 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>--wrap / --nowrap</code></td>
- <td>Enforces wrapped (or not wrapped) alignment formatting.</td>
- <td></td>
- <td align="center">✓</td>
- </tr>
+ <tr valign="top">
+ <td><code>‑‑help / -h</code></td>
+ <td>Display a help statement</td>
+ </tr>
-
- <tr>
- <td><code>--structure <em>filename/URL</em></code></td>
- <td>Load a structure file <em>filename</em> or URL <em>URL</em> associated with a sequence in the open alignment. The sequence to be associated with can be specified with a following <code>--seqid</code> argument, or the subval modifier <code>seqid=<em>ID</em></code> can be used. A subval <em>INDEX</em> can also be used to specify the <em>INDEX-th</em> sequence in the open alignment.</td>
- <td>
+ <tr valign="top">
+ <td><code>‑‑headless</code></td>
+ <td>Run Jalview in headless mode. No GUI interface will be created and Jalview will quit after all arguments have been processed.</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑jabaws <em>URL</em></code></td>
+ <td>Set a different URL to connect to a JABAWS server.</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑news / ‑‑nonews</code></td>
+ <td>Show (or don't show) the news feed.</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑splash / ‑‑nosplash</code></td>
+ <td>Show (or don't show) the About Jalview splash screen.</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑questionnaire / ‑‑noquestionnaire</code></td>
+ <td>Show (or don't show) the questionnaire if one is available.</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑usagestats / ‑‑nousagestats</code></td>
+ <td>Send (or don't send) initial launch usage stats. <em>Note: usage stats are useful for future funding for Jalview!</em></td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑webservicediscovery / ‑‑nowebservicediscovery</code></td>
+ <td>Attempt (or don't attempt) to connect to JABAWS web services.</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑props <em>filename</em></code></td>
+ <td>Use file <em>filename</em> as the preferences file <em>instead</em> of the usual <code>~/.jalview_properties</code> file.</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑debug</code></td>
+ <td>Start Jalview in debug log level.</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑quiet</code></td>
+ <td>Stop all output to STDOUT (after the Java Virtual Machine has started). Use <code>‑‑quiet</code> a second time to stop all output to STDERR.</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑initsubstitutions / ‑‑noinitsubstitutions</code></td>
+ <td>Assume that <code>‑‑substitutions</code> are initially enabled (or initially disabled).</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑jvmmempc=<em>PERCENT</em></code></td>
+ <td>
+ <em>Only available with standalone executable jar or jalview.bin.Launcher.</em>
+ <br/>
+ Limit maximum heap size (memory) to PERCENT% of total physical memory detected.
+ This defaults to 90 if total physical memory can be detected.
+ <br/>
+ The equals sign ("=") separator must be used with no spaces.
+ <br/>
+ See <a href="../memory.html">Memory usage settings for Jalview</a> for more details.
+ </td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑jvmmemmax=<em>MAXMEMORY</em></code></td>
+ <td>
+ <em>Only available with standalone executable jar or jalview.bin.Launcher.</em>
+ <br/>
+ Limit maximum heap size (memory) to MAXMEMORY. MAXMEMORY can be specified in bytes, kilobytes(k), megabytes(m),
+ gigabytes(g) or if you're lucky enough, terabytes(t).
+ This defaults to 32g if total physical memory can be detected, or to 8g if total physical memory cannot be detected.
+ <br/>
+ The equals sign ("=") separator must be used with no spaces.
+ <br/>
+ See <a href="../memory.html">Memory usage settings for Jalview</a> for more details.
+ </td>
+ </tr>
+
+ </table>
+
+
+ <h2>Opening an alignment</h2>
+
+ <table border="1" cellpadding="3">
+ <tr valign="top">
+ <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 valign="top">
+ <td><code>‑‑open <em>filename/URL ...</em></code></td>
+ <td>
+ Opens one or more alignment files <em>filename</em> or URLs <em>URL</em> in new alignment windows.
+ </td>
+ <td>
+ <code>
+ colour=<em>name</em>,
+ <br/>
+ title=<em>string</em>,
+ <br/>
+ features=<em>filename</em>,
+ <br/>
+ annotations=<em>filename</em>,
+ <br/>
+ tree=<em>filename</em>,
+ <br/>
+ showannotations,
+ <br/>
+ showssannotations,
+ <br/>
+ sortbytree,
+ <br/>
+ wrap
+ </code>
+ </td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑append <em>filename/URL ...</em></code></td>
+ <td>Appends one or more alignment files <em>filename</em> or URLs <em>URL</em> to the open alignment window (or opens a new alignment if none already open).</td>
+ <td>
<code>
- seqid=<em>sequenceid</em></code> or <code><em>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>--seqid <em>ID</em></code></td>
- <td>Specify the sequence name for the preceding <code>--structure</code> to be associated with.</td>
- <td></td>
- <td align="center">✓</td>
- </tr>
-
-
- <tr>
- <td><code>--paematrix <em>filename</em></code></td>
- <td>Add a PAE json matrix file <em>filename</em> to the preceding <code>--structure</code>.</td>
- <td></td>
- <td align="center">✓</td>
- </tr>
+ colour=<em>name</em>,
+ <br/>
+ title=<em>string</em>,
+ <br/>
+ features=<em>filename</em>,
+ <br/>
+ annotations=<em>filename</em>,
+ <br/>
+ tree=<em>filename</em>,
+ <br/>
+ showannotations,
+ <br/>
+ showssannotations,
+ <br/>
+ sortbytree,
+ <br/>
+ wrap
+ </code>.
+ </td>
+ <td align="center">✓</td>
+ </tr>
-
- <tr>
- <td><code>--tempfac <em>name</em></code></td>
- <td>Set the type of temperature factor. Possible values for <em>name</em> are
- <code>default</code>,
- <code>plddt</code>
- </td>
- <td></td>
- <td align="center">✓</td>
- </tr>
-
-
- <tr>
- <td><code>--structureviewer <em>name</em></code></td>
- <td>Set the structure viewer to use to open the 3d structure file specified in previous <code>--structure</code> to <em>name</em>. Possible values of <em>name</em> are:
- <br/>
+ <tr valign="top">
+ <td><code>‑‑title <em>"string""</em></code></td>
+ <td>Specifies the title for the open alignment window as <em>string</em>.</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑colour <em>name</em></code></td>
+ <td>Applies the colour scheme <em>name</em> to the open alignment window. Valid values for <em>name</em> are:
+ <br/>
+ <code>clustal</code>,
+ <br/>
+ <code>blosum62</code>,
+ <br/>
+ <code>pc-identity</code>,
+ <br/>
+ <code>zappo</code>,
+ <br/>
+ <code>taylor</code>,
+ <br/>
+ <code>gecos-flower</code>,
+ <br/>
+ <code>gecos-blossom</code>,
+ <br/>
+ <code>gecos-sunset</code>,
+ <br/>
+ <code>gecos-ocean</code>,
+ <br/>
+ <code>hydrophobic</code>,
+ <br/>
+ <code>helix-propensity</code>,
+ <br/>
+ <code>strand-propensity</code>,
+ <br/>
+ <code>turn-propensity</code>,
+ <br/>
+ <code>buried-index</code>,
+ <br/>
+ <code>nucleotide</code>,
+ <br/>
+ <code>nucleotide-ambiguity</code>,
+ <br/>
+ <code>purine-pyrimidine</code>,
+ <br/>
+ <code>rna-helices</code>,
+ <br/>
+ <code>t-coffee-scores</code>,
+ <br/>
+ <code>sequence-id</code>.
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑features <em>filename/URL</em></code></td>
+ <td>Add a feature file <em>filename</em> or URL <em>URL</em> to the open alignment.</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+
+
+ <tr valign="top">
+ <td><code>‑‑tree <em>filename/URL</em></code></td>
+ <td>Add a tree file <em>filename</em> or URL <em>URL</em> to the open alignment.</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr valign="top">
+ <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 valign="top">
+ <td><code>‑‑annotations <em>filename/URL</em></code></td>
+ <td>Add an annotations file <em>filename</em> or URL <em>URL</em> to the open alignment.</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑showannotations / ‑‑noshowannotations</code></td>
+ <td>Enforces showing (or not showing) alignment annotations.</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑wrap / ‑‑nowrap</code></td>
+ <td>Enforces wrapped (or not wrapped) alignment formatting.</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑nostructure</code></td>
+ <td>Do not open or process any 3D structure in the <code>‑‑open</code> or <code>‑‑append</code> files.</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ </table>
+
+
+ <h2>Adding a 3D structure</h2>
+
+ <table border="1" cellpadding="3">
+ <tr valign="top">
+ <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 valign="top">
+ <td><code>‑‑structure <em>filename/URL</em></code></td>
+ <td>Load a structure file <em>filename</em> or URL <em>URL</em> associated with a sequence in the open alignment. The sequence to be associated with can be specified with a following <code>‑‑seqid</code> argument, or the subval modifier <code>seqid=<em>ID</em></code> can be used. A subval <em>INDEX</em> can also be used to specify the <em>INDEX-th</em> sequence in the open alignment.</td>
+ <td>
+ <code>
+ seqid=<em>id</em></code> or <code><em>INDEX</em>,
+ <br/>
+ paefile=<em>filename</em>,
+ <br/>
+ tempfac=<em>name</em>,
+ <br/>
+ showssannotations,
+ <br/>
+ notempfac,
+ <br/>
+ structureviewer=<em>name</em>
+ </code></td>
+ <td align="center">✓</td>
+ </tr>
+
+
+ <tr valign="top">
+ <td><code>‑‑seqid <em>ID</em></code></td>
+ <td>Specify the sequence name for the preceding <code>‑‑structure</code> to be associated with.</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+
+ <tr valign="top">
+ <td><code>‑‑paematrix <em>filename</em></code></td>
+ <td>Add a PAE json matrix file <em>filename</em> to the preceding <code>‑‑structure</code>.</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+
+ <tr valign="top">
+ <td><code>‑‑tempfac <em>name</em></code></td>
+ <td>Set the type of temperature factor. Valid values for <em>name</em> are:
+ <br/>
+ <code>default</code>,
+ <br/>
+ <code>plddt</code>
+ </td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+
+ <tr valign="top">
+ <td><code>‑‑structureviewer <em>name</em></code></td>
+ <td>Set the structure viewer to use to open the 3d structure file specified in previous <code>‑‑structure</code> to <em>name</em>. Valid values of <em>name</em> are:
+ <br/>
<code>none</code>,
<br/>
<code>jmol</code>,
<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:
+ </td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+
+ <tr valign="top">
+ <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 valign="top">
+ <td><code>‑‑showssannotations / ‑‑noshowssannotations</code></td>
+ <td>Do not show secondary structure annotations for the preceding <code>‑‑structure</code></td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ </table>
+
+
+ <h2>Outputting files</h2>
+
+ <table border="1" cellpadding="3">
+ <tr valign="top">
+ <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 valign="top">
+ <td><code>‑‑image <em>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:
+ <br/>
+ <code>svg</code>,
+ <br/>
+ <code>png</code>,
+ <br/>
+ <code>eps</code>,
+ <br/>
+ <code>html</code>,
+ <br/>
+ <code>biojs</code>.
+ </td>
+ <td>
+ <code>type=<em>name</em>,
+ <code>textrenderer=<em>name</em>
+ </td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑type <em>name</em></code></td>
+ <td>Set the image format for the preceding <code>‑‑image</code> to <em>name</em>. Valid values for <em>name</em> are:
+ <br/>
+ <code>svg</code>,
+ <br/>
+ <code>png</code>,
+ <br/>
+ <code>eps</code>,
+ <br/>
+ <code>html</code>,
+ <br/>
+ <code>biojs</code>.
+ </td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑textrenderer <em>name</em></code></td>
+ <td>Sets whether text in a vector image format (SVG, HTML, EPS) should be rendered as text or vector line-art. Valid values for <em>name</em> are:
+ <br/>
<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>
-
-
-
+ <br/>
+ <code>lineart</code>.
+ </td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑output <em>filename</em></code></td>
+ <td>Export the open alignment to file <em>filename</em>. The format <em>name</em> is specified by the subval modifier <code>format=<em>name</em></code>, a following <code>‑‑format <em>name</em></code> argument or guessed from the file extension. Valid format names (and file extensions) are:
+ <br/>
+ <code>fasta</code> (<code>fa, fasta, mfa, fastq</code>),
+ <br/>
+ <code>pfam</code> (<code>pfam</code>),
+ <br/>
+ <code>stockholm</code> (<code>sto, stk</code>),
+ <br/>
+ <code>pir</code> (<code>pir</code>),
+ <br/>
+ <code>blc</code> (<code>blc</code>),
+ <br/>
+ <code>amsa</code> (<code>amsa</code>),
+ <br/>
+ <code>json</code> (<code>json</code>),
+ <br/>
+ <code>pileup</code> (<code>pileup</code>),
+ <br/>
+ <code>msf</code> (<code>msf</code>),
+ <br/>
+ <code>clustal</code> (<code>aln</code>),
+ <br/>
+ <code>phylip</code> (<code>phy</code>),
+ <br/>
+ <code>jalview</code> (<code>jvp, jar</code>).
+ </td>
+ <td><code>format=<em>name</em></code></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑format <em>name</em></code></td>
+ <td>Sets the format for the preceding <code>‑‑output</code> file. Valid formats are:
+ <br/>
+ <code>fasta</code>,
+ <br/>
+ <code>pfam</code>,
+ <br/>
+ <code>stockholm</code>,
+ <br/>
+ <code>pir</code>,
+ <br/>
+ <code>blc</code>,
+ <br/>
+ <code>amsa</code>,
+ <br/>
+ <code>json</code>,
+ <br/>
+ <code>pileup</code>,
+ <br/>
+ <code>msf</code>,
+ <br/>
+ <code>clustal</code>,
+ <br/>
+ <code>phylip</code>,
+ <br/>
+ <code>jalview</code>.
+ </td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr valign="top">
+ <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 valign="top">
+ <td><code>‑‑backups / ‑‑nobackups</code></td>
+ <td>Enable (or disable) writing backup files when saving an <code>‑‑output</code> file. This applies to the current open alignment -- to apply to all <code>‑‑output</code> and <code>‑‑image</code> files, use after <code>‑‑all</code>.</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑overwrite / ‑‑nooverwrite</code></td>
+ <td>Enable (or disable) overwriting of output files without backups enabled. This applies to the current open alignment -- to apply to all <code>‑‑output</code> and <code>‑‑image</code> files, use after <code>‑‑all</code>.</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑close</code></td>
+ <td>Close the current open alignment window. This occurs after other output arguments. This applies to the current open alignment -- to apply to all <code>‑‑output</code> and <code>‑‑image</code> files, use after <code>‑‑all</code>.</td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ </table>
+
+
+ <h2>Controlling flow of arguments</h2>
+
+ <table border="1" cellpadding="3">
+ <tr valign="top">
+ <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 valign="top">
+ <td><code>‑‑new</code></td>
+ <td>Move on to a new alignment window. This will ensure <code>‑‑append</code> will start a new alignment window and other linked arguments will apply to the new alignment window.</td>
+ <td></td>
+ <td align="center"></td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑substitutions / ‑‑nosubstitutions</code></td>
+ <td>The following argument values allow (or don't allow) subsituting filename parts. This is initially true. Valid substitutions are
+ <code>{basename}</code> - the filename-without-extension of the currently <code>‑‑open</code>ed file (or first <code>‑‑append</code>ed file),
+ <br/>
+ <code>{dirname}</code>, - the directory (folder) name of the currently <code>‑‑open</code>ed file (or first <code>‑‑append</code>ed file),
+ <br/>
+ <code>{argfilebasename}</code> - the filename-without-extension of the current <code>‑‑argfile</code>,
+ <br/>
+ <code>{argfiledirname}</code> - the directory (folder) name of the current <code>‑‑argfile</code>,
+ <br/>
+ <code>{n}</code> - the value of the index counter (starting at 0).
+ <br/>
+ <code>{++n}</code> - increase and substitute the value of the index counter,
+ <br/>
+ <code>{}</code> - the value of the current alignment window <em>default</em> index.
+ </td>
+ <td></td>
+ <td align="center"></td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑argfile <em>filename</em></code></td>
+ <td>
+ Open one or more files <em>filename</em> and read, line-by-line, as arguments to Jalview.
+ <br/>
+ <strong>Note</strong> that if you use one or more <code>‑‑argfile</code> arguments then all other non-initialising arguments will be ignored.
+ </td>
+ <td></td>
+ <td align="center"></td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑npp</code></td>
+ <td>Increase the index counter used in argument value substitutions.</td>
+ <td></td>
+ <td align="center"></td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑all</code></td>
+ <td>Apply the following output arguments to <em>all</em> sets of linked arguments.</td>
+ <td></td>
+ <td align="center"></td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑quit</code></td>
+ <td>After all files have been opened, appended and output, quit Jalview. In <code>‑‑headless</code> mode this already happens.</td>
+ <td></td>
+ <td align="center"></td>
+ </tr>
+
</table>
git://source.jalview.org / jalview.git / blobdiff