+
+
+ <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>sub-value modifiers</strong> (optional)</td>
+ <td><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 sub-value modifier <code>seqid=<em>ID</em></code> can be used. A sub-value <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>,
+ <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 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>
+
+ <tr valign="top">
+ <td><code>‑‑close</code></td>
+ <td>Close the open alignment window. This occurs after other output, processing and image export 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>Processing alignments</h2>
+
+ <table border="1" cellpadding="3">
+ <tr valign="top">
+ <td><strong>argument</strong></td>
+ <td><strong>action</strong></td>
+ <td><strong>sub-value modifiers</strong> (optional)</td>
+ <td><strong>linked</strong> (optional)</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>
+ </table>
+
+
+ <h2>Outputting alignment files</h2>
+
+ <table border="1" cellpadding="3">
+ <tr valign="top">
+ <td><strong>argument</strong></td>
+ <td><strong>action</strong></td>
+ <td><strong>sub-value modifiers</strong> (optional)</td>
+ <td><strong>linked</strong> (optional)</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 sub-value 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>‑‑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>
+
+ </table>
+
+
+ <h2>Exporting image files</h2>
+
+ <table border="1" cellpadding="3">
+ <tr valign="top">
+ <td><strong>argument</strong></td>
+ <td><strong>action</strong></td>
+ <td><strong>sub-value modifiers</strong> (optional)</td>
+ <td><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 sub-value 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>,
+ <code>scale=<em>number</em>,
+ <code>width=<em>number</em>,
+ <code>height=<em>number</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>,
+ <br/>
+ <code>lineart</code>.
+ </td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑scale <em>number</em></code></td>
+ <td>Sets a scaling for bitmap image format (PNG). Should be given as a floating point number. This can also be set as a sub-value modifier to the <code>--image</code> value. If used in conjunction with <code>--width</code> and <code>--height</code> then the smallest scaling will be used (<code>scale</code>, <code>width</code> and <code>height</code> provide bounds for the image).
+ </td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑width <em>number</em></code></td>
+ <td>Sets a width for bitmap image format (PNG) with the height maintaining the aspect ratio. Should be given as a positive integer. This can also be set as a sub-value modifier to the <code>--image</code> value. If used in conjunction with <code>--scale</code> and <code>--height</code> then the smallest scaling will be used (<code>scale</code>, <code>width</code> and <code>height</code> provide bounds for the image).
+ </td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑height <em>number</em></code></td>
+ <td>Sets a height for bitmap image format (PNG) with the width maintaining the aspect ratio. Should be given as a positive integer. This can also be set as a sub-value modifier to the <code>--image</code> value. If used in conjunction with <code>--scale</code> and <code>--width</code> then the smallest scaling will be used (<code>scale</code>, <code>width</code> and <code>height</code> provide bounds for the image).</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>
+
+ </table>
+
+
+ <h2>Exporting 3D structure image files (<code>jmol</code> only)</h2>
+
+ <table border="1" cellpadding="3">
+ <tr valign="top">
+ <td><strong>argument</strong></td>
+ <td><strong>action</strong></td>
+ <td><strong>sub-value modifiers</strong> (optional)</td>
+ <td><strong>linked</strong> (optional)</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑structureimage <em>filename</em></code></td>
+ <td>Export an image of a 3D structure opened in JMOL. Image formats can be:
+ <br/>
+ <code>svg</code>,
+ <br/>
+ <code>png</code>,
+ <br/>
+ <code>eps</code>.
+ </td>
+ <td>
+ <code>structureimagetype=<em>name</em>,
+ <code>structureimagetextrenderer=<em>name</em>,
+ <code>structureimagescale=<em>number</em>,
+ <code>structureimagewidth=<em>number</em>,
+ <code>structureimageheight=<em>number</em>
+ </td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑structureimagetype <em>name</em></code></td>
+ <td>Set the structure image format for the preceding --structureimage. Valid values are:
+ <br/>
+ <code>svg</code>,
+ <br/>
+ <code>png</code>,
+ <br/>
+ <code>eps</code>.
+ </td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑structureimagetextrenderer <em>name</em></code></td>
+ <td>Sets whether text in a vector structure image format (SVG, EPS) should be rendered as text or vector line-art. Possible values are:
+ <br/>
+ <code>text</code>,
+ <br/>
+ <code>lineart</code>.
+ </td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑structureimagescale <em>number</em></code></td>
+ <td>Sets a scaling for bitmap structure image format (PNG). Should be given as a floating point number. If used in conjunction with --structureimagewidth and --structureimageheight then the smallest scaling will be used (structureimagescale, structureimagewidth and structureimageheight provide bounds for the structure image).
+ </td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑structureimagewidth <em>number</em></code></td>
+ <td>Sets a width for bitmap structure image format (PNG) with the height maintaining the aspect ratio. Should be given as a positive integer. If used in conjunction with --structureimagescale and --structureimageheight then the smallest scaling will be used (structureimagescale, structureimagewidth and structureimageheight provide bounds for the structure image).
+ </td>
+ <td></td>
+ <td align="center">✓</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑structureimageheight <em>number</em></code></td>
+ <td>Sets a height for bitmap structure image format (PNG) with the width maintaining the aspect ratio. Should be given as a positive integer. If used in conjunction with --structureimagescale and --structureimagewidth then the smallest scaling will be used (structureimagescale, structureimagewidth and structureimageheight provide bounds for the structure image).
+ </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>
+ </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.
+ <br/>
+ <em>Note</em> that <code>--open</code> already starts a new alignment window for each file it opens.
+ </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>
+ </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/>
+ Values in an argfile should be given with an equals sign ("=") separator with no spaces.
+ <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>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑npp</code></td>
+ <td>Increase the index counter used in argument value substitutions.</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑all / ‑‑noall</code></td>
+ <td>Apply (or stop applying) the following output arguments to <em>all</em> sets of linked arguments.</td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑allstructures / ‑‑noallstructures</code></td>
+ <td>
+ Apply (or stop applying) the following 3D structure formatting arguments to all structures <em>within the current open alignment</em>. Whilst <code>--allstructures</code> will continue to operate for a <code>--new</code> alignment, the structure formatting arguments must be set again for each new alignment.
+ </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>
+ </tr>
+
+ </table>
+