* 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>
<title>Jalview Command Line Arguments (next generation)</title>
<body>
- <h1>Jalview Command Line Arguments (version 2.11.3.0 and later)</h1>
+ <h1>Jalview Command Line Arguments (next generation)</h1>
<p>
For a summary of Jalview command line arguments see <a href="clarguments-ng-summary.html">Summary
<p>
The old command line arguments can still be used (see
<a href="clarguments.html">the old page on command line arguments</a>) so
- existing scripts utilising them should not break.
+ existing scripts utilising them should not break. <strong>These will be removed</strong> in a future version of Jalview.
</p>
<p>
<strong>Note!</strong> If you use command line arguments without any dashes and
<em>don't</em> use the bare-word argument <code>open</code> then all
your arguments will be interpreted as alignment files to be opened by the
- new command line argument process.
+ new command line argument process!
</p>
<p>
if (orgtimeout == null)
{
orgtimeout = "30";
- System.out.println("# INFO: Setting default net timeout to "
- + orgtimeout + " seconds.");
+ Console.debug("Setting default net timeout to " + orgtimeout
+ + " seconds.");
}
String remoteVersion = null;
if (remoteBuildPropertiesUrl.startsWith("http"))
// Show secondary structure annotations?
boolean showSSAnnotations = ArgParser.getFromSubValArgOrPref(avm,
- Arg.SSANNOTATIONS, av.getSubVals(), null,
+ Arg.SHOWSSANNOTATIONS, av.getSubVals(), null,
"STRUCT_FROM_PDB", true);
af.setAnnotationsVisibility(showSSAnnotations, true, false);
af.getCurrentView().getAlignment(), hideThese, null,
false, false);
}
- else
- /*
- * comment out hacky approach up to here and add this line: if
- * (showTemperatureFactor)
- */
- {
- /*
- if (avm.containsArg(Arg.TEMPFAC_LABEL))
- {
- AlignmentAnnotation aa = AlignmentUtils
- .getFirstSequenceAnnotationOfType(
- af.getCurrentView().getAlignment(),
- AlignmentAnnotation.LINE_GRAPH);
- String label = avm.getValue(Arg.TEMPFAC_LABEL);
- if (aa != null)
- {
- aa.label = label;
- }
- else
- {
- Console.info(
- "Could not find annotation to apply tempfac_label '"
- + label);
- }
- }
- */
- }
// store the AlignFrame for this id
afMap.put(id, af);
// showing annotations from structure file or not
boolean ssFromStructure = ArgParser.getFromSubValArgOrPref(avm,
- Arg.SSANNOTATIONS, subVals, null, "STRUCT_FROM_PDB",
+ Arg.SHOWSSANNOTATIONS, subVals, null, "STRUCT_FROM_PDB",
true);
// get TEMPFAC type from subvals or Arg.TEMPFAC in case user Adds
return null;
if (subVals != null)
{
- if (subVals.has("seqid"))
+ if (subVals.has(Arg.SEQID.getName()))
{
- seq = al.findName(subVals.get("seqid"));
+ seq = al.findName(subVals.get(Arg.SEQID.getName()));
}
else if (-1 < subVals.getIndex()
&& subVals.getIndex() < al.getSequences().size())
if (!Platform.isJS())
{
- System.err
- .println("Setting initial log level to " + logLevel.name());
+ if (!Jalview.getInstance().quiet())
+ {
+ System.err.println(
+ "Setting initial log level to " + logLevel.name());
+ }
Log4j.init(logLevel);
}
// log output
public static AlignFrame currentAlignFrame;
+ public ArgParser argparser = null;
+
+ public BootstrapArgs bootstrapArgs = null;
+
+ private boolean QUIET = false;
+
+ public boolean quiet()
+ {
+ return QUIET;
+ }
+
static
{
if (!Platform.isJS())
if (args == null)
args = new String[] {};
- // Move any new getdown-launcher-new.jar into place over old
- // getdown-launcher.jar
- String appdirString = System.getProperty("getdownappdir");
- if (appdirString != null && appdirString.length() > 0)
- {
- final File appdir = new File(appdirString);
- new Thread()
- {
- @Override
- public void run()
- {
- LaunchUtil.upgradeGetdown(
- new File(appdir, "getdown-launcher-old.jar"),
- new File(appdir, "getdown-launcher.jar"),
- new File(appdir, "getdown-launcher-new.jar"));
- }
- }.start();
- }
-
// get args needed before proper ArgParser
- BootstrapArgs bootstrapArgs = BootstrapArgs.getBootstrapArgs(args);
+ bootstrapArgs = BootstrapArgs.getBootstrapArgs(args);
if (!Platform.isJS())
{
// are we being --quiet ?
if (bootstrapArgs.contains(Arg.QUIET))
{
+ QUIET = true;
OutputStream devNull = new OutputStream()
{
System.setErr(new PrintStream(devNull));
}
}
- }
-
- System.out
- .println("Java version: " + System.getProperty("java.version"));
- System.out.println("Java Home: " + System.getProperty("java.home"));
- System.out.println(System.getProperty("os.arch") + " "
- + System.getProperty("os.name") + " "
- + System.getProperty("os.version"));
- String val = System.getProperty("sys.install4jVersion");
- if (val != null)
- {
- System.out.println("Install4j version: " + val);
+ if (bootstrapArgs.contains(Arg.HELP))
+ {
+ QUIET = true;
+ }
}
- val = System.getProperty("installer_template_version");
- if (val != null)
+
+ // Move any new getdown-launcher-new.jar into place over old
+ // getdown-launcher.jar
+ String appdirString = System.getProperty("getdownappdir");
+ if (appdirString != null && appdirString.length() > 0)
{
- System.out.println("Install4j template version: " + val);
+ final File appdir = new File(appdirString);
+ new Thread()
+ {
+ @Override
+ public void run()
+ {
+ LaunchUtil.upgradeGetdown(
+ new File(appdir, "getdown-launcher-old.jar"),
+ new File(appdir, "getdown-launcher.jar"),
+ new File(appdir, "getdown-launcher-new.jar"));
+ }
+ }.start();
}
- val = System.getProperty("launcher_version");
- if (val != null)
+
+ if (!quiet())
{
- System.out.println("Launcher version: " + val);
+ System.out.println(
+ "Java version: " + System.getProperty("java.version"));
+ System.out.println("Java Home: " + System.getProperty("java.home"));
+ System.out.println(System.getProperty("os.arch") + " "
+ + System.getProperty("os.name") + " "
+ + System.getProperty("os.version"));
+
+ String val = System.getProperty("sys.install4jVersion");
+ if (val != null)
+ {
+ System.out.println("Install4j version: " + val);
+ }
+ val = System.getProperty("installer_template_version");
+ if (val != null)
+ {
+ System.out.println("Install4j template version: " + val);
+ }
+ val = System.getProperty("launcher_version");
+ if (val != null)
+ {
+ System.out.println("Launcher version: " + val);
+ }
}
if (Platform.isLinux() && LaunchUtils.getJavaVersion() < 11)
"test/jalview/bin/testProps.jvprops", usrPropsFile);
}
- // new ArgParser
- ArgParser argparser;
// --argfile=... -- OVERRIDES ALL NON-BOOTSTRAP ARGS
if (bootstrapArgs.contains(Arg.ARGFILE))
{
jvmmemmax = arg.substring(
MemorySetting.MAX_HEAPSIZE_PROPERTY_NAME.length() + 2);
}
+ // --doubledash versions
+ else if (arg.startsWith("--"
+ + MemorySetting.MAX_HEAPSIZE_PERCENT_PROPERTY_NAME + "="))
+ {
+ jvmmempc = arg.substring(
+ MemorySetting.MAX_HEAPSIZE_PERCENT_PROPERTY_NAME.length()
+ + 3);
+ }
+ else if (arg.startsWith(
+ "--" + MemorySetting.MAX_HEAPSIZE_PROPERTY_NAME + "="))
+ {
+ jvmmemmax = arg.substring(
+ MemorySetting.MAX_HEAPSIZE_PROPERTY_NAME.length() + 3);
+ }
+ // retain arg
else
{
arguments.add(arg);
import java.util.ArrayList;
import java.util.Arrays;
import java.util.EnumSet;
+import java.util.Iterator;
import java.util.List;
import java.util.Locale;
import java.util.stream.Collectors;
+import jalview.bin.Cache;
+import jalview.util.ChannelProperties;
+
public enum Arg
{
- HELP("h"), CALCULATION, MENUBAR, STATUS, SHOWOVERVIEW, SHOWANNOTATIONS,
- COLOUR("color"), FEATURES, ANNOTATIONS, GROOVY, GROUPS, HEADLESS, JABAWS,
- DISPLAY, NEWS, SORTBYTREE, USAGESTATS, APPEND, OPEN, PROPS, QUESTIONNAIRE,
- SETPROP, TREE, VDOC, VSESS, OUTPUT, SSANNOTATIONS, NOTEMPFAC, TEMPFAC,
- TITLE, PAEMATRIX, WRAP, NOSTRUCTURE, STRUCTURE, STRUCTUREVIEWER, IMAGE,
- TYPE, FORMAT, OVERWRITE, TEXTRENDERER, QUIT, CLOSE, DEBUG("d"), TRACE,
- QUIET("q"), ARGFILE, NEW, NPP("n++"), SUBSTITUTIONS, INITSUBSTITUTIONS,
- NIL, SPLASH, SETARGFILE, UNSETARGFILE, WEBSERVICEDISCOVERY, ALL, BACKUPS,
- TESTOUTPUT, SEQID;
+
+ // Initialising arguments (BOOTSTRAP)
+ HELP("Display this help statement", Opt.UNARY, Opt.BOOTSTRAP),
+ HEADLESS(
+ "Run Jalview in headless mode. No GUI interface will be created and Jalview will quit after all arguments have been processed.",
+ Opt.UNARY, Opt.BOOTSTRAP),
+ JABAWS("Set a different URL to connect to a JABAWS server.", Opt.STRING,
+ Opt.BOOTSTRAP),
+ NEWS("Show (or don't show) the news feed.", true, Opt.BOOLEAN,
+ Opt.BOOTSTRAP),
+ SPLASH("Show (or don't show) the About Jalview splash screen.", true,
+ Opt.BOOLEAN, Opt.BOOTSTRAP),
+ QUESTIONNAIRE(
+ "Show (or don't show) the questionnaire if one is available.",
+ true, Opt.BOOLEAN, Opt.BOOTSTRAP),
+ USAGESTATS("Send (or don't send) initial launch usage stats.", true,
+ Opt.BOOLEAN, Opt.BOOTSTRAP),
+ WEBSERVICEDISCOVERY(
+ "Attempt (or don't attempt) to connect to JABAWS web services.",
+ true, Opt.BOOLEAN, Opt.BOOTSTRAP),
+ PROPS("Use file filename as the preferences file instead of the usual ~/.jalview_properties file.",
+ Opt.STRING, Opt.BOOTSTRAP),
+ DEBUG("Start Jalview in debug log level.", Opt.BOOLEAN, Opt.BOOTSTRAP),
+ TRACE("Start Jalview in trace log level.", Opt.BOOLEAN, Opt.BOOTSTRAP,
+ Opt.SECRET),
+ QUIET("Stop all output to STDOUT (after the Java Virtual Machine has started). Use ‑‑quiet a second time to stop all output to STDERR.",
+ Opt.UNARY, Opt.MULTI, Opt.BOOTSTRAP),
+ INITSUBSTITUTIONS(
+ "Assume that ‑‑substitutions are initially enabled (or initially disabled).",
+ true, Opt.BOOLEAN, Opt.BOOTSTRAP, Opt.NOACTION),
+
+ // Opening an alignment
+ OPEN("Opens one or more alignment files filename or URLs URL in new alignment windows.",
+ Opt.STRING, Opt.LINKED, Opt.INCREMENTDEFAULTCOUNTER, Opt.MULTI,
+ Opt.GLOB, Opt.ALLOWSUBSTITUTIONS, Opt.INPUT),
+ APPEND("Appends one or more alignment files filename or URLs URL to the open alignment window (or opens a new alignment if none already open).",
+ Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.GLOB,
+ Opt.ALLOWSUBSTITUTIONS, Opt.INPUT),
+ TITLE("Specifies the title for the open alignment window as string.",
+ Opt.STRING, Opt.LINKED),
+ COLOUR("Applies the colour scheme to the open alignment window. Valid values are:\n"
+ + "clustal,\n" + "blosum62,\n" + "pc-identity,\n" + "zappo,\n"
+ + "taylor,\n" + "gecos-flower,\n" + "gecos-blossom,\n"
+ + "gecos-sunset,\n" + "gecos-ocean,\n" + "hydrophobic,\n"
+ + "helix-propensity,\n" + "strand-propensity,\n"
+ + "turn-propensity,\n" + "buried-index,\n" + "nucleotide,\n"
+ + "nucleotide-ambiguity,\n" + "purine-pyrimidine,\n"
+ + "rna-helices,\n" + "t-coffee-scores,\n" + "sequence-id.",
+ Opt.STRING, Opt.LINKED),
+ FEATURES("Add a feature file filename or URL URL to the open alignment.",
+ Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS),
+ TREE("Add a tree file filename or URL URL to the open alignment.",
+ Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS),
+ SORTBYTREE(
+ "Enforces sorting (or not sorting) the alignment in the order of an attached phylogenetic tree.",
+ true, Opt.LINKED, Opt.BOOLEAN),
+ ANNOTATIONS(
+ "Add an annotations file filename or URL URL to the open alignment.",
+ Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS),
+ SHOWANNOTATIONS(
+ "Enforces showing (or not showing) alignment annotations.",
+ Opt.BOOLEAN, Opt.LINKED),
+ WRAP("Enforces wrapped (or not wrapped) alignment formatting.",
+ Opt.BOOLEAN, Opt.LINKED),
+ NOSTRUCTURE(
+ "Do not open or process any 3D structure in the ‑‑open or ‑‑append files.",
+ Opt.UNARY, Opt.LINKED),
+
+ // Adding a 3D structure
+ STRUCTURE(
+ "Load a structure file filename or URL URL associated with a sequence in the open alignment. The sequence to be associated with can be specified with a following --seqid argument, or the subval modifier seqid=ID can be used. A subval INDEX can also be used to specify the INDEX-th sequence in the open alignment.",
+ Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS),
+ SEQID("Specify the sequence name for the preceding --structure to be associated with.",
+ Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS),
+ PAEMATRIX(
+ "Add a PAE json matrix file filename to the preceding --structure.",
+ Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS),
+ TEMPFAC("Set the type of temperature factor. Possible values for name are default, plddt.",
+ Opt.STRING, Opt.LINKED),
+ STRUCTUREVIEWER(
+ "Set the structure viewer to use to open the 3d structure file specified in previous --structure to name. Possible values of name are:\n"
+ + "none, jmol, chimera, chimerax, pymol.",
+ Opt.STRING, Opt.LINKED, Opt.MULTI),
+ NOTEMPFAC(
+ "Do not show the temperature factor annotation for the preceding --structure.",
+ Opt.UNARY, Opt.LINKED),
+ SHOWSSANNOTATIONS(null, Opt.BOOLEAN, Opt.LINKED),
+
+ // Outputting files
+ IMAGE("Output an image of the open alignment window. Format is specified by the subval modifier, a following --type argument or guessed from the file extension. Valid formats/extensions are: svg, png, eps, html, biojs.",
+ Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS, Opt.ALLOWALL,
+ Opt.REQUIREINPUT),
+ TYPE("Set the image format for the preceding --image to name. Valid values for name are: svg, png, eps, html, biojs.",
+ Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
+ TEXTRENDERER(
+ "Sets whether text in a vector image format (SVG, HTML, EPS) should be rendered as text or vector line-art. Possible values for name are: text, lineart.",
+ Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
+ OUTPUT("Export the open alignment to file filename. The format name is specified by the subval modifier format=name, a following --format name argument or guessed from the file extension. Valid format names (and file extensions) are:\n"
+ + "fasta (fa, fasta, mfa, fastq),\n" + "pfam (pfam),\n"
+ + "stockholm (sto, stk),\n" + "pir (pir),\n" + "blc (blc),\n"
+ + "amsa (amsa),\n" + "json (json),\n" + "pileup (pileup),\n"
+ + "msf (msf),\n" + "clustal (aln),\n" + "phylip (phy),\n"
+ + "jalview (jvp, jar).", Opt.STRING, Opt.LINKED,
+ Opt.ALLOWSUBSTITUTIONS, Opt.ALLOWALL, Opt.REQUIREINPUT),
+ FORMAT("Sets the format for the preceding --output file. Valid formats are:\n"
+ + "fasta,\n" + "pfam,\n" + "stockholm,\n" + "pir,\n" + "blc,\n"
+ + "amsa,\n" + "json,\n" + "pileup,\n" + "msf,\n" + "clustal,\n"
+ + "phylip,\n" + "jalview.", Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
+ GROOVY("Process a groovy script in the file for the open alignment.",
+ Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS),
+ BACKUPS("Enable (or disable) writing backup files when saving an ‑‑output file. This applies to the current open alignment -- to apply to all ‑‑output and ‑‑image files, use after ‑‑all.",
+ true, Opt.BOOLEAN, Opt.LINKED, Opt.ALLOWALL),
+ OVERWRITE(
+ "Enable (or disable) overwriting of output files without backups enabled. This applies to the current open alignment -- to apply to all ‑‑output and ‑‑image files, use after ‑‑all.",
+ Opt.BOOLEAN, Opt.LINKED, Opt.ALLOWALL),
+ CLOSE("Close the current open alignment window. This occurs after other output arguments. This applies to the current open alignment -- to apply to all ‑‑output and ‑‑image files, use after ‑‑all.",
+ Opt.UNARY, Opt.LINKED, Opt.ALLOWALL),
+
+ // controlling flow of arguments
+ NEW("Move on to a new alignment window. This will ensure --append will start a new alignment window and other linked arguments will apply to the new alignment window.",
+ Opt.UNARY, Opt.MULTI, Opt.NOACTION, Opt.INCREMENTDEFAULTCOUNTER),
+ SUBSTITUTIONS(
+ "The following argument values allow (or don't allow) subsituting filename parts. This is initially true. Valid substitutions are {basename} - the filename-without-extension of the currently --opened file (or first --appended file),\n"
+ + "{dirname}, - the directory (folder) name of the currently --opened file (or first --appended file),\n"
+ + "{argfilebasename} - the filename-without-extension of the current --argfile,\n"
+ + "{argfiledirname} - the directory (folder) name of the current --argfile,\n"
+ + "{n} - the value of the index counter (starting at 0).\n"
+ + "{++n} - increase and substitute the value of the index counter,\n"
+ + "{} - the value of the current alignment window default index.",
+ true, Opt.BOOLEAN, Opt.MULTI, Opt.NOACTION),
+ ARGFILE("Open one or more files filename and read, line-by-line, as arguments to Jalview.\n"
+ + "Note that if you use one or more --argfile arguments then all other non-initialising arguments will be ignored.",
+ Opt.STRING, Opt.MULTI, Opt.BOOTSTRAP, Opt.GLOB,
+ Opt.ALLOWSUBSTITUTIONS),
+ NPP("Increase the index counter used in argument value substitutions.",
+ Opt.UNARY, Opt.MULTI, Opt.NOACTION),
+ ALL("Apply the following output arguments to all sets of linked arguments.",
+ Opt.BOOLEAN, Opt.MULTI, Opt.NOACTION),
+ QUIT("After all files have been opened, appended and output, quit Jalview. In ‑‑headless mode this already happens.",
+ Opt.UNARY),
+
+ // secret options
+ TESTOUTPUT(
+ "Allow specific stdout information. For testing purposes only.",
+ Opt.UNARY, Opt.BOOTSTRAP, Opt.SECRET), // do not show this to the user
+ SETPROP("Set an individual Java System property.", Opt.STRING, Opt.MULTI,
+ Opt.BOOTSTRAP, Opt.SECRET), // not in use yet
+ NIL("This argument does nothing on its own, but can be used with linkedIds.",
+ Opt.UNARY, Opt.LINKED, Opt.MULTI, Opt.NOACTION, Opt.SECRET),
+
+ // private options (inserted during arg processing)
+ SETARGFILE(
+ "Sets the current value of the argfilename. Inserted before argfilecontents.",
+ Opt.UNARY, Opt.LINKED, Opt.STRING, Opt.MULTI, Opt.PRIVATE,
+ Opt.NOACTION),
+ UNSETARGFILE(
+ "Unsets the current value of the argfilename. Inserted after argfile contents.",
+ Opt.UNARY, Opt.LINKED, Opt.MULTI, Opt.PRIVATE, Opt.NOACTION),
+
+ // these last two have no purpose in the normal Jalview application but are
+ // used by jalview.bin.Launcher to set memory settings. They are not used by
+ // argparser but are here for Usage statement reasons.
+ JVMMEMPC(
+ "Only available with standalone executable jar or jalview.bin.Launcher.\n"
+ + "Limit maximum heap size (memory) to PERCENT% of total physical memory detected. This defaults to 90 if total physical memory can be detected.\n"
+ + "The equals sign (\"=\") separator must be used with no spaces.",
+ Opt.NOACTION, Opt.BOOTSTRAP, Opt.STRING),
+ JVMMEMMAX(
+ "Only available with standalone executable jar or jalview.bin.Launcher.\n"
+ + "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.\n"
+ + "The equals sign (\"=\") separator must be used with no spaces.",
+ Opt.NOACTION, Opt.BOOTSTRAP, Opt.STRING),
+
+ ;
public static enum Opt
{
// SubVals and values.
PRIVATE, // This Arg is used internally, and cannot be specified by the
// user.
+ SECRET, // This Arg is used by development processes and although it can be
+ // set by the user, it is not displayed to the user.
ALLOWALL, // This Arg can use the '*' linkedId to apply to all known
// linkedIds
INCREMENTDEFAULTCOUNTER, // If an Arg has this option and the default
// input (i.e. --open or --append)
}
- static
- {
- HELP.setOptions("Display this help message", Opt.UNARY, Opt.BOOTSTRAP);
- CALCULATION.setOptions(true, Opt.BOOLEAN); // default "true" implies only
- // expecting "--nocalculation"
- MENUBAR.setOptions(true, Opt.BOOLEAN);
- STATUS.setOptions(true, Opt.BOOLEAN);
- SHOWOVERVIEW.setOptions(Opt.UNARY, Opt.LINKED);
- SHOWANNOTATIONS.setOptions(Opt.BOOLEAN, Opt.LINKED);
- COLOUR.setOptions(Opt.STRING, Opt.LINKED);
- FEATURES.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI,
- Opt.ALLOWSUBSTITUTIONS);
- ANNOTATIONS.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI,
- Opt.ALLOWSUBSTITUTIONS);
- TREE.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI,
- Opt.ALLOWSUBSTITUTIONS);
- GROOVY.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI,
- Opt.ALLOWSUBSTITUTIONS);
- GROUPS.setOptions(Opt.STRING, Opt.LINKED);
- HEADLESS.setOptions(Opt.UNARY, Opt.BOOTSTRAP);
- TESTOUTPUT.setOptions(Opt.UNARY, Opt.BOOTSTRAP);
- JABAWS.setOptions(Opt.STRING, Opt.BOOTSTRAP);
- DISPLAY.setOptions(true, Opt.BOOLEAN);
- NEWS.setOptions(true, Opt.BOOLEAN, Opt.BOOTSTRAP);
- SPLASH.setOptions(true, Opt.BOOLEAN, Opt.BOOTSTRAP);
- SORTBYTREE.setOptions(true, Opt.LINKED, Opt.BOOLEAN);
- QUESTIONNAIRE.setOptions(true, Opt.BOOLEAN, Opt.BOOTSTRAP);
- USAGESTATS.setOptions(true, Opt.BOOLEAN, Opt.BOOTSTRAP);
- WEBSERVICEDISCOVERY.setOptions(true, Opt.BOOLEAN, Opt.BOOTSTRAP);
- APPEND.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.GLOB,
- Opt.ALLOWSUBSTITUTIONS, Opt.INPUT);
- OPEN.setOptions(Opt.STRING, Opt.LINKED, Opt.INCREMENTDEFAULTCOUNTER,
- Opt.MULTI, Opt.GLOB, Opt.ALLOWSUBSTITUTIONS, Opt.INPUT);
- PROPS.setOptions(Opt.STRING, Opt.BOOTSTRAP);
- SETPROP.setOptions(Opt.STRING, Opt.MULTI, Opt.BOOTSTRAP);
-
- VDOC.setOptions(Opt.UNARY);
- VSESS.setOptions(Opt.UNARY);
-
- OUTPUT.setOptions(Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS,
- Opt.ALLOWALL, Opt.REQUIREINPUT);
-
- SSANNOTATIONS.setOptions(Opt.BOOLEAN, Opt.LINKED);
- NOTEMPFAC.setOptions(Opt.UNARY, Opt.LINKED);
- TEMPFAC.setOptions(Opt.STRING, Opt.LINKED);
- TITLE.setOptions(Opt.STRING, Opt.LINKED);
- PAEMATRIX.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI,
- Opt.ALLOWSUBSTITUTIONS);
- SEQID.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI,
- Opt.ALLOWSUBSTITUTIONS);
- NOSTRUCTURE.setOptions(Opt.UNARY, Opt.LINKED);
- STRUCTURE.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI,
- Opt.ALLOWSUBSTITUTIONS);
- STRUCTUREVIEWER.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI);
- WRAP.setOptions(Opt.BOOLEAN, Opt.LINKED);
- IMAGE.setOptions(Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS,
- Opt.ALLOWALL, Opt.REQUIREINPUT);
- TYPE.setOptions(Opt.STRING, Opt.LINKED, Opt.ALLOWALL);
- FORMAT.setOptions(Opt.STRING, Opt.LINKED, Opt.ALLOWALL);
- TEXTRENDERER.setOptions(Opt.STRING, Opt.LINKED, Opt.ALLOWALL);
- QUIT.setOptions(Opt.UNARY);
- OVERWRITE.setOptions(Opt.BOOLEAN, Opt.LINKED, Opt.ALLOWALL);
- BACKUPS.setOptions(true, Opt.BOOLEAN, Opt.LINKED, Opt.ALLOWALL);
- CLOSE.setOptions(Opt.UNARY, Opt.LINKED, Opt.ALLOWALL);
- DEBUG.setOptions(Opt.BOOLEAN, Opt.BOOTSTRAP);
- TRACE.setOptions(Opt.BOOLEAN, Opt.BOOTSTRAP);
- QUIET.setOptions(Opt.UNARY, Opt.MULTI, Opt.BOOTSTRAP);
- ARGFILE.setOptions(Opt.STRING, Opt.MULTI, Opt.BOOTSTRAP, Opt.GLOB,
- Opt.ALLOWSUBSTITUTIONS);
- NEW.setOptions(Opt.UNARY, Opt.MULTI, Opt.NOACTION,
- Opt.INCREMENTDEFAULTCOUNTER);
- NPP.setOptions(Opt.UNARY, Opt.MULTI, Opt.NOACTION);
- SUBSTITUTIONS.setOptions(Opt.BOOLEAN, Opt.MULTI, Opt.NOACTION);
- INITSUBSTITUTIONS.setOptions(true, Opt.BOOLEAN, Opt.BOOTSTRAP,
- Opt.NOACTION); // defaulting substitutions to true
- NIL.setOptions(Opt.UNARY, Opt.LINKED, Opt.MULTI, Opt.NOACTION);
- SETARGFILE.setOptions(Opt.STRING, Opt.MULTI, Opt.PRIVATE, Opt.NOACTION);
- UNSETARGFILE.setOptions(Opt.MULTI, Opt.PRIVATE, Opt.NOACTION);
- ALL.setOptions(Opt.BOOLEAN, Opt.MULTI, Opt.NOACTION);
-
- }
-
private final String[] argNames;
private Opt[] argOptions;
private String description = null;
- private Arg()
+ private Arg(String description, Opt... options)
{
- this(new String[0]);
+ this(null, description, false, options);
}
- private Arg(String... names)
+ private Arg(String description, boolean defaultBoolean, Opt... options)
{
- int length = (names == null || names.length == 0
- || (names.length == 1 && names[0] == null)) ? 1
- : names.length + 1;
- this.argNames = new String[length];
- this.argNames[0] = this.getName();
- if (length > 1)
- System.arraycopy(names, 0, this.argNames, 1, names.length);
+ this(null, description, defaultBoolean, options);
+ }
+
+ private Arg(String alternativeName, String description, Opt... options)
+ {
+ this(alternativeName, description, false, options);
+ }
+
+ private Arg(String alternativeName, String description,
+ boolean defaultBoolean, Opt... options)
+ {
+ this.argNames = alternativeName != null
+ ? new String[]
+ { this.getName(), alternativeName }
+ : new String[]
+ { this.getName() };
+ this.description = description;
+ this.defaultBoolValue = defaultBoolean;
+ this.setOptions(options);
}
public String argString()
protected void setOptions(Opt... options)
{
- setOptions("", false, options);
- }
-
- protected void setOptions(String desc, Opt... options)
- {
- setOptions(desc, false, options);
- }
-
- protected void setOptions(boolean defaultBoolValue, Opt... options)
- {
- setOptions("", defaultBoolValue, options);
- }
-
- protected void setOptions(String desc, boolean defaultBoolValue,
- Opt... options)
- {
- this.description = desc;
- this.defaultBoolValue = defaultBoolValue;
this.argOptions = options;
}
return defaultBoolValue;
}
- private void setDescription(String d)
- {
- description = d;
- }
-
protected String getDescription()
{
return description;
{
StringBuilder sb = new StringBuilder();
- sb.append("Usage: jalview [args]");
+ sb.append(ChannelProperties.getProperty("app_name"));
+ String version = Cache.getDefault("VERSION", null);
+ if (version != null)
+ {
+ sb.append(" version ");
+ sb.append(Cache.getDefault("VERSION", "unknown"));
+ }
+ sb.append(System.lineSeparator());
+ sb.append("Usage: jalview [files...] [args]");
+ sb.append(System.lineSeparator());
sb.append(System.lineSeparator());
int maxArgLength = 0;
for (Arg a : EnumSet.allOf(Arg.class))
{
- if (a.hasOption(Opt.PRIVATE))
+ if (a.hasOption(Opt.PRIVATE) || a.hasOption(Opt.SECRET))
continue;
+
StringBuilder argSb = new StringBuilder();
argSb.append(a.hasOption(Opt.BOOLEAN) ? booleanArgString(a)
: a.argString());
// might want to sort these
for (Arg a : EnumSet.allOf(Arg.class))
{
- if (a.hasOption(Opt.PRIVATE))
+ if (a.hasOption(Opt.PRIVATE) || a.hasOption(Opt.SECRET))
continue;
StringBuilder argSb = new StringBuilder();
argSb.append(a.hasOption(Opt.BOOLEAN) ? booleanArgString(a)
: a.argString());
if (a.hasOption(Opt.STRING))
argSb.append("=value");
- sb.append(String.format("%-" + maxArgLength + "s - %s",
- argSb.toString(), a.getDescription()));
+ Iterator<String> descLines = null;
+ if (a.getDescription() != null)
+ {
+ descLines = Arrays.stream(a.getDescription().split("\\n"))
+ .iterator();
+ }
+ sb.append(String.format("%-" + maxArgLength + "s", argSb.toString()));
+ boolean first = true;
+ if (descLines != null)
+ {
+ while (descLines.hasNext())
+ {
+ if (first)
+ sb.append(" - ");
+ else
+ sb.append(" ".repeat(maxArgLength + 3));
+ sb.append(descLines.next());
+ sb.append(System.lineSeparator());
+ first = false;
+ }
+ }
List<String> options = new ArrayList<>();
options.add("allows substitutions");
}
+ if (a.hasOption(Opt.PRIVATE))
+ {
+ options.add("for internal use only");
+ }
+
+ if (a.hasOption(Opt.SECRET))
+ {
+ options.add("for development use only");
+ }
+
if (options.size() > 0)
{
- sb.append(" (");
+ if (first)
+ sb.append(" - ");
+ else
+ sb.append(" ".repeat(maxArgLength + 3));
+ sb.append("(");
sb.append(String.join("; ", options));
sb.append(')');
+ sb.append(System.lineSeparator());
}
sb.append(System.lineSeparator());
}
{
if (key == null)
key = a.getName();
+ String nokey = ArgParser.NEGATESTRING + key;
if (sv != null && sv.has(key) && sv.get(key) != null)
return sv.get(key).toLowerCase(Locale.ROOT).equals("true");
+
+ if (sv != null && sv.has(key) && sv.get(key) != null)
+ return sv.get(key).toLowerCase(Locale.ROOT).equals("true");
+
+ // check for negative boolean (subval "no..." will be "true")
+ if (sv != null && sv.has(nokey) && sv.get(nokey) != null)
+ return !sv.get(nokey).toLowerCase(Locale.ROOT).equals("true");
+
if (avm != null && avm.containsArg(a))
return avm.getBoolean(a);
+
return pref != null ? Cache.getDefault(pref, def) : def;
}
// specify an id in the subValues so wouldn't need to be guessed).
ArgValue closestAv = null;
int thisArgIndex = thisAv.getArgIndex();
+ if (!containsArg(a))
+ return null;
ArgValues compareAvs = this.getArgValues(a);
int closestNextIndex = Integer.MAX_VALUE;
for (ArgValue av : compareAvs.getArgValueList())
+ "--colour=gecos-flower "
+ "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
+ "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
- + "--nossannotations "
+ + "--noshowssannotations "
+ "--props=test/jalview/bin/commandsTest2.jvprops1 ",
15, 4, 1 },
{ "--nonews --nosplash --debug " + "--append=examples/uniref50.fa "
+ "--colour=gecos-flower "
+ "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
+ "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
- + "--noshowannotations " + "--nossannotations "
+ + "--noshowannotations " + "--noshowssannotations "
+ "--props=test/jalview/bin/commandsTest2.jvprops1 ",
15, 0, 1 },
{ "--nonews --nosplash --debug " + "--append=examples/uniref50.fa "
+ "--colour=gecos-flower "
+ "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
+ "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
- + "--noshowannotations " + "--nossannotations "
+ + "--noshowannotations " + "--noshowssannotations "
+ "--props=test/jalview/bin/commandsTest2.jvprops1 ",
15, 0, 1 },
{ "--nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --argfile=test/jalview/bin/commandsTest2.argfile1 ",
--substitutions
--append=examples/test_fab41.result/sample.a2m
--showannotations
---ssannotations
+--showssannotations
--colour=gecos-flower
--structure=[viewer=jmol,tempfac=plddt,paematrix={dirname}/test_fab41_unrelaxed_rank_1_model_3_scores.json]{dirname}/test_fab41_unrelaxed_rank_1_model_3.pdb
--structure={dirname}/test_fab41_unrelaxed_rank_2_model_4.pdb
--substitutions
--append=examples/test_fab41.result/sample.a2m
--noshowannotations
---nossannotations
+--noshowssannotations
--colour=gecos-flower
--structure=[tempfac=plddt,paematrix={dirname}/test_fab41_unrelaxed_rank_1_model_3_scores.json]{dirname}/test_fab41_unrelaxed_rank_1_model_3.pdb
--structureviewer=none
git://source.jalview.org / jalview.git / commitdiff