3 * Jalview is distributed in the hope that it will be useful, but
4 * WITHOUT ANY WARRANTY; without even the implied warranty
5 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
6 * PURPOSE. See the GNU General Public License for more details.
8 * You should have received a copy of the GNU General Public License
9 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
10 * The Jalview Authors are detailed in the 'AUTHORS' file.
12 <title>Jalview Command Line Arguments: summary</title>
15 <h1>Jalview Command Line Arguments: summary</h1>
18 Jalview Command Line Arguments: summary
20 <a href="clarguments-intro.html">Jalview Command Line Arguments: introduction</a>
22 <a href="clarguments-basic.html">Jalview Command Line Arguments: basic usage</a>
24 <a href="clarguments-advanced.html">Jalview Command Line Arguments: advanced usage</a>
26 <a href="clarguments-argfiles.html">Jalview Command Line Arguments: argfiles</a>
32 <h2>Initialising arguments</h2>
34 <table border="1" cellpadding="3">
36 <td><strong>argument</strong></td>
37 <td><strong>action</strong></td>
41 <td><code>‑‑help / -h</code></td>
42 <td>Display a help statement</td>
46 <td><code>‑‑headless</code></td>
47 <td>Run Jalview in headless mode. No GUI interface will be created and Jalview will quit after all arguments have been processed.</td>
51 <td><code>‑‑jabaws <em>URL</em></code></td>
52 <td>Set a different URL to connect to a JABAWS server.</td>
56 <td><code>‑‑news / ‑‑nonews</code></td>
57 <td>Show (or don't show) the news feed.</td>
61 <td><code>‑‑splash / ‑‑nosplash</code></td>
62 <td>Show (or don't show) the About Jalview splash screen.</td>
66 <td><code>‑‑questionnaire / ‑‑noquestionnaire</code></td>
67 <td>Show (or don't show) the questionnaire if one is available.</td>
71 <td><code>‑‑usagestats / ‑‑nousagestats</code></td>
72 <td>Send (or don't send) initial launch usage stats. <em>Note: usage stats are useful for future funding for Jalview!</em></td>
76 <td><code>‑‑webservicediscovery / ‑‑nowebservicediscovery</code></td>
77 <td>Attempt (or don't attempt) to connect to JABAWS web services.</td>
81 <td><code>‑‑props <em>filename</em></code></td>
82 <td>Use file <em>filename</em> as the preferences file <em>instead</em> of the usual <code>~/.jalview_properties</code> file.</td>
86 <td><code>‑‑debug</code></td>
87 <td>Start Jalview in debug log level.</td>
91 <td><code>‑‑quiet</code></td>
92 <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>
96 <td><code>‑‑initsubstitutions / ‑‑noinitsubstitutions</code></td>
97 <td>Set <code>‑‑substitutions</code> to be initially enabled (or initially disabled).</td>
101 <td><code>‑‑jvmmempc=<em>PERCENT</em></code></td>
103 <em>Only available with standalone executable jar or jalview.bin.Launcher.</em>
105 Limit maximum heap size (memory) to PERCENT% of total physical memory detected.
106 This defaults to 90 if total physical memory can be detected.
108 The equals sign ("=") separator must be used with no spaces.
110 See <a href="../memory.html">Memory usage settings for Jalview</a> for more details.
115 <td><code>‑‑jvmmemmax=<em>MAXMEMORY</em></code></td>
117 <em>Only available with standalone executable jar or jalview.bin.Launcher.</em>
119 Limit maximum heap size (memory) to MAXMEMORY. MAXMEMORY can be specified in bytes, kilobytes(k), megabytes(m),
120 gigabytes(g) or if you're lucky enough, terabytes(t).
121 This defaults to 32g if total physical memory can be detected, or to 8g if total physical memory cannot be detected.
123 The equals sign ("=") separator must be used with no spaces.
125 See <a href="../memory.html">Memory usage settings for Jalview</a> for more details.
132 <h2>Opening an alignment</h2>
134 <table border="1" cellpadding="3">
136 <td><strong>argument</strong></td>
137 <td><strong>action</strong></td>
138 <td><strong>sub-value modifiers</strong> (optional)</td>
139 <td><strong>linked</strong> (optional)</td>
143 <td><code>‑‑open <em>filename/URL ...</em></code></td>
145 Opens one or more alignment files <em>filename</em> or URLs <em>URL</em> in new alignment windows.
149 colour=<em>name</em>,
151 title=<em>string</em>,
153 features=<em>filename</em>,
155 annotations=<em>filename</em>,
157 tree=<em>filename</em>,
168 <td align="center">✓</td>
172 <td><code>‑‑append <em>filename/URL ...</em></code></td>
173 <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>
176 colour=<em>name</em>,
178 title=<em>string</em>,
180 features=<em>filename</em>,
182 annotations=<em>filename</em>,
184 tree=<em>filename</em>,
195 <td align="center">✓</td>
199 <td><code>‑‑title <em>"string""</em></code></td>
200 <td>Specifies the title for the open alignment window as <em>string</em>.</td>
202 <td align="center">✓</td>
206 <td><code>‑‑colour <em>name</em></code></td>
207 <td>Applies the colour scheme <em>name</em> to the open alignment window. Valid values for <em>name</em> are:
209 <code>clustal</code>,
211 <code>blosum62</code>,
213 <code>pc-identity</code>,
219 <code>gecos-flower</code>,
221 <code>gecos-blossom</code>,
223 <code>gecos-sunset</code>,
225 <code>gecos-ocean</code>,
227 <code>hydrophobic</code>,
229 <code>helix-propensity</code>,
231 <code>strand-propensity</code>,
233 <code>turn-propensity</code>,
235 <code>buried-index</code>,
237 <code>nucleotide</code>,
239 <code>nucleotide-ambiguity</code>,
241 <code>purine-pyrimidine</code>,
243 <code>rna-helices</code>,
245 <code>t-coffee-scores</code>,
247 <code>sequence-id</code>.
249 <td align="center">✓</td>
253 <td><code>‑‑features <em>filename/URL</em></code></td>
254 <td>Add a feature file <em>filename</em> or URL <em>URL</em> to the open alignment.</td>
256 <td align="center">✓</td>
262 <td><code>‑‑tree <em>filename/URL</em></code></td>
263 <td>Add a tree file <em>filename</em> or URL <em>URL</em> to the open alignment.</td>
265 <td align="center">✓</td>
269 <td><code>‑‑sortbytree / ‑‑nosortbytree</code></td>
270 <td>Enforces sorting (or not sorting) the alignment in the order of an attached phylogenetic tree.</td>
272 <td align="center">✓</td>
277 <td><code>‑‑annotations <em>filename/URL</em></code></td>
278 <td>Add an annotations file <em>filename</em> or URL <em>URL</em> to the open alignment.</td>
280 <td align="center">✓</td>
284 <td><code>‑‑showannotations / ‑‑noshowannotations</code></td>
285 <td>Enforces showing (or not showing) alignment annotations.</td>
287 <td align="center">✓</td>
291 <td><code>‑‑wrap / ‑‑nowrap</code></td>
292 <td>Enforces wrapped (or not wrapped) alignment formatting.</td>
294 <td align="center">✓</td>
298 <td><code>‑‑nostructure</code></td>
299 <td>Do not open or process any 3D structure in the <code>‑‑open</code> or <code>‑‑append</code> files.</td>
301 <td align="center">✓</td>
307 <h2>Adding a 3D structure</h2>
309 <table border="1" cellpadding="3">
311 <td><strong>argument</strong></td>
312 <td><strong>action</strong></td>
313 <td><strong>sub-value modifiers</strong> (optional)</td>
314 <td><strong>linked</strong> (optional)</td>
318 <td><code>‑‑structure <em>filename/URL</em></code></td>
319 <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>
322 seqid=<em>id</em></code> or <code><em>INDEX</em>,
324 paefile=<em>filename</em>,
326 tempfac=<em>name</em>,
334 structureviewer=<em>name</em>
336 <td align="center">✓</td>
341 <td><code>‑‑seqid <em>ID</em></code></td>
342 <td>Specify the sequence name for the preceding <code>‑‑structure</code> to be associated with.</td>
344 <td align="center">✓</td>
349 <td><code>‑‑paematrix <em>filename</em></code></td>
350 <td>Add a PAE json matrix file <em>filename</em> to the preceding <code>‑‑structure</code>.</td>
352 <td align="center">✓</td>
357 <td><code>‑‑tempfac <em>name</em></code></td>
358 <td>Set the type of temperature factor. Valid values for <em>name</em> are:
360 <code>default</code>,
365 <td align="center">✓</td>
370 <td><code>‑‑structureviewer <em>name</em></code></td>
371 <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:
377 <code>chimera</code> <em>- requires installation, might need configuring in Preferences</em>,
379 <code>chimerax</code> <em>- requires installation, might need configuring in Preferences</em>,
381 <code>pymol</code> <em>- requires installation, might need configuring in Preferences</em>
384 <td align="center">✓</td>
390 <td><code>‑‑notempfac</code></td>
391 <td>Do not show the temperature factor annotation for the preceding <code>‑‑structure</code></td>
393 <td align="center">✓</td>
399 <td><code>‑‑showssannotations / ‑‑noshowssannotations</code></td>
400 <td>Do not show secondary structure annotations for the preceding <code>‑‑structure</code></td>
402 <td align="center">✓</td>
408 <h2>Outputting files</h2>
410 <table border="1" cellpadding="3">
412 <td><strong>argument</strong></td>
413 <td><strong>action</strong></td>
414 <td><strong>sub-value modifiers</strong> (optional)</td>
415 <td><strong>linked</strong> (optional)</td>
419 <td><code>‑‑output <em>filename</em></code></td>
420 <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:
422 <code>fasta</code> (<code>fa, fasta, mfa, fastq</code>),
424 <code>pfam</code> (<code>pfam</code>),
426 <code>stockholm</code> (<code>sto, stk</code>),
428 <code>pir</code> (<code>pir</code>),
430 <code>blc</code> (<code>blc</code>),
432 <code>amsa</code> (<code>amsa</code>),
434 <code>json</code> (<code>json</code>),
436 <code>pileup</code> (<code>pileup</code>),
438 <code>msf</code> (<code>msf</code>),
440 <code>clustal</code> (<code>aln</code>),
442 <code>phylip</code> (<code>phy</code>),
444 <code>jalview</code> (<code>jvp, jar</code>).
446 <td><code>format=<em>name</em></code></td>
447 <td align="center">✓</td>
451 <td><code>‑‑format <em>name</em></code></td>
452 <td>Sets the format for the preceding <code>‑‑output</code> file. Valid formats are:
458 <code>stockholm</code>,
472 <code>clustal</code>,
476 <code>jalview</code>.
479 <td align="center">✓</td>
483 <td><code>‑‑image <em>filename</em></code></td>
484 <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:
497 <code>type=<em>name</em>,
498 <code>textrenderer=<em>name</em>,
499 <code>scale=<em>number</em>,
500 <code>width=<em>number</em>,
501 <code>height=<em>number</em>
503 <td align="center">✓</td>
507 <td><code>‑‑type <em>name</em></code></td>
508 <td>Set the image format for the preceding <code>‑‑image</code> to <em>name</em>. Valid values for <em>name</em> are:
521 <td align="center">✓</td>
525 <td><code>‑‑textrenderer <em>name</em></code></td>
526 <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:
530 <code>lineart</code>.
533 <td align="center">✓</td>
537 <td><code>‑‑scale <em>number</em></code></td>
538 <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>
540 <td align="center">✓</td>
544 <td><code>‑‑width <em>number</em></code></td>
545 <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>
547 <td align="center">✓</td>
551 <td><code>‑‑height <em>number</em></code></td>
552 <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>
554 <td align="center">✓</td>
558 <td><code>‑‑groovy <em>filename</em></code></td>
559 <td>Process a groovy script in the file for the open alignment.</td>
561 <td align="center">✓</td>
565 <td><code>‑‑backups / ‑‑nobackups</code></td>
566 <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>
568 <td align="center">✓</td>
572 <td><code>‑‑overwrite / ‑‑nooverwrite</code></td>
573 <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>
575 <td align="center">✓</td>
579 <td><code>‑‑close</code></td>
580 <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>
582 <td align="center">✓</td>
588 <h2>Controlling flow of arguments</h2>
590 <table border="1" cellpadding="3">
592 <td><strong>argument</strong></td>
593 <td><strong>action</strong></td>
597 <td><code>‑‑new</code></td>
599 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.
601 <em>Note</em> that <code>--open</code> already starts a new alignment window for each file it opens.
606 <td><code>‑‑substitutions / ‑‑nosubstitutions</code></td>
607 <td>The following argument values allow (or don't allow) subsituting filename parts. This is initially true. Valid substitutions are
608 <code>{basename}</code> - the filename-without-extension of the currently <code>‑‑open</code>ed file (or first <code>‑‑append</code>ed file),
610 <code>{dirname}</code>, - the directory (folder) name of the currently <code>‑‑open</code>ed file (or first <code>‑‑append</code>ed file),
612 <code>{argfilebasename}</code> - the filename-without-extension of the current <code>‑‑argfile</code>,
614 <code>{argfiledirname}</code> - the directory (folder) name of the current <code>‑‑argfile</code>,
616 <code>{n}</code> - the value of the index counter (starting at 0).
618 <code>{++n}</code> - increase and substitute the value of the index counter,
620 <code>{}</code> - the value of the current alignment window <em>default</em> index.
625 <td><code>‑‑argfile <em>filename</em></code></td>
627 Open one or more files <em>filename</em> and read, line-by-line, as arguments to Jalview.
629 Values in an argfile should be given with an equals sign ("=") separator with no spaces.
631 <strong>Note</strong> that if you use one or more <code>‑‑argfile</code> arguments then all other non-initialising arguments will be ignored.
636 <td><code>‑‑npp</code></td>
637 <td>Increase the index counter used in argument value substitutions.</td>
641 <td><code>‑‑all</code></td>
642 <td>Apply the following output arguments to <em>all</em> sets of linked arguments.</td>
646 <td><code>‑‑quit</code></td>
647 <td>After all files have been opened, appended and output, quit Jalview. In <code>‑‑headless</code> mode this already happens.</td>