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>Summary of Command Line Arguments (next generation)</title>
15 <h1>Summary of Command Line Arguments (next generation)</h1>
18 See <a href="clarguments-ng.html">Jalview Command Line Arguments (next generation)</a>
19 for more explanation about using Jalview's command line arguments.
26 <h2>Initialising arguments</h2>
28 <table border="1" cellpadding="3">
30 <td><strong>argument</strong></td>
31 <td><strong>action</strong></td>
35 <td><code>‑‑help / -h</code></td>
36 <td>Display a help statement</td>
40 <td><code>‑‑headless</code></td>
41 <td>Run Jalview in headless mode. No GUI interface will be created and Jalview will quit after all arguments have been processed.</td>
45 <td><code>‑‑jabaws <em>URL</em></code></td>
46 <td>Set a different URL to connect to a JABAWS server.</td>
50 <td><code>‑‑news / ‑‑nonews</code></td>
51 <td>Show (or don't show) the news feed.</td>
55 <td><code>‑‑splash / ‑‑nosplash</code></td>
56 <td>Show (or don't show) the About Jalview splash screen.</td>
60 <td><code>‑‑questionnaire / ‑‑noquestionnaire</code></td>
61 <td>Show (or don't show) the questionnaire if one is available.</td>
65 <td><code>‑‑usagestats / ‑‑nousagestats</code></td>
66 <td>Send (or don't send) initial launch usage stats. <em>Note: usage stats are useful for future funding for Jalview!</em></td>
70 <td><code>‑‑webservicediscovery / ‑‑nowebservicediscovery</code></td>
71 <td>Attempt (or don't attempt) to connect to JABAWS web services.</td>
75 <td><code>‑‑props <em>filename</em></code></td>
76 <td>Use file <em>filename</em> as the preferences file <em>instead</em> of the usual <code>~/.jalview_properties</code> file.</td>
80 <td><code>‑‑debug</code></td>
81 <td>Start Jalview in debug log level.</td>
85 <td><code>‑‑quiet</code></td>
86 <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>
90 <td><code>‑‑initsubstitutions / ‑‑noinitsubstitutions</code></td>
91 <td>Assume that <code>‑‑substitutions</code> are initially enabled (or initially disabled).</td>
95 <td><code>‑‑jvmmempc=<em>PERCENT</em></code></td>
97 <em>Only available with standalone executable jar or jalview.bin.Launcher.</em>
99 Limit maximum heap size (memory) to PERCENT% of total physical memory detected.
100 This defaults to 90 if total physical memory can be detected.
102 The equals sign ("=") separator must be used with no spaces.
104 See <a href="../memory.html">Memory usage settings for Jalview</a> for more details.
109 <td><code>‑‑jvmmemmax=<em>MAXMEMORY</em></code></td>
111 <em>Only available with standalone executable jar or jalview.bin.Launcher.</em>
113 Limit maximum heap size (memory) to MAXMEMORY. MAXMEMORY can be specified in bytes, kilobytes(k), megabytes(m),
114 gigabytes(g) or if you're lucky enough, terabytes(t).
115 This defaults to 32g if total physical memory can be detected, or to 8g if total physical memory cannot be detected.
117 The equals sign ("=") separator must be used with no spaces.
119 See <a href="../memory.html">Memory usage settings for Jalview</a> for more details.
126 <h2>Opening an alignment</h2>
128 <table border="1" cellpadding="3">
130 <td><strong>argument</strong></td>
131 <td><strong>action</strong></td>
132 <td><strong>subval modifiers</strong> (optional)</td>
133 <td align="center"><strong>linked</strong> (optional)</td>
137 <td><code>‑‑open <em>filename/URL ...</em></code></td>
139 Opens one or more alignment files <em>filename</em> or URLs <em>URL</em> in new alignment windows.
143 colour=<em>name</em>,
145 title=<em>string</em>,
147 features=<em>filename</em>,
149 annotations=<em>filename</em>,
151 tree=<em>filename</em>,
162 <td align="center">✓</td>
166 <td><code>‑‑append <em>filename/URL ...</em></code></td>
167 <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>
170 colour=<em>name</em>,
172 title=<em>string</em>,
174 features=<em>filename</em>,
176 annotations=<em>filename</em>,
178 tree=<em>filename</em>,
189 <td align="center">✓</td>
193 <td><code>‑‑title <em>"string""</em></code></td>
194 <td>Specifies the title for the open alignment window as <em>string</em>.</td>
196 <td align="center">✓</td>
200 <td><code>‑‑colour <em>name</em></code></td>
201 <td>Applies the colour scheme <em>name</em> to the open alignment window. Valid values for <em>name</em> are:
203 <code>clustal</code>,
205 <code>blosum62</code>,
207 <code>pc-identity</code>,
213 <code>gecos-flower</code>,
215 <code>gecos-blossom</code>,
217 <code>gecos-sunset</code>,
219 <code>gecos-ocean</code>,
221 <code>hydrophobic</code>,
223 <code>helix-propensity</code>,
225 <code>strand-propensity</code>,
227 <code>turn-propensity</code>,
229 <code>buried-index</code>,
231 <code>nucleotide</code>,
233 <code>nucleotide-ambiguity</code>,
235 <code>purine-pyrimidine</code>,
237 <code>rna-helices</code>,
239 <code>t-coffee-scores</code>,
241 <code>sequence-id</code>.
243 <td align="center">✓</td>
247 <td><code>‑‑features <em>filename/URL</em></code></td>
248 <td>Add a feature file <em>filename</em> or URL <em>URL</em> to the open alignment.</td>
250 <td align="center">✓</td>
256 <td><code>‑‑tree <em>filename/URL</em></code></td>
257 <td>Add a tree file <em>filename</em> or URL <em>URL</em> to the open alignment.</td>
259 <td align="center">✓</td>
263 <td><code>‑‑sortbytree / ‑‑nosortbytree</code></td>
264 <td>Enforces sorting (or not sorting) the alignment in the order of an attached phylogenetic tree.</td>
266 <td align="center">✓</td>
271 <td><code>‑‑annotations <em>filename/URL</em></code></td>
272 <td>Add an annotations file <em>filename</em> or URL <em>URL</em> to the open alignment.</td>
274 <td align="center">✓</td>
278 <td><code>‑‑showannotations / ‑‑noshowannotations</code></td>
279 <td>Enforces showing (or not showing) alignment annotations.</td>
281 <td align="center">✓</td>
285 <td><code>‑‑wrap / ‑‑nowrap</code></td>
286 <td>Enforces wrapped (or not wrapped) alignment formatting.</td>
288 <td align="center">✓</td>
292 <td><code>‑‑nostructure</code></td>
293 <td>Do not open or process any 3D structure in the <code>‑‑open</code> or <code>‑‑append</code> files.</td>
295 <td align="center">✓</td>
301 <h2>Adding a 3D structure</h2>
303 <table border="1" cellpadding="3">
305 <td><strong>argument</strong></td>
306 <td><strong>action</strong></td>
307 <td><strong>subval modifiers</strong> (optional)</td>
308 <td align="center"><strong>linked</strong> (optional)</td>
312 <td><code>‑‑structure <em>filename/URL</em></code></td>
313 <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>
316 seqid=<em>id</em></code> or <code><em>INDEX</em>,
318 paefile=<em>filename</em>,
320 tempfac=<em>name</em>,
326 structureviewer=<em>name</em>
328 <td align="center">✓</td>
333 <td><code>‑‑seqid <em>ID</em></code></td>
334 <td>Specify the sequence name for the preceding <code>‑‑structure</code> to be associated with.</td>
336 <td align="center">✓</td>
341 <td><code>‑‑paematrix <em>filename</em></code></td>
342 <td>Add a PAE json matrix file <em>filename</em> to the preceding <code>‑‑structure</code>.</td>
344 <td align="center">✓</td>
349 <td><code>‑‑tempfac <em>name</em></code></td>
350 <td>Set the type of temperature factor. Valid values for <em>name</em> are:
352 <code>default</code>,
357 <td align="center">✓</td>
362 <td><code>‑‑structureviewer <em>name</em></code></td>
363 <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:
369 <code>chimera</code> <em>- requires installation, might need configuring in Preferences</em>,
371 <code>chimerax</code> <em>- requires installation, might need configuring in Preferences</em>,
373 <code>pymol</code> <em>- requires installation, might need configuring in Preferences</em>
376 <td align="center">✓</td>
381 <td><code>‑‑notempfac</code></td>
382 <td>Do not show the temperature factor annotation for the preceding <code>‑‑structure</code></td>
384 <td align="center">✓</td>
389 <td><code>‑‑showssannotations / ‑‑noshowssannotations</code></td>
390 <td>Do not show secondary structure annotations for the preceding <code>‑‑structure</code></td>
392 <td align="center">✓</td>
398 <h2>Outputting files</h2>
400 <table border="1" cellpadding="3">
402 <td><strong>argument</strong></td>
403 <td><strong>action</strong></td>
404 <td><strong>subval modifiers</strong> (optional)</td>
405 <td align="center"><strong>linked</strong> (optional)</td>
409 <td><code>‑‑image <em>filename</em></code></td>
410 <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:
423 <code>type=<em>name</em>,
424 <code>textrenderer=<em>name</em>
426 <td align="center">✓</td>
430 <td><code>‑‑type <em>name</em></code></td>
431 <td>Set the image format for the preceding <code>‑‑image</code> to <em>name</em>. Valid values for <em>name</em> are:
444 <td align="center">✓</td>
448 <td><code>‑‑textrenderer <em>name</em></code></td>
449 <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:
453 <code>lineart</code>.
456 <td align="center">✓</td>
460 <td><code>‑‑output <em>filename</em></code></td>
461 <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:
463 <code>fasta</code> (<code>fa, fasta, mfa, fastq</code>),
465 <code>pfam</code> (<code>pfam</code>),
467 <code>stockholm</code> (<code>sto, stk</code>),
469 <code>pir</code> (<code>pir</code>),
471 <code>blc</code> (<code>blc</code>),
473 <code>amsa</code> (<code>amsa</code>),
475 <code>json</code> (<code>json</code>),
477 <code>pileup</code> (<code>pileup</code>),
479 <code>msf</code> (<code>msf</code>),
481 <code>clustal</code> (<code>aln</code>),
483 <code>phylip</code> (<code>phy</code>),
485 <code>jalview</code> (<code>jvp, jar</code>).
487 <td><code>format=<em>name</em></code></td>
488 <td align="center">✓</td>
492 <td><code>‑‑format <em>name</em></code></td>
493 <td>Sets the format for the preceding <code>‑‑output</code> file. Valid formats are:
499 <code>stockholm</code>,
513 <code>clustal</code>,
517 <code>jalview</code>.
520 <td align="center">✓</td>
524 <td><code>‑‑groovy <em>filename</em></code></td>
525 <td>Process a groovy script in the file for the open alignment.</td>
527 <td align="center">✓</td>
531 <td><code>‑‑backups / ‑‑nobackups</code></td>
532 <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>
534 <td align="center">✓</td>
538 <td><code>‑‑overwrite / ‑‑nooverwrite</code></td>
539 <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>
541 <td align="center">✓</td>
545 <td><code>‑‑close</code></td>
546 <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>
548 <td align="center">✓</td>
554 <h2>Controlling flow of arguments</h2>
556 <table border="1" cellpadding="3">
558 <td><strong>argument</strong></td>
559 <td><strong>action</strong></td>
560 <td><strong>subval modifiers</strong> (optional)</td>
561 <td align="center"><strong>linked</strong> (optional)</td>
565 <td><code>‑‑new</code></td>
566 <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>
568 <td align="center"></td>
572 <td><code>‑‑substitutions / ‑‑nosubstitutions</code></td>
573 <td>The following argument values allow (or don't allow) subsituting filename parts. This is initially true. Valid substitutions are
574 <code>{basename}</code> - the filename-without-extension of the currently <code>‑‑open</code>ed file (or first <code>‑‑append</code>ed file),
576 <code>{dirname}</code>, - the directory (folder) name of the currently <code>‑‑open</code>ed file (or first <code>‑‑append</code>ed file),
578 <code>{argfilebasename}</code> - the filename-without-extension of the current <code>‑‑argfile</code>,
580 <code>{argfiledirname}</code> - the directory (folder) name of the current <code>‑‑argfile</code>,
582 <code>{n}</code> - the value of the index counter (starting at 0).
584 <code>{++n}</code> - increase and substitute the value of the index counter,
586 <code>{}</code> - the value of the current alignment window <em>default</em> index.
589 <td align="center"></td>
593 <td><code>‑‑argfile <em>filename</em></code></td>
595 Open one or more files <em>filename</em> and read, line-by-line, as arguments to Jalview.
597 <strong>Note</strong> that if you use one or more <code>‑‑argfile</code> arguments then all other non-initialising arguments will be ignored.
600 <td align="center"></td>
604 <td><code>‑‑npp</code></td>
605 <td>Increase the index counter used in argument value substitutions.</td>
607 <td align="center"></td>
611 <td><code>‑‑all</code></td>
612 <td>Apply the following output arguments to <em>all</em> sets of linked arguments.</td>
614 <td align="center"></td>
618 <td><code>‑‑quit</code></td>
619 <td>After all files have been opened, appended and output, quit Jalview. In <code>‑‑headless</code> mode this already happens.</td>
621 <td align="center"></td>