Jalview Command Line Arguments: summary

Jalview Command Line Arguments: summary
Jalview Command Line Arguments: introduction
Jalview Command Line Arguments: basic usage
Jalview Command Line Arguments: advanced usage
Jalview Command Line Arguments: argfiles

Initialising arguments

argument action
‑‑help / -h Display a help statement
‑‑headless Run Jalview in headless mode. No GUI interface will be created and Jalview will quit after all arguments have been processed.
‑‑jabaws URL Set a different URL to connect to a JABAWS server.
‑‑news / ‑‑nonews Show (or don't show) the news feed.
‑‑splash / ‑‑nosplash Show (or don't show) the About Jalview splash screen.
‑‑questionnaire / ‑‑noquestionnaire Show (or don't show) the questionnaire if one is available.
‑‑usagestats / ‑‑nousagestats Send (or don't send) initial launch usage stats. Note: usage stats are useful for future funding for Jalview!
‑‑webservicediscovery / ‑‑nowebservicediscovery Attempt (or don't attempt) to connect to JABAWS web services.
‑‑props filename Use file filename as the preferences file instead of the usual ~/.jalview_properties file.
‑‑debug Start Jalview in debug log level.
‑‑quiet Stop all output to STDOUT (after the Java Virtual Machine has started). Use ‑‑quiet a second time to stop all output to STDERR.
‑‑initsubstitutions / ‑‑noinitsubstitutions Set ‑‑substitutions to be initially enabled (or initially disabled).
‑‑jvmmempc=PERCENT Limit maximum heap size (memory) to PERCENT% of total physical memory detected. This defaults to 90 if total physical memory can be detected.
The equals sign ("=") separator must be used with no spaces.
See Memory usage settings for Jalview for more details.
‑‑jvmmemmax=MAXMEMORY 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.
The equals sign ("=") separator must be used with no spaces.
See Memory usage settings for Jalview for more details.

Opening an alignment

argument action sub-value modifiers (optional) linked (optional)
‑‑open filename/URL ... Opens one or more alignment files filename or URLs URL in new alignment windows. colour=name,
title=string,
features=filename,
annotations=filename,
tree=filename,
showannotations,
showssannotations,
sortbytree,
wrap 		✓
‑‑append filename/URL ... Appends one or more alignment files filename or URLs URL to the open alignment window (or opens a new alignment if none already open). colour=name,
title=string,
features=filename,
annotations=filename,
tree=filename,
showannotations,
showssannotations,
sortbytree,
wrap 		✓
‑‑title "string"" Specifies the title for the open alignment window as string. ✓
‑‑colour name Applies the colour scheme name to the open alignment window. Valid values for name are:
clustal,
blosum62,
pc-identity,
zappo,
taylor,
gecos-flower,
gecos-blossom,
gecos-sunset,
gecos-ocean,
hydrophobic,
helix-propensity,
strand-propensity,
turn-propensity,
buried-index,
nucleotide,
nucleotide-ambiguity,
purine-pyrimidine,
rna-helices,
t-coffee-scores,
sequence-id. 		✓
‑‑features filename/URL Add a feature file filename or URL URL to the open alignment. ✓
‑‑tree filename/URL Add a tree file filename or URL URL to the open alignment. ✓
‑‑sortbytree / ‑‑nosortbytree Enforces sorting (or not sorting) the alignment in the order of an attached phylogenetic tree. ✓
‑‑annotations filename/URL Add an annotations file filename or URL URL to the open alignment. ✓
‑‑showannotations / ‑‑noshowannotations Enforces showing (or not showing) alignment annotations. ✓
‑‑wrap / ‑‑nowrap Enforces wrapped (or not wrapped) alignment formatting. ✓
‑‑nostructure Do not open or process any 3D structure in the ‑‑open or ‑‑append files. ✓

Adding a 3D structure

argument action sub-value modifiers (optional) linked (optional)
‑‑structure filename/URL 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 sub-value modifier seqid=ID can be used. A sub-value INDEX can also be used to specify the INDEX-th sequence in the open alignment. seqid=id or INDEX,
paefile=filename,
tempfac=name,
showssannotations,
structureviewer=name 		✓
‑‑seqid ID Specify the sequence name for the preceding ‑‑structure to be associated with. ✓
‑‑paematrix filename Add a PAE json matrix file filename to the preceding ‑‑structure. ✓
‑‑tempfac name Set the type of temperature factor. Valid values for name are:
default,
plddt 		✓
‑‑structureviewer name Set the structure viewer to use to open the 3d structure file specified in previous ‑‑structure to name. Valid values of name are:
none,
jmol,
chimera - requires installation, might need configuring in Preferences,
chimerax - requires installation, might need configuring in Preferences,
pymol - requires installation, might need configuring in Preferences 		✓
‑‑showssannotations / ‑‑noshowssannotations Do not show secondary structure annotations for the preceding ‑‑structure ✓

Outputting files

argument action sub-value modifiers (optional) linked (optional)
‑‑output filename Export the open alignment to file filename. The format name is specified by the sub-value modifier format=name, a following ‑‑format name argument or guessed from the file extension. Valid format names (and file extensions) are:
fasta (fa, fasta, mfa, fastq),
pfam (pfam),
stockholm (sto, stk),
pir (pir),
blc (blc),
amsa (amsa),
json (json),
pileup (pileup),
msf (msf),
clustal (aln),
phylip (phy),
jalview (jvp, jar). 		format=name ✓
‑‑format name Sets the format for the preceding ‑‑output file. Valid formats are:
fasta,
pfam,
stockholm,
pir,
blc,
amsa,
json,
pileup,
msf,
clustal,
phylip,
jalview. 		✓
‑‑image filename Output an image of the open alignment window. Format is specified by the sub-value modifier, a following ‑‑type argument or guessed from the file extension. Valid formats/extensions are:
svg,
png,
eps,
html,
biojs. 		type=name, textrenderer=name, scale=number, width=number, height=number ✓
‑‑type name Set the image format for the preceding ‑‑image to name. Valid values for name are:
svg,
png,
eps,
html,
biojs. 		✓
‑‑textrenderer name Sets whether text in a vector image format (SVG, HTML, EPS) should be rendered as text or vector line-art. Valid values for name are:
text,
lineart. 		✓
‑‑scale number 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 --image value. If used in conjunction with --width and --height then the smallest scaling will be used (scale, width and height provide bounds for the image). ✓
‑‑width number 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 --image value. If used in conjunction with --scale and --height then the smallest scaling will be used (scale, width and height provide bounds for the image). ✓
‑‑height number 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 --image value. If used in conjunction with --scale and --width then the smallest scaling will be used (scale, width and height provide bounds for the image). ✓
‑‑groovy filename Process a groovy script in the file for the open alignment. ✓
‑‑backups / ‑‑nobackups 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. ✓
‑‑overwrite / ‑‑nooverwrite 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. ✓
‑‑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. ✓

Controlling flow of arguments

argument action
‑‑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.
Note that --open already starts a new alignment window for each file it opens.
‑‑substitutions / ‑‑nosubstitutions 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),
{dirname}, - the directory (folder) name of the currently ‑‑opened file (or first ‑‑appended file),
{argfilebasename} - the filename-without-extension of the current ‑‑argfile,
{argfiledirname} - the directory (folder) name of the current ‑‑argfile,
{n} - the value of the index counter (starting at 0).
{++n} - increase and substitute the value of the index counter,
{} - the value of the current alignment window default index.
‑‑argfile filename Open one or more files filename and read, line-by-line, as arguments to Jalview.
Values in an argfile should be given with an equals sign ("=") separator with no spaces.
Note that if you use one or more ‑‑argfile arguments then all other non-initialising arguments will be ignored.
‑‑npp Increase the index counter used in argument value substitutions.
‑‑all / ‑‑noall Apply (or stop applying) the following output arguments to all sets of linked arguments.
‑‑quit After all files have been opened, appended and output, quit Jalview. In ‑‑headless mode this already happens.