Command Line: introduction
Command Line: basic usage
Command Line: advanced usage
Command Line: argument files
Command Line: reference
| argument | action |
‑‑help / -h
|
Display a help statement. |
‑‑help‑config | Help for arguments used to configure Jalview from startup |
‑‑help‑opening | Help for arguments used to open and format alignments |
‑‑help‑structure | Help for arguments used to add and format 3D structure data |
‑‑help‑process | Help for arguments used to process an alignment once opened |
‑‑help‑output | Help for arguments used to save data from a processed alignment |
‑‑help‑image | Help for arguments used to export an image of an alignment |
‑‑help‑structureimage | Help for arguments used to export an image of an structure |
‑‑help‑flow | Help for arguments that control processing of the other arguments |
‑‑help‑all | Help for all arguments |
‑‑headless |
Run Jalview in headless mode. In headless mode, no GUI interface will be created and Jalview will quit after all arguments have been processed.
If you use a command line argument to specify an output file of some kind ( ‑‑output, ‑‑image or ‑‑structureimage) then headless mode will be assumed. If you don't want this behaviour use ‑‑gui.
|
‑‑gui |
Force Jalview to run in graphical mode. This can be used to counter the assumption of headless mode when an argument that creates an output file is used. ‑‑gui takes precedence over ‑‑headless. |
‑‑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. |
‑‑javaconsole / ‑‑nojavaconsole |
Show (/ or don't show) the Java Console. Using one of these overrides any saved Preference. |
‑‑questionnaire / ‑‑noquestionnaire |
Show (/ or don't show) the questionnaire if one is available. |
‑‑nousagestats |
Don't send usage stats via Google analytics for this session. Note: usage stats are useful for future funding for Jalview! |
‑‑nostartupfile |
Don't show the default startup file. |
‑‑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. |
‑‑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. |
| 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,
|
✓ |
‑‑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" |
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 include:
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.
Names of user defined schemes will also work, and jalview colour scheme specifications like: ‑‑colour "D,E=red; K,R,H=0022FF; C,c=yellow"
| ✓ | |
‑‑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. |
✓ |
| 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,
|
✓ |
‑‑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 |
✓ | |
‑‑close |
Close the open alignment window. This occurs after other output, processing and image export arguments. This applies to the current open alignment -- to apply to all ‑‑output and ‑‑image files, use after ‑‑all. |
✓ |
| argument | action | sub-value modifiers (optional) | linked (optional) |
‑‑groovy filename |
Process a groovy script in the file for the open alignment. | ✓ |
| 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).
To output directly to STDOUT (console output) use the filename - (a single hyphen). In this case all STDOUT messages will instead go to STDERR. If no format is supplied then Fasta will be assumed.
|
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.
|
✓ | |
‑‑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. |
✓ | |
‑‑mkdirs |
Enable automatic creation of new directories and parent directories for filenames given, or created through substitutions, in ‑‑output, ‑‑image or ‑‑structureimage arguments.
| ✓ |
| argument | action | sub-value modifiers (optional) | linked (optional) |
‑‑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,
|
✓ |
‑‑structureimage filename |
Export an image of a 3D structure opened in JMOL (currently jmol only). Each ‑‑structureimage filename will output a file for each ‑‑structureimage that has been applied to the open alignment window. In this situation, to avoid overwriting the same file with each structure, additional substitutions {structuredirname}, {structurebasename} and {structureextname} are available being substituted with the directory path, file basename and file extension of each structure file. Image formats can be:
svg,
png,
eps.
|
type=name,
|
✓ |
‑‑type name |
Set the image format for the preceding ‑‑image or ‑‑structureimage 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. Applies to the preceding ‑‑image or ‑‑structureimage. 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. Applies to the preceding ‑‑image or ‑‑structureimage. This can also be set as a sub-value modifier to the ‑‑image or ‑‑structureimage value. If used in conjunction with ‑‑width and ‑‑height then the smallest size 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. Applies to the preceding ‑‑image or ‑‑structureimage. Should be given as a positive integer. This can also be set as a sub-value modifier to the ‑‑image or ‑‑structureimage value. If used in conjunction with ‑‑scale and ‑‑height then the smallest size 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. Applies to the preceding ‑‑image or ‑‑structureimage. Should be given as a positive integer. This can also be set as a sub-value modifier to the ‑‑image or ‑‑structureimage value. If used in conjunction with ‑‑scale and ‑‑width then the smallest size will be used (scale, width and height provide bounds for the image). |
✓ | |
‑‑bgcolour name |
Only applies to structure images (opened with jmol structure viewer). Sets the background colour of the preceding ‑‑structureimage. name should be either a named colour (e.g. white, cyan) known to Jmol, or can be given as a six digit RGB hex string (e.g. ffffff, 00ffff). This can also be set as a sub-value modifier to the ‑‑structureimage value. |
✓ | |
‑‑groovy filename |
Process a groovy script in the file for the open alignment. | ✓ |
| 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),
{extension}, - the extension of the filename 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,
{structurebasename} - the filename-without-extension of the ‑‑structure file. Only available to ‑‑structureimage .
{structuredirname}, - the directory (folder) name of the ‑‑structure file. Only available to ‑‑structureimage .
{structureextension}, - the extension of the filename of the ‑‑structure file. Only available to ‑‑structureimage .
{n} - the value of the index counter (starting at 0).
{++n} - increase and substitute the value of the index counter.
{m} - the value of the on-the-fly counter (starting at 0). Only available to ‑‑structureimage .
{++m} - increase and substitute the (incremented) value of the on-the-fly counter. Only available to ‑‑structureimage .
{} - 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. |
‑‑allstructures / ‑‑noallstructures |
Apply (or stop applying) the following 3D structure formatting arguments to all structures within the current open alignment. Whilst ‑‑allstructures will continue to operate for a ‑‑new alignment, the structure formatting arguments must be set again for each new alignment.
|
‑‑quit |
After all files have been opened, appended and output, quit Jalview. In ‑‑headless mode this already happens. |