X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Fclarguments-ng-summary.html;fp=help%2Fhelp%2Fhtml%2Ffeatures%2Fclarguments-ng-summary.html;h=0000000000000000000000000000000000000000;hb=5eca2a7ffd0c6b38898655d8b1c95310535cdfc8;hp=c7b5be777b5ab207c730a631afd9b2e8b4d345bd;hpb=ec24991b1786e17158a43f713c8ae9c4f8647393;p=jalview.git diff --git a/help/help/html/features/clarguments-ng-summary.html b/help/help/html/features/clarguments-ng-summary.html deleted file mode 100644 index c7b5be7..0000000 --- a/help/help/html/features/clarguments-ng-summary.html +++ /dev/null @@ -1,624 +0,0 @@ - - -Summary of Command Line Arguments (next generation) - - -

Summary of Command Line Arguments (next generation)

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- See Jalview Command Line Arguments (next generation) - for more explanation about using Jalview's command line arguments. -

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Initialising arguments

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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`	Assume that `‑‑substitutions` are initially enabled (or initially disabled).
`‑‑jvmmempc=PERCENT`	- Only available with standalone executable jar or jalview.bin.Launcher. - - 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`	- Only available with standalone executable jar or jalview.bin.Launcher. - - 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. -

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Opening an alignment

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argument	action	subval 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.		✓

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Adding a 3D structure

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argument	action	subval 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 subval modifier `seqid=ID` can be used. A subval INDEX can also be used to specify the INDEX-th sequence in the open alignment.	- `- seqid=id` or `INDEX, - - paefile=filename, - - tempfac=name, - - showssannotations, - - notempfac, - - 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 -		✓
`‑‑notempfac`	Do not show the temperature factor annotation for the preceding `‑‑structure`		✓
`‑‑showssannotations / ‑‑noshowssannotations`	Do not show secondary structure annotations for the preceding `‑‑structure`		✓

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Outputting files

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argument	action	subval modifiers (optional)	linked (optional)
`‑‑image filename`	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`. -	- `type=name, - textrenderer=name -`	✓
`‑‑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`. -		✓
`‑‑output filename`	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: - - `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`. -		✓
`‑‑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`.		✓

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Controlling flow of arguments

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argument	action	subval modifiers (optional)	linked (optional)
`‑‑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.
`‑‑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 `‑‑open`ed file (or first `‑‑append`ed file), - - `{dirname}`, - the directory (folder) name of the currently `‑‑open`ed file (or first `‑‑append`ed 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. - - 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`	Apply 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.