X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2Fargparser%2FArg.java;h=b69ed614bf94b0e1d1cb66731f7dadfe5f2d501a;hb=24148ee604dd03ceaeab63c123f3afc5cc2a57a7;hp=c502eecb665819b3ce860e7b97ea8f6782a05cd7;hpb=4fd4608b88401dbb1a86a29f8d607c7481145e27;p=jalview.git diff --git a/src/jalview/bin/argparser/Arg.java b/src/jalview/bin/argparser/Arg.java index c502eec..b69ed61 100644 --- a/src/jalview/bin/argparser/Arg.java +++ b/src/jalview/bin/argparser/Arg.java @@ -19,7 +19,7 @@ public enum Arg // Initialising arguments (BOOTSTRAP) HELP(Type.HELP, "h", "Display basic help", Opt.UNARY, Opt.BOOTSTRAP, - Opt.HASTYPE, Opt.MULTI), + Opt.HASTYPE, Opt.MULTIVALUE), /* * Other --help-type Args will be added by the static block. */ @@ -29,8 +29,8 @@ public enum Arg Opt.UNARY, Opt.BOOTSTRAP), HEADLESS(Type.CONFIG, "Run Jalview in headless mode. No GUI interface will be created and Jalview will quit after all arguments have been processed. " - + "Headless mode is assumed if an output file is to be generated, this can be overridden with --noheadless or --gui.", - Opt.BOOLEAN, Opt.BOOTSTRAP), + + "Headless mode is assumed if an output file is to be generated, this can be overridden with --gui.", + Opt.UNARY, Opt.BOOTSTRAP), GUI(Type.CONFIG, "Do not run Jalview in headless mode. This overrides the assumption of headless mode when an output file is to be generated.", Opt.UNARY, Opt.BOOTSTRAP), @@ -44,9 +44,10 @@ public enum Arg QUESTIONNAIRE(Type.CONFIG, "Show (or don't show) the questionnaire if one is available.", true, Opt.BOOLEAN, Opt.BOOTSTRAP), - USAGESTATS(Type.CONFIG, - "Send (or don't send) initial launch usage stats.", true, - Opt.BOOLEAN, Opt.BOOTSTRAP), + NOUSAGESTATS(Type.CONFIG, "Don't send initial launch usage stats.", + Opt.UNARY, Opt.BOOTSTRAP), + NOSTARTUPFILE(Type.CONFIG, "Don't show the default startup file.", + Opt.UNARY, Opt.BOOTSTRAP), WEBSERVICEDISCOVERY(Type.CONFIG, "Attempt (or don't attempt) to connect to JABAWS web services.", true, Opt.BOOLEAN, Opt.BOOTSTRAP), @@ -61,26 +62,30 @@ public enum Arg Opt.BOOTSTRAP, Opt.SECRET), QUIET(Type.CONFIG, "q", "Stop all output to STDOUT (after the Java Virtual Machine has started). Use ‑‑quiet a second time to stop all output to STDERR.", - Opt.UNARY, Opt.MULTI, Opt.BOOTSTRAP), + Opt.UNARY, Opt.MULTIVALUE, Opt.BOOTSTRAP), INITSUBSTITUTIONS(Type.CONFIG, "Set ‑‑substitutions to be initially enabled (or initially disabled).", true, Opt.BOOLEAN, Opt.BOOTSTRAP, Opt.NOACTION, Opt.SECRET), + P(Type.CONFIG, "Set a Jalview preference value for this session.", + Opt.PREFIXKEV, Opt.PRESERVECASE, Opt.STRING, Opt.BOOTSTRAP, + Opt.MULTIVALUE, Opt.NOACTION, Opt.SECRET), // keep this secret for + // now. // Opening an alignment OPEN(Type.OPENING, "Opens one or more alignment files or URLs in new alignment windows.", - Opt.STRING, Opt.LINKED, Opt.INCREMENTDEFAULTCOUNTER, Opt.MULTI, - Opt.GLOB, Opt.ALLOWSUBSTITUTIONS, Opt.INPUT, Opt.STORED, - Opt.PRIMARY), + Opt.STRING, Opt.LINKED, Opt.INCREMENTDEFAULTCOUNTER, + Opt.MULTIVALUE, Opt.GLOB, Opt.ALLOWSUBSTITUTIONS, Opt.INPUT, + Opt.STORED, Opt.PRIMARY), APPEND(Type.OPENING, "Appends one or more alignment files or URLs to the open alignment window (or opens a new alignment if none already open).", - Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.GLOB, + Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.GLOB, Opt.ALLOWSUBSTITUTIONS, Opt.INPUT, Opt.PRIMARY), TITLE(Type.OPENING, "Specifies the title for the open alignment window as string.", - Opt.STRING, Opt.LINKED), + Opt.STRING, Opt.LINKED, Opt.ALLOWMULTIID), COLOUR(Type.OPENING, "color", // being a bit soft on the Americans! - "Applies the colour scheme to the open alignment window. Valid values are:\n" + "Applies the colour scheme to the open alignment window. Valid values include:\n" + "clustal,\n" + "blosum62,\n" + "pc-identity,\n" + "zappo,\n" + "taylor,\n" + "gecos-flower,\n" + "gecos-blossom,\n" + "gecos-sunset,\n" @@ -89,99 +94,122 @@ public enum Arg + "turn-propensity,\n" + "buried-index,\n" + "nucleotide,\n" + "nucleotide-ambiguity,\n" + "purine-pyrimidine,\n" + "rna-helices,\n" - + "t-coffee-scores,\n" + "sequence-id.", - Opt.STRING, Opt.LINKED, Opt.ALLOWALL), + + "t-coffee-scores,\n" + "sequence-id.\n" + "\n" + + "Names of user defined colourschemes will also work,\n" + + "and jalview colourscheme specifications like\n" + + "--colour=\"D,E=red; K,R,H=0022FF; C,c=yellow\"", + Opt.STRING, Opt.LINKED, Opt.ALLOWMULTIID), FEATURES(Type.OPENING, "Add a feature file or URL to the open alignment.", - Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS), + Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWSUBSTITUTIONS, + Opt.ALLOWMULTIID), TREE(Type.OPENING, "Add a tree file or URL to the open alignment.", - Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS), + Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWSUBSTITUTIONS, + Opt.ALLOWMULTIID), SORTBYTREE(Type.OPENING, "Enforces sorting (or not sorting) the open alignment in the order of an attached phylogenetic tree.", - true, Opt.LINKED, Opt.BOOLEAN, Opt.ALLOWALL), + true, Opt.LINKED, Opt.BOOLEAN, Opt.ALLOWMULTIID), ANNOTATIONS(Type.OPENING, "Add an annotations file or URL to the open alignment.", - Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS), + Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWSUBSTITUTIONS, + Opt.ALLOWMULTIID), SHOWANNOTATIONS(Type.OPENING, "Enforces showing (or not showing) alignment annotations.", - Opt.BOOLEAN, Opt.LINKED, Opt.ALLOWALL), + Opt.BOOLEAN, Opt.LINKED, Opt.ALLOWMULTIID, Opt.ALLOWMULTIID), WRAP(Type.OPENING, "Enforces wrapped (or not wrapped) alignment formatting.", - Opt.BOOLEAN, Opt.LINKED, Opt.ALLOWALL), + Opt.BOOLEAN, Opt.LINKED, Opt.ALLOWMULTIID, Opt.ALLOWMULTIID), NOSTRUCTURE(Type.OPENING, "Do not open or process any 3D structure in the ‑‑open or ‑‑append files.", - Opt.UNARY, Opt.LINKED, Opt.ALLOWALL), + Opt.UNARY, Opt.LINKED, Opt.ALLOWMULTIID, Opt.ALLOWMULTIID), // Adding a 3D structure STRUCTURE(Type.STRUCTURE, "Load a structure file or URL associated with a sequence in the open alignment.\n" + "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.", - Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS, - Opt.PRIMARY), + Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWSUBSTITUTIONS, + Opt.PRIMARY, Opt.ALLOWMULTIID), SEQID(Type.STRUCTURE, "Specify the sequence name for the preceding --structure to be associated with.", - Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS), + Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWSUBSTITUTIONS, + Opt.ALLOWMULTIID), PAEMATRIX(Type.STRUCTURE, "Add a PAE json matrix file to the preceding --structure.", - Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS), + Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWSUBSTITUTIONS, + Opt.ALLOWMULTIID), TEMPFAC(Type.STRUCTURE, "Set the type of temperature factor. Possible values are:\n" + "default,\n" + "plddt.", - Opt.STRING, Opt.LINKED), + Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWMULTIID), STRUCTUREVIEWER(Type.STRUCTURE, "Set the structure viewer to use to open the 3D structure file specified in previous --structure to name. Possible values of name are:\n" + "none,\n" + "jmol,\n" + "chimera,\n" + "chimerax,\n" + "pymol.", - Opt.STRING, Opt.LINKED, Opt.MULTI), + Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWMULTIID), NOTEMPFAC(Type.STRUCTURE, "Do not show the temperature factor annotation for the preceding --structure.", - Opt.UNARY, Opt.LINKED, Opt.ALLOWALL, Opt.SECRET), // keep this secret - // until it works! + Opt.UNARY, Opt.LINKED, Opt.ALLOWMULTIID, Opt.SECRET), // keep this + // secret until + // it works! SHOWSSANNOTATIONS(Type.STRUCTURE, null, Opt.BOOLEAN, Opt.LINKED, - Opt.ALLOWALL), + Opt.ALLOWMULTIID), // Outputting files IMAGE(Type.IMAGE, "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:\n" + "svg,\n" + "png,\n" + "eps,\n" + "html,\n" + "biojs.", - Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS, Opt.ALLOWALL, - Opt.REQUIREINPUT, Opt.OUTPUTFILE, Opt.PRIMARY), + Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS, Opt.MULTIVALUE, + Opt.ALLOWMULTIID, Opt.REQUIREINPUT, Opt.OUTPUTFILE, Opt.PRIMARY), + STRUCTUREIMAGE(Type.IMAGE, + "Export an image of a 3D structure opened in JMOL", Opt.STRING, + Opt.LINKED, Opt.MULTIVALUE, Opt.OUTPUTFILE, Opt.ALLOWMULTIID, + Opt.PRIMARY), TYPE(Type.IMAGE, - "Set the image format for the preceding --image. Valid values are:\n" - + "svg,\n" + "png,\n" + "eps,\n" + "html,\n" + "biojs.", - Opt.STRING, Opt.LINKED, Opt.ALLOWALL), + "Set the image format for the preceding " + Arg.IMAGE.argString() + + " or " + Arg.STRUCTUREIMAGE.argString() + + ". Valid values are:\n" + "svg,\n" + "png,\n" + "eps,\n" + + "html,\n" + "biojs.", + Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWMULTIID), TEXTRENDERER(Type.IMAGE, "Sets whether text in a vector image format (SVG, HTML, EPS) should be rendered as text or vector line-art. Possible values are:\n" + "text,\n" + "lineart.", - Opt.STRING, Opt.LINKED, Opt.ALLOWALL), + Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWMULTIID), SCALE(Type.IMAGE, "Sets a scaling for bitmap image format (PNG). Should be given as a floating point number. If used in conjunction with --width and --height then the smallest scaling will be used (scale, width and height provide bounds for the image).", - Opt.STRING, Opt.LINKED, Opt.ALLOWALL), + Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWMULTIID), WIDTH(Type.IMAGE, "Sets a width for bitmap image format (PNG) with the height maintaining the aspect ratio. Should be given as a positive integer. If used in conjunction with --scale and --height then the smallest scaling will be used (scale, width and height provide bounds for the image).", - Opt.STRING, Opt.LINKED, Opt.ALLOWALL), + Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWMULTIID), HEIGHT(Type.IMAGE, "Sets a height for bitmap image format (PNG) with the width maintaining the aspect ratio. Should be given as a positive integer. If used in conjunction with --scale and --width then the smallest scaling will be used (scale, width and height provide bounds for the image).", - Opt.STRING, Opt.LINKED, Opt.ALLOWALL), - STRUCTUREIMAGE(Type.STRUCTUREIMAGE, - "Export an image of a 3D structure opened in JMOL", Opt.STRING, - Opt.LINKED, Opt.MULTI, Opt.OUTPUTFILE), - STRUCTUREIMAGETYPE(Type.STRUCTUREIMAGE, + Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWMULTIID), + IMAGECOLOUR(Type.IMAGE, "imagecolor", // being a bit soft on the Americans! + "Applies the colour scheme to the open alignment window for this image, otherwise the value of " + + Arg.COLOUR.argString() + + " (or none) will apply. Valid values are the same as " + + Arg.COLOUR.argString() + ".", + Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWMULTIID), + BGCOLOUR(Type.IMAGE, "bgcolor", // being a bit soft on the Americans! + "Applies a background colour to the structure image. Valid values are named colours or #RRGGBB.", + Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWMULTIID), + /* + STRUCTUREIMAGETYPE(Type.IMAGE, "Set the structure image format for the preceding --structureimage. Valid values are:\n" + "svg,\n" + "png,\n" + "eps,\n" + "html,\n" + "biojs.", - Opt.STRING, Opt.LINKED, Opt.ALLOWALL), - STRUCTUREIMAGETEXTRENDERER(Type.STRUCTUREIMAGE, + Opt.STRING, Opt.LINKED, Opt.ALLOWMULTIID), + STRUCTUREIMAGETEXTRENDERER(Type.IMAGE, "Sets whether text in a vector structure image format (SVG, EPS) should be rendered as text or vector line-art. Possible values are:\n" + "text,\n" + "lineart.", - Opt.STRING, Opt.LINKED, Opt.ALLOWALL), - STRUCTUREIMAGESCALE(Type.STRUCTUREIMAGE, + Opt.STRING, Opt.LINKED, Opt.ALLOWMULTIID), + STRUCTUREIMAGESCALE(Type.IMAGE, "Sets a scaling for bitmap structure image format (PNG). Should be given as a floating point number. If used in conjunction with --structureimagewidth and --structureimageheight then the smallest scaling will be used (structureimagescale, structureimagewidth and structureimageheight provide bounds for the structure image).", - Opt.STRING, Opt.LINKED, Opt.ALLOWALL), - STRUCTUREIMAGEWIDTH(Type.STRUCTUREIMAGE, + Opt.STRING, Opt.LINKED, Opt.ALLOWMULTIID), + STRUCTUREIMAGEWIDTH(Type.IMAGE, "Sets a width for bitmap structure image format (PNG) with the height maintaining the aspect ratio. Should be given as a positive integer. If used in conjunction with --structureimagescale and --structureimageheight then the smallest scaling will be used (structureimagescale, structureimagewidth and structureimageheight provide bounds for the structure image).", - Opt.STRING, Opt.LINKED, Opt.ALLOWALL), - STRUCTUREIMAGEHEIGHT(Type.STRUCTUREIMAGE, + Opt.STRING, Opt.LINKED, Opt.ALLOWMULTIID), + STRUCTUREIMAGEHEIGHT(Type.IMAGE, "Sets a height for bitmap structure image format (PNG) with the width maintaining the aspect ratio. Should be given as a positive integer. If used in conjunction with --structureimagescale and --structureimagewidth then the smallest scaling will be used (structureimagescale, structureimagewidth and structureimageheight provide bounds for the structure image).", - Opt.STRING, Opt.LINKED, Opt.ALLOWALL), + Opt.STRING, Opt.LINKED, Opt.ALLOWMULTIID), + */ OUTPUT(Type.OUTPUT, "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:\n" @@ -191,32 +219,36 @@ public enum Arg + "pileup (pileup),\n" + "msf (msf),\n" + "clustal (aln),\n" + "phylip (phy),\n" + "jalview (jvp, jar).", - Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS, Opt.ALLOWALL, - Opt.REQUIREINPUT, Opt.OUTPUTFILE, Opt.PRIMARY), + Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS, Opt.ALLOWMULTIID, + Opt.REQUIREINPUT, Opt.OUTPUTFILE, Opt.STDOUT, Opt.PRIMARY), FORMAT(Type.OUTPUT, "Sets the format for the preceding --output file. Valid formats are:\n" + "fasta,\n" + "pfam,\n" + "stockholm,\n" + "pir,\n" + "blc,\n" + "amsa,\n" + "json,\n" + "pileup,\n" + "msf,\n" + "clustal,\n" + "phylip,\n" + "jalview.", - Opt.STRING, Opt.LINKED, Opt.ALLOWALL), + Opt.STRING, Opt.LINKED, Opt.ALLOWMULTIID), GROOVY(Type.PROCESS, "Process a groovy script in the file for the open alignment.", - Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS, - Opt.ALLOWALL), + Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWSUBSTITUTIONS, + Opt.ALLOWMULTIID), BACKUPS(Type.OUTPUT, "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.", - true, Opt.BOOLEAN, Opt.LINKED, Opt.ALLOWALL), + true, Opt.BOOLEAN, Opt.LINKED, Opt.ALLOWMULTIID), OVERWRITE(Type.OUTPUT, "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.", - Opt.BOOLEAN, Opt.LINKED, Opt.ALLOWALL), + Opt.BOOLEAN, Opt.LINKED, Opt.ALLOWMULTIID), CLOSE(Type.OPENING, "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.", - Opt.UNARY, Opt.LINKED, Opt.ALLOWALL), + Opt.UNARY, Opt.LINKED, Opt.ALLOWMULTIID), + MKDIRS(Type.OUTPUT, + "Automatically create directories when outputting a file to a new directory.", + Opt.UNARY, Opt.LINKED, Opt.ALLOWMULTIID), // controlling flow of arguments NEW(Type.FLOW, "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.", - Opt.UNARY, Opt.MULTI, Opt.NOACTION, Opt.INCREMENTDEFAULTCOUNTER), + Opt.UNARY, Opt.MULTIVALUE, Opt.NOACTION, + Opt.INCREMENTDEFAULTCOUNTER), SUBSTITUTIONS(Type.FLOW, "The following argument values allow (or don't allow) subsituting filename parts. This is initially true. Valid substitutions are:\n" + "{basename} - the filename-without-extension of the currently --opened file (or first --appended file),\n" @@ -226,22 +258,22 @@ public enum Arg + "{n} - the value of the index counter (starting at 0).\n" + "{++n} - increase and substitute the value of the index counter,\n" + "{} - the value of the current alignment window default index.", - true, Opt.BOOLEAN, Opt.MULTI, Opt.NOACTION), + true, Opt.BOOLEAN, Opt.MULTIVALUE, Opt.NOACTION), ARGFILE(Type.FLOW, "Open one or more files filename and read, line-by-line, as arguments to Jalview.\n" + "Values in an argfile should be given with an equals sign (\"=\") separator with no spaces.\n" + "Note that if you use one or more --argfile arguments then all other non-initialising arguments will be ignored.", - Opt.STRING, Opt.MULTI, Opt.BOOTSTRAP, Opt.GLOB, + Opt.STRING, Opt.MULTIVALUE, Opt.BOOTSTRAP, Opt.GLOB, Opt.ALLOWSUBSTITUTIONS), NPP(Type.FLOW, "n++", "Increase the index counter used in argument value substitutions.", - Opt.UNARY, Opt.MULTI, Opt.NOACTION), + Opt.UNARY, Opt.MULTIVALUE, Opt.NOACTION), ALL(Type.FLOW, "Apply the following output arguments to all sets of linked arguments.", - Opt.BOOLEAN, Opt.MULTI, Opt.NOACTION), + Opt.BOOLEAN, Opt.MULTIVALUE, Opt.NOACTION), OPENED(Type.FLOW, "Apply the following output arguments to all of the last --open'ed set of linked arguments.", - Opt.BOOLEAN, Opt.MULTI, Opt.NOACTION), + Opt.BOOLEAN, Opt.MULTIVALUE, Opt.NOACTION), QUIT(Type.FLOW, "After all files have been opened, appended and output, quit Jalview. In ‑‑headless mode this already happens.", Opt.UNARY), @@ -250,26 +282,27 @@ public enum Arg Opt.UNARY, Opt.SECRET), ALLSTRUCTURES(Type.FLOW, "Apply the following 3D structure formatting arguments to all structures within the open alignment.", - Opt.BOOLEAN, Opt.MULTI, Opt.NOACTION), + Opt.BOOLEAN, Opt.MULTIVALUE, Opt.NOACTION), // secret options TESTOUTPUT(Type.CONFIG, "Allow specific stdout information. For testing purposes only.", Opt.UNARY, Opt.BOOTSTRAP, Opt.SECRET), // do not show this to the user SETPROP(Type.CONFIG, "Set an individual Java System property.", - Opt.STRING, Opt.MULTI, Opt.BOOTSTRAP, Opt.SECRET), // not in use yet + Opt.STRING, Opt.MULTIVALUE, Opt.BOOTSTRAP, Opt.SECRET), // not in use + // yet NIL(Type.FLOW, "This argument does nothing on its own, but can be used with linkedIds.", - Opt.UNARY, Opt.LINKED, Opt.MULTI, Opt.NOACTION, Opt.SECRET), + Opt.UNARY, Opt.LINKED, Opt.MULTIVALUE, Opt.NOACTION, Opt.SECRET), // private options (inserted during arg processing) SETARGFILE(Type.FLOW, "Sets the current value of the argfilename. Inserted before argfilecontents.", - Opt.UNARY, Opt.LINKED, Opt.STRING, Opt.MULTI, Opt.PRIVATE, + Opt.UNARY, Opt.LINKED, Opt.STRING, Opt.MULTIVALUE, Opt.PRIVATE, Opt.NOACTION), UNSETARGFILE(Type.FLOW, "Unsets the current value of the argfilename. Inserted after argfile contents.", - Opt.UNARY, Opt.LINKED, Opt.MULTI, Opt.PRIVATE, Opt.NOACTION), + Opt.UNARY, Opt.LINKED, Opt.MULTIVALUE, Opt.PRIVATE, Opt.NOACTION), // these last two have no purpose in the normal Jalview application but are // used by jalview.bin.Launcher to set memory settings. They are not used by @@ -287,57 +320,151 @@ public enum Arg public static enum Opt { - BOOLEAN, // This Arg can be specified as --arg or --noarg to give true or - // false. A default can be given with setOptions(bool, Opt....). - // Use ArgParser.isSet(Arg) to see if this arg was not specified. - STRING, // This Arg can accept a value either through --arg=value or --arg - // value. - UNARY, // This Arg is a boolean value, true if present, false if not. Like - // BOOLEAN but without the --noarg option. - MULTI, // This Arg can be specified multiple times. Multiple values are - // stored in the ArgValuesMap (along with their positional index) for - // each linkedId. - LINKED, // This Arg can be linked to others through a --arg[linkedId] or - // --arg[linkedId]=value. If no linkedId is specified then the - // current default linkedId will be used. - NODUPLICATEVALUES, // This Arg can only have one value (per linkedId). The - // first value will be used and subsequent values ignored - // with a warning. - BOOTSTRAP, // This Arg value(s) can be determined at an earlier stage than - // non-BOOTSTRAP Args. Substitutions do not happen in BOOTSTRAP - // Args and they cannot be linked or contain SubVals. See - // jalview.bin.argparser.BootstrapArgs. - GLOB, // This Arg can expand wildcard filename "globs" (e.g. - // path/*/filename*). If the Arg value is given as --arg filename* - // then the shell will have expanded the glob already, but if - // specified as --arg=filename* then the Java glob expansion method - // will be used (see FileUtils.getFilenamesFromGlob()). Note that this - // might be different from the shell expansion rules. - NOACTION, // This Arg does not perform a data task, usually used to control - // flow in ArgParser.parse(args). - ALLOWSUBSTITUTIONS, // This Arg allows substitutions in its linkedId, - // SubVals and values. - PRIVATE, // This Arg is used internally, and cannot be specified by the - // user. - SECRET, // This Arg is used by development processes and although it can be - // set by the user, it is not displayed to the user. - ALLOWALL, // This Arg can use the '*' linkedId to apply to all known - // linkedIds - INCREMENTDEFAULTCOUNTER, // If an Arg has this option and the default - // linkedId is used, the defaultLinkedIdCounter is - // incremented *first*. - INPUT, // This Arg counts as an input for REQUIREINPUT - REQUIREINPUT, // This Arg can only be applied via --all if there is an - // input (i.e. --open or --append) - OUTPUTFILE, // This Arg provides an output filename. With Opt.ALLOWALL *.ext - // is - // shorthand for --all --output={basename}.ext - STORED, // This Arg resets and creates a new set of "opened" linkedIds - HELP, // This Arg is a --help type arg - PRIMARY, // This Arg is the main Arg for its type - HASTYPE, // This Arg can have an Arg.Type assigned to it (and no value) - FIRST, // Move this arg to the first in usage statement (within type) - LAST, // Move this arg to the end in usage statement (within type) + /* + * A BOOLEAN Arg can be specified as --arg or --noarg to give true or false. + * A default can be given with setOptions(bool, Opt....). + * Use ArgParser.isSet(Arg) to see if this arg was not specified. + */ + BOOLEAN("can be negated with " + ArgParser.DOUBLEDASH + + ArgParser.NEGATESTRING + "..."), + + /* + * A STRING Arg will take a value either through --arg=value or --arg value. + */ + STRING("expects a value"), + /* + * A UNARY Arg is a boolean value, true if present, false if not. + * Like BOOLEAN but without the --noarg option. + */ + UNARY(null), + /* + * A MULTI Arg can be specified multiple times. + * Multiple values are stored in the ArgValuesMap (along with their positional index) for each linkedId. + */ + MULTIVALUE("can be specified multiple times"), + /* + * A Linked Arg can be linked to others through a --arg[linkedId] or --arg[linkedId]=value. + * If no linkedId is specified then the current default linkedId will be used. + */ + LINKED("is linked to an alignment"), + /* + * A NODUPLICATES Arg can only have one value (per linkedId). + * The first value will be used and subsequent values ignored with a warning. + */ + NODUPLICATEVALUES("cannot have the same value more than once"), + /* + * A BOOTSTRAP Arg value(s) can be determined at an earlier stage than non-BOOTSTRAP Args. + * Substitutions do not happen in BOOTSTRAP Args and they cannot be linked or contain SubVals. + * See jalview.bin.argparser.BootstrapArgs. + */ + BOOTSTRAP("a configuration argument"), + /* + * A GLOB Arg can expand wildcard filename "globs" (e.g. path/* /filename*). + * If the Arg value is given as --arg filename* then the shell will have expanded the glob already, + * but if specified as --arg=filename* then the Java glob expansion method will be used + * (see FileUtils.getFilenamesFromGlob()). + * Note that this might be different from the shell expansion rules. + */ + GLOB("can take multiple filenames with wildcards"), + /* + * A NOACTION Arg does not perform a data task, + * usually used to control flow in ArgParser.parse(args). + */ + NOACTION(null), + /* + * An ALLOWSUBSTITUTIONS Arg allows substitutions in its linkedId, + * SubVals and values. + */ + ALLOWSUBSTITUTIONS("values can use substitutions"), + /* + * A PRIVATE Arg is used internally, and cannot be specified by the user. + */ + PRIVATE(null), + /* + * A SECRET Arg is used by development processes and although it can be set by the user, + * it is not displayed to the user. + */ + SECRET(null), + /* + * An ALLOWALL Arg can use the '*' linkedId to apply to all known linkedIds + */ + ALLOWMULTIID("can be used with " + ArgParser.DOUBLEDASH + "all"), + /* + * If an Arg has the INCREMENTDEFAULTCOUNTER option and the default linkedId is used, + * the defaultLinkedIdCounter is incremented *first*. + */ + INCREMENTDEFAULTCOUNTER("starts a new default alignment"), + /* + * An INPUT Arg counts as an input for REQUIREINPUT + */ + INPUT(null), + /* + * A REQUIREINPUT Arg can only be applied via --all if there is an input + * (i.e. --open or --append) + */ + REQUIREINPUT(null), + /* + * An OUTPUTFILE Arg provides an output filename. With Opt.ALLOWALL *.ext is shorthand for + * --all --output={basename}.ext + */ + OUTPUTFILE("output file --headless will be assumed unless --gui used"), + /* + * A STDOUT Arg can take an output filename that can be '-' to mean print to STDOUT. + */ + STDOUT("allows the output filename '" + ArgParser.STDOUTFILENAME + + "' to mean output to STDOUT"), + /* + * A STORED Arg resets and creates a new set of "opened" linkedIds + */ + STORED(null), + /* + * A HELP Arg is a --help type arg + */ + HELP("provides a help statement"), + /* + * A PRIMARY Arg is the main Arg for its type + */ + PRIMARY("is a primary argument for its type"), + /* + * A HASTYPE Arg can have an Arg.Type assigned to its ArgValue + */ + HASTYPE(null), + /* + * A FIRST arg gets moved to appear first in the usage statement (within type) + */ + FIRST(null), + /* + * A LAST arg gets moved to appear last in the usage statement (within type) + */ + LAST(null), + /* + * After other args are checked, the following args can prefix a KEY=VALUE argument + */ + PREFIXKEV("prefixes key=value"), + /* + * do not lowercase the name when getting the arg name or arg string + */ + PRESERVECASE(null), + // + ; + + private String description; + + private Opt() + { + description = null; + } + + private Opt(String description) + { + this.description = description; + } + + public String description() + { + return description; + } + } public static enum Type @@ -350,8 +477,9 @@ public enum Arg STRUCTURE("arguments used to add and format 3D structure data"), PROCESS("arguments used to process an alignment once opened"), OUTPUT("arguments used to save data from a processed alignment"), - IMAGE("arguments used to export an image of an alignment"), - STRUCTUREIMAGE("arguments used to export an image of an structure"), + IMAGE("arguments used to export an image of an alignment or structure"), + // IMAGE("arguments used to export an image of an alignment"), + // STRUCTUREIMAGE("arguments used to export an image of an structure"), FLOW("arguments that control processing of the other arguments"), // ALL("all arguments"), // mostly just a place-holder for --help-all NONE, // mostly a place-holder for --help @@ -405,15 +533,15 @@ public enum Arg private Arg(Type type, String alternativeName, String description, boolean defaultBoolean, Opt... options) { + this.type = type; + this.description = description; + this.defaultBoolValue = defaultBoolean; + this.setOptions(options); this.argNames = alternativeName != null ? new String[] { this.getName(), alternativeName } : new String[] { this.getName() }; - this.type = type; - this.description = description; - this.defaultBoolValue = defaultBoolean; - this.setOptions(options); } public String argString() @@ -463,7 +591,9 @@ public enum Arg public String getName() { - return this.name().toLowerCase(Locale.ROOT).replace('_', '-'); + String name = hasOption(Opt.PRESERVECASE) ? this.name() + : this.name().toLowerCase(Locale.ROOT); + return name.replace('_', '-'); } @Override @@ -627,7 +757,7 @@ public enum Arg } } - appendArgUsage(sb, a, maxArgLength); + appendArgUsage(sb, a, maxArgLength, Platform.consoleWidth()); if (argsI.hasNext()) { @@ -639,69 +769,71 @@ public enum Arg } private static void appendArgUsage(StringBuilder sb, Arg a, - int maxArgLength) + int maxArgLength, int maxWidth) { boolean first = appendArgAndDescription(sb, null, null, a, maxArgLength); List options = new ArrayList<>(); - if (a.hasOption(Opt.BOOLEAN)) - { - options.add("default " + (a.getDefaultBoolValue() ? a.argString() - : a.negateArgString())); - } - - if (a.hasOption(Opt.MULTI)) + for (Opt o : EnumSet.allOf(Opt.class)) { - options.add("multiple"); - } - - if (a.hasOption(Opt.LINKED)) - { - options.add("can be linked"); - } - - if (a.hasOption(Opt.GLOB)) - { - options.add("allows file globs"); - } - - if (a.hasOption(Opt.ALLOWSUBSTITUTIONS)) - { - options.add("allows substitutions"); - } - - if (a.hasOption(Opt.ALLOWALL)) - { - options.add("can be applied to all linked arguments"); - } - - if (a.hasOption(Opt.PRIVATE)) - { - options.add("for internal use only"); - } - - if (a.hasOption(Opt.SECRET)) - { - options.add("for development use only"); + if (a.hasOption(o) && o.description() != null) + { + options.add(o.description()); + } } + final String optDisplaySeparator = "; "; if (options.size() > 0) { + int linelength = 0; + String spacing = String.format("%-" + + (maxArgLength + ARGDESCRIPTIONSEPARATOR.length()) + "s", + ""); if (first) { sb.append(ARGDESCRIPTIONSEPARATOR); + linelength += maxArgLength + ARGDESCRIPTIONSEPARATOR.length(); } else { - sb.append(String.format("%-" - + (maxArgLength + ARGDESCRIPTIONSEPARATOR.length()) + "s", - "")); + sb.append(spacing); + linelength += spacing.length(); + } + if (options.size() > 0) + { + boolean optFirst = true; + Iterator optionsI = options.listIterator(); + while (optionsI.hasNext()) + { + String desc = optionsI.next(); + if (optFirst) + { + sb.append("("); + linelength += 1; + } + int descLength = desc.length() + + (optionsI.hasNext() ? optDisplaySeparator.length() : 0); + if (linelength + descLength > maxWidth) + { + sb.append(System.lineSeparator()); + linelength = 0; + sb.append(spacing); + linelength += spacing.length(); + } + // sb.append(linelength + "+" + desc.length() + " "); + sb.append(desc); + linelength += desc.length(); + if (optionsI.hasNext()) + { + sb.append(optDisplaySeparator); + linelength += optDisplaySeparator.length(); + } + optFirst = false; + } + sb.append(')'); + sb.append(System.lineSeparator()); } - sb.append("("); - sb.append(String.join("; ", options)); - sb.append(')'); - sb.append(System.lineSeparator()); } } @@ -711,7 +843,16 @@ public enum Arg argSb.append( a.hasOption(Opt.BOOLEAN) ? booleanArgString(a) : a.argString()); if (a.hasOption(Opt.STRING)) - argSb.append("=value"); + { + if (a.hasOption(Opt.PREFIXKEV)) + { + argSb.append("key=value"); + } + else + { + argSb.append("=value"); + } + } return argSb.toString(); }