From: Ben Soares Date: Thu, 18 May 2023 15:28:29 +0000 (+0100) Subject: JAL-629 Added 'Type' to args and argvalues X-Git-Tag: Release_2_11_4_0~317 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=92c48abf7079358345432e020b72d025fc14f75d;p=jalview.git JAL-629 Added 'Type' to args and argvalues --- diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java index 50ff7c3..dcdb4c0 100644 --- a/src/jalview/bin/Commands.java +++ b/src/jalview/bin/Commands.java @@ -561,6 +561,9 @@ public class Commands StructureChooser.openStructureFileForSequence(null, null, ap, seq, false, structureFilepath, tft, paeFilepath, false, ssFromStructure, false, viewerType); + + String structureImage = ArgParser.getValueFromSubValOrArg(avm, av, + Arg.STRUCTUREIMAGE, subVals); } } } diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index cf73c81..8bc3e1b 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -68,6 +68,7 @@ import groovy.lang.Binding; import groovy.util.GroovyScriptEngine; import jalview.bin.argparser.Arg; import jalview.bin.argparser.Arg.Opt; +import jalview.bin.argparser.Arg.Type; import jalview.bin.argparser.ArgParser; import jalview.bin.argparser.BootstrapArgs; import jalview.ext.so.SequenceOntology; @@ -473,7 +474,7 @@ public class Jalview if (bootstrapArgs.contains(Arg.ARGFILE)) { argparser = ArgParser.parseArgFiles( - bootstrapArgs.getList(Arg.ARGFILE), + bootstrapArgs.getValueList(Arg.ARGFILE), bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS), bootstrapArgs); } @@ -491,9 +492,11 @@ public class Jalview * @j2sIgnore */ { - if (bootstrapArgs.contains(Arg.HELP)) + if (bootstrapArgs.containsType(Type.HELP)) { - System.out.println(Arg.usage()); + System.out.println("##### HERE"); + System.out + .println(Arg.usage(bootstrapArgs.getArgsOfType(Type.HELP))); Jalview.exit(null, 0); } if (aparser.contains("help") || aparser.contains("h")) @@ -547,7 +550,7 @@ public class Jalview List setprops = new ArrayList<>(); if (bootstrapArgs.contains(Arg.SETPROP)) { - setprops = bootstrapArgs.getList(Arg.SETPROP); + setprops = bootstrapArgs.getValueList(Arg.SETPROP); } else { diff --git a/src/jalview/bin/argparser/Arg.java b/src/jalview/bin/argparser/Arg.java index a18057c..a7fc0f7 100644 --- a/src/jalview/bin/argparser/Arg.java +++ b/src/jalview/bin/argparser/Arg.java @@ -2,6 +2,8 @@ package jalview.bin.argparser; import java.util.ArrayList; import java.util.Arrays; +import java.util.Collections; +import java.util.Comparator; import java.util.EnumSet; import java.util.Iterator; import java.util.List; @@ -15,52 +17,64 @@ public enum Arg { // Initialising arguments (BOOTSTRAP) - HELP("h", "Display this help statement", Opt.UNARY, Opt.BOOTSTRAP), - VERSION("v", + HELP(Type.HELP, "h", "Display this help statement", Opt.UNARY, + Opt.BOOTSTRAP, Opt.HASTYPE), + /* + * Other --help-type Args will be added by the static block. + */ + VERSION(Type.CONFIG, "v", "Display the version of " + ChannelProperties.getProperty("app_name"), Opt.UNARY, Opt.BOOTSTRAP), - HEADLESS( + HEADLESS(Type.CONFIG, "Run Jalview in headless mode. No GUI interface will be created and Jalview will quit after all arguments have been processed.", Opt.UNARY, Opt.BOOTSTRAP), - JABAWS("Set a different URL to connect to a JABAWS server.", Opt.STRING, - Opt.BOOTSTRAP), - NEWS("Show (or don't show) the news feed.", true, Opt.BOOLEAN, - Opt.BOOTSTRAP), - SPLASH("Show (or don't show) the About Jalview splash screen.", true, + JABAWS(Type.CONFIG, "Set a different URL to connect to a JABAWS server.", + Opt.STRING, Opt.BOOTSTRAP), + NEWS(Type.CONFIG, "Show (or don't show) the news feed.", true, + Opt.BOOLEAN, Opt.BOOTSTRAP), + SPLASH(Type.CONFIG, + "Show (or don't show) the About Jalview splash screen.", true, Opt.BOOLEAN, Opt.BOOTSTRAP), - QUESTIONNAIRE( + QUESTIONNAIRE(Type.CONFIG, "Show (or don't show) the questionnaire if one is available.", true, Opt.BOOLEAN, Opt.BOOTSTRAP), - USAGESTATS("Send (or don't send) initial launch usage stats.", true, + USAGESTATS(Type.CONFIG, + "Send (or don't send) initial launch usage stats.", true, Opt.BOOLEAN, Opt.BOOTSTRAP), - WEBSERVICEDISCOVERY( + WEBSERVICEDISCOVERY(Type.CONFIG, "Attempt (or don't attempt) to connect to JABAWS web services.", true, Opt.BOOLEAN, Opt.BOOTSTRAP), - PROPS("Use a file as the preferences file instead of the usual ~/" - + ChannelProperties.getProperty("preferences.filename") - + " file.", Opt.STRING, Opt.BOOTSTRAP), - DEBUG("d", "Start Jalview in debug log level.", Opt.BOOLEAN, + PROPS(Type.CONFIG, + "Use a file as the preferences file instead of the usual ~/" + + ChannelProperties.getProperty("preferences.filename") + + " file.", + Opt.STRING, Opt.BOOTSTRAP), + DEBUG(Type.CONFIG, "d", "Start Jalview in debug log level.", Opt.BOOLEAN, Opt.BOOTSTRAP), - TRACE("Start Jalview in trace log level.", Opt.BOOLEAN, Opt.BOOTSTRAP, - Opt.SECRET), - QUIET("q", + TRACE(Type.CONFIG, "Start Jalview in trace log level.", Opt.BOOLEAN, + 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), - INITSUBSTITUTIONS( + INITSUBSTITUTIONS(Type.CONFIG, "Set ‑‑substitutions to be initially enabled (or initially disabled).", - true, Opt.BOOLEAN, Opt.BOOTSTRAP, Opt.NOACTION), + true, Opt.BOOLEAN, Opt.BOOTSTRAP, Opt.NOACTION, Opt.SECRET), // Opening an alignment - OPEN("Opens one or more alignment files or URLs in new alignment windows.", + 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), - APPEND("Appends one or more alignment files or URLs to the open alignment window (or opens a new alignment if none already open).", + 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.ALLOWSUBSTITUTIONS, Opt.INPUT), - TITLE("Specifies the title for the open alignment window as string.", + Opt.ALLOWSUBSTITUTIONS, Opt.INPUT, Opt.PRIMARY), + TITLE(Type.OPENING, + "Specifies the title for the open alignment window as string.", Opt.STRING, Opt.LINKED), - COLOUR("color", // being a bit soft on the Americans! + COLOUR(Type.OPENING, "color", // being a bit soft on the Americans! "Applies the colour scheme to the open alignment window. Valid values are:\n" + "clustal,\n" + "blosum62,\n" + "pc-identity,\n" + "zappo,\n" + "taylor,\n" + "gecos-flower,\n" @@ -72,92 +86,116 @@ public enum Arg + "purine-pyrimidine,\n" + "rna-helices,\n" + "t-coffee-scores,\n" + "sequence-id.", Opt.STRING, Opt.LINKED, Opt.ALLOWALL), - FEATURES("Add a feature file or URL to the open alignment.", Opt.STRING, - Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS), - TREE("Add a tree file or URL to the open alignment.", Opt.STRING, - Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS), - SORTBYTREE( + FEATURES(Type.OPENING, "Add a feature file or URL to the open alignment.", + Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS), + TREE(Type.OPENING, "Add a tree file or URL to the open alignment.", + Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS), + 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), - ANNOTATIONS("Add an annotations file or URL to the open alignment.", + ANNOTATIONS(Type.OPENING, + "Add an annotations file or URL to the open alignment.", Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS), - SHOWANNOTATIONS( + SHOWANNOTATIONS(Type.OPENING, "Enforces showing (or not showing) alignment annotations.", Opt.BOOLEAN, Opt.LINKED, Opt.ALLOWALL), - WRAP("Enforces wrapped (or not wrapped) alignment formatting.", + WRAP(Type.OPENING, + "Enforces wrapped (or not wrapped) alignment formatting.", Opt.BOOLEAN, Opt.LINKED, Opt.ALLOWALL), - NOSTRUCTURE( + NOSTRUCTURE(Type.OPENING, "Do not open or process any 3D structure in the ‑‑open or ‑‑append files.", Opt.UNARY, Opt.LINKED, Opt.ALLOWALL), // Adding a 3D structure - 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), + SEQID(Type.STRUCTURE, + "Specify the sequence name for the preceding --structure to be associated with.", Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS), - SEQID("Specify the sequence name for the preceding --structure to be associated with.", - Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS), - PAEMATRIX("Add a PAE json matrix file to the preceding --structure.", + PAEMATRIX(Type.STRUCTURE, + "Add a PAE json matrix file to the preceding --structure.", Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS), - TEMPFAC("Set the type of temperature factor. Possible values are:\n" - + "default,\n" + "plddt.", Opt.STRING, Opt.LINKED), - STRUCTUREVIEWER( - "Set the structure viewer to use to open the 3d structure file specified in previous --structure to name. Possible values of name are:\n" + TEMPFAC(Type.STRUCTURE, + "Set the type of temperature factor. Possible values are:\n" + + "default,\n" + "plddt.", + Opt.STRING, Opt.LINKED), + 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), - NOTEMPFAC( + STRUCTUREIMAGE(Type.STRUCTURE, + "Export an image of a 3D structure opened in JMOL", Opt.STRING, + Opt.LINKED, Opt.MULTI), + 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! - SHOWSSANNOTATIONS(null, Opt.BOOLEAN, Opt.LINKED, Opt.ALLOWALL), + SHOWSSANNOTATIONS(Type.STRUCTURE, null, Opt.BOOLEAN, Opt.LINKED, + Opt.ALLOWALL), // Outputting files - 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.", + 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.OUTPUT), - TYPE("Set the image format for the preceding --image to name. Valid values for name are: svg,\n" - + "png,\n" + "eps,\n" + "html,\n" + "biojs.", Opt.STRING, - Opt.LINKED, Opt.ALLOWALL), - TEXTRENDERER( + Opt.REQUIREINPUT, Opt.OUTPUT, Opt.PRIMARY), + TYPE(Type.IMAGE, + "Set the image format for the preceding --image to name. Valid values for name are: svg,\n" + + "png,\n" + "eps,\n" + "html,\n" + "biojs.", + Opt.STRING, Opt.LINKED, Opt.ALLOWALL), + 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 for name are:\n" + "text,\n" + "lineart.", Opt.STRING, Opt.LINKED, Opt.ALLOWALL), - SCALE("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).", + 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), + 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), - WIDTH("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).", + 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), - HEIGHT("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).", + 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" + + "fasta (fa, fasta, mfa, fastq),\n" + "pfam (pfam),\n" + + "stockholm (sto, stk),\n" + "pir (pir),\n" + + "blc (blc),\n" + "amsa (amsa),\n" + "json (json),\n" + + "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.OUTPUT, 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), - 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" - + "fasta (fa, fasta, mfa, fastq),\n" + "pfam (pfam),\n" - + "stockholm (sto, stk),\n" + "pir (pir),\n" + "blc (blc),\n" - + "amsa (amsa),\n" + "json (json),\n" + "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.OUTPUT), - FORMAT("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), - GROOVY("Process a groovy script in the file for the open alignment.", + GROOVY(Type.PROCESS, + "Process a groovy script in the file for the open alignment.", Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS, Opt.ALLOWALL), - BACKUPS("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.", + 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), - OVERWRITE( + 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), - 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.", + 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), // controlling flow of arguments - 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.", + 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), - SUBSTITUTIONS( + SUBSTITUTIONS(Type.FLOW, "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),\n" + "{dirname}, - the directory (folder) name of the currently --opened file (or first --appended file),\n" + "{argfilebasename} - the filename-without-extension of the current --argfile,\n" @@ -166,47 +204,52 @@ public enum Arg + "{++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), - ARGFILE("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.", + 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.ALLOWSUBSTITUTIONS), - NPP("n++", + NPP(Type.FLOW, "n++", "Increase the index counter used in argument value substitutions.", Opt.UNARY, Opt.MULTI, Opt.NOACTION), - ALL("Apply the following output arguments to all sets of linked arguments.", + ALL(Type.FLOW, + "Apply the following output arguments to all sets of linked arguments.", Opt.BOOLEAN, Opt.MULTI, Opt.NOACTION), - OPENED("Apply the following output arguments to all of the last --open'ed set of linked arguments.", + 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), - QUIT("After all files have been opened, appended and output, quit Jalview. In ‑‑headless mode this already happens.", + QUIT(Type.FLOW, + "After all files have been opened, appended and output, quit Jalview. In ‑‑headless mode this already happens.", Opt.UNARY), // secret options - TESTOUTPUT( + 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("Set an individual Java System property.", Opt.STRING, Opt.MULTI, - Opt.BOOTSTRAP, Opt.SECRET), // not in use yet - NIL("This argument does nothing on its own, but can be used with linkedIds.", + SETPROP(Type.CONFIG, "Set an individual Java System property.", + Opt.STRING, Opt.MULTI, 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), // private options (inserted during arg processing) - SETARGFILE( + SETARGFILE(Type.FLOW, "Sets the current value of the argfilename. Inserted before argfilecontents.", Opt.UNARY, Opt.LINKED, Opt.STRING, Opt.MULTI, Opt.PRIVATE, Opt.NOACTION), - UNSETARGFILE( + UNSETARGFILE(Type.FLOW, "Unsets the current value of the argfilename. Inserted after argfile contents.", Opt.UNARY, Opt.LINKED, Opt.MULTI, 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 // argparser but are here for Usage statement reasons. - JVMMEMPC( + JVMMEMPC(Type.CONFIG, "Limit maximum heap size (memory) to PERCENT% of total physical memory detected. This defaults to 90 if total physical memory can be detected.\n" + "The equals sign (\"=\") separator must be used with no spaces.", Opt.NOACTION, Opt.BOOTSTRAP, Opt.STRING), - JVMMEMMAX( + JVMMEMMAX(Type.CONFIG, "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.\n" + "The equals sign (\"=\") separator must be used with no spaces.", Opt.NOACTION, Opt.BOOTSTRAP, Opt.STRING), @@ -260,32 +303,75 @@ public enum Arg OUTPUT, // 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) + } + + public static enum Type + { + // Type restricts argument to certain usage output + CONFIG("Arguments user to configure " + + ChannelProperties.getProperty("app_name") + " from startup"), + OPENING("Arguments used to open and format alignments"), + 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"), + FLOW("Arguments that control processing of the other arguments"), + ALL("All arguments"), // mostly just a place-holder for --help-all + HELP("Arguments to provide help text"); + + private String description; + + private Type(String description) + { + this.description = description; + } + + public String description() + { + return description; + } + } + + static + { + for (Type t : EnumSet.allOf(Type.class)) + { + String type = t.name(); + + } } private final String[] argNames; private Opt[] argOptions; - private boolean defaultBoolValue = false; + private boolean defaultBoolValue; + + private String description; - private String description = null; + private Type type; - private Arg(String description, Opt... options) + private Arg(Type type, String description, Opt... options) { - this(null, description, false, options); + this(type, null, description, false, options); } - private Arg(String description, boolean defaultBoolean, Opt... options) + private Arg(Type type, String description, boolean defaultBoolean, + Opt... options) { - this(null, description, defaultBoolean, options); + this(type, null, description, defaultBoolean, options); } - private Arg(String alternativeName, String description, Opt... options) + private Arg(Type type, String alternativeName, String description, + Opt... options) { - this(alternativeName, description, false, options); + this(type, alternativeName, description, false, options); } - private Arg(String alternativeName, String description, + private Arg(Type type, String alternativeName, String description, boolean defaultBoolean, Opt... options) { this.argNames = alternativeName != null @@ -293,6 +379,7 @@ public enum Arg { this.getName(), alternativeName } : new String[] { this.getName() }; + this.type = type; this.description = description; this.defaultBoolValue = defaultBoolean; this.setOptions(options); @@ -328,6 +415,7 @@ public enum Arg if (getNames().length > 0) sb.append('"'); sb.append(")\n"); + sb.append("\nType: " + type.name()); sb.append("\nOpt: "); // map List to List for the String.join List optList = Arrays.asList(argOptions).stream() @@ -365,6 +453,16 @@ public enum Arg return false; } + public boolean hasAllOptions(Opt... opts) + { + for (Opt o : opts) + { + if (!this.hasOption(o)) + return false; + } + return true; + } + protected void setOptions(Opt... options) { this.argOptions = options; @@ -375,6 +473,11 @@ public enum Arg return defaultBoolValue; } + public Type getType() + { + return this.type; + } + protected String getDescription() { return description; @@ -393,6 +496,11 @@ public enum Arg public static final String usage() { + return usage(null); + } + + public static final String usage(List helpArgs) + { StringBuilder sb = new StringBuilder(); sb.append(ChannelProperties.getProperty("app_name")); @@ -407,6 +515,10 @@ public enum Arg sb.append(System.lineSeparator()); sb.append(System.lineSeparator()); + // PROGRAM THIS! + Type type = Type.HELP; + Iterator typeArgs = Arg.getAllOfType(type); + int maxArgLength = 0; for (Arg a : EnumSet.allOf(Arg.class)) { @@ -512,4 +624,77 @@ public enum Arg } return sb.toString(); } + + protected static Iterator getAllOfType(Type type) + { + return getAllOfType(type, new Opt[] {}); + } + + protected static Iterator getAllOfType(Type type, Opt... options) + { + Opt[] opts = options == null ? new Opt[] {} : options; + return EnumSet.allOf(Arg.class).stream().filter(a -> { + if (a.getType() != type) + return false; + for (Opt o : opts) + { + if (!a.hasOption(o)) + return false; + } + return true; + }).iterator(); + } + + private static List sortForDisplay(Type... types) + { + List argsToSort; + // if no types provided, do all + if (types == null || types.length == 0) + { + argsToSort = Arrays + .asList(EnumSet.allOf(Arg.class).toArray(new Arg[] {})); + } + else + { + argsToSort = new ArrayList<>(); + for (Type type : types) + { + Arg.getAllOfType(type).forEachRemaining(a -> argsToSort.add(a)); + } + } + + Collections.sort(argsToSort, new ArgComparator()); + return argsToSort; + } + + protected int compareForDisplay(Arg other) + { + if (other == null) + return 1; + // first compare types (in order of appearance) + int i = this.getType().compareTo(other.getType()); + if (i == 0) + { + // next prioritise primary arguments + i = this.hasOption(Opt.PRIMARY) + ? (other.hasOption(Opt.PRIMARY) ? 0 : 1) + : (other.hasOption(Opt.PRIMARY) ? -1 : 0); + if (i == 0) + { + // finally order of appearance in enum declarations + i = this.compareTo(other); + } + } + return i; + } + +} + +class ArgComparator implements Comparator +{ + @Override + public int compare(Arg a, Arg b) + { + return a.compareForDisplay(b); + } } \ No newline at end of file diff --git a/src/jalview/bin/argparser/ArgParser.java b/src/jalview/bin/argparser/ArgParser.java index e6bd917..4e1793d 100644 --- a/src/jalview/bin/argparser/ArgParser.java +++ b/src/jalview/bin/argparser/ArgParser.java @@ -38,11 +38,14 @@ import jalview.bin.Cache; import jalview.bin.Console; import jalview.bin.Jalview; import jalview.bin.argparser.Arg.Opt; +import jalview.bin.argparser.Arg.Type; import jalview.util.FileUtils; import jalview.util.HttpUtils; public class ArgParser { + protected static final String SINGLEDASH = "-"; + protected static final String DOUBLEDASH = "--"; protected static final char EQUALS = '='; @@ -105,10 +108,6 @@ public class ArgParser // --argfile name private static final String ARGFILEDIRNAME = "{argfiledirname}"; - // an output file wildcard to signify --output=*.ext is really --all --output - // {basename}.ext - private static final String OUTPUTWILDCARD = "*."; - // flag to say whether {n} subtitutions in output filenames should be made. // Turn on and off with --substitutions and --nosubstitutions // Start with it on @@ -148,8 +147,7 @@ public class ArgParser if (argMap.containsKey(argName)) { Console.warn("Trying to add argument name multiple times: '" - + argName + "'"); // RESTORE THIS WHEN - // MERGED + + argName + "'"); if (argMap.get(argName) != a) { Console.error( @@ -246,13 +244,17 @@ public class ArgParser openEachInitialFilenames = false; } - String argName = null; - String val = null; - List globVals = null; // for Opt.GLOB only - SubVals globSubVals = null; // also for use by Opt.GLOB only - String linkedId = null; + // look for double-dash, e.g. --arg if (arg.startsWith(DOUBLEDASH)) { + String argName = null; + String val = null; + List globVals = null; // for Opt.GLOB only + SubVals globSubVals = null; // also for use by Opt.GLOB only + String linkedId = null; + Type type = null; + + // look for equals e.g. --arg=value int equalPos = arg.indexOf(EQUALS); if (equalPos > -1) { @@ -263,17 +265,32 @@ public class ArgParser { argName = arg.substring(DOUBLEDASH.length()); } + + // look for linked ID e.g. --arg[linkedID] int idOpen = argName.indexOf('['); int idClose = argName.indexOf(']'); - if (idOpen > -1 && idClose == argName.length() - 1) { linkedId = argName.substring(idOpen + 1, idClose); argName = argName.substring(0, idOpen); } + // look for type modification e.g. --help-opening + int dashPos = argName.indexOf(SINGLEDASH); + if (dashPos > -1) + { + String potentialArgName = argName.substring(0, dashPos); + Arg potentialArg = argMap.get(potentialArgName); + if (potentialArg != null && potentialArg.hasOption(Opt.HASTYPE)) + { + argName = argName.substring(0, dashPos); + String typeName = argName.substring(dashPos + 1); + type = Type.valueOf(typeName); + } + } + Arg a = argMap.get(argName); - // check for boolean prepended by "no" + // check for boolean prepended by "no" e.g. --nowrap boolean negated = false; if (a == null && argName.startsWith(NEGATESTRING) && argMap .containsKey(argName.substring(NEGATESTRING.length()))) @@ -416,7 +433,6 @@ public class ArgParser } String autoCounterString = null; - boolean usingAutoCounterLinkedId = false; String defaultLinkedId = defaultLinkedId(false); boolean usingDefaultLinkedId = false; if (a.hasOption(Opt.LINKED)) @@ -469,7 +485,6 @@ public class ArgParser autoCounterString = Integer.toString(linkedIdAutoCounter); linkedId = linkedId.replace(LINKEDIDAUTOCOUNTER, autoCounterString); - usingAutoCounterLinkedId = true; Console.debug( "Changing linkedId to '" + linkedId + "' from " + arg); } @@ -479,7 +494,6 @@ public class ArgParser autoCounterString = Integer.toString(++linkedIdAutoCounter); linkedId = linkedId.replace(INCREMENTLINKEDIDAUTOCOUNTER, autoCounterString); - usingAutoCounterLinkedId = true; Console.debug( "Changing linkedId to '" + linkedId + "' from " + arg); } @@ -527,7 +541,7 @@ public class ArgParser { String v = gve.nextElement(); SubVals vsv = new SubVals(globSubVals, v); - addValue(linkedId, avs, vsv, v, argIndex++, true); + addValue(linkedId, type, avs, vsv, v, argIndex++, true); // if we're using defaultLinkedId and the arg increments the // counter: if (gve.hasMoreElements() && usingDefaultLinkedId @@ -543,17 +557,17 @@ public class ArgParser } else { - addValue(linkedId, avs, val, argIndex, true); + addValue(linkedId, type, avs, val, argIndex, true); } } else if (a.hasOption(Opt.BOOLEAN)) { - setBoolean(linkedId, avs, !negated, argIndex); + setBoolean(linkedId, type, avs, !negated, argIndex); setNegated(linkedId, avs, negated); } else if (a.hasOption(Opt.UNARY)) { - setBoolean(linkedId, avs, true, argIndex); + setBoolean(linkedId, type, avs, true, argIndex); } // remove the '*' or 'open*' linkedId that should be empty if it was @@ -981,37 +995,37 @@ public class ArgParser // the following methods look for the "*" linkedId and add the argvalue to all // linkedId ArgValues if it does. // This version inserts the subvals sv into all created values - private void addValue(String linkedId, ArgValues avs, SubVals sv, - String v, int argIndex, boolean doSubs) + private void addValue(String linkedId, Type type, ArgValues avs, + SubVals sv, String v, int argIndex, boolean doSubs) { - this.argValueOperation(Op.ADDVALUE, linkedId, avs, sv, v, false, + this.argValueOperation(Op.ADDVALUE, linkedId, type, avs, sv, v, false, argIndex, doSubs); } - private void addValue(String linkedId, ArgValues avs, String v, + private void addValue(String linkedId, Type type, ArgValues avs, String v, int argIndex, boolean doSubs) { - this.argValueOperation(Op.ADDVALUE, linkedId, avs, null, v, false, + this.argValueOperation(Op.ADDVALUE, linkedId, type, avs, null, v, false, argIndex, doSubs); } - private void setBoolean(String linkedId, ArgValues avs, boolean b, - int argIndex) + private void setBoolean(String linkedId, Type type, ArgValues avs, + boolean b, int argIndex) { - this.argValueOperation(Op.SETBOOLEAN, linkedId, avs, null, null, b, - argIndex, false); + this.argValueOperation(Op.SETBOOLEAN, linkedId, type, avs, null, null, + b, argIndex, false); } private void setNegated(String linkedId, ArgValues avs, boolean b) { - this.argValueOperation(Op.SETNEGATED, linkedId, avs, null, null, b, 0, - false); + this.argValueOperation(Op.SETNEGATED, linkedId, null, avs, null, null, + b, 0, false); } private void incrementCount(String linkedId, ArgValues avs) { - this.argValueOperation(Op.INCREMENTCOUNT, linkedId, avs, null, null, - false, 0, false); + this.argValueOperation(Op.INCREMENTCOUNT, linkedId, null, avs, null, + null, false, 0, false); } private enum Op @@ -1022,8 +1036,9 @@ public class ArgParser // The following operations look for the "*" and "open*" linkedIds and add the // argvalue to all appropriate linkedId ArgValues if it does. // If subvals are supplied, they are inserted into all new set values. - private void argValueOperation(Op op, String linkedId, ArgValues avs, - SubVals sv, String v, boolean b, int argIndex, boolean doSubs) + private void argValueOperation(Op op, String linkedId, Type type, + ArgValues avs, SubVals sv, String v, boolean b, int argIndex, + boolean doSubs) { Arg a = avs.arg(); @@ -1079,7 +1094,7 @@ public class ArgParser val = makeSubstitutions(v, id); sv = new SubVals(sv, val); } - tavs.addValue(sv, val, argIndex, true); + tavs.addValue(sv, type, val, argIndex, true); } else { @@ -1087,13 +1102,13 @@ public class ArgParser { val = makeSubstitutions(v, id); } - tavs.addValue(val, argIndex, true); + tavs.addValue(type, val, argIndex, true); } finaliseStoringArgValue(id, tavs); break; case SETBOOLEAN: - tavs.setBoolean(b, argIndex, true); + tavs.setBoolean(type, b, argIndex, true); finaliseStoringArgValue(id, tavs); break; @@ -1125,7 +1140,7 @@ public class ArgParser val = makeSubstitutions(v, linkedId); sv = new SubVals(sv, val); } - avs.addValue(sv, val, argIndex, false); + avs.addValue(sv, type, val, argIndex, false); } else { @@ -1133,13 +1148,13 @@ public class ArgParser { val = makeSubstitutions(v, linkedId); } - avs.addValue(val, argIndex, false); + avs.addValue(type, val, argIndex, false); } finaliseStoringArgValue(linkedId, avs); break; case SETBOOLEAN: - avs.setBoolean(b, argIndex, false); + avs.setBoolean(type, b, argIndex, false); finaliseStoringArgValue(linkedId, avs); break; diff --git a/src/jalview/bin/argparser/ArgValue.java b/src/jalview/bin/argparser/ArgValue.java index 1643713..f76b757 100644 --- a/src/jalview/bin/argparser/ArgValue.java +++ b/src/jalview/bin/argparser/ArgValue.java @@ -1,5 +1,8 @@ package jalview.bin.argparser; +import jalview.bin.argparser.Arg.Opt; +import jalview.bin.argparser.Arg.Type; + /** * A helper class to keep an index of argument position with argument values */ @@ -11,26 +14,45 @@ public class ArgValue implements Comparable private String value; + /* + * Type type is only really used by --help-type + */ + private Type type = null; + // This id is set by a subVal id= to identify the product of this ArgValue // later. Set but not currently used. private String id; private SubVals subVals; - protected ArgValue(Arg a, SubVals sv, String content, int argIndex) + protected ArgValue(Arg a, SubVals sv, Type type, String content, + int argIndex) { this.arg = a; this.value = content; this.argIndex = argIndex; this.subVals = sv == null ? new SubVals("") : sv; + this.setType(type); } - protected ArgValue(Arg a, String value, int argIndex) + protected ArgValue(Arg a, Type type, String value, int argIndex) { this.arg = a; this.argIndex = argIndex; this.subVals = new SubVals(value); this.value = getSubVals().getContent(); + this.setType(type); + } + + protected void setType(Type t) + { + if (this.getArg().hasOption(Opt.HASTYPE)) + this.type = t; + } + + public Type getType() + { + return type; } public Arg getArg() @@ -76,7 +98,7 @@ public class ArgValue implements Comparable } @Override - public int compareTo(ArgValue o) + public final int compareTo(ArgValue o) { return this.getArgIndex() - o.getArgIndex(); } diff --git a/src/jalview/bin/argparser/ArgValues.java b/src/jalview/bin/argparser/ArgValues.java index f2c299c..f25fc9a 100644 --- a/src/jalview/bin/argparser/ArgValues.java +++ b/src/jalview/bin/argparser/ArgValues.java @@ -8,6 +8,7 @@ import java.util.stream.Collectors; import jalview.bin.Console; import jalview.bin.argparser.Arg.Opt; +import jalview.bin.argparser.Arg.Type; public class ArgValues { @@ -31,6 +32,11 @@ public class ArgValues private Map idMap = new HashMap<>(); + /* + * Type type is only really used by --help-type + */ + private Type type = null; + protected ArgValues(Arg a) { this.arg = a; @@ -53,6 +59,17 @@ public class ArgValues return arg; } + protected void setType(Type t) + { + if (this.arg().hasOption(Opt.HASTYPE)) + this.type = t; + } + + public Type getType() + { + return type; + } + protected int getCount() { return argCount; @@ -76,8 +93,10 @@ public class ArgValues return this.negated; } - protected void setBoolean(boolean b, int i, boolean beingSetByWildcard) + protected void setBoolean(Type t, boolean b, int i, + boolean beingSetByWildcard) { + this.setType(t); // don't overwrite a wildcard set boolean with a non-wildcard set boolean if (boolIndex >= 0 && !this.setByWildcard && beingSetByWildcard) return; @@ -117,15 +136,16 @@ public class ArgValues return sb.toString(); } - protected void addValue(String val, int argIndex, boolean wildcard) + protected void addValue(Type type, String val, int argIndex, + boolean wildcard) { - addArgValue(new ArgValue(arg(), val, argIndex), wildcard); + addArgValue(new ArgValue(arg(), type, val, argIndex), wildcard); } - protected void addValue(SubVals sv, String content, int argIndex, - boolean wildcard) + protected void addValue(SubVals sv, Type type, String content, + int argIndex, boolean wildcard) { - addArgValue(new ArgValue(arg(), sv, content, argIndex), wildcard); + addArgValue(new ArgValue(arg(), sv, type, content, argIndex), wildcard); } protected void addArgValue(ArgValue av, boolean beingSetByWildcard) diff --git a/src/jalview/bin/argparser/BootstrapArgs.java b/src/jalview/bin/argparser/BootstrapArgs.java index 14b7fe6..1c54355 100644 --- a/src/jalview/bin/argparser/BootstrapArgs.java +++ b/src/jalview/bin/argparser/BootstrapArgs.java @@ -1,6 +1,7 @@ package jalview.bin.argparser; import java.io.File; +import java.util.AbstractMap; import java.util.ArrayList; import java.util.Arrays; import java.util.HashMap; @@ -8,14 +9,16 @@ import java.util.HashSet; import java.util.List; import java.util.Map; import java.util.Set; +import java.util.stream.Collectors; import jalview.bin.argparser.Arg.Opt; +import jalview.bin.argparser.Arg.Type; import jalview.util.FileUtils; public class BootstrapArgs { // only need one - private Map> bootstrapArgMap = new HashMap<>(); + private Map>> bootstrapArgMap = new HashMap<>(); private Set argFiles = new HashSet<>(); @@ -54,12 +57,16 @@ public class BootstrapArgs for (int i = 0; i < args.size(); i++) { String arg = args.get(i); - String argName = null; - String val = null; + // look for double-dash, e.g. --arg if (arg.startsWith(ArgParser.DOUBLEDASH)) { + String argName = null; + String val = null; + Type type = null; // remove "--" arg = arg.substring(ArgParser.DOUBLEDASH.length()); + + // look for equals e.g. --arg=value int equalPos = arg.indexOf(ArgParser.EQUALS); if (equalPos > -1 && ArgParser.argMap.containsKey(arg.substring(0, equalPos))) @@ -80,6 +87,22 @@ public class BootstrapArgs argName = arg; val = "true"; } + else + { + // look for type modification e.g. --help-opening + int dashPos = arg.indexOf(ArgParser.SINGLEDASH); + if (dashPos > -1) + { + String potentialArgName = arg.substring(0, dashPos); + Arg potentialArg = ArgParser.argMap.get(potentialArgName); + if (potentialArg != null && potentialArg.hasOption(Opt.HASTYPE)) + { + argName = arg.substring(0, dashPos); + String typeName = arg.substring(dashPos + 1); + type = Type.valueOf(typeName); + } + } + } Arg a = ArgParser.argMap.get(argName); @@ -108,7 +131,7 @@ public class BootstrapArgs vals.add(val); } } - addAll(a, vals); + addAll(a, type, vals); if (a == Arg.ARGFILE) { @@ -121,7 +144,7 @@ public class BootstrapArgs } else { - add(a, val); + add(a, type, val); } } } @@ -132,14 +155,55 @@ public class BootstrapArgs return bootstrapArgMap.containsKey(a); } - public List getList(Arg a) + public boolean containsType(Type t) + { + for (List> l : bootstrapArgMap.values()) + { + for (Map.Entry e : l) + { + if (e.getKey() == t) + return true; + } + } + return false; + } + + public List getArgsOfType(Type t) + { + return getArgsOfType(t, new Opt[] {}); + } + + public List getArgsOfType(Type t, Opt... opts) + { + List args = new ArrayList<>(); + for (Arg a : bootstrapArgMap.keySet()) + { + if (!a.hasAllOptions(opts)) + continue; + + List> l = bootstrapArgMap.get(a); + if (l.stream().anyMatch(e -> e.getKey() == t)) + { + args.add(a); + } + } + return args; + } + + public List> getList(Arg a) { return bootstrapArgMap.get(a); } - private List getOrCreateList(Arg a) + public List getValueList(Arg a) { - List l = getList(a); + return bootstrapArgMap.get(a).stream().map(e -> e.getValue()) + .collect(Collectors.toList()); + } + + private List> getOrCreateList(Arg a) + { + List> l = getList(a); if (l == null) { l = new ArrayList<>(); @@ -148,7 +212,7 @@ public class BootstrapArgs return l; } - private void putList(Arg a, List l) + private void putList(Arg a, List> l) { bootstrapArgMap.put(a, l); } @@ -159,28 +223,36 @@ public class BootstrapArgs * and the arg is not MULTI (so first expressed value is * retained). */ - private void add(Arg a, String s) + private void add(Arg a, Type t, String s) { - List l = getOrCreateList(a); + List> l = getOrCreateList(a); if (a.hasOption(Opt.MULTI) || l.size() == 0) { - l.add(s); + l.add(entry(t, s)); } } - private void addAll(Arg a, List al) + private void addAll(Arg a, Type t, List al) { - List l = getOrCreateList(a); + List> l = getOrCreateList(a); if (a.hasOption(Opt.MULTI)) { - l.addAll(al); + for (String s : al) + { + l.add(entry(t, s)); + } } else if (l.size() == 0 && al.size() > 0) { - l.add(al.get(0)); + l.add(entry(t, al.get(0))); } } + private static Map.Entry entry(Type t, String s) + { + return new AbstractMap.SimpleEntry(t, s); + } + /* * Retrieves the first value even if MULTI. * A convenience for non-MULTI args. @@ -189,8 +261,8 @@ public class BootstrapArgs { if (!bootstrapArgMap.containsKey(a)) return null; - List aL = bootstrapArgMap.get(a); - return (aL == null || aL.size() == 0) ? null : aL.get(0); + List> aL = bootstrapArgMap.get(a); + return (aL == null || aL.size() == 0) ? null : aL.get(0).getValue(); } public boolean getBoolean(Arg a, boolean d) diff --git a/test/jalview/bin/CommandsTest2.java b/test/jalview/bin/CommandsTest2.java index f056da2..bd63232 100644 --- a/test/jalview/bin/CommandsTest2.java +++ b/test/jalview/bin/CommandsTest2.java @@ -26,7 +26,7 @@ public class CommandsTest2 @BeforeClass(alwaysRun = true) public static void setUpBeforeClass() throws Exception { - Cache.loadProperties("test/jalview/bin/commandsTest2.jvprops"); + Cache.loadProperties("test/jalview/bin/commandsTest.jvprops"); Date oneHourFromNow = new Date( System.currentTimeMillis() + 3600 * 1000); Cache.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED", oneHourFromNow); diff --git a/test/jalview/bin/argparser/ArgParserTest.java b/test/jalview/bin/argparser/ArgParserTest.java index 259acac..bc2be78 100644 --- a/test/jalview/bin/argparser/ArgParserTest.java +++ b/test/jalview/bin/argparser/ArgParserTest.java @@ -97,7 +97,7 @@ public class ArgParserTest } else if (a == Arg.ARGFILE) { - List filenames = b.getList(a); + List filenames = b.getValueList(a); boolean found = false; for (String s : filenames) {