X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2Fargparser%2FArgParser.java;h=fd42bb24a506e3903c3fbbac38317c9d1cdc98d6;hb=85240f268c71a9d0dc91dc196a93cb10d29794d3;hp=e08ae035840c72597eb822086086f30b30b4193a;hpb=55dc379e013ee8d6199e531b8e3d9482d33acfd4;p=jalview.git diff --git a/src/jalview/bin/argparser/ArgParser.java b/src/jalview/bin/argparser/ArgParser.java index e08ae03..fd42bb2 100644 --- a/src/jalview/bin/argparser/ArgParser.java +++ b/src/jalview/bin/argparser/ArgParser.java @@ -26,86 +26,159 @@ import java.nio.file.Files; import java.nio.file.Paths; import java.util.ArrayList; import java.util.Arrays; +import java.util.Collections; import java.util.EnumSet; +import java.util.Enumeration; import java.util.HashMap; import java.util.List; -import java.util.Locale; import java.util.Map; -import jalview.bin.Cache; import jalview.bin.Console; import jalview.bin.Jalview; +import jalview.bin.Jalview.ExitCode; 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 = '='; + public static final char EQUALS = '='; + + public static final String STDOUTFILENAME = "-"; protected static final String NEGATESTRING = "no"; - // the default linked id prefix used for no id (not even square braces) + /** + * the default linked id prefix used for no id (ie when not even square braces + * are provided) + */ protected static final String DEFAULTLINKEDIDPREFIX = "JALVIEW:"; - // the counter added to the default linked id prefix + /** + * the linkedId string used to match all linkedIds seen so far + */ + protected static final String MATCHALLLINKEDIDS = "*"; + + /** + * the linkedId string used to match all of the last --open'ed linkedIds + */ + protected static final String MATCHOPENEDLINKEDIDS = "open*"; + + /** + * the counter added to the default linked id prefix + */ private int defaultLinkedIdCounter = 0; - // the substitution string used to use the defaultLinkedIdCounter + /** + * the substitution string used to use the defaultLinkedIdCounter + */ private static final String DEFAULTLINKEDIDCOUNTER = "{}"; - // the counter added to the default linked id prefix. NOW using - // linkedIdAutoCounter - // private int openLinkedIdCounter = 0; - - // the linked id prefix used for --open files. NOW the same as DEFAULT + /** + * the linked id prefix used for --open files. NOW the same as DEFAULT + */ protected static final String OPENLINKEDIDPREFIX = DEFAULTLINKEDIDPREFIX; - // the counter used for {n} substitutions + /** + * the counter used for {n} substitutions + */ private int linkedIdAutoCounter = 0; - // the linked id substitution string used to increment the idCounter (and use - // the incremented value) + /** + * the linked id substitution string used to increment the idCounter (and use + * the incremented value) + */ private static final String INCREMENTLINKEDIDAUTOCOUNTER = "{++n}"; - // the linked id substitution string used to use the idCounter + /** + * the linked id substitution string used to use the idCounter + */ private static final String LINKEDIDAUTOCOUNTER = "{n}"; - // the linked id substitution string used to use the base filename of --append - // or --open + /** + * the linked id substitution string used to use the filename extension of + * --append or --open + */ + private static final String LINKEDIDEXTENSION = "{extension}"; + + /** + * the linked id substitution string used to use the base filename of --append + */ + /** or --open */ private static final String LINKEDIDBASENAME = "{basename}"; - // the linked id substitution string used to use the dir path of --append - // or --open + /** + * the linked id substitution string used to use the dir path of --append or + * --open + */ private static final String LINKEDIDDIRNAME = "{dirname}"; - // the current argfile + /** + * the current argfile + */ private String argFile = null; - // the linked id substitution string used to use the dir path of the latest - // --argfile name + /** + * the linked id substitution string used to use the dir path of the latest + */ + /** --argfile name */ private static final String ARGFILEBASENAME = "{argfilebasename}"; - // the linked id substitution string used to use the dir path of the latest - // --argfile name + /** + * the linked id substitution string used to use the dir path of the latest + * --argfile name + */ private static final String ARGFILEDIRNAME = "{argfiledirname}"; - // flag to say whether {n} subtitutions in output filenames should be made. - // Turn on and off with --subs and --nosubs - private boolean substitutions = false; + /** + * flag to say whether {n} subtitutions in output filenames should be made. + * Turn on and off with --substitutions and --nosubstitutions Start with it on + */ + private boolean substitutions = true; + + /** + * flag to say whether the default linkedId is the current default linked id + * + * or ALL linkedIds + */ + private boolean allLinkedIds = false; + + /** + * flag to say whether the structure arguments should be applied to all + * structures with this linked id + */ + private boolean allStructures = false; protected static final Map argMap; protected Map linkedArgs = new HashMap<>(); - protected List linkedOrder = null; + protected List linkedOrder = new ArrayList<>(); + + protected List storedLinkedIds = new ArrayList<>(); - protected List argList; + protected List argList = new ArrayList<>(); private static final char ARGFILECOMMENT = '#'; + private int argIndex = 0; + + private BootstrapArgs bootstrapArgs = null; + + private boolean oldArguments = false; + + private boolean mixedArguments = false; + + /** + * saved examples of mixed arguments + */ + private String[] mixedExamples = new String[] { null, null }; + static { argMap = new HashMap<>(); @@ -116,8 +189,7 @@ 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( @@ -135,27 +207,32 @@ public class ArgParser public ArgParser(String[] args) { - this(args, false); + this(args, false, null); } - public ArgParser(String[] args, boolean initsubstitutions) + public ArgParser(String[] args, boolean initsubstitutions, + BootstrapArgs bsa) { - // Make a mutable new ArrayList so that shell globbing parser works. - // (When shell file globbing is used, there are a sequence of non-Arg - // arguments (which are the expanded globbed filenames) that need to be - // consumed by the --append/--argfile/etc Arg which is most easily done by - // removing these filenames from the list one at a time. This can't be done - // with an ArrayList made with only Arrays.asList(String[] args). ) - this(new ArrayList<>(Arrays.asList(args)), initsubstitutions); + /* + * Make a mutable new ArrayList so that shell globbing parser works. + * (When shell file globbing is used, there are a sequence of non-Arg + * arguments (which are the expanded globbed filenames) that need to be + * consumed by the --append/--argfile/etc Arg which is most easily done + * by removing these filenames from the list one at a time. This can't be + * done with an ArrayList made with only Arrays.asList(String[] args) as + * that is not mutable. ) + */ + this(new ArrayList<>(Arrays.asList(args)), initsubstitutions, false, + bsa); } public ArgParser(List args, boolean initsubstitutions) { - this(args, initsubstitutions, false); + this(args, initsubstitutions, false, null); } public ArgParser(List args, boolean initsubstitutions, - boolean allowPrivate) + boolean allowPrivate, BootstrapArgs bsa) { // do nothing if there are no "--" args and (some "-" args || >0 arg is // "open") @@ -166,19 +243,44 @@ public class ArgParser if (arg.startsWith(DOUBLEDASH)) { dd = true; - break; + if (mixedExamples[1] == null) + { + mixedExamples[1] = arg; + } } - else if (arg.startsWith("-") || arg.equals("open")) + else if ((arg.startsWith("-") && !arg.equals(STDOUTFILENAME)) + || arg.equals("open")) { d = true; + if (mixedExamples[0] == null) + { + mixedExamples[0] = arg; + } } } - if (d && !dd) + if (d) + { + if (dd) + { + mixedArguments = true; + } + else + { + oldArguments = true; + } + } + + if (oldArguments || mixedArguments) { // leave it to the old style -- parse an empty list parse(new ArrayList(), false, false); return; } + + if (bsa != null) + this.bootstrapArgs = bsa; + else + this.bootstrapArgs = BootstrapArgs.getBootstrapArgs(args); parse(args, initsubstitutions, allowPrivate); } @@ -186,35 +288,42 @@ public class ArgParser boolean allowPrivate) { this.substitutions = initsubstitutions; - int argIndex = 0; - boolean openEachInitialFilenames = true; - for (int i = 0; i < args.size(); i++) - { - String arg = args.get(i); - // If the first arguments do not start with "--" or "-" or is "open" and - // is a filename that exists it is probably a file/list of files to open - // so we fake an Arg.OPEN argument and when adding files only add the - // single arg[i] and increment the defaultLinkedIdCounter so that each of - // these files is opened separately. - if (openEachInitialFilenames && !arg.startsWith(DOUBLEDASH) - && !arg.startsWith("-") && (new File(arg).exists() - || HttpUtils.startsWithHttpOrHttps(arg))) - { - arg = Arg.OPEN.argString(); - } - else + /* + * If the first argument does not start with "--" or "-" or is not "open", + * and is a filename that exists or a URL, it is probably a file/list of + * files to open so we insert an Arg.OPEN argument before it. This will + * mean the list of files at the start of the arguments are all opened + * separately. + */ + if (args.size() > 0) + { + String arg0 = args.get(0); + if (arg0 != null + && (!arg0.startsWith(DOUBLEDASH) && !arg0.startsWith("-") + && !arg0.equals("open") && (new File(arg0).exists() + || HttpUtils.startsWithHttpOrHttps(arg0)))) { - openEachInitialFilenames = false; + // insert "--open" at the start + args.add(0, Arg.OPEN.argString()); } + } - 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; + for (int i = 0; i < args.size(); i++) + { + String arg = args.get(i); + + // 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) { @@ -225,31 +334,80 @@ 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)) + { + String typeName = argName.substring(dashPos + 1); + try + { + type = Type.valueOf(typeName); + } catch (IllegalArgumentException e) + { + type = Type.INVALID; + } + argName = argName.substring(0, dashPos); + } + } + 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()))) + if (a == null) { - argName = argName.substring(NEGATESTRING.length()); - a = argMap.get(argName); - negated = true; + if (argName.startsWith(NEGATESTRING) && argMap + .containsKey(argName.substring(NEGATESTRING.length()))) + { + argName = argName.substring(NEGATESTRING.length()); + a = argMap.get(argName); + negated = true; + } + else + { + // after all other args, look for Opt.PREFIXKEV args if still not + // found + for (Arg potentialArg : EnumSet.allOf(Arg.class)) + { + if (potentialArg.hasOption(Opt.PREFIXKEV) && argName != null + && argName.startsWith(potentialArg.getName()) + && equalPos > -1) + { + val = argName.substring(potentialArg.getName().length()) + + EQUALS + val; + argName = argName.substring(0, + potentialArg.getName().length()); + a = potentialArg; + break; + } + } + } } // check for config errors if (a == null) { // arg not found - Console.error("Argument '" + arg + "' not recognised. Ignoring."); + Console.error("Argument '" + arg + "' not recognised. Exiting."); + Jalview.exit( + "Invalid argument used." + System.lineSeparator() + "Use" + + System.lineSeparator() + "jalview " + + Arg.HELP.argString() + System.lineSeparator() + + "for a usage statement.", + ExitCode.INVALID_ARGUMENT); continue; } if (a.hasOption(Opt.PRIVATE) && !allowPrivate) @@ -306,7 +464,7 @@ public class ArgParser { // There is no "=" so value is next arg or args (possibly shell // glob-expanded) - if ((openEachInitialFilenames ? i : i + 1) >= args.size()) + if (i + 1 >= args.size()) { // no value to take for arg, which wants a value Console.error("Argument '" + a.getName() @@ -321,8 +479,7 @@ public class ArgParser { // if this is the first argument with a file list at the start of // the args we add filenames from index i instead of i+1 - globVals = getShellGlobbedFilenameValues(a, args, - openEachInitialFilenames ? i : i + 1); + globVals = getShellGlobbedFilenameValues(a, args, i + 1); } else { @@ -333,11 +490,7 @@ public class ArgParser // make NOACTION adjustments // default and auto counter increments - if (a == Arg.NEWFRAME) - { - defaultLinkedIdCounter++; - } - else if (a == Arg.NPP) + if (a == Arg.NPP) { linkedIdAutoCounter++; } @@ -353,25 +506,56 @@ public class ArgParser { argFile = null; } + else if (a == Arg.ALL) + { + allLinkedIds = !negated; + } + else if (a == Arg.ALLSTRUCTURES) + { + allStructures = !negated; + } + + if (a.hasOption(Opt.STORED)) + { + // reset the lastOpenedLinkedIds list + this.storedLinkedIds = new ArrayList<>(); + } + + // this is probably only Arg.NEW and Arg.OPEN + if (a.hasOption(Opt.INCREMENTDEFAULTCOUNTER)) + { + // use the next default prefixed OPENLINKEDID + defaultLinkedId(true); + } String autoCounterString = null; - boolean usingAutoCounterLinkedId = false; - String defaultLinkedId = new StringBuilder(DEFAULTLINKEDIDPREFIX) - .append(Integer.toString(defaultLinkedIdCounter)) - .toString(); + String defaultLinkedId = defaultLinkedId(false); boolean usingDefaultLinkedId = false; if (a.hasOption(Opt.LINKED)) { if (linkedId == null) { - if (a == Arg.OPEN) + if (a.hasOption(Opt.OUTPUTFILE) && a.hasOption(Opt.ALLOWMULTIID) + && val.contains(MATCHALLLINKEDIDS)) { - // use the next default prefixed OPENLINKEDID - // NOW using the linkedIdAutoCounter - defaultLinkedIdCounter++; - linkedId = new StringBuilder(OPENLINKEDIDPREFIX) - .append(Integer.toString(defaultLinkedIdCounter)) - .toString(); + // --output=*.ext is shorthand for --output {basename}.ext + // --output=*/*.ext is shorthand for + // --output {dirname}/{basename}.ext + // (or --image=*.ext) + linkedId = allLinkedIds ? MATCHALLLINKEDIDS + : MATCHOPENEDLINKEDIDS; + val = FileUtils.convertWildcardsToPath(val, MATCHALLLINKEDIDS, + LINKEDIDDIRNAME, LINKEDIDBASENAME); + } + else if (allLinkedIds && a.hasOption(Opt.ALLOWMULTIID)) + { + linkedId = MATCHALLLINKEDIDS; + } + else if (a.hasOption(Opt.ALLOWMULTIID) + && this.storedLinkedIds != null + && this.storedLinkedIds.size() > 0) + { + linkedId = MATCHOPENEDLINKEDIDS; } else { @@ -382,36 +566,34 @@ public class ArgParser + arg); } } - else if (linkedId.contains(LINKEDIDAUTOCOUNTER)) - { - // turn {n} to the autoCounter - autoCounterString = Integer.toString(linkedIdAutoCounter); - linkedId = linkedId.replace(LINKEDIDAUTOCOUNTER, - autoCounterString); - usingAutoCounterLinkedId = true; - Console.debug( - "Changing linkedId to '" + linkedId + "' from " + arg); - } - else if (linkedId.contains(INCREMENTLINKEDIDAUTOCOUNTER)) + else { - // turn {++n} to the incremented autoCounter - autoCounterString = Integer.toString(++linkedIdAutoCounter); - linkedId = linkedId.replace(INCREMENTLINKEDIDAUTOCOUNTER, - autoCounterString); - usingAutoCounterLinkedId = true; - Console.debug( - "Changing linkedId to '" + linkedId + "' from " + arg); + if (linkedId.contains(LINKEDIDAUTOCOUNTER)) + { + // turn {n} to the autoCounter + autoCounterString = Integer.toString(linkedIdAutoCounter); + linkedId = linkedId.replace(LINKEDIDAUTOCOUNTER, + autoCounterString); + Console.debug("Changing linkedId to '" + linkedId + "' from " + + arg); + } + if (linkedId.contains(INCREMENTLINKEDIDAUTOCOUNTER)) + { + // turn {++n} to the incremented autoCounter + autoCounterString = Integer.toString(++linkedIdAutoCounter); + linkedId = linkedId.replace(INCREMENTLINKEDIDAUTOCOUNTER, + autoCounterString); + Console.debug("Changing linkedId to '" + linkedId + "' from " + + arg); + } } } - if (!linkedArgs.containsKey(linkedId)) - linkedArgs.put(linkedId, new ArgValuesMap()); - - // do not continue for NOACTION args + // do not continue in this block for NOACTION args if (a.hasOption(Opt.NOACTION)) continue; - ArgValuesMap avm = linkedArgs.get(linkedId); + ArgValuesMap avm = getOrCreateLinkedArgValuesMap(linkedId); // not dealing with both NODUPLICATEVALUES and GLOB if (a.hasOption(Opt.NODUPLICATEVALUES) && avm.hasValue(a, val)) @@ -423,8 +605,9 @@ public class ArgParser } // check for unique id - SubVals idsv = new SubVals(val); - String id = idsv.get(ArgValues.ID); + SubVals subvals = new SubVals(val); + boolean addNewSubVals = false; + String id = subvals.get(ArgValues.ID); if (id != null && avm.hasId(a, id)) { Console.error("Argument '" + a.argString() @@ -432,7 +615,20 @@ public class ArgParser continue; } - boolean argIndexIncremented = false; + // set allstructures to all non-primary structure options in this linked + // id if --allstructures has been set + if (allStructures && (a.getType() == Type.STRUCTURE + // || a.getType() == Type.STRUCTUREIMAGE) + ) && !a.hasOption(Opt.PRIMARY)) + { + if (!subvals.has(Arg.ALLSTRUCTURES.getName())) + // && !subvals.has("structureid")) + { + subvals.put(Arg.ALLSTRUCTURES.getName(), "true"); + addNewSubVals = true; + } + } + ArgValues avs = avm.getOrCreateArgValues(a); // store appropriate String value(s) @@ -441,50 +637,89 @@ public class ArgParser if (a.hasOption(Opt.GLOB) && globVals != null && globVals.size() > 0) { - for (String v : globVals) + Enumeration gve = Collections.enumeration(globVals); + while (gve.hasMoreElements()) { - v = makeSubstitutions(v, linkedId); + String v = gve.nextElement(); SubVals vsv = new SubVals(globSubVals, v); - avs.addValue(vsv, v, argIndex++); - argIndexIncremented = true; + addValue(linkedId, type, avs, vsv, v, argIndex++, true); + // if we're using defaultLinkedId and the arg increments the + // counter: + if (gve.hasMoreElements() && usingDefaultLinkedId + && a.hasOption(Opt.INCREMENTDEFAULTCOUNTER)) + { + // increment the default linkedId + linkedId = defaultLinkedId(true); + // get new avm and avs + avm = linkedArgs.get(linkedId); + avs = avm.getOrCreateArgValues(a); + } } } else { - avs.addValue(makeSubstitutions(val, linkedId), argIndex); + // addValue(linkedId, type, avs, val, argIndex, true); + addValue(linkedId, type, avs, addNewSubVals ? subvals : null, + val, argIndex, true); } } else if (a.hasOption(Opt.BOOLEAN)) { - avs.setBoolean(!negated, argIndex); - avs.setNegated(negated); + setBoolean(linkedId, type, avs, !negated, argIndex); + setNegated(linkedId, avs, negated); } else if (a.hasOption(Opt.UNARY)) { - avs.setBoolean(true, argIndex); + setBoolean(linkedId, type, avs, true, argIndex); } - avs.incrementCount(); - if (!argIndexIncremented) - argIndex++; - // store in appropriate place - if (a.hasOption(Opt.LINKED)) + // remove the '*' or 'open*' linkedId that should be empty if it was + // created + if ((MATCHALLLINKEDIDS.equals(linkedId) + || MATCHOPENEDLINKEDIDS.equals(linkedId)) + && linkedArgs.containsKey(linkedId)) { - // store the order of linkedIds - if (linkedOrder == null) - linkedOrder = new ArrayList<>(); - if (!linkedOrder.contains(linkedId)) - linkedOrder.add(linkedId); + linkedArgs.remove(linkedId); } + } + } + } - // store arg in the list of args used - if (argList == null) - argList = new ArrayList<>(); - if (!argList.contains(a)) - argList.add(a); + private void finaliseStoringArgValue(String linkedId, ArgValues avs) + { + Arg a = avs.arg(); + incrementCount(linkedId, avs); + argIndex++; + + // store in appropriate place + if (a.hasOption(Opt.LINKED)) + { + // store the order of linkedIds + if (!linkedOrder.contains(linkedId)) + linkedOrder.add(linkedId); + } + // store arg in the list of args used + if (!argList.contains(a)) + argList.add(a); + } + + private String defaultLinkedId(boolean increment) + { + String defaultLinkedId = new StringBuilder(DEFAULTLINKEDIDPREFIX) + .append(Integer.toString(defaultLinkedIdCounter)).toString(); + if (increment) + { + while (linkedArgs.containsKey(defaultLinkedId)) + { + defaultLinkedIdCounter++; + defaultLinkedId = new StringBuilder(DEFAULTLINKEDIDPREFIX) + .append(Integer.toString(defaultLinkedIdCounter)) + .toString(); } } + getOrCreateLinkedArgValuesMap(defaultLinkedId); + return defaultLinkedId; } public String makeSubstitutions(String val, String linkedId) @@ -523,6 +758,10 @@ public class ArgParser { rest = rest.replace(LINKEDIDBASENAME, avm.getBasename()); } + if (rest.contains(LINKEDIDEXTENSION)) + { + rest = rest.replace(LINKEDIDEXTENSION, avm.getExtension()); + } if (rest.contains(LINKEDIDDIRNAME)) { rest = rest.replace(LINKEDIDDIRNAME, avm.getDirname()); @@ -567,9 +806,24 @@ public class ArgParser return vals; } + public BootstrapArgs getBootstrapArgs() + { + return bootstrapArgs; + } + public boolean isSet(Arg a) { - return a.hasOption(Opt.LINKED) ? isSet("", a) : isSet(null, a); + return a.hasOption(Opt.LINKED) ? isSetAtAll(a) : isSet(null, a); + } + + public boolean isSetAtAll(Arg a) + { + for (String linkedId : linkedOrder) + { + if (isSet(linkedId, a)) + return true; + } + return false; } public boolean isSet(String linkedId, Arg a) @@ -578,7 +832,7 @@ public class ArgParser return avm == null ? false : avm.containsArg(a); } - public boolean getBool(Arg a) + public boolean getBoolean(Arg a) { if (!a.hasOption(Opt.BOOLEAN) && !a.hasOption(Opt.UNARY)) { @@ -597,12 +851,12 @@ public class ArgParser return avs == null ? a.getDefaultBoolValue() : avs.getBoolean(); } - public List linkedIds() + public List getLinkedIds() { return linkedOrder; } - public ArgValuesMap linkedArgs(String id) + public ArgValuesMap getLinkedArgs(String id) { return linkedArgs.get(id); } @@ -613,16 +867,16 @@ public class ArgParser StringBuilder sb = new StringBuilder(); sb.append("UNLINKED\n"); sb.append(argValuesMapToString(linkedArgs.get(null))); - if (linkedIds() != null) + if (getLinkedIds() != null) { sb.append("LINKED\n"); - for (String id : linkedIds()) + for (String id : getLinkedIds()) { // already listed these as UNLINKED args if (id == null) continue; - ArgValuesMap avm = linkedArgs(id); + ArgValuesMap avm = getLinkedArgs(id); sb.append("ID: '").append(id).append("'\n"); sb.append(argValuesMapToString(avm)); } @@ -645,7 +899,7 @@ public class ArgParser } public static ArgParser parseArgFiles(List argFilenameGlobs, - boolean initsubstitutions) + boolean initsubstitutions, BootstrapArgs bsa) { List argFiles = new ArrayList<>(); @@ -655,11 +909,11 @@ public class ArgParser argFiles.addAll(FileUtils.getFilesFromGlob(pattern)); } - return parseArgFileList(argFiles, initsubstitutions); + return parseArgFileList(argFiles, initsubstitutions, bsa); } public static ArgParser parseArgFileList(List argFiles, - boolean initsubstitutions) + boolean initsubstitutions, BootstrapArgs bsa) { List argsList = new ArrayList<>(); for (File argFile : argFiles) @@ -668,7 +922,7 @@ public class ArgParser { String message = Arg.ARGFILE.argString() + EQUALS + "\"" + argFile.getPath() + "\": File does not exist."; - Jalview.exit(message, 2); + Jalview.exit(message, ExitCode.FILE_NOT_FOUND); } try { @@ -682,12 +936,12 @@ public class ArgParser { String message = Arg.ARGFILE.argString() + "=\"" + argFile.getPath() + "\": File could not be read."; - Jalview.exit(message, 3); + Jalview.exit(message, ExitCode.FILE_NOT_READABLE); } } // Third param "true" uses Opt.PRIVATE args --setargile=argfile and // --unsetargfile - return new ArgParser(argsList, initsubstitutions, true); + return new ArgParser(argsList, initsubstitutions, true, bsa); } protected static List readArgFile(File argFile) @@ -708,69 +962,245 @@ public class ArgParser String message = Arg.ARGFILE.argString() + "=\"" + argFile.getPath() + "\": File could not be read."; Console.debug(message, e); - Jalview.exit(message, 3); + Jalview.exit(message, ExitCode.FILE_NOT_READABLE); } } return args; } - public static enum Position + // 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, Type type, ArgValues avs, + SubVals sv, String v, int argIndex, boolean doSubs) + { + this.argValueOperation(Op.ADDVALUE, linkedId, type, avs, sv, v, false, + argIndex, doSubs); + } + + private void setBoolean(String linkedId, Type type, ArgValues avs, + boolean b, int argIndex) + { + this.argValueOperation(Op.SETBOOLEAN, linkedId, type, avs, null, null, + b, argIndex, false); + } + + private void setNegated(String linkedId, ArgValues avs, boolean b) { - FIRST, BEFORE, AFTER + this.argValueOperation(Op.SETNEGATED, linkedId, null, avs, null, null, + b, 0, false); } - public static String getValueFromSubValOrArg(ArgValuesMap avm, Arg a, - SubVals sv) + private void incrementCount(String linkedId, ArgValues avs) { - return getFromSubValArgOrPref(avm, a, sv, null, null, null); + this.argValueOperation(Op.INCREMENTCOUNT, linkedId, null, avs, null, + null, false, 0, false); } - public static String getFromSubValArgOrPref(ArgValuesMap avm, Arg a, - SubVals sv, String key, String pref, String def) + private enum Op { - return getFromSubValArgOrPref(avm, a, Position.FIRST, null, sv, key, - pref, def); + ADDVALUE, SETBOOLEAN, SETNEGATED, INCREMENTCOUNT } - public static String getFromSubValArgOrPref(ArgValuesMap avm, Arg a, - Position pos, ArgValue av, SubVals sv, String key, String pref, - String def) + private void argValueOperation(Op op, String linkedId, Type type, + ArgValues avs, SubVals sv, String v, boolean b, int argIndex, + boolean doSubs) { - if (key == null) - key = a.getName(); - if (sv != null && sv.has(key) && sv.get(key) != null) - return sv.get(key); - if (avm != null && avm.containsArg(a)) + // default to merge subvals if subvals are provided + argValueOperation(op, linkedId, type, avs, sv, true, v, b, argIndex, + doSubs); + } + + /** + * 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. + * + * @param op + * The ArgParser.Op operation + * @param linkedId + * The String linkedId from the ArgValuesMap + * @param type + * The Arg.Type to attach to this ArgValue + * @param avs + * The ArgValues for this linkedId + * @param sv + * Use these SubVals on the ArgValue + * @param merge + * Merge the SubVals with any existing on the value. False will + * replace unless sv is null + * @param v + * The value of the ArgValue (may contain subvals). + * @param b + * The boolean value of the ArgValue. + * @param argIndex + * The argIndex for the ArgValue. + * @param doSubs + * Whether to perform substitutions on the subvals and value. + */ + private void argValueOperation(Op op, String linkedId, Type type, + ArgValues avs, SubVals sv, boolean merge, String v, boolean b, + int argIndex, boolean doSubs) + { + Arg a = avs.arg(); + + List wildcardLinkedIds = null; + if (a.hasOption(Opt.ALLOWMULTIID)) + { + switch (linkedId) + { + case MATCHALLLINKEDIDS: + wildcardLinkedIds = getLinkedIds(); + break; + case MATCHOPENEDLINKEDIDS: + wildcardLinkedIds = this.storedLinkedIds; + break; + } + } + + // if we're not a wildcard linkedId and the arg is marked to be stored, add + // to storedLinkedIds + if (linkedId != null && wildcardLinkedIds == null + && a.hasOption(Opt.STORED) + && !storedLinkedIds.contains(linkedId)) + { + storedLinkedIds.add(linkedId); + } + + // if we are a wildcard linkedId, apply the arg and value to all appropriate + // linkedIds + if (wildcardLinkedIds != null) + { + for (String id : wildcardLinkedIds) + { + // skip incorrectly stored wildcard ids! + if (id == null || MATCHALLLINKEDIDS.equals(id) + || MATCHOPENEDLINKEDIDS.equals(id)) + { + continue; + } + ArgValuesMap avm = linkedArgs.get(id); + // don't set an output if there isn't an input + if (a.hasOption(Opt.REQUIREINPUT) + && !avm.hasArgWithOption(Opt.INPUT)) + continue; + + ArgValues tavs = avm.getOrCreateArgValues(a); + switch (op) + { + + case ADDVALUE: + String val = v; + if (sv != null) + { + if (doSubs) + { + sv = new SubVals(sv, val, merge); + val = makeSubstitutions(sv.getContent(), id); + } + tavs.addValue(sv, type, val, argIndex, true); + } + else + { + if (doSubs) + { + val = makeSubstitutions(v, id); + } + tavs.addValue(type, val, argIndex, true); + } + finaliseStoringArgValue(id, tavs); + break; + + case SETBOOLEAN: + tavs.setBoolean(type, b, argIndex, true); + finaliseStoringArgValue(id, tavs); + break; + + case SETNEGATED: + tavs.setNegated(b, true); + break; + + case INCREMENTCOUNT: + tavs.incrementCount(); + break; + + default: + break; + + } + + } + } + else // no wildcard linkedId -- do it simpler { - String val = null; - if (pos == Position.FIRST && avm.getValue(a) != null) - return avm.getValue(a); - else if (pos == Position.BEFORE - && avm.getClosestPreviousArgValueOfArg(av, a) != null) - return avm.getClosestPreviousArgValueOfArg(av, a).getValue(); - else if (pos == Position.AFTER - && avm.getClosestNextArgValueOfArg(av, a) != null) - return avm.getClosestNextArgValueOfArg(av, a).getValue(); + switch (op) + { + case ADDVALUE: + String val = v; + if (sv != null) + { + if (doSubs) + { + val = makeSubstitutions(v, linkedId); + sv = new SubVals(sv, val); + } + avs.addValue(sv, type, val, argIndex, false); + } + else + { + if (doSubs) + { + val = makeSubstitutions(v, linkedId); + } + avs.addValue(type, val, argIndex, false); + } + finaliseStoringArgValue(linkedId, avs); + break; + + case SETBOOLEAN: + avs.setBoolean(type, b, argIndex, false); + finaliseStoringArgValue(linkedId, avs); + break; + + case SETNEGATED: + avs.setNegated(b, false); + break; + + case INCREMENTCOUNT: + avs.incrementCount(); + break; + + default: + break; + } } - return pref != null ? Cache.getDefault(pref, def) : def; } - public static boolean getBoolFromSubValOrArg(ArgValuesMap avm, Arg a, - SubVals sv) + private ArgValuesMap getOrCreateLinkedArgValuesMap(String linkedId) + { + if (linkedArgs.containsKey(linkedId) + && linkedArgs.get(linkedId) != null) + return linkedArgs.get(linkedId); + + linkedArgs.put(linkedId, new ArgValuesMap(linkedId)); + return linkedArgs.get(linkedId); + } + + public boolean isOldStyle() + { + return oldArguments; + } + + public boolean isMixedStyle() { - return getFromSubValArgOrPref(avm, a, sv, null, null, false); + return mixedArguments; } - public static boolean getFromSubValArgOrPref(ArgValuesMap avm, Arg a, - SubVals sv, String key, String pref, boolean def) + public String[] getMixedExamples() { - if (key == null) - key = a.getName(); - if (sv != null && sv.has(key) && sv.get(key) != null) - return sv.get(key).toLowerCase(Locale.ROOT).equals("true"); - if (avm != null && avm.containsArg(a)) - return avm.getBoolean(a); - return pref != null ? Cache.getDefault(pref, def) : def; + return mixedExamples; } } \ No newline at end of file