X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2Fargparser%2FArgParser.java;h=e08ae035840c72597eb822086086f30b30b4193a;hb=6dafac1b9bcc7265b0fb1641f7474a6c81b24119;hp=ff238da584dc2680cd95a6d626b9f276d5f48992;hpb=d42b7588a34477b24ce97ba75788536e74e6cf86;p=jalview.git diff --git a/src/jalview/bin/argparser/ArgParser.java b/src/jalview/bin/argparser/ArgParser.java index ff238da..e08ae03 100644 --- a/src/jalview/bin/argparser/ArgParser.java +++ b/src/jalview/bin/argparser/ArgParser.java @@ -29,12 +29,15 @@ import java.util.Arrays; import java.util.EnumSet; 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.argparser.Arg.Opt; import jalview.util.FileUtils; +import jalview.util.HttpUtils; public class ArgParser { @@ -50,25 +53,32 @@ public class ArgParser // the counter added to the default linked id prefix private int defaultLinkedIdCounter = 0; - // the linked id prefix used for --opennew files - protected static final String OPENNEWLINKEDIDPREFIX = "OPENNEW:"; + // the substitution string used to use the defaultLinkedIdCounter + private static final String DEFAULTLINKEDIDCOUNTER = "{}"; - // the counter added to the default linked id prefix - private int opennewLinkedIdCounter = 0; + // 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 + protected static final String OPENLINKEDIDPREFIX = DEFAULTLINKEDIDPREFIX; + + // 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) - private static final String INCREMENTAUTOCOUNTERLINKEDID = "{++n}"; + private static final String INCREMENTLINKEDIDAUTOCOUNTER = "{++n}"; // the linked id substitution string used to use the idCounter - private static final String AUTOCOUNTERLINKEDID = "{n}"; + private static final String LINKEDIDAUTOCOUNTER = "{n}"; - // the linked id substitution string used to use the base filename of --open - // or --opennew + // 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 --open - // or --opennew + // the linked id substitution string used to use the dir path of --append + // or --open private static final String LINKEDIDDIRNAME = "{dirname}"; // the current argfile @@ -82,8 +92,6 @@ public class ArgParser // --argfile name private static final String ARGFILEDIRNAME = "{argfiledirname}"; - private int linkedIdAutoCounter = 0; - // flag to say whether {n} subtitutions in output filenames should be made. // Turn on and off with --subs and --nosubs private boolean substitutions = false; @@ -96,6 +104,8 @@ public class ArgParser protected List argList; + private static final char ARGFILECOMMENT = '#'; + static { argMap = new HashMap<>(); @@ -133,7 +143,7 @@ public class ArgParser // 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 --open/--argfile/etc Arg which is most easily done by + // 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); @@ -147,7 +157,8 @@ public class ArgParser public ArgParser(List args, boolean initsubstitutions, boolean allowPrivate) { - // do nothing if there are no "--" args and some "-" args + // do nothing if there are no "--" args and (some "-" args || >0 arg is + // "open") boolean d = false; boolean dd = false; for (String arg : args) @@ -157,7 +168,7 @@ public class ArgParser dd = true; break; } - else if (arg.startsWith("-")) + else if (arg.startsWith("-") || arg.equals("open")) { d = true; } @@ -187,9 +198,10 @@ public class ArgParser // 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()) + && !arg.startsWith("-") && (new File(arg).exists() + || HttpUtils.startsWithHttpOrHttps(arg))) { - arg = Arg.OPENNEW.argString(); + arg = Arg.OPEN.argString(); } else { @@ -278,7 +290,7 @@ public class ArgParser if (a.hasOption(Opt.GLOB)) { // strip off and save the SubVals to be added individually later - globSubVals = ArgParser.getSubVals(val); + globSubVals = new SubVals(val); // make substitutions before looking for files String fileGlob = makeSubstitutions(globSubVals.getContent(), linkedId); @@ -321,7 +333,7 @@ public class ArgParser // make NOACTION adjustments // default and auto counter increments - if (a == Arg.INCREMENT) + if (a == Arg.NEWFRAME) { defaultLinkedIdCounter++; } @@ -352,13 +364,14 @@ public class ArgParser { if (linkedId == null) { - if (a == Arg.OPENNEW) + if (a == Arg.OPEN) { - // use the next default prefixed OPENNEWLINKEDID - linkedId = new StringBuilder(OPENNEWLINKEDIDPREFIX) - .append(Integer.toString(opennewLinkedIdCounter)) + // use the next default prefixed OPENLINKEDID + // NOW using the linkedIdAutoCounter + defaultLinkedIdCounter++; + linkedId = new StringBuilder(OPENLINKEDIDPREFIX) + .append(Integer.toString(defaultLinkedIdCounter)) .toString(); - opennewLinkedIdCounter++; } else { @@ -369,21 +382,21 @@ public class ArgParser + arg); } } - else if (linkedId.contains(AUTOCOUNTERLINKEDID)) + else if (linkedId.contains(LINKEDIDAUTOCOUNTER)) { // turn {n} to the autoCounter autoCounterString = Integer.toString(linkedIdAutoCounter); - linkedId = linkedId.replace(AUTOCOUNTERLINKEDID, + linkedId = linkedId.replace(LINKEDIDAUTOCOUNTER, autoCounterString); usingAutoCounterLinkedId = true; Console.debug( "Changing linkedId to '" + linkedId + "' from " + arg); } - else if (linkedId.contains(INCREMENTAUTOCOUNTERLINKEDID)) + else if (linkedId.contains(INCREMENTLINKEDIDAUTOCOUNTER)) { // turn {++n} to the incremented autoCounter autoCounterString = Integer.toString(++linkedIdAutoCounter); - linkedId = linkedId.replace(INCREMENTAUTOCOUNTERLINKEDID, + linkedId = linkedId.replace(INCREMENTLINKEDIDAUTOCOUNTER, autoCounterString); usingAutoCounterLinkedId = true; Console.debug( @@ -410,7 +423,7 @@ public class ArgParser } // check for unique id - SubVals idsv = ArgParser.getSubVals(val); + SubVals idsv = new SubVals(val); String id = idsv.get(ArgValues.ID); if (id != null && avm.hasId(a, id)) { @@ -474,9 +487,9 @@ public class ArgParser } } - private String makeSubstitutions(String val, String linkedId) + public String makeSubstitutions(String val, String linkedId) { - if (!this.substitutions) + if (!this.substitutions || val == null) return val; String subvals; @@ -494,14 +507,15 @@ public class ArgParser subvals = ""; rest = val; } - if (rest.contains(AUTOCOUNTERLINKEDID)) - rest = rest.replace(AUTOCOUNTERLINKEDID, + if (rest.contains(LINKEDIDAUTOCOUNTER)) + rest = rest.replace(LINKEDIDAUTOCOUNTER, String.valueOf(linkedIdAutoCounter)); - if (rest.contains(INCREMENTAUTOCOUNTERLINKEDID)) - rest = rest.replace(INCREMENTAUTOCOUNTERLINKEDID, + if (rest.contains(INCREMENTLINKEDIDAUTOCOUNTER)) + rest = rest.replace(INCREMENTLINKEDIDAUTOCOUNTER, String.valueOf(++linkedIdAutoCounter)); - if (rest.contains("{}")) - rest = rest.replace("{}", String.valueOf(defaultLinkedIdCounter)); + if (rest.contains(DEFAULTLINKEDIDCOUNTER)) + rest = rest.replace(DEFAULTLINKEDIDCOUNTER, + String.valueOf(defaultLinkedIdCounter)); ArgValuesMap avm = linkedArgs.get(linkedId); if (avm != null) { @@ -630,11 +644,6 @@ public class ArgParser return sb.toString(); } - public static SubVals getSubVals(String item) - { - return new SubVals(item); - } - public static ArgParser parseArgFiles(List argFilenameGlobs, boolean initsubstitutions) { @@ -667,7 +676,7 @@ public class ArgParser .append(EQUALS).append(argFile.getCanonicalPath()) .toString(); argsList.add(setargfile); - argsList.addAll(Files.readAllLines(Paths.get(argFile.getPath()))); + argsList.addAll(readArgFile(argFile)); argsList.add(Arg.UNSETARGFILE.argString()); } catch (IOException e) { @@ -681,4 +690,87 @@ public class ArgParser return new ArgParser(argsList, initsubstitutions, true); } + protected static List readArgFile(File argFile) + { + List args = new ArrayList<>(); + if (argFile != null && argFile.exists()) + { + try + { + for (String line : Files.readAllLines(Paths.get(argFile.getPath()))) + { + if (line != null && line.length() > 0 + && line.charAt(0) != ARGFILECOMMENT) + args.add(line); + } + } catch (IOException e) + { + String message = Arg.ARGFILE.argString() + "=\"" + argFile.getPath() + + "\": File could not be read."; + Console.debug(message, e); + Jalview.exit(message, 3); + } + } + return args; + } + + public static enum Position + { + FIRST, BEFORE, AFTER + } + + public static String getValueFromSubValOrArg(ArgValuesMap avm, Arg a, + SubVals sv) + { + return getFromSubValArgOrPref(avm, a, sv, null, null, null); + } + + public static String getFromSubValArgOrPref(ArgValuesMap avm, Arg a, + SubVals sv, String key, String pref, String def) + { + return getFromSubValArgOrPref(avm, a, Position.FIRST, null, sv, key, + pref, def); + } + + public static String getFromSubValArgOrPref(ArgValuesMap avm, Arg a, + Position pos, ArgValue av, SubVals sv, String key, String pref, + String def) + { + 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)) + { + 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(); + } + return pref != null ? Cache.getDefault(pref, def) : def; + } + + public static boolean getBoolFromSubValOrArg(ArgValuesMap avm, Arg a, + SubVals sv) + { + return getFromSubValArgOrPref(avm, a, sv, null, null, false); + } + + public static boolean getFromSubValArgOrPref(ArgValuesMap avm, Arg a, + SubVals sv, String key, String pref, boolean def) + { + 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; + } + } \ No newline at end of file