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 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 = '=';
+ public static final char EQUALS = '=';
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 linkedId string used to match all linkedIds seen so far
+ /**
+ * the linkedId string used to match all linkedIds seen so far
+ */
protected static final String MATCHALLLINKEDIDS = "*";
- // the counter added to the default linked id prefix
+ /**
+ * 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
+ /**
+ * 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 default linkedId is the current default linked id
+ * or OPENED linkedIds
+ */
+ private boolean openedLinkedIds = 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<String, Arg> argMap;
protected Map<String, ArgValuesMap> linkedArgs = new HashMap<>();
- protected List<String> linkedOrder = null;
+ protected List<String> linkedOrder = new ArrayList<>();
- protected List<Arg> argList;
+ protected List<String> storedLinkedIds = new ArrayList<>();
+
+ protected List<Arg> argList = new ArrayList<>();
private static final char ARGFILECOMMENT = '#';
+ private int argIndex = 0;
+
+ private BootstrapArgs bootstrapArgs = null;
+
static
{
argMap = new HashMap<>();
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(
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
// 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);
+ this(new ArrayList<>(Arrays.asList(args)), initsubstitutions, false,
+ bsa);
}
public ArgParser(List<String> args, boolean initsubstitutions)
{
- this(args, initsubstitutions, false);
+ this(args, initsubstitutions, false, null);
}
public ArgParser(List<String> args, boolean initsubstitutions,
- boolean allowPrivate)
+ boolean allowPrivate, BootstrapArgs bsa)
{
// do nothing if there are no "--" args and (some "-" args || >0 arg is
// "open")
parse(new ArrayList<String>(), false, false);
return;
}
+ if (bsa != null)
+ this.bootstrapArgs = bsa;
+ else
+ this.bootstrapArgs = BootstrapArgs.getBootstrapArgs(args);
parse(args, initsubstitutions, allowPrivate);
}
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
+ // If the first arguments do not start with "--" or "-" or is not "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()
+ && !arg.startsWith("-") && !arg.equals("open")
+ && (new File(arg).exists()
|| HttpUtils.startsWithHttpOrHttps(arg)))
{
arg = Arg.OPEN.argString();
openEachInitialFilenames = false;
}
- String argName = null;
- String val = null;
- List<String> 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<String> 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)
{
{
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.", 13);
continue;
}
if (a.hasOption(Opt.PRIVATE) && !allowPrivate)
// make NOACTION adjustments
// default and auto counter increments
- if (a == Arg.NEWFRAME)
- {
- defaultLinkedIdCounter++;
- }
- else if (a == Arg.NPP)
+ if (a == Arg.NPP)
{
linkedIdAutoCounter++;
}
{
argFile = null;
}
- else if (a == Arg.ALLFRAMES)
+ else if (a == Arg.ALL)
{
allLinkedIds = !negated;
+ openedLinkedIds = false;
+ }
+ else if (a == Arg.OPENED)
+ {
+ openedLinkedIds = !negated;
+ allLinkedIds = false;
+ }
+ 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.ALLOWALL)
+ && val.startsWith(MATCHALLLINKEDIDS))
+ {
+ // --output=*.ext is shorthand for --all --output {basename}.ext
+ // (or --image=*.ext)
+ allLinkedIds = true;
+ openedLinkedIds = false;
+ linkedId = MATCHALLLINKEDIDS;
+ val = LINKEDIDDIRNAME + File.separator + LINKEDIDBASENAME
+ + val.substring(MATCHALLLINKEDIDS.length());
+ }
+ else if (a.hasOption(Opt.OUTPUTFILE)
+ && a.hasOption(Opt.ALLOWALL)
+ && val.startsWith(MATCHOPENEDLINKEDIDS))
{
- // use the next default prefixed OPENLINKEDID
- // NOW using the linkedIdAutoCounter
- defaultLinkedIdCounter++;
- linkedId = new StringBuilder(OPENLINKEDIDPREFIX)
- .append(Integer.toString(defaultLinkedIdCounter))
- .toString();
+ // --output=open*.ext is shorthand for --opened --output
+ // {basename}.ext
+ // (or --image=open*.ext)
+ openedLinkedIds = true;
+ allLinkedIds = false;
+ linkedId = MATCHOPENEDLINKEDIDS;
+ val = LINKEDIDDIRNAME + File.separator + LINKEDIDBASENAME
+ + val.substring(MATCHOPENEDLINKEDIDS.length());
+ }
+ else if (allLinkedIds && a.hasOption(Opt.ALLOWALL))
+ {
+ linkedId = MATCHALLLINKEDIDS;
+ }
+ else if (openedLinkedIds && a.hasOption(Opt.ALLOWALL))
+ {
+ linkedId = MATCHOPENEDLINKEDIDS;
}
else
{
- if (allLinkedIds && a.hasOption(Opt.ALLOWALL))
- {
- linkedId = this.MATCHALLLINKEDIDS;
- }
- else
- {
- // use default linkedId for linked arguments
- linkedId = defaultLinkedId;
- usingDefaultLinkedId = true;
- Console.debug("Changing linkedId to '" + linkedId
- + "' from " + arg);
- }
+ // use default linkedId for linked arguments
+ linkedId = defaultLinkedId;
+ usingDefaultLinkedId = true;
+ Console.debug("Changing linkedId to '" + linkedId + "' from "
+ + 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))
}
// 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()
continue;
}
- boolean argIndexIncremented = false;
- /* TODO
- * Change all avs.addValue() avs.setBoolean avs.setNegated() avs.incrementCount calls to checkfor linkedId == "*"
- * DONE, need to check
- */
+ // 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)
if (a.hasOption(Opt.GLOB) && globVals != null
&& globVals.size() > 0)
{
- for (String v : globVals)
+ Enumeration<String> gve = Collections.enumeration(globVals);
+ while (gve.hasMoreElements())
{
+ String v = gve.nextElement();
SubVals vsv = new SubVals(globSubVals, v);
- addValue(linkedId, avs, vsv, v, argIndex++, true);
- 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
{
- addValue(linkedId, avs, val, argIndex, true);
+ // addValue(linkedId, type, avs, val, argIndex, true);
+ addValue(linkedId, type, avs, addNewSubVals ? subvals : null,
+ 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);
}
- incrementCount(linkedId, avs);
- 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)
+ && linkedArgs.containsKey(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)
{
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());
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)
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))
{
return avs == null ? a.getDefaultBoolValue() : avs.getBoolean();
}
- public List<String> linkedIds()
+ public List<String> getLinkedIds()
{
return linkedOrder;
}
- public ArgValuesMap linkedArgs(String id)
+ public ArgValuesMap getLinkedArgs(String id)
{
return linkedArgs.get(id);
}
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));
}
}
public static ArgParser parseArgFiles(List<String> argFilenameGlobs,
- boolean initsubstitutions)
+ boolean initsubstitutions, BootstrapArgs bsa)
{
List<File> argFiles = new ArrayList<>();
argFiles.addAll(FileUtils.getFilesFromGlob(pattern));
}
- return parseArgFileList(argFiles, initsubstitutions);
+ return parseArgFileList(argFiles, initsubstitutions, bsa);
}
public static ArgParser parseArgFileList(List<File> argFiles,
- boolean initsubstitutions)
+ boolean initsubstitutions, BootstrapArgs bsa)
{
List<String> argsList = new ArrayList<>();
for (File argFile : argFiles)
}
// 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<String> readArgFile(File argFile)
FIRST, BEFORE, AFTER
}
- public static String getValueFromSubValOrArg(ArgValuesMap avm, Arg a,
- SubVals sv)
+ /**
+ * get from following Arg of type a or subval of same name (lowercase)
+ */
+ public static String getValueFromSubValOrArg(ArgValuesMap avm,
+ ArgValue av, Arg a, SubVals sv)
{
- return getFromSubValArgOrPref(avm, a, sv, null, null, null);
+ return getFromSubValArgOrPref(avm, av, a, sv, null, null, null);
}
- public static String getFromSubValArgOrPref(ArgValuesMap avm, Arg a,
- SubVals sv, String key, String pref, String def)
+ /**
+ * get from following Arg of type a or subval key or preference pref or
+ * default def
+ */
+ public static String getFromSubValArgOrPref(ArgValuesMap avm, ArgValue av,
+ Arg a, SubVals sv, String key, String pref, String def)
{
- return getFromSubValArgOrPref(avm, a, Position.FIRST, null, sv, key,
- pref, def);
+ return getFromSubValArgOrPref(avm, a, Position.AFTER, av, sv, key, pref,
+ def);
}
+ /**
+ * get from following(AFTER), first occurence of (FIRST) or previous (BEFORE)
+ * Arg of type a or subval key or preference pref or default def
+ */
public static String getFromSubValArgOrPref(ArgValuesMap avm, Arg a,
Position pos, ArgValue av, SubVals sv, String key, String pref,
String def)
{
+ return getFromSubValArgOrPrefWithSubstitutions(null, avm, a, pos, av,
+ sv, key, pref, def);
+ }
+
+ public static String getFromSubValArgOrPrefWithSubstitutions(ArgParser ap,
+ ArgValuesMap avm, Arg a, Position pos, ArgValue av, SubVals sv,
+ String key, String pref, String def)
+ {
if (key == null)
key = a.getName();
+ String value = null;
if (sv != null && sv.has(key) && sv.get(key) != null)
- return sv.get(key);
- if (avm != null && avm.containsArg(a))
{
- String val = null;
+ value = ap == null ? sv.get(key)
+ : sv.getWithSubstitutions(ap, avm.getLinkedId(), key);
+ }
+ else if (avm != null && avm.containsArg(a))
+ {
if (pos == Position.FIRST && avm.getValue(a) != null)
- return avm.getValue(a);
+ value = avm.getValue(a);
else if (pos == Position.BEFORE
&& avm.getClosestPreviousArgValueOfArg(av, a) != null)
- return avm.getClosestPreviousArgValueOfArg(av, a).getValue();
+ value = avm.getClosestPreviousArgValueOfArg(av, a).getValue();
else if (pos == Position.AFTER
&& avm.getClosestNextArgValueOfArg(av, a) != null)
- return avm.getClosestNextArgValueOfArg(av, a).getValue();
+ value = avm.getClosestNextArgValueOfArg(av, a).getValue();
+
+ // look for allstructures subval for Type.STRUCTURE*
+ Arg arg = av.getArg();
+ if (value == null && arg.hasOption(Opt.PRIMARY)
+ && arg.getType() == Type.STRUCTURE
+ && !a.hasOption(Opt.PRIMARY) && (a.getType() == Type.STRUCTURE
+ || a.getType() == Type.STRUCTUREIMAGE))
+ {
+ ArgValue av2 = avm.getArgValueOfArgWithSubValKey(a,
+ Arg.ALLSTRUCTURES.getName());
+ if (av2 != null)
+ {
+ value = av2.getValue();
+ }
+ }
+ }
+ if (value == null)
+ {
+ value = pref != null ? Cache.getDefault(pref, def) : def;
}
- return pref != null ? Cache.getDefault(pref, def) : def;
+ return value;
}
public static boolean getBoolFromSubValOrArg(ArgValuesMap avm, Arg a,
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;
+ return getFromSubValArgOrPref(avm, a, sv, key, pref, def, false);
}
- // the following methods look for the "*" linkedId and add the argvalue to all
- // linkedId ArgValues if it does
- private void addValue(String linkedId, ArgValues avs, SubVals sv,
- String v, int argIndex, boolean doSubs)
+ public static boolean getFromSubValArgOrPref(ArgValuesMap avm, Arg a,
+ SubVals sv, String key, String pref, boolean def,
+ boolean invertPref)
{
- Arg a = avs.arg();
- if (MATCHALLLINKEDIDS.equals(linkedId) && a.hasOption(Opt.ALLOWALL))
+ if ((key == null && a == null) || (sv == null && a == null))
+ return false;
+
+ boolean usingArgKey = false;
+ if (key == null)
{
- for (String id : linkedOrder)
+ key = a.getName();
+ usingArgKey = true;
+ }
+
+ String nokey = ArgParser.NEGATESTRING + key;
+
+ // look for key or nokey in subvals first (if using Arg check options)
+ if (sv != null)
+ {
+ // check for true boolean
+ if (sv.has(key) && sv.get(key) != null)
{
- ArgValuesMap avm = linkedArgs.get(id);
- ArgValues tavs = avm.getArgValues(a);
- String val = v;
- if (doSubs)
+ if (usingArgKey)
{
- val = makeSubstitutions(v, linkedId);
- sv = new SubVals(sv, val);
+ if (!(a.hasOption(Opt.BOOLEAN) || a.hasOption(Opt.UNARY)))
+ {
+ Console.debug(
+ "Looking for boolean in subval from non-boolean/non-unary Arg "
+ + a.getName());
+ return false;
+ }
}
- tavs.addValue(sv, val, argIndex);
+ return sv.get(key).toLowerCase(Locale.ROOT).equals("true");
}
- }
- else
- {
- String val = v;
- if (doSubs)
+
+ // check for negative boolean (subval "no..." will be "true")
+ if (sv.has(nokey) && sv.get(nokey) != null)
{
- val = makeSubstitutions(v, linkedId);
- sv = new SubVals(sv, val);
+ if (usingArgKey)
+ {
+ if (!(a.hasOption(Opt.BOOLEAN)))
+ {
+ Console.debug(
+ "Looking for negative boolean in subval from non-boolean Arg "
+ + a.getName());
+ return false;
+ }
+ }
+ return !sv.get(nokey).toLowerCase(Locale.ROOT).equals("true");
}
- avs.addValue(sv, val, argIndex);
}
+
+ // check argvalues
+ if (avm != null && avm.containsArg(a))
+ return avm.getBoolean(a);
+
+ // return preference or default
+ boolean prefVal = pref != null ? Cache.getDefault(pref, def) : false;
+ return pref != null ? (invertPref ? !prefVal : prefVal) : def;
}
- private void addValue(String linkedId, ArgValues avs, String v,
+ // 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 addValue(String linkedId, Type type, ArgValues avs, String v,
int argIndex, boolean doSubs)
{
- Arg a = avs.arg();
- if (MATCHALLLINKEDIDS.equals(linkedId) && a.hasOption(Opt.ALLOWALL))
- {
- for (String id : linkedOrder)
- {
- ArgValuesMap avm = linkedArgs.get(id);
- ArgValues tavs = avm.getArgValues(a);
- String val = doSubs ? makeSubstitutions(v, linkedId) : v;
- tavs.addValue(val, argIndex);
- }
- }
- else
- {
- String val = doSubs ? makeSubstitutions(v, linkedId) : v;
- avs.addValue(val, argIndex);
- }
+ 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)
{
- Arg a = avs.arg();
- if (MATCHALLLINKEDIDS.equals(linkedId) && a.hasOption(Opt.ALLOWALL))
- {
- for (String id : linkedOrder)
- {
- ArgValuesMap avm = linkedArgs.get(id);
- ArgValues tavs = avm.getArgValues(a);
- tavs.setBoolean(b, argIndex);
- }
- }
- else
- {
- avs.setBoolean(b, argIndex);
- }
+ 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, null, avs, null, null,
+ b, 0, false);
+ }
+
+ private void incrementCount(String linkedId, ArgValues avs)
+ {
+ this.argValueOperation(Op.INCREMENTCOUNT, linkedId, null, avs, null,
+ null, false, 0, false);
+ }
+
+ private enum Op
+ {
+ ADDVALUE, SETBOOLEAN, SETNEGATED, INCREMENTCOUNT
+ }
+
+ private void argValueOperation(Op op, String linkedId, Type type,
+ ArgValues avs, SubVals sv, String v, boolean b, int argIndex,
+ boolean doSubs)
+ {
+ // 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();
- if (MATCHALLLINKEDIDS.equals(linkedId) && a.hasOption(Opt.ALLOWALL))
+
+ List<String> wildcardLinkedIds = null;
+ if (a.hasOption(Opt.ALLOWALL))
{
- for (String id : linkedOrder)
+ switch (linkedId)
{
- ArgValuesMap avm = linkedArgs.get(id);
- ArgValues tavs = avm.getArgValues(a);
- tavs.setNegated(b);
+ case MATCHALLLINKEDIDS:
+ wildcardLinkedIds = getLinkedIds();
+ break;
+ case MATCHOPENEDLINKEDIDS:
+ wildcardLinkedIds = this.storedLinkedIds;
+ break;
}
}
- else
+
+ // 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))
{
- avs.setNegated(b);
+ storedLinkedIds.add(linkedId);
}
- }
- private void incrementCount(String linkedId, ArgValues avs)
- {
- Arg a = avs.arg();
- if (MATCHALLLINKEDIDS.equals(linkedId) && a.hasOption(Opt.ALLOWALL))
+ // if we are a wildcard linkedId, apply the arg and value to all appropriate
+ // linkedIds
+ if (wildcardLinkedIds != null)
{
- for (String id : linkedOrder)
+ for (String id : wildcardLinkedIds)
{
+ // skip incorrectly stored wildcard ids!
+ if (id == null || MATCHALLLINKEDIDS.equals(id)
+ || MATCHOPENEDLINKEDIDS.equals(id))
+ continue;
ArgValuesMap avm = linkedArgs.get(id);
- ArgValues tavs = avm.getArgValues(a);
- tavs.incrementCount();
+ // 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
+ else // no wildcard linkedId -- do it simpler
{
- avs.incrementCount();
+ 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;
+ }
}
}
+ 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);
+ }
+
}
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff