import java.net.URLDecoder;
import java.util.ArrayList;
import java.util.Arrays;
+import java.util.Collection;
import java.util.Collections;
import java.util.EnumSet;
import java.util.Enumeration;
USAGESTATS, OPEN, OPEN2, PROPS, QUESTIONNAIRE, SETPROP, TREE, VDOC,
VSESS, OUTPUT, OUTPUTTYPE, SSANNOTATION, NOTEMPFAC, TEMPFAC,
TEMPFAC_LABEL, TEMPFAC_DESC, TEMPFAC_SHADING, TITLE, PAEMATRIX, WRAP,
- NOSTRUCTURE, STRUCTURE;
+ NOSTRUCTURE, STRUCTURE, IMAGE, QUIT, DEBUG("d");
static
{
TEMPFAC.setOptions(Opt.STRING, Opt.LINKED);
TEMPFAC_LABEL.setOptions(Opt.STRING, Opt.LINKED);
TEMPFAC_DESC.setOptions(Opt.STRING, Opt.LINKED);
- TEMPFAC_SHADING.setOptions(Opt.STRING, Opt.LINKED);
+ TEMPFAC_SHADING.setOptions(Opt.BOOLEAN, Opt.LINKED);
TITLE.setOptions(Opt.STRING, Opt.LINKED);
PAEMATRIX.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI);
NOSTRUCTURE.setOptions(Opt.UNARY, Opt.LINKED);
STRUCTURE.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI);
WRAP.setOptions(Opt.BOOLEAN, Opt.LINKED);
+ IMAGE.setOptions(Opt.STRING, Opt.LINKED);
+ QUIT.setOptions(Opt.UNARY);
+ DEBUG.setOptions(Opt.BOOLEAN);
}
private final String[] argNames;
private boolean negated = false;
- private List<String> argsList;
+ private int singleArgIndex = -1;
+
+ private List<Integer> argsIndexes;
+
+ private List<ArgValue> argsList;
protected ArgValues(Arg a)
{
this.arg = a;
- this.argsList = new ArrayList<String>();
+ this.argsList = new ArrayList<ArgValue>();
this.boolValue = arg.getDefaultBoolValue();
}
{
sb.append("Values:");
boolean first = true;
- for (String v : argsList)
+ for (ArgValue av : argsList)
{
+ String v = av.getValue();
if (!first)
sb.append(",");
sb.append("\n '");
protected void addValue()
{
- addValue(null);
+ addValue(null, -1);
}
- protected void addValue(String val)
+ protected void addValue(String val, int argIndex)
{
- addValue(val, false);
+ addValue(val, argIndex, false);
}
- protected void addValue(String val, boolean noDuplicates)
+ protected void addValue(String val, int argIndex, boolean noDuplicates)
{
if ((!arg.hasOption(Opt.MULTI) && argsList.size() > 0)
|| (noDuplicates && argsList.contains(val)))
return;
if (argsList == null)
{
- Console.warn("** inst");
- argsList = new ArrayList<String>();
+ argsList = new ArrayList<ArgValue>();
}
- argsList.add(val);
+ argsList.add(new ArgValue(val, argIndex));
}
protected boolean hasValue(String val)
return argsList.contains(val);
}
- protected String getValue()
+ protected ArgValue getArgValue()
{
if (arg.hasOption(Opt.MULTI))
Console.warn("Requesting single value for multi value argument");
return argsList.size() > 0 ? argsList.get(0) : null;
}
- protected List<String> getValues()
+ /*
+ protected String getValue()
+ {
+ ArgValue av = getArgValue();
+ return av == null ? null : av.getValue();
+ }
+ */
+
+ protected List<ArgValue> getArgValueList()
{
return argsList;
}
// new style
Enumeration<String> argE = Collections.enumeration(Arrays.asList(args));
- ARG: while (argE.hasMoreElements())
+ int argIndex = 0;
+ while (argE.hasMoreElements())
{
String arg = argE.nextElement();
String argName = null;
{
// arg not found
Console.error("Argument '" + arg + "' not recognised. Ignoring.");
- continue ARG;
+ continue;
}
if (!a.hasOption(Opt.BOOLEAN) && negated)
{
// used "no" with a non-boolean option
Console.error("Argument '--" + NEGATESTRING + argName
+ "' not a boolean option. Ignoring.");
- continue ARG;
+ continue;
}
if (!a.hasOption(Opt.STRING) && equalPos > -1)
{
Console.error("Argument '--" + argName
+ "' does not expect a value (given as '" + arg
+ "'). Ignoring.");
- continue ARG;
+ continue;
}
if (!a.hasOption(Opt.LINKED) && linkedId != null)
{
Console.error("Argument '--" + argName
+ "' does not expect a linked id (given as '" + arg
+ "'). Ignoring.");
- continue ARG;
+ continue;
}
if (a.hasOption(Opt.STRING) && equalPos == -1)
// no value to take for arg, which wants a value
Console.error("Argument '" + a.getName()
+ "' requires a value, none given. Ignoring.");
- continue ARG;
+ continue;
}
val = argE.nextElement();
}
// store appropriate value
if (a.hasOption(Opt.STRING))
{
- values.addValue(val);
+ values.addValue(val, argIndex);
}
else if (a.hasOption(Opt.BOOLEAN))
{
public boolean getBool(Arg a)
{
- if (!a.hasOption(Opt.BOOLEAN))
+ if (!a.hasOption(Opt.BOOLEAN) && !a.hasOption(Opt.UNARY))
{
Console.warn("Getting boolean from non boolean Arg '" + a.getName()
+ "'.");
return sb.toString();
}
- public static SubId getSubId(String item)
+ public static SubVals getSubVals(String item)
{
- return new SubId(item);
+ return new SubVals(item);
+ }
+
+ /**
+ * A helper class to keep an index of argument position with argument values
+ */
+ public static class ArgValue
+ {
+ private int argIndex;
+
+ private String value;
+
+ protected ArgValue(String value, int argIndex)
+ {
+ this.value = value;
+ this.argIndex = argIndex;
+ }
+
+ protected String getValue()
+ {
+ return value;
+ }
+
+ protected int getArgIndex()
+ {
+ return argIndex;
+ }
}
/**
* the strings keyName and keyValue, and the content after the square brackets
* (if present). Values not set `will be -1 or null.
*/
- public static class SubId
+ public static class SubVals
{
- protected int index = 0;
+ private static int NOTSET = -1;
- protected String keyName = null;
+ private int index = NOTSET;
- protected String keyValue = null;
+ private Map<String, String> subVals = null;
- protected String content = null;
+ private static char SEPARATOR = ';';
- public SubId()
- {
- }
+ private String content = null;
- public SubId(String item)
+ public SubVals(String item)
{
- this.parseVal(item);
+ this.parseVals(item);
}
- public void parseVal(String item)
+ public void parseVals(String item)
{
if (item.indexOf('[') == 0 && item.indexOf(']') > 1)
{
int openBracket = item.indexOf('[');
int closeBracket = item.indexOf(']');
- String indexString = item.substring(openBracket + 1, closeBracket);
+ String subvalsString = item.substring(openBracket + 1,
+ closeBracket);
this.content = item.substring(closeBracket + 1);
- int equals = indexString.indexOf('=');
- if (equals > -1)
- {
- this.keyName = indexString.substring(0, equals);
- this.keyValue = indexString.substring(equals + 1);
- this.index = -1;
- }
- else
+ boolean setIndex = false;
+ for (String subvalString : subvalsString
+ .split(Character.toString(SEPARATOR)))
{
- try
+ int equals = subvalString.indexOf('=');
+ if (equals > -1)
{
- this.index = Integer.parseInt(indexString);
- } catch (NumberFormatException e)
+ if (subVals == null)
+ subVals = new HashMap<>();
+ subVals.put(subvalString.substring(0, equals),
+ subvalString.substring(equals + 1));
+ }
+ else
{
- Console.warn("Failed to obtain sequenced id or index from '"
- + item + "'. Setting index=0 and using content='"
- + content + "'.");
+ try
+ {
+ this.index = Integer.parseInt(subvalString);
+ setIndex = true;
+ } catch (NumberFormatException e)
+ {
+ Console.warn("Failed to obtain subvalue or index from '"
+ + item + "'. Setting index=0 and using content='"
+ + content + "'.");
+ }
}
}
+ if (!setIndex)
+ this.index = NOTSET;
}
else
{
this.content = item;
}
}
+
+ public boolean notSet()
+ {
+ // notSet is true if content present but nonsensical
+ return index == NOTSET && subVals == null;
+ }
+
+ public String get(String key)
+ {
+ return subVals == null ? null : subVals.get(key);
+ }
+
+ public boolean has(String key)
+ {
+ return subVals == null ? false : subVals.containsKey(key);
+ }
+
+ public int getIndex()
+ {
+ return index;
+ }
+
+ public String getContent()
+ {
+ return content;
+ }
+ }
+
+ /**
+ * Helper class to allow easy extraction of information about specific
+ * argument values (without having to check for null etc all the time)
+ */
+ protected static class ArgValuesMap
+ {
+ protected Map<Arg, ArgValues> m;
+
+ protected ArgValuesMap(Map<Arg, ArgValues> map)
+ {
+ this.m = map;
+ }
+
+ protected ArgValues getArgValues(Arg a)
+ {
+ return m == null ? null : m.get(a);
+ }
+
+ protected List<ArgValue> getArgValueList(Arg a)
+ {
+ ArgValues av = getArgValues(a);
+ return av == null ? null : av.getArgValueList();
+ }
+
+ protected ArgValue getArgValue(Arg a)
+ {
+ List<ArgValue> vals = getArgValueList(a);
+ return (vals == null || vals.size() == 0) ? null : vals.get(0);
+ }
+
+ protected String getValue(Arg a)
+ {
+ ArgValue av = getArgValue(a);
+ return av == null ? null : av.getValue();
+ }
+
+ protected boolean hasValue(Arg a)
+ {
+ if (!m.containsKey(a))
+ return false;
+ return getArgValue(a) != null;
+ }
+
+ protected boolean getBoolean(Arg a)
+ {
+ ArgValues av = getArgValues(a);
+ return av == null ? false : av.getBoolean();
+ }
+
+ protected ArgValue getClosestPreviousArgValueOfArg(ArgValue thisAv,
+ Arg a)
+ {
+ ArgValue closestAv = null;
+ int thisArgIndex = thisAv.getArgIndex();
+ ArgValues compareAvs = this.getArgValues(a);
+ int closestPreviousIndex = -1;
+ for (ArgValue av : compareAvs.getArgValueList())
+ {
+ int argIndex = av.getArgIndex();
+ if (argIndex < thisArgIndex && argIndex > closestPreviousIndex)
+ {
+ closestPreviousIndex = argIndex;
+ closestAv = av;
+ }
+ }
+ return closestAv;
+ }
+ }
+
+ private static final Collection<Arg> bootstrapArgs = new ArrayList(
+ Arrays.asList(Arg.PROPS, Arg.DEBUG));
+
+ public static Map<Arg, String> bootstrapArgs(String[] args)
+ {
+ Map<Arg, String> bootstrapArgMap = new HashMap<>();
+ if (args == null)
+ return bootstrapArgMap;
+ Enumeration<String> argE = Collections.enumeration(Arrays.asList(args));
+ while (argE.hasMoreElements())
+ {
+ String arg = argE.nextElement();
+ String argName = null;
+ String val = null;
+ if (arg.startsWith("--"))
+ {
+ int equalPos = arg.indexOf('=');
+ if (equalPos > -1)
+ {
+ argName = arg.substring(2, equalPos);
+ val = arg.substring(equalPos + 1);
+ }
+ else
+ {
+ argName = arg.substring(2);
+ }
+ Arg a = argMap.get(argName);
+ if (a != null && bootstrapArgs.contains(a))
+ bootstrapArgMap.put(a, val);
+ }
+ }
+ return bootstrapArgMap;
}
}
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff