+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.bin.argparser;
import java.io.File;
import java.util.AbstractMap;
import java.util.ArrayList;
import java.util.Arrays;
+import java.util.EnumSet;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
private Set<File> argFiles = new HashSet<>();
+ private Set<Opt> argsOptions = new HashSet<>();
+
+ private Set<Type> argsTypes = new HashSet<>();
+
+ private boolean outputToStdout = false;
+
public static BootstrapArgs getBootstrapArgs(String[] args)
{
List<String> argList = new ArrayList<>(Arrays.asList(args));
{
if (argFiles.contains(inArgFile))
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Looped argfiles detected: '" + inArgFile.getPath() + "'");
return;
}
}
}
- if (ArgParser.argMap.containsKey(argName) && val == null)
+ // after all other args, look for Opt.PREFIX args if still not found
+ if (!ArgParser.argMap.containsKey(argName))
{
- val = "true";
+ for (Arg potentialArg : EnumSet.allOf(Arg.class))
+ {
+ if (potentialArg.hasOption(Opt.PREFIXKEV) && argName != null
+ && argName.startsWith(potentialArg.getName())
+ && val != null)
+ {
+ val = argName.substring(potentialArg.getName().length())
+ + ArgParser.EQUALS + val;
+ argName = argName.substring(0,
+ potentialArg.getName().length());
+ break;
+ }
+ }
}
Arg a = ArgParser.argMap.get(argName);
+ if (a != null)
+ {
+ for (Opt opt : a.getOptions())
+ {
+ if (!argsOptions.contains(opt))
+ {
+ argsOptions.add(opt);
+ }
+ }
+ for (Type t : a.getTypes())
+ {
+ if (!argsTypes.contains(t))
+ {
+ argsTypes.add(t);
+ }
+ }
+ }
+
if (a == null || !a.hasOption(Opt.BOOTSTRAP))
{
- // not a valid bootstrap arg
+ // not a bootstrap arg
+
+ // make a check for an output going to stdout
+ if (a != null && a.hasOption(Opt.OUTPUTFILE)
+ && a.hasOption(Opt.STDOUT))
+ {
+ if (val == null && i + 1 < args.size())
+ {
+ val = args.get(i + 1);
+ }
+ if (val.startsWith("[") && val.indexOf(']') > 0)
+ {
+ val = val.substring(val.indexOf(']') + 1);
+ }
+
+ if (ArgParser.STDOUTFILENAME.equals(val))
+ {
+ this.outputToStdout = true;
+ }
+ }
+
continue;
}
}
else
{
+ if (val == null)
+ {
+ val = "true";
+ }
+
add(a, type, val);
}
}
}
+
+ // if in an argfile, remove it from the hashset so it can be re-used in
+ // another argfile
+ if (inArgFile != null)
+ {
+ argFiles.remove(inArgFile);
+ }
}
public boolean contains(Arg a)
private void add(Arg a, Type t, String s)
{
List<Map.Entry<Type, String>> l = getOrCreateList(a);
- if (a.hasOption(Opt.MULTI) || l.size() == 0)
+ if (a.hasOption(Opt.MULTIVALUE) || l.size() == 0)
{
l.add(entry(t, s));
}
private void addAll(Arg a, Type t, List<String> al)
{
List<Map.Entry<Type, String>> l = getOrCreateList(a);
- if (a.hasOption(Opt.MULTI))
+ if (a.hasOption(Opt.MULTIVALUE))
{
for (String s : al)
{
* Retrieves the first value even if MULTI.
* A convenience for non-MULTI args.
*/
- public String get(Arg a)
+ public String getValue(Arg a)
{
if (!bootstrapArgMap.containsKey(a))
return null;
{
if (!bootstrapArgMap.containsKey(a))
return d;
- return Boolean.parseBoolean(get(a));
+ return Boolean.parseBoolean(getValue(a));
}
public boolean getBoolean(Arg a)
return false;
}
if (bootstrapArgMap.containsKey(a))
- return Boolean.parseBoolean(get(a));
+ {
+ return Boolean.parseBoolean(getValue(a));
+ }
else
+ {
return a.getDefaultBoolValue();
+ }
+ }
+
+ public boolean argsHaveOption(Opt opt)
+ {
+ return argsOptions.contains(opt);
+ }
+
+ public boolean argsHaveType(Type type)
+ {
+ return argsTypes.contains(type);
+ }
+
+ public boolean isHeadless()
+ {
+ boolean isHeadless = false;
+ if (this.argsHaveType(Type.HELP))
+ {
+ // --help, --help-all, ... specified => headless
+ isHeadless = true;
+ }
+ else if (this.contains(Arg.VERSION))
+ {
+ // --version specified => headless
+ isHeadless = true;
+ }
+ else if (this.contains(Arg.GUI))
+ {
+ // --gui specified => forced NOT headless
+ isHeadless = !this.getBoolean(Arg.GUI);
+ }
+ else if (this.contains(Arg.HEADLESS))
+ {
+ // --headless has been specified on the command line => headless
+ isHeadless = this.getBoolean(Arg.HEADLESS);
+ }
+ else if (this.argsHaveOption(Opt.OUTPUTFILE))
+ {
+ // --output file.fa, --image pic.png, --structureimage struct.png =>
+ // assume headless unless above has been already specified
+ isHeadless = true;
+ }
+ return isHeadless;
+ }
+
+ public boolean outputToStdout()
+ {
+ return this.outputToStdout;
}
}
git://source.jalview.org / jalview.git / blobdiff