+ ArgValuesMap avm = argParser.getLinkedArgs(id);
+ AlignFrame af = afMap.get(id);
+
+ if (af == null)
+ {
+ addWarn("Did not have an alignment window for id=" + id);
+ return false;
+ }
+
+ Boolean isError = Boolean.valueOf(false);
+
+ if (avm.containsArg(Arg.OUTPUT))
+ {
+ for (ArgValue av : avm.getArgValueList(Arg.OUTPUT))
+ {
+ String val = av.getValue();
+ SubVals subVals = av.getSubVals();
+ String fileName = subVals.getContent();
+ boolean stdout = ArgParser.STDOUTFILENAME.equals(fileName);
+ File file = new File(fileName);
+
+ String name = af.getName();
+ String format = ArgParser.getValueFromSubValOrArg(avm, av,
+ Arg.FORMAT, subVals);
+ FileFormats ffs = FileFormats.getInstance();
+ List<String> validFormats = ffs.getWritableFormats(false);
+
+ FileFormatI ff = null;
+ if (format == null && fileName != null)
+ {
+ FORMAT: for (String fname : validFormats)
+ {
+ FileFormatI tff = ffs.forName(fname);
+ String[] extensions = tff.getExtensions().split(",");
+ for (String ext : extensions)
+ {
+ if (fileName.toLowerCase(Locale.ROOT).endsWith("." + ext))
+ {
+ ff = tff;
+ format = ff.getName();
+ break FORMAT;
+ }
+ }
+ }
+ }
+ if (ff == null && format != null)
+ {
+ ff = ffs.forName(format);
+ }
+ if (ff == null)
+ {
+ if (stdout)
+ {
+ ff = FileFormat.Fasta;
+ }
+ else
+ {
+ StringBuilder validSB = new StringBuilder();
+ for (String f : validFormats)
+ {
+ if (validSB.length() > 0)
+ validSB.append(", ");
+ validSB.append(f);
+ FileFormatI tff = ffs.forName(f);
+ validSB.append(" (");
+ validSB.append(tff.getExtensions());
+ validSB.append(")");
+ }
+
+ addError("No valid format specified for "
+ + Arg.OUTPUT.argString() + ". Valid formats are "
+ + validSB.toString() + ".");
+ continue;
+ }
+ }
+
+ boolean success = checksBeforeWritingToFile(avm, subVals, true,
+ fileName, ff.getName(), isError);
+ if (!success)
+ {
+ continue;
+ }
+
+ boolean backups = ArgParser.getFromSubValArgOrPref(avm, Arg.BACKUPS,
+ subVals, null,
+ Platform.isHeadless() ? null : BackupFiles.ENABLED,
+ !Platform.isHeadless());
+
+ Console.info("Writing " + fileName);
+
+ af.saveAlignment(fileName, ff, stdout, backups);
+ if (af.isSaveAlignmentSuccessful())
+ {
+ Console.debug("Written alignment '" + name + "' in "
+ + ff.getName() + " format to '" + file + "'");
+ }
+ else
+ {
+ addError("Error writing file '" + file + "' in " + ff.getName()
+ + " format!");
+ isError = true;
+ continue;
+ }
+
+ }
+ }
+ return !isError;
+ }
+
+ private SequenceI getSpecifiedSequence(AlignFrame af, ArgValuesMap avm,
+ ArgValue av)
+ {
+ SubVals subVals = av.getSubVals();
+ ArgValue idAv = avm.getClosestNextArgValueOfArg(av, Arg.SEQID);
+ SequenceI seq = null;
+ if (subVals == null && idAv == null)
+ return null;
+ if (af == null || af.getCurrentView() == null)
+ {
+ return null;
+ }