/*.................................................................................................................*/
void getArguments(
MultipartEntityBuilder builder,
StringBuffer sb,
String fileName,
String LOCproteinModel,
String LOCdnaModel,
String LOCotherOptions,
int LOCbootstrapreps,
int LOCbootstrapSeed,
int LOCnumRuns,
String LOCoutgroupTaxSetString,
String LOCMultipleModelFile,
boolean preflight) {
if (builder == null) return;
/*
if (preflight)
arguments += " -n preflight.out ";
else
arguments += " -s " + fileName + " -n file.out ";
*/
if (isProtein) {
if (StringUtil.blank(LOCproteinModel))
addArgument(builder, sb, "vparam.protein_opts_", "PROTGAMMAJTT");
else addArgument(builder, sb, "vparam.protein_opts_", LOCproteinModel);
} else if (StringUtil.blank(LOCdnaModel))
addArgument(builder, sb, "vparam.dna_gtrcat_", "GTRGAMMA");
else addArgument(builder, sb, "vparam.dna_gtrcat_", "GTRGAMMA");
// builder.addTextBody("vparam.dna_gtrcat_",LOCdnaModel);
/*
if (StringUtil.notEmpty(LOCMultipleModelFile))
arguments += " -q " + ShellScriptUtil.protectForShellScript(LOCMultipleModelFile);
if (!StringUtil.blank(LOCotherOptions))
arguments += " " + LOCotherOptions;
*/
addArgument(builder, sb, "vparam.provide_parsimony_seed_", "1");
addArgument(builder, sb, "vparam.parsimony_seed_val_", "" + randomIntSeed);
if (bootstrapOrJackknife()) {
if (LOCbootstrapreps > 0) {
addArgument(builder, sb, "vparam.choose_bootstrap_", "b");
addArgument(builder, sb, "vparam.bootstrap_value_", "" + LOCbootstrapreps);
addArgument(builder, sb, "vparam.seed_value_", "" + LOCbootstrapSeed);
// addArgument(builder, sb, "vparam.bootstrap_",""+LOCbootstrapreps);
// addArgument(builder, sb, "vparam.mulparambootstrap_seed_",""+LOCbootstrapSeed);
} else Debugg.println("TOO FEW BOOTSTRAP REPS");
} else {
addArgument(builder, sb, "vparam.specify_runs_", "1");
addArgument(builder, sb, "vparam.altrun_number_", "" + LOCnumRuns);
// if (RAxML814orLater)
// addArgument(builder, sb, "vparam.mesquite_output_","1");
}
TaxaSelectionSet outgroupSet = null;
if (!StringUtil.blank(LOCoutgroupTaxSetString)) {
outgroupSet =
(TaxaSelectionSet) taxa.getSpecsSet(LOCoutgroupTaxSetString, TaxaSelectionSet.class);
if (outgroupSet != null)
addArgument(builder, sb, "vparam.outgroup_", outgroupSet.getStringList(",", true));
arguments += " -o " + outgroupSet.getStringList(",", true);
}
}
