private List<String> constructArguments()
throws IOException, XMLStreamException, URISyntaxException, UnspecifiedPladipusException {
File peptideShakerJar = getJar();
ArrayList<String> cmdArgs = new ArrayList<>();
cmdArgs.add("java");
cmdArgs.add("-Xmx" + MemoryWarningSystem.getAllowedRam() + "M");
cmdArgs.add("-cp");
cmdArgs.add(peptideShakerJar.getAbsolutePath());
cmdArgs.add("eu.isas.peptideshaker.cmd.PeptideShakerCLI");
// check if folder exists
File outputFolder = new File(parameters.get("output_folder"));
outputFolder.mkdirs();
// check if reports are requested
if (parameters.containsKey("reports")) {
File outputReportFolder = new File(outputFolder, "reports");
if (outputReportFolder.mkdirs()) {
parameters.put("out_reports", outputReportFolder.getAbsolutePath());
}
}
for (AllowedPeptideShakerParams aParameter : AllowedPeptideShakerParams.values()) {
if (parameters.containsKey(aParameter.getId())) {
cmdArgs.add("-" + aParameter.getId());
cmdArgs.add(parameters.get(aParameter.getId()));
} else if (aParameter.isMandatory()) {
throw new IllegalArgumentException("Missing mandatory parameter : " + aParameter.id);
}
}
// check if spectra need to be exported
if (parameters.containsKey("spectrum_folder")) {
File exportFolder = new File(parameters.get("spectrum_folder"));
exportFolder.mkdirs();
}
// also add these for other possible CLI's?
for (AllowedPeptideShakerFollowUpParams aParameter :
AllowedPeptideShakerFollowUpParams.values()) {
if (parameters.containsKey(aParameter.getId())) {
cmdArgs.add("-" + aParameter.getId());
cmdArgs.add(parameters.get(aParameter.getId()));
}
}
for (Map.Entry<String, String> aParameter : parameters.entrySet()) {
cmdArgs.add("-" + aParameter.getKey());
cmdArgs.add(parameters.get(aParameter.getValue()));
}
return cmdArgs;
}
