/**
* Get the non-terminal modifications as a string in the Tide format.
*
* @param modifications the modifications to check
* @param fixed if the modifications are to to be added as fixed or variable
* @return the non-terminal modifications as a string in the Tide forma
*/
private String getNonTerminalModifications(ArrayList<String> modifications, boolean fixed) {
// tide ptm pattern: [max_per_peptide]residues[+/-]mass_change
String nonTerminalModifications = "";
for (String ptmName : modifications) {
PTM ptm = ptmFactory.getPTM(ptmName);
if (!ptm.isNTerm() && !ptm.isCTerm()) {
if (!nonTerminalModifications.isEmpty()) {
nonTerminalModifications += ",";
}
// add the number of allowed ptms per peptide
if (!fixed) {
nonTerminalModifications +=
tideParameters
.getMaxVariablePtmsPerTypePerPeptide(); // @TODO: make this modification specific?
}
// add the residues affected
AminoAcidPattern ptmPattern = ptm.getPattern();
if (ptmPattern != null && ptmPattern.length() > 0) {
for (Character aminoAcid : ptmPattern.getAminoAcidsAtTarget()) {
nonTerminalModifications += aminoAcid;
}
}
// add the ptm mass
if (ptm.getRoundedMass() > 0) {
nonTerminalModifications += "+";
}
nonTerminalModifications += ptm.getRoundedMass();
}
}
return nonTerminalModifications;
}
/**
* Constructor.
*
* @param tideFolder the Tide folder
* @param searchParameters the search parameters
* @param waitingHandler the waiting handler
* @throws IOException thrown of there are problems creating the Tide parameter file
*/
public TideIndexProcessBuilder(
File tideFolder, SearchParameters searchParameters, WaitingHandler waitingHandler)
throws IOException {
this.waitingHandler = waitingHandler;
this.searchParameters = searchParameters;
tideParameters =
(TideParameters)
searchParameters.getIdentificationAlgorithmParameter(Advocate.tide.getIndex());
this.fastaFile = searchParameters.getFastaFile();
// make sure that the tide file is executable
File tide = new File(tideFolder.getAbsolutePath() + File.separator + EXECUTABLE_FILE_NAME);
tide.setExecutable(true);
// full path to executable
process_name_array.add(tide.getAbsolutePath());
process_name_array.add("tide-index");
// add the fasta file
process_name_array.add(searchParameters.getFastaFile().getAbsolutePath());
// the name of the index file
process_name_array.add(
tideParameters.getFastIndexFolderName()); // @TODO: put in the user temp folder instead?
// overwrite existing files
process_name_array.add("--overwrite");
process_name_array.add("T");
// add the modifications
String nonTerminalMods = getNonTerminalModifications();
if (!nonTerminalMods.isEmpty()) {
process_name_array.add("--mods-spec");
process_name_array.add(getNonTerminalModifications());
}
String nTermMods = getTerminalModifications(true);
if (!nTermMods.isEmpty()) {
process_name_array.add("--nterm-peptide-mods-spec");
process_name_array.add(nTermMods);
}
String cTermMods = getTerminalModifications(false);
if (!cTermMods.isEmpty()) {
process_name_array.add("--cterm-peptide-mods-spec");
process_name_array.add(cTermMods);
}
// the max number of modifications per peptide
if (tideParameters.getMaxVariablePtmsPerPeptide() != null) {
process_name_array.add("--max-mods");
process_name_array.add(tideParameters.getMaxVariablePtmsPerPeptide().toString());
}
// the decoy format
process_name_array.add("--decoy-format");
process_name_array.add(tideParameters.getDecoyFormat());
if (!tideParameters.getDecoyFormat().equalsIgnoreCase("none")) {
process_name_array.add("--keep-terminal-aminos");
process_name_array.add(tideParameters.getKeepTerminalAminoAcids());
process_name_array.add("--seed");
process_name_array.add(tideParameters.getDecoySeed().toString());
}
// missed cleavages
process_name_array.add("--missed-cleavages");
process_name_array.add("" + searchParameters.getnMissedCleavages());
// set the output directory
process_name_array.add("--output-dir");
process_name_array.add(tideParameters.getOutputFolderName());
// create peptide list
process_name_array.add("--peptide-list");
if (tideParameters.getPrintPeptides()) {
process_name_array.add("T");
} else {
process_name_array.add("F");
}
// use parameter file
// process_name_array.add("--parameter-file");
// process_name_array.add("a file"); // @TODO: implement?
//
// output verbosity
process_name_array.add("--verbosity");
process_name_array.add("" + tideParameters.getVerbosity());
// peptide lengths
process_name_array.add("--min-length");
process_name_array.add(tideParameters.getMinPeptideLength().toString());
process_name_array.add("--max-length");
process_name_array.add(tideParameters.getMaxPeptideLength().toString());
// peptide masses
process_name_array.add("--min-mass");
process_name_array.add(tideParameters.getMinPrecursorMass().toString());
process_name_array.add("--max-mass");
process_name_array.add(tideParameters.getMaxPrecursorMass().toString());
// monoisotopic precursor mass
process_name_array.add("--monoisotopic-precursor");
if (tideParameters.getMonoisotopicPrecursor()) {
process_name_array.add("T");
} else {
process_name_array.add("F");
}
// include starting peptide both with and without the initial m
process_name_array.add("--clip-nterm-methionine");
if (tideParameters.getClipNtermMethionine()) {
process_name_array.add("T");
} else {
process_name_array.add("F");
}
// enzyme
// note: Tide enzymes not supported:
// elastase ([ALIV]|{P}), clostripain ([R]|[]), iodosobenzoate ([W]|[]),
// proline-endopeptidase ([P]|[]),
// staph-protease ([E]|[]), pepsin-a ([FL]|{P}), elastase-trypsin-chymotrypsin
// ([ALIVKRWFY]|{P})
if (searchParameters.getEnzyme().getName().equals("Trypsin")) {
process_name_array.add("--enzyme");
process_name_array.add("trypsin");
} else if (searchParameters.getEnzyme().getName().equals("Trypsin, no P rule")) {
process_name_array.add("--enzyme");
process_name_array.add("trypsin/p");
} else if (searchParameters.getEnzyme().getName().equals("Chymotrypsin (FYWL)")) {
process_name_array.add("--enzyme");
process_name_array.add("chymotrypsin");
} else if (searchParameters.getEnzyme().getName().equals("CNBr")) {
process_name_array.add("--enzyme");
process_name_array.add("cyanogen-bromide");
} else if (searchParameters.getEnzyme().getName().equals("Asp-N")) {
process_name_array.add("--enzyme");
process_name_array.add("asp-n");
} else if (searchParameters.getEnzyme().getName().equals("Lys-C")) {
process_name_array.add("--enzyme");
process_name_array.add("lys-c");
} else if (searchParameters.getEnzyme().getName().equals("Lys-N (K)")) {
process_name_array.add("--enzyme");
process_name_array.add("lys-n");
} else if (searchParameters.getEnzyme().getName().equals("Arg-C")) {
process_name_array.add("--enzyme");
process_name_array.add("arg-c");
} else if (searchParameters.getEnzyme().getName().equals("Glu-C (DE)")) {
process_name_array.add("--enzyme");
process_name_array.add("glu-c");
} else if (searchParameters.getEnzyme().getName().equals("Unspecific")) {
process_name_array.add("--enzyme");
process_name_array.add("no-enzyme");
} else {
process_name_array.add("--custom-enzyme");
process_name_array.add(searchParameters.getEnzyme().getXTandemFormat());
}
// full or partial enzyme digestion
process_name_array.add("--digestion");
process_name_array.add(tideParameters.getDigestionType());
process_name_array.trimToSize();
// print the command to the log file
System.out.println(
System.getProperty("line.separator")
+ System.getProperty("line.separator")
+ "tide index command: ");
for (Object currentElement : process_name_array) {
System.out.print(currentElement + " ");
}
System.out.println(System.getProperty("line.separator"));
pb = new ProcessBuilder(process_name_array);
pb.directory(tideFolder);
// set error out and std out to same stream
pb.redirectErrorStream(true);
}