/**
* Create the parameters file.
*
* @param searchParametersFile the file where to save the search parameters
* @return the parameters file
* @throws IOException exception thrown whenever an error occurred while writing the configuration
* file
*/
private File createParametersFile(File searchParametersFile) throws IOException {
File andromedaTempFolder = new File(andromedaTempFolderPath);
String fileName;
try {
fileName = Util.removeExtension(searchParametersFile.getName()) + ".apar";
} catch (Exception e) {
fileName = "SearchGUI.apar";
}
File parameterFile = new File(andromedaTempFolder, fileName);
BufferedWriter bw = new BufferedWriter(new FileWriter(parameterFile));
try {
boolean semiSpecific = false;
DigestionPreferences digestionPreferences = searchParameters.getDigestionPreferences();
if (digestionPreferences.getCleavagePreference()
== DigestionPreferences.CleavagePreference.enzyme) {
Enzyme enzyme = digestionPreferences.getEnzymes().get(0);
String enzymeName = enzyme.getName();
bw.write("enzymes=" + enzymeName); // @TODO: support multiple enzymes?
bw.newLine();
if (digestionPreferences.getSpecificity(enzyme.getName())
== DigestionPreferences.Specificity.semiSpecific
|| digestionPreferences.getSpecificity(enzyme.getName())
== DigestionPreferences.Specificity.specificCTermOnly
|| digestionPreferences.getSpecificity(enzyme.getName())
== DigestionPreferences.Specificity.specificNTermOnly) {
semiSpecific = true;
}
} else if (digestionPreferences.getCleavagePreference()
== DigestionPreferences.CleavagePreference.unSpecific) {
bw.write("enzyme mode=unspecific");
bw.newLine();
} else {
// whole enzyme
// @TODO: what to put here..?
}
if (semiSpecific) {
bw.write("enzyme mode=semispecific"); // @TODO: support: Semispecific Free N-terminus and
// Semispecific Free C-terminus
} else {
bw.write("enzyme mode=specific");
}
bw.newLine();
PtmSettings modificationProfile = searchParameters.getPtmSettings();
StringBuilder list = new StringBuilder();
for (String ptmName : modificationProfile.getVariableModifications()) {
if (list.length() > 0) {
list.append(",");
}
list.append(ptmName);
}
bw.write("variable modifications=" + list);
bw.newLine();
list = new StringBuilder();
for (String ptmName : modificationProfile.getFixedModifications()) {
if (list.length() > 0) {
list.append(",");
}
list.append(ptmName);
}
bw.write("fixed modifications=" + list);
bw.newLine();
bw.write("label modifications="); // @TODO: support labels
bw.newLine();
if (!modificationProfile.getRefinementVariableModifications().isEmpty()) {
bw.write("has additional variable modifications=True");
bw.newLine();
list = new StringBuilder();
for (String ptmName : modificationProfile.getRefinementVariableModifications()) {
if (list.length() > 0) {
list.append(",");
}
list.append(ptmName);
}
bw.write("additional variable modifications=" + list);
bw.newLine();
bw.write("additional variable modification proteins=");
bw.newLine();
} else {
bw.write("has additional variable modifications=False");
bw.newLine();
bw.write("additional variable modifications=");
bw.newLine();
bw.write("additional variable modification proteins=");
bw.newLine();
}
bw.write("peptide mass tolerance=" + searchParameters.getPrecursorAccuracy());
bw.newLine();
bw.write("max peptide mass=" + andromedaParameters.getMaxPeptideMass());
bw.newLine();
bw.write("max combinations=" + andromedaParameters.getMaxCombinations());
bw.newLine();
if (searchParameters.isPrecursorAccuracyTypePpm()) {
bw.write("peptide mass tolerance Unit=ppm");
} else {
bw.write("peptide mass tolerance Unit=Da");
}
bw.newLine();
bw.write("fragment mass tolerance=" + searchParameters.getFragmentIonAccuracy());
bw.newLine();
if (searchParameters.getFragmentAccuracyType() == SearchParameters.MassAccuracyType.PPM) {
bw.write("fragment mass tolerance Unit=ppm");
} else {
bw.write("fragment mass tolerance Unit=Da");
}
bw.newLine();
bw.write("top peaks=" + andromedaParameters.getTopPeaks());
bw.newLine();
bw.write("top peaks window=" + andromedaParameters.getTopPeaksWindow());
bw.newLine();
if (digestionPreferences.getCleavagePreference()
== DigestionPreferences.CleavagePreference.enzyme) {
Integer missedCleavages = null;
for (Enzyme enzyme : digestionPreferences.getEnzymes()) {
int enzymeMissedCleavages = digestionPreferences.getnMissedCleavages(enzyme.getName());
if (missedCleavages == null || enzymeMissedCleavages > missedCleavages) {
missedCleavages = enzymeMissedCleavages;
}
}
bw.write("max missed cleavages=" + missedCleavages);
bw.newLine();
}
bw.write("fasta file=\"" + searchParameters.getFastaFile().getAbsolutePath() + "\"");
bw.newLine();
bw.write("decoy mode=" + andromedaParameters.getDecoyMode());
bw.newLine();
bw.write("include contaminants=False");
bw.newLine();
if (andromedaParameters.isIncludeWater()) {
bw.write("include water=True");
} else {
bw.write("include water=False");
}
bw.newLine();
if (andromedaParameters.isIncludeAmmonia()) {
bw.write("include ammonia=True");
} else {
bw.write("include ammonia=False");
}
bw.newLine();
if (andromedaParameters.isDependentLosses()) {
bw.write("dependent losses=True");
} else {
bw.write("dependent losses=False");
}
bw.newLine();
bw.write("special aas=");
bw.newLine();
if (andromedaParameters.isFragmentAll()) {
bw.write("fragment all=True");
} else {
bw.write("fragment all=False");
}
bw.newLine();
if (andromedaParameters.isEmpiricalCorrection()) {
bw.write("empirical correction=True");
} else {
bw.write("empirical correction=False");
}
bw.newLine();
if (andromedaParameters.isHigherCharge()) {
bw.write("higher charges=True");
} else {
bw.write("higher charges=False");
}
bw.newLine();
bw.write("fragmentation type=" + andromedaParameters.getFragmentationMethod().name);
bw.newLine();
bw.write("max number of modifications=" + andromedaParameters.getMaxNumberOfModifications());
bw.newLine();
bw.write("min peptide length no enzyme=" + andromedaParameters.getMinPeptideLengthNoEnzyme());
bw.newLine();
bw.write("max peptide length no enzyme=" + andromedaParameters.getMaxPeptideLengthNoEnzyme());
bw.newLine();
if (andromedaParameters.isEqualIL()) {
bw.write("equal il=True");
} else {
bw.write("equal il=False");
}
bw.newLine();
bw.write("number of candidates=" + andromedaParameters.getNumberOfCandidates());
bw.newLine();
} finally {
bw.close();
}
return parameterFile;
}
/**
* Creates the enzyme configuration file.
*
* @param andromedaFolder the Andromeda installation folder
* @throws IOException exception thrown whenever an error occurred while writing the file.
*/
public static void createEnzymesFile(File andromedaFolder) throws IOException {
EnzymeFactory enzymeFactory = EnzymeFactory.getInstance();
File file = new File(andromedaFolder, "conf");
file = new File(file, "enzymes.xml");
BufferedWriter bw = new BufferedWriter(new FileWriter(file));
int index = 0;
String date = "0001-01-01T00:00:00";
try {
bw.write("<?xml version=\"1.0\" encoding=\"utf-8\"?>");
bw.newLine();
bw.write(
"<enzymes xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xmlns:xsd=\"http://www.w3.org/2001/XMLSchema\">");
bw.newLine();
for (Enzyme enzyme : enzymeFactory.getEnzymes()) {
bw.write(
" <enzyme index=\""
+ index
+ "\" title=\""
+ enzyme.getName()
+ "\" description=\""
+ enzyme.getDescription()
+ "\" create_date=\""
+ date
+ "\" last_modified_date=\""
+ date
+ "\" user=\"SearchGUI\">");
bw.newLine();
bw.write(" <specificity>");
bw.newLine();
ArrayList<Character> aaBefore = new ArrayList<Character>(enzyme.getAminoAcidBefore());
if (aaBefore.isEmpty()) {
for (char aa : AminoAcid.getUniqueAminoAcids()) {
aaBefore.add(aa);
}
}
ArrayList<Character> aaAfter = new ArrayList<Character>(enzyme.getAminoAcidAfter());
if (aaAfter.isEmpty()) {
for (char aa : AminoAcid.getUniqueAminoAcids()) {
aaAfter.add(aa);
}
}
for (Character aa1 : aaBefore) {
for (Character aa2 : aaAfter) {
if (!enzyme.getRestrictionBefore().contains(aa1)
&& !enzyme.getRestrictionAfter().contains(aa2)) {
bw.write(" <string>" + aa1 + aa2 + "</string>");
bw.newLine();
}
}
}
bw.write(" </specificity>");
bw.newLine();
bw.write(" </enzyme>");
bw.newLine();
index++;
}
bw.write("</enzymes>");
bw.newLine();
} finally {
bw.close();
}
}