/** Loads the modifications from the modification file. */
public void resetPtmFactory() {
// reset ptm factory
ptmFactory.reloadFactory();
ptmFactory = PTMFactory.getInstance();
try {
ptmFactory.importModifications(new File(resource, PeptideShaker.MODIFICATIONS_FILE), false);
} catch (Exception e) {
e.printStackTrace();
}
try {
ptmFactory.importModifications(
new File(resource, PeptideShaker.USER_MODIFICATIONS_FILE), true);
} catch (Exception e) {
e.printStackTrace();
}
}
/**
* Get the 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
* @param nTerm true if the modifications are n-terminal, false if c-terminal
* @return the terminal modifications as a string in the Tide format
*/
private String getTerminalModifications(
ArrayList<String> modifications, boolean fixed, boolean nTerm) {
String terminalModifications = "";
for (String ptmName : modifications) {
PTM ptm = ptmFactory.getPTM(ptmName);
if ((ptm.isNTerm() && nTerm) || (ptm.isCTerm() && !nTerm)) {
if (!terminalModifications.isEmpty()) {
terminalModifications += ",";
}
// add the number of allowed ptms per peptide
if (!fixed) {
terminalModifications += "1";
}
// add the residues affected
AminoAcidPattern ptmPattern = ptm.getPattern();
String tempPtmPattern = "";
if (ptmPattern != null && ptmPattern.length() > 0) {
for (Character aminoAcid : ptmPattern.getAminoAcidsAtTarget()) {
tempPtmPattern += aminoAcid;
}
}
if (tempPtmPattern.length() == 0) {
tempPtmPattern = "X";
}
terminalModifications += tempPtmPattern;
// add the ptm mass
if (ptm.getRoundedMass() > 0) {
terminalModifications += "+";
}
terminalModifications += ptm.getRoundedMass();
}
}
return terminalModifications;
}
/**
* Creates the Andromeda PTM file and saves the PTM indexes in the search parameters.
*
* @param andromedaFolder the Andromeda installation folder
* @param identificationParameters the identification parameters
* @param identificationParametersFile the file where to save the search parameters
* @throws IOException exception thrown whenever an error occurs while writing to the file.
* @throws java.lang.ClassNotFoundException exception thrown whenever an error occurred while
* saving the search parameters
*/
public static void createPtmFile(
File andromedaFolder,
IdentificationParameters identificationParameters,
File identificationParametersFile)
throws IOException, ClassNotFoundException {
File file = new File(andromedaFolder, "conf");
file = new File(file, "modifications.xml");
BufferedWriter bw = new BufferedWriter(new FileWriter(file));
int index = 0;
String date = "0001-01-01T00:00:00";
PTMFactory ptmFactory = PTMFactory.getInstance();
SearchParameters searchParameters = identificationParameters.getSearchParameters();
AndromedaParameters andromedaParameters =
(AndromedaParameters)
searchParameters.getIdentificationAlgorithmParameter(Advocate.andromeda.getIndex());
try {
bw.write("<?xml version=\"1.0\" encoding=\"utf-8\"?>");
bw.newLine();
bw.write(
"<modifications xmlns:xsd=\"http://www.w3.org/2001/XMLSchema\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\">");
bw.newLine();
// add the default ptms
for (String ptmName : ptmFactory.getDefaultModifications()) {
PTM ptm = ptmFactory.getPTM(ptmName);
writePtm(bw, date, ptm, index);
andromedaParameters.setPtmIndex(ptmName, index);
index++;
}
// add the user ptms
for (String ptmName : ptmFactory.getUserModifications()) {
PTM ptm = ptmFactory.getPTM(ptmName);
writePtm(bw, date, ptm, index);
andromedaParameters.setPtmIndex(ptmName, index);
index++;
}
bw.write("</modifications>");
bw.newLine();
} finally {
bw.close();
}
IdentificationParameters.saveIdentificationParameters(
identificationParameters, identificationParametersFile);
}
/**
* 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;
}
/**
* Calling this method will run the configured PeptideShaker process.
*
* @return returns 1 if the process was canceled
*/
public Object call() {
PathSettingsCLIInputBean pathSettingsCLIInputBean =
followUpCLIInputBean.getPathSettingsCLIInputBean();
if (pathSettingsCLIInputBean.getLogFolder() != null) {
redirectErrorStream(pathSettingsCLIInputBean.getLogFolder());
}
if (pathSettingsCLIInputBean.hasInput()) {
PathSettingsCLI pathSettingsCLI = new PathSettingsCLI(pathSettingsCLIInputBean);
pathSettingsCLI.setPathSettings();
} else {
try {
setPathConfiguration();
} catch (Exception e) {
System.out.println(
"An error occurred when the setting path configurations. Default paths will be used.");
e.printStackTrace();
}
}
setDbFolder(PeptideShaker.getMatchesFolder());
try {
ArrayList<PathKey> errorKeys = PeptideShakerPathPreferences.getErrorKeys();
if (!errorKeys.isEmpty()) {
System.out.println(
"Unable to write in the following configuration folders. Please use a temporary folder, "
+ "the path configuration command line, or edit the configuration paths from the graphical interface.");
for (PathKey pathKey : errorKeys) {
System.out.println(pathKey.getId() + ": " + pathKey.getDescription());
}
}
} catch (Exception e) {
System.out.println("Unable to load the path configurations. Default paths will be used.");
e.printStackTrace();
}
// Load user preferences
utilitiesUserPreferences = UtilitiesUserPreferences.loadUserPreferences();
// Instantiate factories
PeptideShaker.instantiateFacories(utilitiesUserPreferences);
ptmFactory = PTMFactory.getInstance();
enzymeFactory = EnzymeFactory.getInstance();
// Load resources files
loadSpecies();
waitingHandler = new WaitingHandlerCLIImpl();
String inputFilePath = null;
try {
if (followUpCLIInputBean.getZipFile() != null) {
inputFilePath = followUpCLIInputBean.getZipFile().getAbsolutePath();
loadCpsFromZipFile(
followUpCLIInputBean.getZipFile(), PeptideShaker.getMatchesFolder(), waitingHandler);
} else if (followUpCLIInputBean.getCpsFile() != null) {
inputFilePath = followUpCLIInputBean.getCpsFile().getAbsolutePath();
cpsFile = followUpCLIInputBean.getCpsFile();
loadCpsFile(PeptideShaker.getMatchesFolder(), waitingHandler);
} else {
waitingHandler.appendReport("PeptideShaker project input missing.", true, true);
return 1;
}
} catch (SQLException e) {
waitingHandler.appendReport(
"An error occurred while reading: "
+ inputFilePath
+ ". "
+ "It looks like another instance of PeptideShaker is still connected to the file. "
+ "Please close all instances of PeptideShaker and try again.",
true,
true);
e.printStackTrace();
} catch (Exception e) {
waitingHandler.appendReport(
"An error occurred while reading: " + inputFilePath + ".", true, true);
e.printStackTrace();
try {
PeptideShakerCLI.closePeptideShaker(identification);
} catch (Exception e2) {
waitingHandler.appendReport("An error occurred while closing PeptideShaker.", true, true);
e2.printStackTrace();
}
return 1;
}
// load fasta file
try {
if (!loadFastaFile(waitingHandler)) {
waitingHandler.appendReport(
"The FASTA file was not found. Please provide its location in the command line parameters.",
true,
true);
try {
PeptideShakerCLI.closePeptideShaker(identification);
} catch (Exception e2) {
waitingHandler.appendReport("An error occurred while closing PeptideShaker.", true, true);
e2.printStackTrace();
}
return 1;
}
waitingHandler.appendReport(
"Protein database "
+ identificationParameters
.getProteinInferencePreferences()
.getProteinSequenceDatabase()
.getName()
+ ".",
true,
true);
} catch (Exception e) {
waitingHandler.appendReport("An error occurred while loading the fasta file.", true, true);
e.printStackTrace();
try {
PeptideShakerCLI.closePeptideShaker(identification);
} catch (Exception e2) {
waitingHandler.appendReport("An error occurred while closing PeptideShaker.", true, true);
e2.printStackTrace();
}
return 1;
}
// load the spectrum files
try {
if (!loadSpectrumFiles(waitingHandler)) {
if (identification.getSpectrumFiles().size() > 1) {
waitingHandler.appendReport(
"The spectrum files were not found. Please provide their location in the command line parameters.",
true,
true);
} else {
waitingHandler.appendReport(
"The spectrum file was not found. Please provide its location in the command line parameters",
true,
true);
}
try {
PeptideShakerCLI.closePeptideShaker(identification);
} catch (Exception e2) {
waitingHandler.appendReport("An error occurred while closing PeptideShaker.", true, true);
e2.printStackTrace();
}
return 1;
}
} catch (Exception e) {
waitingHandler.appendReport(
"An error occurred while loading the spectrum file(s).", true, true);
e.printStackTrace();
try {
PeptideShakerCLI.closePeptideShaker(identification);
} catch (Exception e2) {
waitingHandler.appendReport("An error occurred while closing PeptideShaker.", true, true);
e2.printStackTrace();
}
return 1;
}
// Load project specific PTMs
String error =
PeptideShaker.loadModifications(getIdentificationParameters().getSearchParameters());
if (error != null) {
System.out.println(error);
}
// recalibrate spectra
if (followUpCLIInputBean.recalibrationNeeded()) {
try {
CLIExportMethods.recalibrateSpectra(
followUpCLIInputBean, identification, identificationParameters, waitingHandler);
waitingHandler.appendReport("Recalibration process completed.", true, true);
} catch (Exception e) {
waitingHandler.appendReport(
"An error occurred while recalibrating the spectra.", true, true);
e.printStackTrace();
waitingHandler.setRunCanceled();
}
}
// export spectra
if (followUpCLIInputBean.spectrumExportNeeded()) {
try {
CLIExportMethods.exportSpectra(
followUpCLIInputBean,
identification,
waitingHandler,
identificationParameters.getSequenceMatchingPreferences());
waitingHandler.appendReport("Spectrum export completed.", true, true);
} catch (Exception e) {
waitingHandler.appendReport("An error occurred while exporting the spectra.", true, true);
e.printStackTrace();
waitingHandler.setRunCanceled();
}
}
// export protein accessions
if (followUpCLIInputBean.accessionExportNeeded()) {
try {
CLIExportMethods.exportAccessions(
followUpCLIInputBean,
identification,
identificationFeaturesGenerator,
waitingHandler,
filterPreferences);
waitingHandler.appendReport("Protein accessions export completed.", true, true);
} catch (Exception e) {
waitingHandler.appendReport(
"An error occurred while exporting the protein accessions.", true, true);
e.printStackTrace();
waitingHandler.setRunCanceled();
}
}
// export protein details
if (followUpCLIInputBean.fastaExportNeeded()) {
try {
CLIExportMethods.exportFasta(
followUpCLIInputBean,
identification,
identificationFeaturesGenerator,
waitingHandler,
filterPreferences);
waitingHandler.appendReport("Protein details export completed.", true, true);
} catch (Exception e) {
waitingHandler.appendReport(
"An error occurred while exporting the protein details.", true, true);
e.printStackTrace();
waitingHandler.setRunCanceled();
}
}
// progenesis export
if (followUpCLIInputBean.progenesisExportNeeded()) {
try {
CLIExportMethods.exportProgenesis(
followUpCLIInputBean,
identification,
waitingHandler,
identificationParameters.getSequenceMatchingPreferences());
waitingHandler.appendReport("Progenesis export completed.", true, true);
} catch (Exception e) {
waitingHandler.appendReport(
"An error occurred while exporting the Progenesis file.", true, true);
e.printStackTrace();
waitingHandler.setRunCanceled();
}
}
// PepNovo training export
if (followUpCLIInputBean.pepnovoTrainingExportNeeded()) {
try {
CLIExportMethods.exportPepnovoTrainingFiles(
followUpCLIInputBean, identification, identificationParameters, waitingHandler);
waitingHandler.appendReport("PepNovo training export completed.", true, true);
} catch (Exception e) {
waitingHandler.appendReport(
"An error occurred while exporting the PepNovo training file.", true, true);
e.printStackTrace();
waitingHandler.setRunCanceled();
}
}
// inclusion list export
if (followUpCLIInputBean.inclusionListNeeded()) {
try {
CLIExportMethods.exportInclusionList(
followUpCLIInputBean,
identification,
identificationFeaturesGenerator,
identificationParameters.getSearchParameters(),
waitingHandler,
filterPreferences);
} catch (Exception e) {
waitingHandler.appendReport(
"An error occurred while generating the inclusion list.", true, true);
e.printStackTrace();
waitingHandler.setRunCanceled();
}
}
try {
PeptideShakerCLI.closePeptideShaker(identification);
} catch (Exception e2) {
waitingHandler.appendReport("An error occurred while closing PeptideShaker.", true, true);
e2.printStackTrace();
waitingHandler.setRunCanceled();
}
if (!waitingHandler.isRunCanceled()) {
waitingHandler.appendReport("Follow-up export completed.", true, true);
System.exit(
0); // @TODO: Find other ways of cancelling the process? If not cancelled searchgui will
// not stop.
// Note that if a different solution is found, the DummyFrame has to be closed similar to the
// setVisible method in the WelcomeDialog!!
return 0;
} else {
System.exit(
1); // @TODO: Find other ways of cancelling the process? If not cancelled searchgui will
// not stop.
// Note that if a different solution is found, the DummyFrame has to be closed similar to the
// setVisible method in the WelcomeDialog!!
return 1;
}
}
public class PSFileImporter {
private File currentPSFile;
private EnzymeFactory enzymeFactory = EnzymeFactory.getInstance();
private String resource;
/** The spectrum annotator. */
private SpectrumAnnotator spectrumAnnotator = new SpectrumAnnotator();
/** The project details. */
private ProjectDetails projectDetails = null;
/** The spectrum factory. */
private SpectrumFactory spectrumFactory = SpectrumFactory.getInstance(100);
/** The identification to display. */
private Identification identification;
/** The compomics PTM factory. */
private PTMFactory ptmFactory = PTMFactory.getInstance();
/** The parameters of the search. */
private SearchParameters searchParameters = new SearchParameters();
/** The initial processing preferences */
private ProcessingPreferences processingPreferences = new ProcessingPreferences();
/** The annotation preferences. */
private AnnotationPreferences annotationPreferences = new AnnotationPreferences();
/** The spectrum counting preferences. */
private SpectrumCountingPreferences spectrumCountingPreferences =
new SpectrumCountingPreferences();
/** The PTM scoring preferences */
private PTMScoringPreferences ptmScoringPreferences = new PTMScoringPreferences();
/** The identification filter used for this project. */
private IdFilter idFilter = new IdFilter();
/** The actually identified modifications. */
/**
* Returns the modifications found in this project.
*
* @return the modifications found in this project
*/
public ArrayList<String> getFoundModifications() {
if (identifiedModifications == null) {
identifiedModifications = new ArrayList<String>();
for (String peptideKey : identification.getPeptideIdentification()) {
boolean modified = false;
for (String modificationName : Peptide.getModificationFamily(peptideKey)) {
if (!identifiedModifications.contains(modificationName)) {
identifiedModifications.add(modificationName);
modified = true;
}
}
if (!modified && !identifiedModifications.contains(PtmPanel.NO_MODIFICATION)) {
identifiedModifications.add(PtmPanel.NO_MODIFICATION);
}
}
}
return identifiedModifications;
}
private ArrayList<String> identifiedModifications = null;
/** Metrics picked-up while loading the files. */
private Metrics metrics;
/** The display preferences. */
private DisplayPreferences displayPreferences = new DisplayPreferences();
/** The sequence factory. */
private SequenceFactory sequenceFactory = SequenceFactory.getInstance(30000);
/** The filter preferences. */
private FilterPreferences filterPreferences = new FilterPreferences();
/** The compomics experiment. */
private MsExperiment experiment = null;
/** The investigated sample. */
private Sample sample;
/** The replicate number. */
private int replicateNumber;
/** The class used to provide sexy features out of the identification. */
private IdentificationFeaturesGenerator identificationFeaturesGenerator;
/** The last folder opened by the user. Defaults to user.home. */
private String lastSelectedFolder = "user.home";
/** The object cache used for the identification database. */
private ObjectsCache objectsCache;
private com.compomics.util.experiment.ProteomicAnalysis proteomicAnalysis;
private ProgressDialogX progressDialog;
private javax.swing.JProgressBar jprog;
public PSFileImporter(javax.swing.JProgressBar jprog) {
this.progressDialog = new ProgressDialogX(false);
this.jprog = jprog;
}
public void importPeptideShakerFile(File aPsFile, final String resource) {
this.resource = resource;
this.currentPSFile = aPsFile;
loadGeneMapping();
loadEnzymes();
resetPtmFactory();
// setDefaultPreferences(); // @TODO: i tried re-adding this but then we get a null pointer, but
// the two below have to be added or the default neutral losses won't appear
IonFactory.getInstance().addDefaultNeutralLoss(NeutralLoss.H2O);
IonFactory.getInstance().addDefaultNeutralLoss(NeutralLoss.NH3);
// exceptionHandler = new ExceptionHandler(this);
new Thread("ProgressThread") {
@Override
public void run() {
jprog.setValue(10);
}
}.start();
Thread importThread =
new Thread("ImportThread") {
@Override
public void run() {
try {
// reset enzymes, ptms and preferences
loadEnzymes();
resetPtmFactory();
setDefaultPreferences();
try {
// close any open connection to an identification database
if (identification != null) {
identification.close();
}
} catch (Exception e) {
e.printStackTrace();
}
File experimentFile =
new File(
PeptideShaker.SERIALIZATION_DIRECTORY, PeptideShaker.experimentObjectName);
File matchFolder = new File(PeptideShaker.SERIALIZATION_DIRECTORY);
// empty the existing files in the matches folder
if (matchFolder.exists()) {
for (File file : matchFolder.listFiles()) {
if (file.isDirectory()) {
boolean deleted = Util.deleteDir(file);
if (!deleted) {
System.out.println("Failed to delete folder: " + file.getPath());
}
} else {
boolean deleted = file.delete();
if (!deleted) {
System.out.println("Failed to delete file: " + file.getPath());
}
}
}
}
final int BUFFER = 2048;
byte data[] = new byte[BUFFER];
FileInputStream fi = new FileInputStream(currentPSFile);
BufferedInputStream bis = new BufferedInputStream(fi, BUFFER);
try {
ArchiveInputStream tarInput =
new ArchiveStreamFactory().createArchiveInputStream(bis);
ArchiveEntry archiveEntry;
while ((archiveEntry = tarInput.getNextEntry()) != null) {
File destinationFile = new File(archiveEntry.getName());
File destinationFolder = destinationFile.getParentFile();
boolean destFolderExists = true;
if (!destinationFolder.exists()) {
destFolderExists = destinationFolder.mkdirs();
}
if (destFolderExists) {
FileOutputStream fos = new FileOutputStream(destinationFile);
BufferedOutputStream bos = new BufferedOutputStream(fos);
int count;
while ((count = tarInput.read(data, 0, BUFFER)) != -1
&& !progressDialog.isRunCanceled()) {
bos.write(data, 0, count);
}
bos.close();
fos.close();
// int progress = (int) (100 *
// tarInput.getBytesRead() / fileLength);
// progressDialog.setValue(progress);
} else {
System.out.println(
"Folder does not exist: \'"
+ destinationFolder.getAbsolutePath()
+ "\'. User preferences not saved.");
}
}
tarInput.close();
} catch (ArchiveException e) {
// Most likely an old project
experimentFile = currentPSFile;
e.printStackTrace();
}
fi.close();
bis.close();
fi.close();
MsExperiment tempExperiment = ExperimentIO.loadExperiment(experimentFile);
Sample tempSample = null;
PeptideShakerSettings experimentSettings = new PeptideShakerSettings();
if (tempExperiment.getUrParam(experimentSettings) instanceof PSSettings) {
// convert old settings files using utilities version 3.10.68 or older
// convert the old ProcessingPreferences object
PSSettings tempSettings =
(PSSettings) tempExperiment.getUrParam(experimentSettings);
ProcessingPreferences tempProcessingPreferences = new ProcessingPreferences();
tempProcessingPreferences.setProteinFDR(
tempSettings.getProcessingPreferences().getProteinFDR());
tempProcessingPreferences.setPeptideFDR(
tempSettings.getProcessingPreferences().getPeptideFDR());
tempProcessingPreferences.setPsmFDR(
tempSettings.getProcessingPreferences().getPsmFDR());
// convert the old PTMScoringPreferences object
PTMScoringPreferences tempPTMScoringPreferences = new PTMScoringPreferences();
tempPTMScoringPreferences.setaScoreCalculation(
tempSettings.getPTMScoringPreferences().aScoreCalculation());
tempPTMScoringPreferences.setaScoreNeutralLosses(
tempSettings.getPTMScoringPreferences().isaScoreNeutralLosses());
tempPTMScoringPreferences.setFlrThreshold(
tempSettings.getPTMScoringPreferences().getFlrThreshold());
// missing gene refrences
GenePreferences genePreferences = getGenePreferences();
// String selectedSpecies = genePreferences.getCurrentSpecies();
// String speciesDatabase =
// genePreferences.getEnsemblDatabaseName(selectedSpecies);
experimentSettings =
new PeptideShakerSettings(
tempSettings.getSearchParameters(),
tempSettings.getAnnotationPreferences(),
tempSettings.getSpectrumCountingPreferences(),
tempSettings.getProjectDetails(),
tempSettings.getFilterPreferences(),
tempSettings.getDisplayPreferences(),
tempSettings.getMetrics(),
tempProcessingPreferences,
tempSettings.getIdentificationFeaturesCache(),
tempPTMScoringPreferences,
genePreferences,
new IdFilter());
;
} else {
experimentSettings =
(PeptideShakerSettings) tempExperiment.getUrParam(experimentSettings);
}
idFilter = experimentSettings.getIdFilter();
setAnnotationPreferences(experimentSettings.getAnnotationPreferences());
setSpectrumCountingPreferences(experimentSettings.getSpectrumCountingPreferences());
setPtmScoringPreferences(experimentSettings.getPTMScoringPreferences());
setProjectDetails(experimentSettings.getProjectDetails());
setSearchParameters(experimentSettings.getSearchParameters());
setProcessingPreferences(experimentSettings.getProcessingPreferences());
setMetrics(experimentSettings.getMetrics());
setDisplayPreferences(experimentSettings.getDisplayPreferences());
if (experimentSettings.getFilterPreferences() != null) {
setFilterPreferences(experimentSettings.getFilterPreferences());
} else {
setFilterPreferences(new FilterPreferences());
}
if (experimentSettings.getDisplayPreferences() != null) {
setDisplayPreferences(experimentSettings.getDisplayPreferences());
displayPreferences.compatibilityCheck(searchParameters.getModificationProfile());
} else {
setDisplayPreferences(new DisplayPreferences());
displayPreferences.setDefaultSelection(searchParameters.getModificationProfile());
}
ArrayList<Sample> samples = new ArrayList(tempExperiment.getSamples().values());
if (samples.size() == 1) {
tempSample = samples.get(0);
} else {
tempSample = samples.get(0);
String[] sampleNames = new String[samples.size()];
for (int cpt = 0; cpt < sampleNames.length; cpt++) {
sampleNames[cpt] = samples.get(cpt).getReference();
System.out.println(sampleNames[cpt]);
}
SampleSelection sampleSelection =
new SampleSelection(null, true, sampleNames, "sample");
sampleSelection.setVisible(false);
String choice = sampleSelection.getChoice();
for (Sample sampleTemp : samples) {
if (sampleTemp.getReference().equals(choice)) {
tempSample = sampleTemp;
break;
}
}
}
ArrayList<Integer> replicates =
new ArrayList(tempExperiment.getAnalysisSet(tempSample).getReplicateNumberList());
System.out.println(replicates);
int tempReplicate;
if (replicates.size() == 1) {
tempReplicate = replicates.get(0);
} else {
String[] replicateNames = new String[replicates.size()];
for (int cpt = 0; cpt < replicateNames.length; cpt++) {
replicateNames[cpt] = samples.get(cpt).getReference();
}
SampleSelection sampleSelection =
new SampleSelection(null, true, replicateNames, "replicate");
sampleSelection.setVisible(false);
Integer choice = new Integer(sampleSelection.getChoice());
tempReplicate = 0;
}
setProject(tempExperiment, tempSample, tempReplicate);
identificationFeaturesGenerator =
new IdentificationFeaturesGenerator(
identification,
searchParameters,
idFilter,
metrics,
spectrumCountingPreferences);
if (experimentSettings.getIdentificationFeaturesCache() != null) {
identificationFeaturesGenerator.setIdentificationFeaturesCache(
experimentSettings.getIdentificationFeaturesCache());
}
// mainProgressDialog.setTitle("Loading FASTA File. Please
// Wait...");
try {
File providedFastaLocation =
experimentSettings.getSearchParameters().getFastaFile();
String fileName = providedFastaLocation.getName();
File projectFolder = currentPSFile.getParentFile();
File dataFolder = new File(projectFolder, "data");
// try to locate the FASTA file
if (providedFastaLocation.exists()) {
SequenceFactory.getInstance().loadFastaFile(providedFastaLocation);
} else if (new File(projectFolder, fileName).exists()) {
SequenceFactory.getInstance().loadFastaFile(new File(projectFolder, fileName));
experimentSettings
.getSearchParameters()
.setFastaFile(new File(projectFolder, fileName));
} else if (new File(dataFolder, fileName).exists()) {
SequenceFactory.getInstance().loadFastaFile(new File(dataFolder, fileName));
experimentSettings
.getSearchParameters()
.setFastaFile(new File(dataFolder, fileName));
} else {
// return error
System.out.println("fastafile is missing");
}
} catch (Exception e) {
e.printStackTrace();
System.out.println("fastafile is missing");
}
// mainProgressDialog.setTitle("Locating Spectrum Files. Please
// Wait...");
for (String spectrumFileName : identification.getSpectrumFiles()) {
try {
File providedSpectrumLocation = projectDetails.getSpectrumFile(spectrumFileName);
// try to locate the spectrum file
if (providedSpectrumLocation == null || !providedSpectrumLocation.exists()) {
File projectFolder = currentPSFile.getParentFile();
File fileInProjectFolder = new File(projectFolder, spectrumFileName);
File dataFolder = new File(projectFolder, "data");
File fileInDataFolder = new File(dataFolder, spectrumFileName);
File fileInLastSelectedFolder =
new File(getLastSelectedFolder(), spectrumFileName);
if (fileInProjectFolder.exists()) {
projectDetails.addSpectrumFile(fileInProjectFolder);
} else if (fileInDataFolder.exists()) {
projectDetails.addSpectrumFile(fileInDataFolder);
} else if (fileInLastSelectedFolder.exists()) {
projectDetails.addSpectrumFile(fileInLastSelectedFolder);
} else {
System.out.println("error no file");
}
}
} catch (Exception e) {
clearData(true);
// clearPreferences();
e.printStackTrace();
System.out.println("error no file");
return;
}
}
objectsCache = new ObjectsCache();
objectsCache.setAutomatedMemoryManagement(true);
if (identification.isDB()) {
try {
String dbFolder =
new File(resource, PeptideShaker.SERIALIZATION_DIRECTORY).getAbsolutePath();
identification.establishConnection(dbFolder, false, objectsCache);
} catch (Exception e) {
e.printStackTrace();
}
} else {
updateAnnotationPreferencesFromSearchSettings();
annotationPreferences.useAutomaticAnnotation(true);
}
int cpt = 1, nfiles = identification.getSpectrumFiles().size();
for (String fileName : identification.getSpectrumFiles()) {
// mainProgressDialog.setTitle("Importing Spectrum
// Files. Please Wait...");
try {
File mgfFile = projectDetails.getSpectrumFile(fileName);
spectrumFactory.addSpectra(mgfFile, progressDialog);
} catch (Exception e) {
clearData(true);
e.printStackTrace();
return;
}
}
boolean compatibilityIssue =
getSearchParameters().getIonSearched1() == null
|| getSearchParameters().getIonSearched2() == null;
if (compatibilityIssue) {
JOptionPane.showMessageDialog(
null,
"The annotation preferences for this project may have changed.\n\n"
+ "Note that PeptideShaker has substancially improved, we strongly\n"
+ "recommend reprocessing your identification files.",
"Annotation Preferences",
JOptionPane.INFORMATION_MESSAGE);
updateAnnotationPreferencesFromSearchSettings();
}
if (identification.getSpectrumIdentificationMap() == null) {
// 0.18 version, needs update of the spectrum mapping
identification.updateSpectrumMapping();
}
} catch (OutOfMemoryError error) {
System.out.println(
"Ran out of memory! (runtime.maxMemory(): "
+ Runtime.getRuntime().maxMemory()
+ ")");
Runtime.getRuntime().gc();
JOptionPane.showMessageDialog(
null,
"The task used up all the available memory and had to be stopped.\n"
+ "Memory boundaries are set in ../resources/conf/JavaOptions.txt.",
"Out Of Memory Error",
JOptionPane.ERROR_MESSAGE);
error.printStackTrace();
} catch (Exception exp) {
exp.printStackTrace();
}
}
};
importThread.setPriority(Thread.MAX_PRIORITY);
// importThread.start();
// while (importThread.isAlive()) {
// try {
// Thread.currentThread().sleep(100);
//
// } catch (Exception e) {
// e.printStackTrace();
// }
// }
ExecutorService es = Executors.newCachedThreadPool();
es.execute(importThread);
es.shutdown();
try {
boolean finshed = es.awaitTermination(1, TimeUnit.DAYS);
System.gc();
return;
// t.start();
} catch (InterruptedException ex) {
System.err.println(ex.getMessage());
// Logger.getLogger(UpdatedOutputGenerator.class.getName()).log(Level.SEVERE, null, ex);
}
System.gc();
// return;
}
/** Loads the enzymes from the enzyme file into the enzyme factory. */
private void loadEnzymes() {
try {
enzymeFactory.importEnzymes(new File(resource, PeptideShaker.ENZYME_FILE));
} catch (Exception e) {
System.out.println("Not able to load the enzyme file." + "Wrong enzyme file.");
e.printStackTrace();
}
}
/** Loads the modifications from the modification file. */
public void resetPtmFactory() {
// reset ptm factory
ptmFactory.reloadFactory();
ptmFactory = PTMFactory.getInstance();
try {
ptmFactory.importModifications(new File(resource, PeptideShaker.MODIFICATIONS_FILE), false);
} catch (Exception e) {
e.printStackTrace();
}
try {
ptmFactory.importModifications(
new File(resource, PeptideShaker.USER_MODIFICATIONS_FILE), true);
} catch (Exception e) {
e.printStackTrace();
}
}
/** Set the default preferences. */
private void setDefaultPreferences() {
searchParameters = new SearchParameters();
annotationPreferences.setAnnotationLevel(0.75);
annotationPreferences.useAutomaticAnnotation(true);
spectrumCountingPreferences.setSelectedMethod(SpectralCountingMethod.NSAF);
spectrumCountingPreferences.setValidatedHits(true);
IonFactory.getInstance().addDefaultNeutralLoss(NeutralLoss.NH3);
IonFactory.getInstance().addDefaultNeutralLoss(NeutralLoss.H2O);
processingPreferences = new ProcessingPreferences();
ptmScoringPreferences = new PTMScoringPreferences();
}
/** Imports the gene mapping. */
private void loadGeneMapping() {
try {
geneFactory.initialize(new File(resource, GENE_MAPPING_PATH), null);
} catch (Exception e) {
e.printStackTrace();
}
}
/** The path to the gene mapping file. */
private final String GENE_MAPPING_PATH = "/resources/conf/gene_ontology/gene_details_human";
/** The gene factory. */
private GeneFactory geneFactory = GeneFactory.getInstance();
/**
* Updates the new annotation preferences.
*
* @param annotationPreferences the new annotation preferences
*/
public void setAnnotationPreferences(AnnotationPreferences annotationPreferences) {
this.annotationPreferences = annotationPreferences;
}
/**
* Sets new spectrum counting preferences.
*
* @param spectrumCountingPreferences new spectrum counting preferences
*/
public void setSpectrumCountingPreferences(
SpectrumCountingPreferences spectrumCountingPreferences) {
this.spectrumCountingPreferences = spectrumCountingPreferences;
}
/**
* Sets the PTM scoring preferences
*
* @param ptmScoringPreferences the PTM scoring preferences
*/
public void setPtmScoringPreferences(PTMScoringPreferences ptmScoringPreferences) {
this.ptmScoringPreferences = ptmScoringPreferences;
}
/**
* Sets the project details.
*
* @param projectDetails the project details
*/
public void setProjectDetails(ProjectDetails projectDetails) {
this.projectDetails = projectDetails;
}
/**
* Updates the search parameters.
*
* @param searchParameters the new search parameters
*/
public void setSearchParameters(SearchParameters searchParameters) {
this.searchParameters = searchParameters;
PeptideShaker.loadModifications(searchParameters);
}
/**
* Sets the initial processing preferences.
*
* @param processingPreferences the initial processing preferences
*/
public void setProcessingPreferences(ProcessingPreferences processingPreferences) {
this.processingPreferences = processingPreferences;
}
/**
* Sets the metrics saved while loading the files.
*
* @param metrics the metrics saved while loading the files
*/
public void setMetrics(Metrics metrics) {
this.metrics = metrics;
}
/**
* Sets the display preferences to use.
*
* @param displayPreferences the display preferences to use
*/
public void setDisplayPreferences(DisplayPreferences displayPreferences) {
this.displayPreferences = displayPreferences;
}
/**
* Sets the gui filter preferences to use. .\
*
* @param filterPreferences the gui filter preferences to use
*/
public void setFilterPreferences(FilterPreferences filterPreferences) {
this.filterPreferences = filterPreferences;
}
/**
* This method sets the information of the project when opened.
*
* @param experiment the experiment conducted
* @param sample The sample analyzed
* @param replicateNumber The replicate number
*/
public void setProject(MsExperiment experiment, Sample sample, int replicateNumber) {
this.experiment = experiment;
this.sample = sample;
this.replicateNumber = replicateNumber;
ProteomicAnalysis proteomic_Analysis =
experiment.getAnalysisSet(sample).getProteomicAnalysis(replicateNumber);
identification = proteomic_Analysis.getIdentification(IdentificationMethod.MS2_IDENTIFICATION);
}
/**
* Returns the last selected folder.
*
* @return the last selected folder
*/
public String getLastSelectedFolder() {
return lastSelectedFolder;
}
/**
* Set the last selected folder.
*
* @param lastSelectedFolder the folder to set
*/
public void setLastSelectedFolder(String lastSelectedFolder) {
this.lastSelectedFolder = lastSelectedFolder;
}
/**
* Returns the identification displayed.
*
* @return the identification displayed
*/
public com.compomics.util.experiment.identification.Identification getIdentification() {
return identification;
}
/**
* Returns the identification features generator.
*
* @return the identification features generator
*/
public IdentificationFeaturesGenerator getIdentificationFeaturesGenerator() {
return identificationFeaturesGenerator;
}
/**
* Returns the search parameters.
*
* @return the search parameters
*/
public SearchParameters getSearchParameters() {
return searchParameters;
}
/**
* Return the display preferences to use.
*
* @return the display preferences to use
*/
public DisplayPreferences getDisplayPreferences() {
return displayPreferences;
}
public ArrayList<IonMatch> getIonsCurrentlyMatched() throws MzMLUnmarshallerException {
return spectrumAnnotator.getCurrentAnnotation(
annotationPreferences.getIonTypes(),
annotationPreferences.getNeutralLosses(),
annotationPreferences.getValidatedCharges());
}
public SpectrumAnnotator getSpectrumAnnorator() {
return spectrumAnnotator;
}
public void clearData(boolean clearDatabaseFolder) {
projectDetails = null;
spectrumAnnotator = new SpectrumAnnotator();
try {
spectrumFactory.closeFiles();
} catch (Exception e) {
e.printStackTrace();
}
try {
sequenceFactory.closeFile();
} catch (Exception e) {
e.printStackTrace();
}
try {
GOFactory.getInstance().closeFiles();
} catch (Exception e) {
e.printStackTrace();
}
try {
spectrumFactory.clearFactory();
} catch (Exception e) {
e.printStackTrace();
}
try {
sequenceFactory.clearFactory();
} catch (Exception e) {
e.printStackTrace();
}
try {
GOFactory.getInstance().clearFactory();
} catch (Exception e) {
e.printStackTrace();
}
identifiedModifications = null;
if (clearDatabaseFolder) {
clearDatabaseFolder();
}
resetFeatureGenerator();
// set up the tabs/panels
currentPSFile = null;
}
/** Resets the feature generator. */
public void resetFeatureGenerator() {
identificationFeaturesGenerator =
new IdentificationFeaturesGenerator(
identification, searchParameters, idFilter, metrics, spectrumCountingPreferences);
}
/** Clears the database folder. */
private void clearDatabaseFolder() {
boolean databaseClosed = true;
// close the database connection
if (identification != null) {
try {
identification.close();
identification = null;
} catch (SQLException e) {
databaseClosed = false;
e.printStackTrace();
JOptionPane.showMessageDialog(
null, "Failed to close the database.", "Database Error", JOptionPane.WARNING_MESSAGE);
}
}
// empty the matches folder
if (databaseClosed) {
File matchFolder = new File(resource, PeptideShaker.SERIALIZATION_DIRECTORY);
if (matchFolder.exists()) {
File[] tempFiles = matchFolder.listFiles();
if (tempFiles != null) {
for (File currentFile : tempFiles) {
Util.deleteDir(currentFile);
}
}
if (matchFolder.listFiles() != null && matchFolder.listFiles().length > 0) {
JOptionPane.showMessageDialog(
null,
"Failed to empty the database folder:\n" + matchFolder.getPath() + ".",
"Database Cleanup Failed",
JOptionPane.WARNING_MESSAGE);
}
}
}
}
/** Updates the ions used for fragment annotation. */
public void updateAnnotationPreferencesFromSearchSettings() {
annotationPreferences.setPreferencesFromSearchParamaers(searchParameters);
}
/**
* Returns the gene preferences.
*
* @return the gene preferences
*/
public GenePreferences getGenePreferences() {
return genePreferences;
}
private GenePreferences genePreferences = new GenePreferences();
/**
* Returns the experiment.
*
* @return the experiment
*/
public MsExperiment getExperiment() {
return experiment;
}
/*
* Returns the sample.
* @return the sample
*/
public Sample getSample() {
return sample;
}
/**
* Returns the replicate number.
*
* @return the replicateNumber
*/
public int getReplicateNumber() {
return this.replicateNumber;
}
/**
* Returns the desired spectrum.
*
* @param spectrumKey the key of the spectrum
* @return the desired spectrum
*/
public MSnSpectrum getSpectrum(String spectrumKey) {
String spectrumFile = Spectrum.getSpectrumFile(spectrumKey);
String spectrumTitle = Spectrum.getSpectrumTitle(spectrumKey);
try {
return (MSnSpectrum) spectrumFactory.getSpectrum(spectrumFile, spectrumTitle);
} catch (Exception e) {
System.out.println(e.getMessage());
return null;
}
}
}
/**
* Writes the lines corresponding to the given PTM name.
*
* @param writer the writer used to write
* @param mod the name of the modifications of interest
* @param variable a string (see static fields) indicating whether the modification is fixed or
* variable
* @throws IOException
*/
private static void writePtmLine(BufferedWriter writer, String mod, String variable)
throws IOException {
// Get the PTMFactory
PTMFactory ptmFactory = PTMFactory.getInstance();
PTM ptm = ptmFactory.getPTM(mod);
double ptmMass = ptm.getRoundedMass();
if (ptmMass > maxMassOffsetValue) {
String connector = "";
if (ptmMass > 0) {
connector = "+";
}
// Write a line for each residue
if (ptm.getPattern() == null || ptm.getPattern().getAminoAcidsAtTarget().isEmpty()) {
if (variable.equalsIgnoreCase(FIXED_PTM)) {
variable = VARIABLE_PTM; // PepNovo+ does not support fixed PTMs at the terminals...
}
if (ptmFactory.getPTM(mod).getType() == PTM.MODN
|| ptmFactory.getPTM(mod).getType() == PTM.MODNAA
|| ptmFactory.getPTM(mod).getType() == PTM.MODNP
|| ptmFactory.getPTM(mod).getType() == PTM.MODNPAA) {
writer.append("N_TERM" + SEP);
writer.append(ptmMass + SPACE);
writer.append(variable + SPACE);
writer.append("N_TERM" + SPACE);
writer.append("^" + connector + Long.toString(Math.round(ptmMass)) + SPACE);
modIdMap.put(ptm.getName(), "^" + connector + Long.toString(Math.round(ptmMass)));
writer.append(ptm.getName().toUpperCase());
writer.newLine();
} else if (ptmFactory.getPTM(mod).getType() == PTM.MODC
|| ptmFactory.getPTM(mod).getType() == PTM.MODCAA
|| ptmFactory.getPTM(mod).getType() == PTM.MODCP
|| ptmFactory.getPTM(mod).getType() == PTM.MODCPAA) {
writer.append("C_TERM" + SEP);
writer.append(ptmMass + SPACE);
writer.append(variable + SPACE);
writer.append("C_TERM" + SPACE);
writer.append("$" + connector + Long.toString(Math.round(ptmMass)) + SPACE);
modIdMap.put(ptm.getName(), "$" + connector + Long.toString(Math.round(ptmMass)));
writer.append(ptm.getName().toUpperCase());
writer.newLine();
}
} else {
for (Character residue : ptm.getPattern().getAminoAcidsAtTarget()) {
if (ptmFactory.getPTM(mod).getType() == PTM.MODN
|| ptmFactory.getPTM(mod).getType() == PTM.MODNAA
|| ptmFactory.getPTM(mod).getType() == PTM.MODNP
|| ptmFactory.getPTM(mod).getType() == PTM.MODNPAA) {
writer.append(residue + SEP);
writer.append(ptmMass + SPACE);
writer.append(variable + SPACE);
writer.append("+1" + SPACE);
writer.append(residue + connector + Long.toString(Math.round(ptmMass)) + SPACE);
modIdMap.put(ptm.getName(), residue + connector + Long.toString(Math.round(ptmMass)));
} else if (ptmFactory.getPTM(mod).getType() == PTM.MODC
|| ptmFactory.getPTM(mod).getType() == PTM.MODCAA
|| ptmFactory.getPTM(mod).getType() == PTM.MODCP
|| ptmFactory.getPTM(mod).getType() == PTM.MODCPAA) {
writer.append(residue + SEP);
writer.append(ptmMass + SPACE);
writer.append(variable + SPACE);
writer.append("-1" + SPACE);
writer.append(residue + connector + Long.toString(Math.round(ptmMass)) + SPACE);
modIdMap.put(ptm.getName(), residue + connector + Long.toString(Math.round(ptmMass)));
} else {
writer.append(residue + SEP);
writer.append(ptmMass + SPACE);
writer.append(variable + SPACE);
writer.append(ALL_LOCATIONS + SPACE);
writer.append(residue + connector + Long.toString(Math.round(ptmMass)) + SPACE);
modIdMap.put(ptm.getName(), residue + connector + Long.toString(Math.round(ptmMass)));
}
writer.append(ptm.getName().toUpperCase());
writer.newLine();
}
}
}
}
/** Fill the modification ID map. */
private static void fillModIdMap() {
// @TODO: is this method really needed anymore?
modIdMap = new HashMap<String, String>();
PTMFactory ptmFactory = PTMFactory.getInstance();
List<String> mods = new ArrayList<String>();
mods.addAll(ptmFactory.getDefaultModifications());
mods.addAll(ptmFactory.getUserModifications());
// Connector string: plus for positive modifications, minus for negative ones
String connector;
// Write the modifications
for (String mod : mods) {
PTM ptm = ptmFactory.getPTM(mod);
double ptmMass = ptm.getRoundedMass();
if (ptmMass > 0) {
connector = "+";
} else {
connector = "";
}
if (ptm.getPattern() == null || ptm.getPattern().getAminoAcidsAtTarget().isEmpty()) {
if (ptmFactory.getPTM(mod).getType() == PTM.MODN
|| ptmFactory.getPTM(mod).getType() == PTM.MODNAA
|| ptmFactory.getPTM(mod).getType() == PTM.MODNP
|| ptmFactory.getPTM(mod).getType() == PTM.MODNPAA) {
modIdMap.put(ptm.getName(), "^" + connector + Long.toString(Math.round(ptmMass)));
} else if (ptmFactory.getPTM(mod).getType() == PTM.MODC
|| ptmFactory.getPTM(mod).getType() == PTM.MODCAA
|| ptmFactory.getPTM(mod).getType() == PTM.MODCP
|| ptmFactory.getPTM(mod).getType() == PTM.MODCPAA) {
modIdMap.put(ptm.getName(), "$" + connector + Long.toString(Math.round(ptmMass)));
}
} else {
for (Character residue : ptmFactory.getPTM(mod).getPattern().getAminoAcidsAtTarget()) {
if (ptmFactory.getPTM(mod).getType() == PTM.MODN
|| ptmFactory.getPTM(mod).getType() == PTM.MODNAA
|| ptmFactory.getPTM(mod).getType() == PTM.MODNP
|| ptmFactory.getPTM(mod).getType() == PTM.MODNPAA) {
modIdMap.put(ptm.getName(), residue + connector + Long.toString(Math.round(ptmMass)));
} else if (ptmFactory.getPTM(mod).getType() == PTM.MODC
|| ptmFactory.getPTM(mod).getType() == PTM.MODCAA
|| ptmFactory.getPTM(mod).getType() == PTM.MODCP
|| ptmFactory.getPTM(mod).getType() == PTM.MODCPAA) {
modIdMap.put(ptm.getName(), residue + connector + Long.toString(Math.round(ptmMass)));
} else {
modIdMap.put(ptm.getName(), residue + connector + Long.toString(Math.round(ptmMass)));
}
}
}
}
}
/**
* ProcessBuilder for the Tide index generation.
*
* @author Harald Barsnes
*/
public class TideIndexProcessBuilder extends SearchGUIProcessBuilder {
/** The name of the Tide executable. */
public static final String EXECUTABLE_FILE_NAME = "crux";
/** The FASTA file. */
private File fastaFile;
/** The search parameters. */
private SearchParameters searchParameters;
/** The advanced Tide parameters. */
private TideParameters tideParameters;
/** The compomics PTM factory. */
private PTMFactory ptmFactory = PTMFactory.getInstance();
/**
* 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);
}
/**
* Returns a string with the non-terminal modifications as a string in the Tide format.
*
* @return the non-terminal modifications as a string in the Tide format.
*/
private String getNonTerminalModifications() {
String tempFixedNonTerminalModifications =
getNonTerminalModifications(
searchParameters.getPtmSettings().getFixedModifications(), true);
String tempVariableNonTerminalModifications =
getNonTerminalModifications(
searchParameters.getPtmSettings().getVariableModifications(), false);
if (!tempFixedNonTerminalModifications.isEmpty()
&& !tempVariableNonTerminalModifications.isEmpty()) {
tempFixedNonTerminalModifications += "," + tempVariableNonTerminalModifications;
} else if (!tempVariableNonTerminalModifications.isEmpty()) {
return tempVariableNonTerminalModifications;
}
return tempFixedNonTerminalModifications;
}
/**
* 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;
}
/**
* Returns a string with the terminal modifications as a string in the Tide format.
*
* @param nTerm true if the modifications are n-terminal, false if c-terminal
* @return the terminal modifications as a string in the Tide format.
*/
private String getTerminalModifications(boolean nTerm) {
String tempNTermModifications =
getTerminalModifications(
searchParameters.getPtmSettings().getFixedModifications(), true, nTerm);
String tempCTermModifications =
getTerminalModifications(
searchParameters.getPtmSettings().getVariableModifications(), false, nTerm);
if (!tempNTermModifications.isEmpty() && !tempCTermModifications.isEmpty()) {
tempNTermModifications += "," + tempCTermModifications;
} else if (!tempCTermModifications.isEmpty()) {
return tempCTermModifications;
}
return tempNTermModifications;
}
/**
* Get the 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
* @param nTerm true if the modifications are n-terminal, false if c-terminal
* @return the terminal modifications as a string in the Tide format
*/
private String getTerminalModifications(
ArrayList<String> modifications, boolean fixed, boolean nTerm) {
String terminalModifications = "";
for (String ptmName : modifications) {
PTM ptm = ptmFactory.getPTM(ptmName);
if ((ptm.isNTerm() && nTerm) || (ptm.isCTerm() && !nTerm)) {
if (!terminalModifications.isEmpty()) {
terminalModifications += ",";
}
// add the number of allowed ptms per peptide
if (!fixed) {
terminalModifications += "1";
}
// add the residues affected
AminoAcidPattern ptmPattern = ptm.getPattern();
String tempPtmPattern = "";
if (ptmPattern != null && ptmPattern.length() > 0) {
for (Character aminoAcid : ptmPattern.getAminoAcidsAtTarget()) {
tempPtmPattern += aminoAcid;
}
}
if (tempPtmPattern.length() == 0) {
tempPtmPattern = "X";
}
terminalModifications += tempPtmPattern;
// add the ptm mass
if (ptm.getRoundedMass() > 0) {
terminalModifications += "+";
}
terminalModifications += ptm.getRoundedMass();
}
}
return terminalModifications;
}
@Override
public String getType() {
return "Tide Indexing Process";
}
@Override
public String getCurrentlyProcessedFileName() {
return fastaFile.getName();
}
}
