Example 1 with WaitingDialog
use of com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog in project peptide-shaker by compomics.
the class PeptideShakerCLI method call.
@Override
public Object call() {
try {
// set up the waiting handler
if (cliInputBean.isGUI()) {
// set the look and feel
try {
UtilitiesGUIDefaults.setLookAndFeel();
} catch (Exception e) {
// ignore, use default look and feel
}
ArrayList<String> tips;
try {
tips = Tips.getTips();
} catch (Exception e) {
tips = new ArrayList<>();
// do something here?
}
waitingHandler = new WaitingDialog(new DummyFrame("PeptideShaker " + PeptideShaker.getVersion(), "/icons/peptide-shaker.gif"), Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/peptide-shaker.gif")), Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/peptide-shaker-orange.gif")), false, tips, "Importing Data", "PeptideShaker", PeptideShaker.getVersion(), true);
((WaitingDialog) waitingHandler).setCloseDialogWhenImportCompletes(false, false);
((WaitingDialog) waitingHandler).setLocationRelativeTo(null);
Point tempLocation = ((WaitingDialog) waitingHandler).getLocation();
((WaitingDialog) waitingHandler).setLocation((int) tempLocation.getX() + 30, (int) tempLocation.getY() + 30);
new Thread(new Runnable() {
public void run() {
try {
((WaitingDialog) waitingHandler).setVisible(true);
} catch (IndexOutOfBoundsException e) {
// ignore
}
}
}, "ProgressDialog").start();
} else {
waitingHandler = new WaitingHandlerCLIImpl();
}
// @TODO: improve the primary progress display?
int progressCounter = cliInputBean.getIdFiles().size() + cliInputBean.getSpectrumFiles().size();
// establishing the database connection
progressCounter++;
// the FASTA file
progressCounter++;
// the peptide to protein map
progressCounter++;
// computing probabilities etc
progressCounter += 6;
// simplify protein groups
progressCounter++;
// resolving protein inference
progressCounter++;
// correcting protein probabilities, Validating identifications at 1% FDR, Scoring PTMs in peptides, Scoring PTMs in proteins.
progressCounter += 4;
// scoring PTMs in PSMs. Estimating PTM FLR.
progressCounter += 2;
// peptide inference
progressCounter++;
// project zipping
if (cliInputBean.getZipExport() != null) {
progressCounter++;
}
// add one more just to not start at 0%
progressCounter++;
waitingHandler.setMaxPrimaryProgressCounter(progressCounter);
// just to not start at 0%
waitingHandler.increasePrimaryProgressCounter();
// turn off illegal access log messages
try {
Class loggerClass = Class.forName("jdk.internal.module.IllegalAccessLogger");
Field loggerField = loggerClass.getDeclaredField("logger");
Class unsafeClass = Class.forName("sun.misc.Unsafe");
Field unsafeField = unsafeClass.getDeclaredField("theUnsafe");
unsafeField.setAccessible(true);
Object unsafe = unsafeField.get(null);
Long offset = (Long) unsafeClass.getMethod("staticFieldOffset", Field.class).invoke(unsafe, loggerField);
//
unsafeClass.getMethod("putObjectVolatile", Object.class, long.class, Object.class).invoke(unsafe, loggerClass, offset, null);
} catch (Throwable ex) {
// ignore, i.e. simply show the warnings...
// ex.printStackTrace();
}
// turn off the zoodb logging
LoggerContext loggerContext = (LoggerContext) LoggerFactory.getILoggerFactory();
ch.qos.logback.classic.Logger logger = loggerContext.getLogger("org.zoodb");
logger.setLevel(Level.toLevel("ERROR"));
setDbFolder(PeptideShaker.getMatchesFolder());
// Load user parameters
utilitiesUserParameters = UtilitiesUserParameters.loadUserParameters();
// Instantiate factories
PeptideShaker.instantiateFacories(utilitiesUserParameters);
modificationFactory = ModificationFactory.getInstance();
enzymeFactory = EnzymeFactory.getInstance();
// Load resources files
loadSpecies();
// Set the gene mappings
ProteinGeneDetailsProvider geneFactory = new ProteinGeneDetailsProvider();
geneFactory.initialize(PeptideShaker.getJarFilePath());
// Load the species mapping
try {
SpeciesFactory speciesFactory = SpeciesFactory.getInstance();
speciesFactory.initiate(PeptideShaker.getJarFilePath());
} catch (Exception e) {
waitingHandler.appendReport("An error occurred while loading the " + "species mapping. Gene annotation might be impaired. " + getLogFileMessage(), true, true);
e.printStackTrace();
}
// create project
try {
createProject();
} catch (Exception e) {
waitingHandler.appendReport("An error occurred while creating the " + "PeptideShaker project. " + getLogFileMessage(), true, true);
e.printStackTrace();
waitingHandler.setRunCanceled();
}
// see if the project was created or canceled
if (waitingHandler.isRunCanceled()) {
try {
closePeptideShaker(identification);
} catch (Exception e) {
waitingHandler.appendReport("An error occurred while closing PeptideShaker. " + getLogFileMessage(), true, true);
e.printStackTrace();
}
System.exit(1);
return 1;
} else {
waitingHandler.appendReport("Project successfully created.", true, true);
waitingHandler.increasePrimaryProgressCounter();
}
// save project
if (cliInputBean.getOutput() != null) {
try {
psdbFile = cliInputBean.getOutput();
waitingHandler.appendReport("Saving results.", true, true);
saveProject(waitingHandler, true);
waitingHandler.appendReport("Results saved to " + psdbFile.getAbsolutePath() + ".", true, true);
waitingHandler.appendReportEndLine();
} catch (Exception e) {
waitingHandler.appendReport("An exception occurred while saving the project. " + getLogFileMessage(), true, true);
e.printStackTrace();
waitingHandler.setRunCanceled();
}
waitingHandler.increasePrimaryProgressCounter();
}
// finished
waitingHandler.setPrimaryProgressCounterIndeterminate(false);
waitingHandler.setSecondaryProgressCounterIndeterminate(false);
// follow up tasks if needed
FollowUpCLIInputBean followUpCLIInputBean = cliInputBean.getFollowUpCLIInputBean();
// array to be filled with all exported follow-up reports
ArrayList<File> followupAnalysisFiles = new ArrayList<File>();
if (followUpCLIInputBean.followUpNeeded()) {
waitingHandler.appendReport("Starting follow up tasks.", true, true);
// recalibrate spectra
if (followUpCLIInputBean.recalibrationNeeded()) {
waitingHandler.appendReport("Spectrum recalibration.", true, true);
try {
followupAnalysisFiles.addAll(CLIExportMethods.recalibrateSpectra(followUpCLIInputBean, identification, sequenceProvider, msFileHandler, identificationParameters, waitingHandler));
} catch (Exception e) {
waitingHandler.appendReport("An error occurred while recalibrating the spectra. " + getLogFileMessage(), true, true);
e.printStackTrace();
waitingHandler.setRunCanceled();
}
}
// export spectra
if (followUpCLIInputBean.spectrumExportNeeded()) {
waitingHandler.appendReport("Spectrum export.", true, true);
try {
followupAnalysisFiles.addAll(CLIExportMethods.exportSpectra(followUpCLIInputBean, identification, msFileHandler, waitingHandler, identificationParameters.getSequenceMatchingParameters()));
} catch (Exception e) {
waitingHandler.appendReport("An error occurred while exporting the spectra. " + getLogFileMessage(), true, true);
e.printStackTrace();
waitingHandler.setRunCanceled();
}
}
// export protein accessions
if (followUpCLIInputBean.accessionExportNeeded()) {
waitingHandler.appendReport("Protein accession export.", true, true);
try {
followupAnalysisFiles.add(CLIExportMethods.exportAccessions(followUpCLIInputBean, identification, sequenceProvider, waitingHandler, filterParameters));
} catch (Exception e) {
waitingHandler.appendReport("An error occurred while exporting the protein accessions. " + getLogFileMessage(), true, true);
e.printStackTrace();
waitingHandler.setRunCanceled();
}
}
// export protein details
if (followUpCLIInputBean.proteinSequencesExportNeeded()) {
waitingHandler.appendReport("Protein sequences export.", true, true);
try {
followupAnalysisFiles.add(CLIExportMethods.exportProteinSequences(followUpCLIInputBean, identification, sequenceProvider, waitingHandler, filterParameters));
} catch (Exception e) {
waitingHandler.appendReport("An error occurred while exporting the protein details. " + getLogFileMessage(), true, true);
e.printStackTrace();
waitingHandler.setRunCanceled();
}
}
// progenesis export
if (followUpCLIInputBean.progenesisExportNeeded()) {
waitingHandler.appendReport("Progenesis export.", true, true);
try {
followupAnalysisFiles.add(CLIExportMethods.exportProgenesis(followUpCLIInputBean, identification, waitingHandler, sequenceProvider, proteinDetailsProvider, identificationParameters.getSequenceMatchingParameters()));
waitingHandler.appendReport("Progenesis export completed.", true, true);
} catch (Exception e) {
waitingHandler.appendReport("An error occurred while exporting the Progenesis file. " + getLogFileMessage(), true, true);
e.printStackTrace();
waitingHandler.setRunCanceled();
}
}
// inclusion list export
if (followUpCLIInputBean.inclusionListNeeded()) {
waitingHandler.appendReport("Inclusion list export.", true, true);
try {
followupAnalysisFiles.add(CLIExportMethods.exportInclusionList(followUpCLIInputBean, identification, identificationFeaturesGenerator, msFileHandler, identificationParameters.getSearchParameters(), waitingHandler, filterParameters));
} catch (Exception e) {
waitingHandler.appendReport("An error occurred while generating the inclusion list.", true, true);
e.printStackTrace();
waitingHandler.setRunCanceled();
}
}
// proteoforms export
if (followUpCLIInputBean.proteoformsNeeded()) {
waitingHandler.appendReport("Proteoform export.", true, true);
try {
followupAnalysisFiles.add(CLIExportMethods.exportProteoforms(followUpCLIInputBean, identification, waitingHandler));
} catch (Exception e) {
waitingHandler.appendReport("An error occurred while generating the proteoforms list.", true, true);
e.printStackTrace();
waitingHandler.setRunCanceled();
}
}
// DeepLC export
if (followUpCLIInputBean.deepLcExportNeeded()) {
waitingHandler.appendReport("DeepLC export.", true, true);
try {
followupAnalysisFiles.addAll(CLIExportMethods.exportDeepLC(followUpCLIInputBean, identification, identificationParameters.getSearchParameters().getModificationParameters(), identificationParameters.getSequenceMatchingParameters(), sequenceProvider, msFileHandler, waitingHandler));
} catch (Exception e) {
waitingHandler.appendReport("An error occurred while generating the proteoforms list.", true, true);
e.printStackTrace();
waitingHandler.setRunCanceled();
}
}
// ms2pip export
if (followUpCLIInputBean.ms2pipExportNeeded()) {
waitingHandler.appendReport("ms2pip export.", true, true);
try {
followupAnalysisFiles.addAll(CLIExportMethods.exportMs2pip(followUpCLIInputBean, identification, identificationParameters.getSearchParameters(), identificationParameters.getSequenceMatchingParameters(), sequenceProvider, msFileHandler, waitingHandler));
} catch (Exception e) {
waitingHandler.appendReport("An error occurred while generating the proteoforms list.", true, true);
e.printStackTrace();
waitingHandler.setRunCanceled();
}
}
}
// report export if needed
ReportCLIInputBean reportCLIInputBean = cliInputBean.getReportCLIInputBean();
// array to be filled with all exported reports
ArrayList<File> reportFiles = new ArrayList<File>();
if (reportCLIInputBean.exportNeeded()) {
// see if output folder is set, and if not set to the same folder as the psdb file
boolean reportOutputFolderSet = reportCLIInputBean.getReportOutputFolder() != null;
if (!reportOutputFolderSet) {
if (cliInputBean.getOutput() == null) {
// @TODO: ideally this test should be done before starting the processing of the data!
waitingHandler.appendReport("Report output folder not set. Please use -out_reports (or the more general -out option). Processing canceled.", true, true);
System.err.println("Report output folder not set. Please use -out_reports (or the more general -out option). Processing canceled.");
waitingHandler.setRunCanceled();
} else {
reportCLIInputBean.setReportOutputFolder(cliInputBean.getOutput().getParentFile());
reportOutputFolderSet = true;
}
}
if (reportOutputFolderSet) {
waitingHandler.appendReport("Exporting reports.", true, true);
// Export report(s)
if (reportCLIInputBean.exportNeeded()) {
// @TODO: this shall not be hard coded //peptideShakerGUI.getDisplayPreferences().getnAASurroundingPeptides()
int nSurroundingAAs = 2;
for (String reportType : reportCLIInputBean.getReportTypes()) {
waitingHandler.appendReport("Exporting " + reportType + ".", true, true);
try {
reportFiles.add(CLIExportMethods.exportReport(reportCLIInputBean, reportType, projectParameters.getProjectUniqueName(), projectDetails, identification, geneMaps, identificationFeaturesGenerator, identificationParameters, sequenceProvider, proteinDetailsProvider, msFileHandler, nSurroundingAAs, spectrumCountingParameters, waitingHandler));
} catch (Exception e) {
waitingHandler.appendReport("An error occurred while exporting the " + reportType + ". " + getLogFileMessage(), true, true);
e.printStackTrace();
waitingHandler.setRunCanceled();
}
}
}
// export documentation
if (reportCLIInputBean.documentationExportNeeded()) {
waitingHandler.appendReport("Exporting report documentation.", true, true);
for (String reportType : reportCLIInputBean.getReportTypes()) {
try {
CLIExportMethods.exportDocumentation(reportCLIInputBean, reportType, waitingHandler);
} catch (Exception e) {
waitingHandler.appendReport("An error occurred while exporting the documentation for " + reportType + ". " + getLogFileMessage(), true, true);
e.printStackTrace();
waitingHandler.setRunCanceled();
}
}
}
}
}
// export as mzid
MzidCLIInputBean mzidCLIInputBean = cliInputBean.getMzidCLIInputBean();
File mzidFile = mzidCLIInputBean.getOutputFile();
if (mzidFile != null) {
waitingHandler.appendReportEndLine();
waitingHandler.appendReport("Exporting project as mzIdentML.", true, true);
// export mzid file
// make sure that all annotations are included
double currentIntensityLimit = this.getIdentificationParameters().getAnnotationParameters().getAnnotationIntensityLimit();
this.getIdentificationParameters().getAnnotationParameters().setIntensityLimit(0.0);
try {
CLIExportMethods.exportMzId(mzidCLIInputBean, this, waitingHandler);
} catch (Exception e) {
waitingHandler.appendReport("An error occurred while generating the mzid file. " + getLogFileMessage(), true, true);
e.printStackTrace();
waitingHandler.setRunCanceled();
} finally {
// reset the annotation level
this.getIdentificationParameters().getAnnotationParameters().setIntensityLimit(currentIntensityLimit);
}
}
// export project as zip
File zipFile = cliInputBean.getZipExport();
if (zipFile != null) {
waitingHandler.appendReportEndLine();
waitingHandler.appendReport("Zipping project.", true, true);
File parent = zipFile.getParentFile();
try {
parent.mkdirs();
} catch (Exception e) {
waitingHandler.appendReport("An error occurred while creating folder " + parent.getAbsolutePath() + ". " + getLogFileMessage(), true, true);
waitingHandler.setRunCanceled();
}
ArrayList<File> spectrumFiles = new ArrayList<>();
for (String spectrumFileName : getIdentification().getFractions()) {
File spectrumFile = new File(msFileHandler.getFilePaths().get(spectrumFileName));
spectrumFiles.add(spectrumFile);
}
File fastaFile = new File(projectDetails.getFastaFile());
try {
ProjectExport.exportProjectAsZip(zipFile, fastaFile, msFileHandler, followupAnalysisFiles, reportFiles, mzidFile, psdbFile, true, waitingHandler);
final int NUMBER_OF_BYTES_PER_MEGABYTE = 1048576;
double sizeOfZippedFile = Util.roundDouble(((double) zipFile.length() / NUMBER_OF_BYTES_PER_MEGABYTE), 2);
waitingHandler.appendReport("Project zipped to \'" + zipFile.getAbsolutePath() + "\' (" + sizeOfZippedFile + " MB)", true, true);
// export mgf file(s) out of the zip file
boolean mgfExport = cliInputBean.getMgfExport();
if (mgfExport) {
waitingHandler.appendReportEndLine();
waitingHandler.appendReport("Writing mgf file(s) to output folder.", true, true);
int i = 0;
for (String spectrumFileName : msFileHandler.getCmsFilePaths().keySet()) {
if (waitingHandler.isRunCanceled()) {
break;
}
waitingHandler.appendReport("Writing: " + IoUtil.removeExtension(spectrumFileName) + ".mgf" + " (" + (i + 1) + "/" + getIdentification().getFractions().size() + ")", true, true);
File mgfFile = new File(parent, IoUtil.removeExtension(spectrumFileName) + ".mgf");
MsFileExporter.writeMgfFile(msFileHandler, spectrumFileName, mgfFile, waitingHandler);
// writing the index too
MgfIndex mgfIndex = IndexedMgfReader.getMgfIndex(mgfFile, waitingHandler);
File indexFile = new File(parent, IoUtil.removeExtension(mgfIndex.getFileName()) + ".cui");
SerializationUtils.writeObject(mgfIndex, indexFile);
i++;
}
waitingHandler.appendReport("Written mgf file(s) to output folder.", true, true);
}
waitingHandler.increasePrimaryProgressCounter();
} catch (IOException e) {
e.printStackTrace();
waitingHandler.appendReport("An error occurred while attempting to zip project in " + zipFile.getAbsolutePath() + ". " + getLogFileMessage(), true, true);
waitingHandler.setRunCanceled();
}
}
waitingHandler.appendReportEndLine();
try {
closePeptideShaker(identification);
} catch (Exception e) {
waitingHandler.appendReport("An error occurred while closing PeptideShaker. " + getLogFileMessage(), true, true);
e.printStackTrace();
}
saveReport();
} catch (Exception e) {
e.printStackTrace();
if (waitingHandler != null) {
waitingHandler.appendReport("PeptideShaker processing failed. " + getLogFileMessage(), true, true);
saveReport();
waitingHandler.setRunCanceled();
}
}
if (waitingHandler != null && !waitingHandler.isRunCanceled()) {
waitingHandler.appendReport("PeptideShaker process completed.", true, true);
waitingHandler.setSecondaryProgressText("Processing Completed.");
// @TODO: Find other ways of cancelling the process? If not cancelled searchgui will not stop.
System.exit(0);
// 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.out.println("PeptideShaker process failed! " + getLogFileMessage());
// @TODO: Find other ways of cancelling the process? If not cancelled searchgui will not stop.
System.exit(1);
// Note that if a different solution is found, the DummyFrame has to be closed similar to the setVisible method in the WelcomeDialog!!
return 1;
}
}
Also used :
ArrayList(java.util.ArrayList)
WaitingDialog(com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog)
Field(java.lang.reflect.Field)
SpeciesFactory(com.compomics.util.experiment.biology.taxonomy.SpeciesFactory)
MgfIndex(com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex)
ProteinGeneDetailsProvider(com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider)
Point(java.awt.Point)
LoggerContext(ch.qos.logback.classic.LoggerContext)
TimeoutException(java.util.concurrent.TimeoutException)
SQLException(java.sql.SQLException)
Point(java.awt.Point)
WaitingHandlerCLIImpl(com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl)
DummyFrame(com.compomics.util.gui.DummyFrame)
Example 2 with WaitingDialog
use of com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog in project peptide-shaker by compomics.
the class PeptideShakerCLI method createProject.
/**
* Creates the PeptideShaker project based on the identification files
* provided in the command line input
*
* @throws java.io.IOException exception thrown if an error occurs while
* reading or writing a file
* @throws java.lang.InterruptedException exception thrown if a thread is
* interrupted
* @throws java.util.concurrent.TimeoutException exception thrown if a
* process times out
*/
public void createProject() throws IOException, InterruptedException, TimeoutException {
// define new project reference
projectParameters = new ProjectParameters(cliInputBean.getExperimentID());
// set the project details
projectDetails = new ProjectDetails();
projectDetails.setCreationDate(new Date());
projectDetails.setPeptideShakerVersion(new Properties().getVersion());
// set up spectrum provider
msFileHandler = new MsFileHandler();
// get the input files
ArrayList<File> identificationFilesInput = cliInputBean.getIdFiles();
ArrayList<File> dataFolders = new ArrayList<>();
ArrayList<File> spectrumFiles = cliInputBean.getSpectrumFiles();
File fastaFile = null;
// Extract data from zip files, try to find the search parameter and spectrum files
ArrayList<File> identificationFiles = new ArrayList<>();
IdentificationParameters tempIdentificationParameters = null;
for (File inputFile : identificationFilesInput) {
File parentFile = inputFile.getParentFile();
if (!dataFolders.contains(parentFile)) {
dataFolders.add(parentFile);
}
File dataFolder = new File(parentFile, "mgf");
if (dataFolder.exists() && !dataFolders.contains(dataFolder)) {
dataFolders.add(dataFolder);
}
dataFolder = new File(parentFile, "mzml");
if (dataFolder.exists() && !dataFolders.contains(dataFolder)) {
dataFolders.add(dataFolder);
}
dataFolder = new File(parentFile, "cms");
if (dataFolder.exists() && !dataFolders.contains(dataFolder)) {
dataFolders.add(dataFolder);
}
dataFolder = new File(parentFile, "fasta");
if (dataFolder.exists() && !dataFolders.contains(dataFolder)) {
dataFolders.add(dataFolder);
}
dataFolder = new File(parentFile, PeptideShaker.DATA_DIRECTORY);
if (dataFolder.exists() && !dataFolders.contains(dataFolder)) {
dataFolders.add(dataFolder);
}
String fileName = inputFile.getName();
if (fileName.toLowerCase().endsWith(".zip")) {
waitingHandler.appendReport("Unzipping " + fileName + ".", true, true);
String newName = PsZipUtils.getTempFolderName(fileName);
String parentFolder = PsZipUtils.getUnzipParentFolder();
if (parentFolder == null) {
parentFolder = parentFile.getAbsolutePath();
}
File parentFolderFile = new File(parentFolder, PsZipUtils.getUnzipSubFolder());
File destinationFolder = new File(parentFolderFile, newName);
destinationFolder.mkdir();
TempFilesManager.registerTempFolder(parentFolderFile);
ZipUtils.unzip(inputFile, destinationFolder, waitingHandler);
if (waitingHandler instanceof WaitingHandlerCLIImpl) {
waitingHandler.appendReportEndLine();
}
dataFolder = new File(destinationFolder, PeptideShaker.DATA_DIRECTORY);
if (dataFolder.exists() && !dataFolders.contains(dataFolder)) {
dataFolders.add(dataFolder);
}
dataFolder = new File(destinationFolder, ".mgf");
if (dataFolder.exists() && !dataFolders.contains(dataFolder)) {
dataFolders.add(dataFolder);
}
dataFolder = new File(parentFile, "mzml");
if (dataFolder.exists() && !dataFolders.contains(dataFolder)) {
dataFolders.add(dataFolder);
}
dataFolder = new File(destinationFolder, ".cms");
if (dataFolder.exists() && !dataFolders.contains(dataFolder)) {
dataFolders.add(dataFolder);
}
dataFolder = new File(destinationFolder, ".fasta");
if (dataFolder.exists() && !dataFolders.contains(dataFolder)) {
dataFolders.add(dataFolder);
}
for (File unzippedFile : destinationFolder.listFiles()) {
String nameLowerCase = unzippedFile.getName().toLowerCase();
if (nameLowerCase.endsWith(".omx") || nameLowerCase.endsWith(".t.xml") || nameLowerCase.endsWith(".pep.xml") || nameLowerCase.endsWith(".dat") || nameLowerCase.endsWith(".mzid") || nameLowerCase.endsWith(".ms-amanda.csv") || nameLowerCase.endsWith(".res") || nameLowerCase.endsWith(".tide-search.target.txt") || nameLowerCase.endsWith(".tags") || nameLowerCase.endsWith(".pnovo.txt") || nameLowerCase.endsWith(".novor.csv") || nameLowerCase.endsWith(".psm") || nameLowerCase.endsWith(".omx.gz") || nameLowerCase.endsWith(".t.xml.gz") || nameLowerCase.endsWith(".pep.xml.gz") || nameLowerCase.endsWith(".mzid.gz") || nameLowerCase.endsWith(".ms-amanda.csv.gz") || nameLowerCase.endsWith(".res.gz") || nameLowerCase.endsWith(".tide-search.target.txt.gz") || nameLowerCase.endsWith(".tags.gz") || nameLowerCase.endsWith(".pnovo.txt.gz") || nameLowerCase.endsWith(".novor.csv.gz") || nameLowerCase.endsWith(".psm.gz")) {
identificationFiles.add(unzippedFile);
} else if (nameLowerCase.endsWith(".par")) {
try {
tempIdentificationParameters = IdentificationParameters.getIdentificationParameters(unzippedFile);
ValidationQcParameters validationQCParameters = tempIdentificationParameters.getIdValidationParameters().getValidationQCParameters();
if (validationQCParameters == null || validationQCParameters.getPsmFilters() == null || validationQCParameters.getPeptideFilters() == null || validationQCParameters.getProteinFilters() == null || validationQCParameters.getPsmFilters().isEmpty() && validationQCParameters.getPeptideFilters().isEmpty() && validationQCParameters.getProteinFilters().isEmpty()) {
MatchesValidator.setDefaultMatchesQCFilters(validationQCParameters);
}
} catch (Exception e) {
e.printStackTrace();
waitingHandler.appendReport("An error occurred while parsing the parameters file " + unzippedFile.getName() + ". " + getLogFileMessage(), true, true);
waitingHandler.setRunCanceled();
}
}
}
} else {
identificationFiles.add(inputFile);
}
}
// list the spectrum files found
HashSet<String> dataFileNamesRequired = new HashSet<>();
for (File spectrumFile : spectrumFiles) {
dataFileNamesRequired.add(IoUtil.getFileName(spectrumFile));
}
for (File dataFolder : dataFolders) {
for (File file : dataFolder.listFiles()) {
String name = file.getName();
if (name.endsWith(".mgf") || name.endsWith(".mgf.gz") || name.endsWith(".mzml") || name.endsWith(".mzml.gz") || name.endsWith(".cms")) {
if (!dataFileNamesRequired.contains(name)) {
spectrumFiles.add(file);
dataFileNamesRequired.add(name);
}
} else if (name.endsWith(".fasta")) {
if (!dataFileNamesRequired.contains(name)) {
fastaFile = file;
dataFileNamesRequired.add(name);
}
}
}
}
// Load the spectrum files
for (File spectrumFile : spectrumFiles) {
File folder = CmsFolder.getParentFolder() == null ? spectrumFile.getParentFile() : new File(CmsFolder.getParentFolder());
msFileHandler.register(spectrumFile, folder, waitingHandler);
}
// If there is a specific fasta file chosen, it is used insted of the one included in the searchgui zip
if (cliInputBean.getFastaFile() != null) {
fastaFile = cliInputBean.getFastaFile();
}
// get the identification parameters
IdentificationParametersInputBean identificationParametersInputBean = cliInputBean.getIdentificationParametersInputBean();
if (tempIdentificationParameters != null && identificationParametersInputBean.getInputFile() == null) {
identificationParametersInputBean.setIdentificationParameters(tempIdentificationParameters);
identificationParametersInputBean.updateIdentificationParameters();
}
identificationParameters = identificationParametersInputBean.getIdentificationParameters();
ValidationQcParameters validationQCParameters = identificationParameters.getIdValidationParameters().getValidationQCParameters();
if (validationQCParameters == null || validationQCParameters.getPsmFilters() == null || validationQCParameters.getPeptideFilters() == null || validationQCParameters.getProteinFilters() == null || validationQCParameters.getPsmFilters().isEmpty() && validationQCParameters.getPeptideFilters().isEmpty() && validationQCParameters.getProteinFilters().isEmpty()) {
MatchesValidator.setDefaultMatchesQCFilters(validationQCParameters);
}
if (identificationParameters == null) {
waitingHandler.appendReport("Identification parameters not found!", true, true);
waitingHandler.setRunCanceled();
}
SearchParameters searchParameters = identificationParameters.getSearchParameters();
String error = PeptideShaker.loadModifications(searchParameters);
if (error != null) {
System.out.println(error);
}
// try to locate the fasta file
if (fastaFile == null) {
waitingHandler.appendReport("FASTA file not set (or not in zip file)!", true, true);
waitingHandler.setRunCanceled();
} else if (!fastaFile.exists()) {
boolean found = false;
// look in the database folder
try {
File tempDbFolder = utilitiesUserParameters.getDbFolder();
File newFile = new File(tempDbFolder, fastaFile.getName());
if (newFile.exists()) {
fastaFile = newFile;
projectDetails.setFastaFile(fastaFile);
found = true;
}
} catch (Exception e) {
e.printStackTrace();
}
if (!found) {
// look in the data folders
for (File dataFolder : dataFolders) {
File newFile = new File(dataFolder, fastaFile.getName());
if (newFile.exists()) {
fastaFile = newFile;
projectDetails.setFastaFile(fastaFile);
found = true;
break;
}
}
if (!found) {
waitingHandler.appendReport("FASTA file \'" + fastaFile.getName() + "\' not found.", true, true);
waitingHandler.setRunCanceled();
}
}
} else {
projectDetails.setFastaFile(fastaFile);
}
// get the summary information for the FASTA file
try {
// get the FASTA summary
FastaSummary fastaSummary = loadFastaFile(waitingHandler);
// set the background species
identificationParameters.getGeneParameters().setBackgroundSpeciesFromFastaSummary(fastaSummary);
} catch (IOException e) {
e.printStackTrace();
waitingHandler.appendReport("An error occurred while parsing the FASTA file.", true, true);
waitingHandler.setRunCanceled();
}
// set the processing settings
ProcessingParameters processingParameters = new ProcessingParameters();
Integer nThreads = cliInputBean.getnThreads();
if (nThreads != null) {
processingParameters.setnThreads(nThreads);
}
// set the spectrum counting prefrences
spectrumCountingParameters = new SpectrumCountingParameters();
// set the project type
projectType = cliInputBean.getProjectType();
// check the project reference
for (String forbiddenChar : Util.FORBIDDEN_CHARACTERS) {
if (cliInputBean.getExperimentID().contains(forbiddenChar)) {
waitingHandler.appendReport("The project name cannot not contain " + forbiddenChar + ".", true, true);
waitingHandler.setRunCanceled();
}
}
// incrementing the counter for a new PeptideShaker start run via CLI
if (utilitiesUserParameters.isAutoUpdate()) {
Util.sendGAUpdate("UA-36198780-1", "startrun-cl", "peptide-shaker-" + PeptideShaker.getVersion());
}
// create a shaker which will perform the analysis
PeptideShaker peptideShaker = new PeptideShaker(projectParameters);
// import the files
int outcome = peptideShaker.importFiles(waitingHandler, identificationFiles, msFileHandler, identificationParameters, projectDetails, processingParameters, exceptionHandler);
if (outcome == 0) {
peptideShaker.createProject(identificationParameters, processingParameters, spectrumCountingParameters, msFileHandler, projectDetails, projectType, waitingHandler, false, exceptionHandler);
}
if (!waitingHandler.isRunCanceled()) {
// identification as created by PeptideShaker
identification = peptideShaker.getIdentification();
// metrics saved while processing the data
metrics = peptideShaker.getMetrics();
// fene maps
geneMaps = peptideShaker.getGeneMaps();
// the identification feature generator
identificationFeaturesGenerator = peptideShaker.getIdentificationFeaturesGenerator();
// the sequence provider
sequenceProvider = peptideShaker.getSequenceProvider();
// the protein details provider
proteinDetailsProvider = peptideShaker.getProteinDetailsProvider();
if (waitingHandler instanceof WaitingDialog) {
projectDetails.setReport(((WaitingDialog) waitingHandler).getReport(null));
((WaitingDialog) waitingHandler).setRunNotFinished();
((WaitingDialog) waitingHandler).setCloseDialogWhenImportCompletes(true, false);
}
} else {
if (waitingHandler instanceof WaitingDialog) {
saveReport();
}
TempFilesManager.deleteTempFolders();
waitingHandler.setWaitingText("PeptideShaker Processing Canceled.");
System.out.println("<CompomicsError>PeptideShaker processing canceled. " + getLogFileMessage() + "</CompomicsError>");
}
}
Also used :
ArrayList(java.util.ArrayList)
WaitingDialog(com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog)
Properties(eu.isas.peptideshaker.utils.Properties)
FastaSummary(com.compomics.util.experiment.io.biology.protein.FastaSummary)
SearchParameters(com.compomics.util.parameters.identification.search.SearchParameters)
IdentificationParameters(com.compomics.util.parameters.identification.IdentificationParameters)
ValidationQcParameters(com.compomics.util.parameters.identification.advanced.ValidationQcParameters)
ProcessingParameters(com.compomics.util.parameters.tools.ProcessingParameters)
MsFileHandler(com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler)
HashSet(java.util.HashSet)
ProjectDetails(eu.isas.peptideshaker.preferences.ProjectDetails)
IdentificationParametersInputBean(com.compomics.cli.identification_parameters.IdentificationParametersInputBean)
SpectrumCountingParameters(com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters)
Date(java.util.Date)
TimeoutException(java.util.concurrent.TimeoutException)
SQLException(java.sql.SQLException)
Point(java.awt.Point)
ProjectParameters(com.compomics.util.experiment.ProjectParameters)
WaitingHandlerCLIImpl(com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl)
PeptideShaker(eu.isas.peptideshaker.PeptideShaker)
Example 3 with WaitingDialog
use of com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog in project peptide-shaker by compomics.
the class PeptideShakerCLI method saveReport.
/**
* Save the peptide shaker report next to the psdb file.
*/
private void saveReport() {
String report;
if (waitingHandler instanceof WaitingDialog) {
report = getExtendedProjectReport(((WaitingDialog) waitingHandler).getReport(null));
} else {
report = getExtendedProjectReport(null);
}
if (report != null) {
if (waitingHandler instanceof WaitingDialog) {
report = "<html><br>";
report += "<b>Report:</b><br>";
report += "<pre>" + ((WaitingDialog) waitingHandler).getReport(null) + "</pre>";
report += "</html>";
}
try {
DateFormat df = new SimpleDateFormat("yyyy-MM-dd HH.mm.ss");
File psReportFile = null;
PathSettingsCLIInputBean pathSettingsCLIInputBean = cliInputBean.getPathSettingsCLIInputBean();
if (getPsdbFile() != null) {
String fileName = "PeptideShaker Report " + getPsdbFile().getName() + " " + df.format(new Date()) + ".html";
psReportFile = new File(getPsdbFile().getParentFile(), fileName);
} else if (cliInputBean.getOutput() != null) {
String fileName = "PeptideShaker Report " + df.format(new Date()) + ".html";
psReportFile = new File(cliInputBean.getOutput().getParentFile(), fileName);
} else if (pathSettingsCLIInputBean.getLogFolder() != null) {
String fileName = "PeptideShaker Report " + df.format(new Date()) + ".html";
psReportFile = new File(pathSettingsCLIInputBean.getLogFolder(), fileName);
}
if (psReportFile != null) {
FileWriter fw = new FileWriter(psReportFile);
try {
fw.write(report);
} finally {
fw.close();
}
}
} catch (Exception ex) {
waitingHandler.appendReport("An error occurred while saving the PeptideShaker report. " + getLogFileMessage(), true, true);
ex.printStackTrace();
}
}
}
Also used :
DateFormat(java.text.DateFormat)
SimpleDateFormat(java.text.SimpleDateFormat)
WaitingDialog(com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog)
SimpleDateFormat(java.text.SimpleDateFormat)
Date(java.util.Date)
TimeoutException(java.util.concurrent.TimeoutException)
SQLException(java.sql.SQLException)
Example 4 with WaitingDialog
use of com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog in project peptide-shaker by compomics.
the class FileImporter method importFiles.
/**
* Imports the identifications from the files.
*
* @param idFiles the identification files
*
* @return 0 if success, 1 if not
*/
public int importFiles(ArrayList<File> idFiles) {
ArrayList<File> sortedIdFiles = idFiles.stream().collect(Collectors.groupingBy(File::getName, TreeMap::new, Collectors.toList())).values().stream().flatMap(List::stream).distinct().collect(Collectors.toCollection(ArrayList::new));
try {
importSequences(identificationParameters.getSequenceMatchingParameters(), identificationParameters.getSearchParameters(), identificationParameters.getFastaParameters(), identificationParameters.getPeptideVariantsParameters(), waitingHandler, exceptionHandler);
if (waitingHandler.isRunCanceled()) {
return 1;
}
GeneParameters geneParameters = identificationParameters.getGeneParameters();
if (geneParameters.getUseGeneMapping()) {
waitingHandler.setSecondaryProgressCounterIndeterminate(true);
waitingHandler.appendReport("Importing gene mappings.", true, true);
importGenes();
} else {
geneMaps = new GeneMaps();
}
if (waitingHandler.isRunCanceled()) {
return 1;
}
waitingHandler.setSecondaryProgressCounterIndeterminate(true);
waitingHandler.appendReport("Establishing local database connection.", true, true);
waitingHandler.increasePrimaryProgressCounter();
if (!waitingHandler.isRunCanceled()) {
waitingHandler.appendReport("Reading identification files.", true, true);
for (File idFile : sortedIdFiles) {
importPsms(idFile);
if (waitingHandler.isRunCanceled()) {
return 1;
}
}
if (nRetained == 0) {
waitingHandler.appendReport("No identification results.", true, true);
waitingHandler.setRunCanceled();
return 1;
}
// get the total number of spectra
int nSpectra = 0;
for (String spectrumFileName : identification.getFractions()) {
nSpectra += spectrumProvider.getSpectrumTitles(spectrumFileName).length;
}
waitingHandler.appendReport("File import completed. " + nPSMs + " first hits imported (" + nTotal + " total) from " + nSpectra + " spectra.", true, true);
waitingHandler.appendReport("[" + nRetained + " first hits passed the initial filtering]", true, true);
}
} catch (OutOfMemoryError error) {
System.out.println("<CompomicsError>PeptideShaker ran out of memory! See the PeptideShaker log for details.</CompomicsError>");
System.err.println("Ran out of memory!");
System.err.println("Memory given to the Java virtual machine: " + Runtime.getRuntime().maxMemory() + ".");
System.err.println("Memory used by the Java virtual machine: " + Runtime.getRuntime().totalMemory() + ".");
System.err.println("Free memory in the Java virtual machine: " + Runtime.getRuntime().freeMemory() + ".");
Runtime.getRuntime().gc();
waitingHandler.appendReportEndLine();
waitingHandler.appendReport("Ran out of memory!", true, true);
waitingHandler.setRunCanceled();
if (waitingHandler instanceof WaitingDialog) {
JOptionPane.showMessageDialog((WaitingDialog) waitingHandler, JOptionEditorPane.getJOptionEditorPane("PeptideShaker used up all the available memory and had to be stopped.<br>" + "Memory boundaries are changed in the the Welcome Dialog (Settings<br>" + "& Help > Settings > Java Memory Settings) or in the Edit menu (Edit<br>" + "Java Options). See also <a href=\"https://compomics.github.io/projects/compomics-utilities/wiki/JavaTroubleShooting.html\">JavaTroubleShooting</a>."), "Out Of Memory", JOptionPane.ERROR_MESSAGE);
}
error.printStackTrace();
return 1;
} catch (Exception e) {
waitingHandler.setRunCanceled();
System.out.println("<CompomicsError>PeptideShaker processing failed. See the PeptideShaker log for details.</CompomicsError>");
if (e instanceof NullPointerException) {
waitingHandler.appendReport("An error occurred while loading the identification files.", true, true);
waitingHandler.appendReport("Please see the error log (Help Menu > Bug Report) for details.", true, true);
} else if (FrameExceptionHandler.getExceptionType(e).equalsIgnoreCase("Protein not found")) {
waitingHandler.appendReport("An error occurred while loading the identification files:", true, true);
waitingHandler.appendReport(e.getLocalizedMessage(), true, true);
waitingHandler.appendReport("Please see https://compomics.github.io/projects/searchgui/wiki/DatabaseHelp.html.", true, true);
} else {
waitingHandler.appendReport("An error occurred while loading the identification files:", true, true);
waitingHandler.appendReport(e.getLocalizedMessage(), true, true);
}
e.printStackTrace();
System.err.println("Free memory: " + Runtime.getRuntime().freeMemory());
return 1;
}
return 0;
}
Also used :
GeneParameters(com.compomics.util.parameters.identification.advanced.GeneParameters)
WaitingDialog(com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog)
File(java.io.File)
GeneMaps(com.compomics.util.experiment.biology.genes.GeneMaps)
TimeoutException(java.util.concurrent.TimeoutException)
IOException(java.io.IOException)
Example 5 with WaitingDialog
use of com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog in project peptide-shaker by compomics.
the class NewDialog method loadButtonActionPerformed.
// </editor-fold>//GEN-END:initComponents
/**
* Tries to process the identification files, closes the dialog and then
* opens the results in the main frame.
*
* @param evt
*/
private void loadButtonActionPerformed(java.awt.event.ActionEvent evt) {
if (validateUserInput()) {
if (welcomeDialog != null) {
welcomeDialog.setVisible(false);
}
this.setVisible(false);
peptideShakerGUI.setVisible(true);
ProjectType projectType = ProjectType.getProjectType(typeCmb.getSelectedItem().toString());
peptideShakerGUI.setIdentificationParameters(identificationParameters);
peptideShakerGUI.setProcessingParameters(processingParameters);
peptideShakerGUI.setDisplayParameters(displayPreferences);
projectDetails = new ProjectDetails();
projectDetails.setCreationDate(new Date());
projectDetails.setPeptideShakerVersion(new eu.isas.peptideshaker.utils.Properties().getVersion());
projectDetails.setFastaFile(fastaFile);
peptideShakerGUI.setProjectDetails(projectDetails);
peptideShakerGUI.setCurentNotes(new ArrayList<>());
peptideShakerGUI.updateNotesNotificationCounter();
peptideShakerGUI.resetDisplayFeaturesGenerator();
peptideShakerGUI.setSpectrumCountingParameters(spectrumCountingPreferences);
peptideShakerGUI.setMsFileHandler(msFileHandler);
ProjectParameters projectParameters = new ProjectParameters(projectNameIdTxt.getText().trim());
// incrementing the counter for a new PeptideShaker start run via GUI
if (peptideShakerGUI.getUtilitiesUserParameters().isAutoUpdate()) {
Util.sendGAUpdate("UA-36198780-1", "startrun-gui", "peptide-shaker-" + PeptideShaker.getVersion());
}
peptideShaker = new PeptideShaker(projectParameters);
ArrayList<String> tips;
try {
tips = Tips.getTips();
} catch (Exception e) {
tips = new ArrayList<>();
// Do something here?
}
WaitingDialog waitingDialog = new WaitingDialog(peptideShakerGUI, Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/peptide-shaker.gif")), Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/peptide-shaker-orange.gif")), true, tips, "Importing Data", "PeptideShaker", PeptideShaker.getVersion(), true);
waitingDialog.setCloseDialogWhenImportCompletes(true, true);
int progressCounter = idFiles.size() + spectrumFiles.size();
// establishing the database connection
progressCounter++;
// the FASTA file
progressCounter++;
// the peptide to protein map
progressCounter++;
// computing probabilities etc
progressCounter += 6;
if (identificationParameters.getProteinInferenceParameters().getSimplifyGroups()) {
// simplify protein groups
progressCounter++;
}
// resolving protein inference
progressCounter++;
// Correcting protein probabilities, Validating identifications at 1% FDR, Scoring PTMs in peptides, Scoring PTMs in proteins.
progressCounter += 4;
// Scoring PTMs in PSMs. Estimating PTM FLR.
progressCounter += 2;
if (identificationParameters.getModificationLocalizationParameters().getAlignNonConfidentModifications()) {
// Peptide inference
progressCounter++;
}
// add one more just to not start at 0%
progressCounter++;
waitingDialog.setMaxPrimaryProgressCounter(progressCounter);
// just to not start at 0%
waitingDialog.increasePrimaryProgressCounter();
boolean needDialog = false;
// load the identification files
if (idFiles.size() > 0) {
needDialog = true;
new Thread(new Runnable() {
public void run() {
ExceptionHandler exceptionHandler = new WaitingDialogExceptionHandler((WaitingDialog) waitingDialog, "https://github.com/compomics/peptide-shaker/issues");
try {
int outcome = peptideShaker.importFiles(waitingDialog, idFiles, msFileHandler, identificationParameters, projectDetails, processingParameters, exceptionHandler);
if (outcome == 0) {
peptideShaker.createProject(identificationParameters, processingParameters, spectrumCountingPreferences, msFileHandler, projectDetails, projectType, waitingDialog, true, exceptionHandler);
} else {
waitingDialog.setRunCanceled();
}
} catch (Exception e) {
exceptionHandler.catchException(e);
waitingDialog.setRunCanceled();
waitingDialog.setWaitingText("Failed to import data or create the project!");
}
}
}, "Import data and create project").start();
}
if (needDialog) {
try {
waitingDialog.setVisible(true);
} catch (IndexOutOfBoundsException e) {
// ignore
}
this.dispose();
}
if (!needDialog || !waitingDialog.isRunCanceled()) {
peptideShakerGUI.setProject(projectParameters);
peptideShakerGUI.setIdentification(peptideShaker.getIdentification());
peptideShakerGUI.setMetrics(peptideShaker.getMetrics());
peptideShakerGUI.setGeneMaps(peptideShaker.getGeneMaps());
peptideShakerGUI.setProjectType(projectType);
peptideShakerGUI.setSequenceProvider(peptideShaker.getSequenceProvider());
peptideShakerGUI.setProteinDetailsProvider(peptideShaker.getProteinDetailsProvider());
peptideShakerGUI.resetDisplayFeaturesGenerator();
peptideShakerGUI.setIdentificationFeaturesGenerator(peptideShaker.getIdentificationFeaturesGenerator());
peptideShakerGUI.displayResults();
// display the overview tab
peptideShakerGUI.initiateDisplay();
peptideShakerGUI.getProjectDetails().setReport(waitingDialog.getReport(null));
this.dispose();
} else if (waitingDialog.isRunCanceled()) {
// close the database
try {
peptideShaker.getIdentification().close(false);
} catch (Exception e) {
System.out.println("Failed to close the database!");
e.printStackTrace();
}
}
}
}
Also used :
ProjectDetails(eu.isas.peptideshaker.preferences.ProjectDetails)
ArrayList(java.util.ArrayList)
WaitingDialog(com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog)
WaitingDialogExceptionHandler(com.compomics.util.exceptions.exception_handlers.WaitingDialogExceptionHandler)
Date(java.util.Date)
WaitingDialogExceptionHandler(com.compomics.util.exceptions.exception_handlers.WaitingDialogExceptionHandler)
ExceptionHandler(com.compomics.util.exceptions.ExceptionHandler)
ProjectParameters(com.compomics.util.experiment.ProjectParameters)
ProjectType(com.compomics.util.parameters.peptide_shaker.ProjectType)
PeptideShaker(eu.isas.peptideshaker.PeptideShaker)
Aggregations
WaitingDialog (com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog)5
TimeoutException (java.util.concurrent.TimeoutException)4
SQLException (java.sql.SQLException)3
ArrayList (java.util.ArrayList)3
Date (java.util.Date)3
ProjectParameters (com.compomics.util.experiment.ProjectParameters)2
WaitingHandlerCLIImpl (com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl)2
PeptideShaker (eu.isas.peptideshaker.PeptideShaker)2
ProjectDetails (eu.isas.peptideshaker.preferences.ProjectDetails)2
Point (java.awt.Point)2
LoggerContext (ch.qos.logback.classic.LoggerContext)1
IdentificationParametersInputBean (com.compomics.cli.identification_parameters.IdentificationParametersInputBean)1
ExceptionHandler (com.compomics.util.exceptions.ExceptionHandler)1
WaitingDialogExceptionHandler (com.compomics.util.exceptions.exception_handlers.WaitingDialogExceptionHandler)1
GeneMaps (com.compomics.util.experiment.biology.genes.GeneMaps)1
ProteinGeneDetailsProvider (com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider)1
SpeciesFactory (com.compomics.util.experiment.biology.taxonomy.SpeciesFactory)1
FastaSummary (com.compomics.util.experiment.io.biology.protein.FastaSummary)1
MsFileHandler (com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler)1
MgfIndex (com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex)1
