/**
* 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;
}
}
/**
* Opens a file chooser where the user can select the database file.
*
* @param evt
*/
private void browseDatabaseSettingsActionPerformed(
java.awt.event.ActionEvent evt) { // GEN-FIRST:event_browseDatabaseSettingsActionPerformed
LastSelectedFolder lastSelectedFolder = peptideShakerGUI.getLastSelectedFolder();
File startLocation = null;
File utilitiesDbFolder = peptideShakerGUI.getUtilitiesUserPreferences().getDbFolder();
if (utilitiesDbFolder != null && utilitiesDbFolder.exists()) {
startLocation = utilitiesDbFolder;
}
if (startLocation == null) {
startLocation = new File(getLastSelectedFolder(lastSelectedFolder));
}
UtilitiesUserPreferences utilitiesUserPreferences =
UtilitiesUserPreferences.loadUserPreferences();
if (utilitiesUserPreferences.getDbFolder() != null
&& utilitiesUserPreferences.getDbFolder().exists()) {
startLocation = utilitiesUserPreferences.getDbFolder();
}
// First check whether a file has already been selected.
// If so, start from that file's parent.
if (databaseSettingsTxt.getText() != null && new File(databaseSettingsTxt.getText()).exists()) {
File temp = new File(databaseSettingsTxt.getText());
startLocation = temp.getParentFile();
}
JFileChooser fc = new JFileChooser(startLocation);
FileFilter filter =
new FileFilter() {
@Override
public boolean accept(File myFile) {
return myFile.getName().toLowerCase().endsWith("fasta")
|| myFile.getName().toLowerCase().endsWith("fas")
|| myFile.isDirectory();
}
@Override
public String getDescription() {
return "Supported formats: FASTA (.fasta or .fas)";
}
};
fc.setFileFilter(filter);
int result = fc.showOpenDialog(this);
if (result == JFileChooser.APPROVE_OPTION) {
File file = fc.getSelectedFile();
if (file.getName().contains(" ")) {
renameFastaFileName(file);
} else {
databaseSettingsTxt.setText(file.getAbsolutePath());
databaseSettingsTxt.setText(file.getAbsolutePath());
}
lastSelectedFolder.setLastSelectedFolder(
SequenceDbDetailsDialog.lastFolderKey, file.getAbsolutePath());
targetDecoySettingsButton.setEnabled(true);
// check if the database contains decoys
if (!file.getAbsolutePath()
.endsWith(
peptideShakerGUI.getUtilitiesUserPreferences().getTargetDecoyFileNameSuffix()
+ ".fasta")) {
int value =
JOptionPane.showConfirmDialog(
this,
"The selected FASTA file does not seem to contain decoy sequences.\n"
+ "Decoys are required by PeptideShaker. Add decoys?",
"Add Decoy Sequences?",
JOptionPane.YES_NO_OPTION);
if (value == JOptionPane.NO_OPTION) {
// do nothing
} else if (value == JOptionPane.YES_OPTION) {
targetDecoySettingsButtonActionPerformed(null);
}
}
validateParametersInput(false);
}
} // GEN-LAST:event_browseDatabaseSettingsActionPerformed
