public class CLIExportMethods extends Object
| Constructor and Description |
|---|
CLIExportMethods() |
| Modifier and Type | Method and Description |
|---|---|
static File |
exportAccessions(FollowUpCLIInputBean followUpCLIInputBean,
com.compomics.util.experiment.identification.Identification identification,
com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
com.compomics.util.waiting.WaitingHandler waitingHandler,
com.compomics.util.gui.filtering.FilterParameters filteringPreferences)
Exports the accessions as specified in the follow-up input bean.
|
static ArrayList<File> |
exportDeepLC(FollowUpCLIInputBean followUpCLIInputBean,
com.compomics.util.experiment.identification.Identification identification,
com.compomics.util.parameters.identification.search.ModificationParameters modificationParameters,
com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters,
com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
com.compomics.util.waiting.WaitingHandler waitingHandler)
Exports files needed by DeepLC.
|
static void |
exportDocumentation(ReportCLIInputBean reportCLIInputBean,
String reportType,
com.compomics.util.waiting.WaitingHandler waitingHandler)
Writes the documentation corresponding to an export given the command
line arguments.
|
static File |
exportInclusionList(FollowUpCLIInputBean followUpCLIInputBean,
com.compomics.util.experiment.identification.Identification identification,
com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator,
com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
com.compomics.util.parameters.identification.search.SearchParameters searchParameters,
com.compomics.util.waiting.WaitingHandler waitingHandler,
com.compomics.util.gui.filtering.FilterParameters filterPreferences)
Exports an inclusion list of the validated hits.
|
static ArrayList<File> |
exportMs2pip(FollowUpCLIInputBean followUpCLIInputBean,
com.compomics.util.experiment.identification.Identification identification,
com.compomics.util.parameters.identification.search.SearchParameters searchParameters,
com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters,
com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
com.compomics.util.waiting.WaitingHandler waitingHandler)
Exports the files needed by ms2pip.
|
static void |
exportMzId(MzidCLIInputBean mzidCLIInputBean,
PsdbParent psbdParent,
com.compomics.util.waiting.WaitingHandler waitingHandler)
Exports the project in the mzIdentML format.
|
static void |
exportPercolator(FollowUpCLIInputBean followUpCLIInputBean,
com.compomics.util.experiment.identification.Identification identification,
com.compomics.util.parameters.identification.search.SearchParameters searchParameters,
com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters,
com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters annotationParameters,
com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters modificationLocalizationParameters,
com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
com.compomics.util.waiting.WaitingHandler waitingHandler)
Exports the files needed by Percolator.
|
static File |
exportProgenesis(FollowUpCLIInputBean followUpCLIInputBean,
com.compomics.util.experiment.identification.Identification identification,
com.compomics.util.waiting.WaitingHandler waitingHandler,
com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider,
com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingPreferences)
Exports the identification in a Progenesis compatible format.
|
static File |
exportProteinSequences(FollowUpCLIInputBean followUpCLIInputBean,
com.compomics.util.experiment.identification.Identification identification,
com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
com.compomics.util.waiting.WaitingHandler waitingHandler,
com.compomics.util.gui.filtering.FilterParameters filteringPreferences)
Exports the protein details in FASTA format as specified in the follow-up
input bean.
|
static File |
exportProteoforms(FollowUpCLIInputBean followUpCLIInputBean,
com.compomics.util.experiment.identification.Identification identification,
com.compomics.util.waiting.WaitingHandler waitingHandler)
Exports proteoforms.
|
static File |
exportReport(ReportCLIInputBean reportCLIInputBean,
String reportType,
String experiment,
ProjectDetails projectDetails,
com.compomics.util.experiment.identification.Identification identification,
com.compomics.util.experiment.biology.genes.GeneMaps geneMaps,
com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator,
com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider,
com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
int nSurroundingAA,
com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters spectrumCountingPreferences,
com.compomics.util.waiting.WaitingHandler waitingHandler)
Writes an export according to the command line settings contained in the
reportCLIInputBean.
|
static ArrayList<File> |
exportSpectra(FollowUpCLIInputBean followUpCLIInputBean,
com.compomics.util.experiment.identification.Identification identification,
com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
com.compomics.util.waiting.WaitingHandler waitingHandler,
com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingPreferences)
Exports the spectra as specified in the follow-up input bean.
|
static ArrayList<File> |
recalibrateSpectra(FollowUpCLIInputBean followUpCLIInputBean,
com.compomics.util.experiment.identification.Identification identification,
com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
com.compomics.util.waiting.WaitingHandler waitingHandler)
Recalibrates spectra as specified in the follow-up input bean.
|
public static ArrayList<File> recalibrateSpectra(FollowUpCLIInputBean followUpCLIInputBean, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.waiting.WaitingHandler waitingHandler) throws IOException
followUpCLIInputBean - the follow up input beanidentification - the identificationsequenceProvider - the sequence providerspectrumProvider - The spectrum provider.identificationParameters - the identification parameterswaitingHandler - a waiting handler to display progressIOException - exception thrown whenever an IO exception occurred
while reading or writing to a filepublic static ArrayList<File> exportSpectra(FollowUpCLIInputBean followUpCLIInputBean, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingPreferences) throws IOException, SQLException, ClassNotFoundException, InterruptedException
followUpCLIInputBean - the follow up input beanidentification - the identificationspectrumProvider - The spectrum provider.waitingHandler - a waiting handler to display progresssequenceMatchingPreferences - the sequence matching preferencesIOException - exception thrown whenever an IO exception occurred
while reading or writing to a fileInterruptedException - exception thrown whenever a threading issue
occurred while interacting with the databaseSQLException - exception thrown whenever an SQL exception occurred
while interacting with the databaseClassNotFoundException - exception thrown whenever an exception
occurred while deserializing an objectpublic static File exportAccessions(FollowUpCLIInputBean followUpCLIInputBean, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.gui.filtering.FilterParameters filteringPreferences) throws IOException
followUpCLIInputBean - the follow up input beanidentification - the identificationsequenceProvider - the FASTA sequence providerwaitingHandler - a waiting handler to display progressfilteringPreferences - the filtering preferencesIOException - exception thrown whenever an IO exception occurred
while reading or writing to a filepublic static File exportProteinSequences(FollowUpCLIInputBean followUpCLIInputBean, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.gui.filtering.FilterParameters filteringPreferences) throws IOException
followUpCLIInputBean - the follow up input beanidentification - the identificationsequenceProvider - the FASTA sequence providerwaitingHandler - a waiting handler to display progressfilteringPreferences - the filtering preferencesIOException - exception thrown whenever an IO exception occurred
while reading or writing to a filepublic static File exportProgenesis(FollowUpCLIInputBean followUpCLIInputBean, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingPreferences) throws IOException
followUpCLIInputBean - the follow up input beanidentification - the identificationwaitingHandler - a waiting handler to display progresssequenceProvider - the sequence providerproteinDetailsProvider - the protein details providersequenceMatchingPreferences - the sequence matching preferencesIOException - exception thrown whenever an IO exception occurred
while reading or writing to a filepublic static File exportProteoforms(FollowUpCLIInputBean followUpCLIInputBean, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.waiting.WaitingHandler waitingHandler)
followUpCLIInputBean - the follow up input beanidentification - the identificationwaitingHandler - a waiting handler to display progresspublic static ArrayList<File> exportDeepLC(FollowUpCLIInputBean followUpCLIInputBean, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.search.ModificationParameters modificationParameters, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.waiting.WaitingHandler waitingHandler)
followUpCLIInputBean - the follow up input beanidentification - the identificationmodificationParameters - The modification parameters.sequenceMatchingParameters - The sequence matching parameters.sequenceProvider - The sequence provider.spectrumProvider - The spectrum provider.waitingHandler - The waiting handler.public static ArrayList<File> exportMs2pip(FollowUpCLIInputBean followUpCLIInputBean, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.waiting.WaitingHandler waitingHandler)
followUpCLIInputBean - the follow up input beanidentification - the identificationsearchParameters - The search parameters.sequenceMatchingParameters - The sequence matching parameters.sequenceProvider - The sequence provider.spectrumProvider - The spectrum provider.waitingHandler - The waiting handler.public static void exportPercolator(FollowUpCLIInputBean followUpCLIInputBean, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters annotationParameters, com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters modificationLocalizationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.waiting.WaitingHandler waitingHandler)
followUpCLIInputBean - the follow up input beanidentification - the identificationsearchParameters - The search parameters.sequenceMatchingParameters - The sequence matching parameters.annotationParameters - The annotation parameters.modificationLocalizationParameters - The modification localization
parameters.sequenceProvider - The sequence provider.spectrumProvider - The spectrum provider.waitingHandler - The waiting handler.public static File exportInclusionList(FollowUpCLIInputBean followUpCLIInputBean, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.gui.filtering.FilterParameters filterPreferences) throws IOException
followUpCLIInputBean - the follow up input beanidentification - the identificationidentificationFeaturesGenerator - the identification features
generatorspectrumProvider - The spectrum provider.searchParameters - the search parameterswaitingHandler - a waiting handler to display progressfilterPreferences - the filter preferencesIOException - exception thrown whenever an IO exception occurred
while reading or writing to a filepublic static File exportReport(ReportCLIInputBean reportCLIInputBean, String reportType, String experiment, ProjectDetails projectDetails, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.biology.genes.GeneMaps geneMaps, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, int nSurroundingAA, com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters spectrumCountingPreferences, com.compomics.util.waiting.WaitingHandler waitingHandler) throws IOException
reportCLIInputBean - the command line settingsreportType - the report typeexperiment - the experiment of the projectprojectDetails - the project details of the projectidentification - the identification of the projectgeneMaps - the gene mapsidentificationFeaturesGenerator - the identification features
generatoridentificationParameters - the identification parameters usedsequenceProvider - the sequence providerproteinDetailsProvider - the protein details providerspectrumProvider - The spectrum provider.nSurroundingAA - the number of amino acids to export on the side of
peptide sequencesspectrumCountingPreferences - the spectrum counting preferenceswaitingHandler - waiting handler displaying feedback to the userIOException - exception thrown whenever an IO exception occurred
while reading or writing to a filepublic static void exportDocumentation(ReportCLIInputBean reportCLIInputBean, String reportType, com.compomics.util.waiting.WaitingHandler waitingHandler) throws IOException
reportCLIInputBean - the command line argumentsreportType - the type of report of interestwaitingHandler - waiting handler displaying feedback to the userIOException - exception thrown whenever an IO exception occurred
while reading or writing to a filepublic static void exportMzId(MzidCLIInputBean mzidCLIInputBean, PsdbParent psbdParent, com.compomics.util.waiting.WaitingHandler waitingHandler) throws IOException
mzidCLIInputBean - the user inputpsbdParent - a psbd file parent allowing accessing the information it
containswaitingHandler - a waiting handler allowing display of progress and
interruption of the exportIOException - exception thrown whenever an IO exception occurred
while reading or writing to a fileCopyright © 2021. All rights reserved.