public class Ms2PipExport extends Object
| Constructor and Description |
|---|
Ms2PipExport() |
| Modifier and Type | Method and Description |
|---|---|
static void |
ms2pipExport(File peprecFile,
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 a ms2pip training file for the given spectrum file.
|
static ArrayList<File> |
ms2pipExport(File peprecFile,
String[] models,
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 ms2pip config and peprec files.
|
static void |
writeConfigFile(File configFile,
String model,
com.compomics.util.parameters.identification.search.SearchParameters searchParameters)
Writes a config file for a given model.
|
public static ArrayList<File> ms2pipExport(File peprecFile, String[] models, 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)
peprecFile - The file where to write the peptides.models - The names of the models to write config files for.identification - The identification object containing the matches.searchParameters - The search parameters.sequenceMatchingParameters - The sequence matching parameters.sequenceProvider - The sequence provider.spectrumProvider - The spectrum provider.waitingHandler - The waiting handler.public static void writeConfigFile(File configFile, String model, com.compomics.util.parameters.identification.search.SearchParameters searchParameters)
configFile - The file where to write.model - The name of the model.searchParameters - The search parameters.public static void ms2pipExport(File peprecFile, 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)
peprecFile - The file where to write the export.identification - The identification object containing the matches.modificationParameters - The modification parameters.sequenceMatchingParameters - The sequence matching parameters.sequenceProvider - The sequence provider.spectrumProvider - The spectrum provider.waitingHandler - The waiting handler.Copyright © 2021. All rights reserved.