public class DeepLcExport extends Object
| Constructor and Description |
|---|
DeepLcExport() |
| Modifier and Type | Method and Description |
|---|---|
static void |
deepLcExport(File destinationFile,
File confidentHitsDestinationFile,
HashSet<Long> keys,
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 DeepLC training file for the given spectrum file.
|
static ArrayList<File> |
deepLcExport(String destinationStem,
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 DeepLC training files for each of the spectrum files.
|
static File |
getConfidentHitsDestinationFile(String destinationStem,
String spectrumFile,
boolean addSuffix)
Returns the file where to write the export for confident hits.
|
static File |
getDestinationFile(String destinationStem,
String spectrumFile,
boolean addSuffix)
Returns the file where to write the export.
|
static ArrayList<File> |
getExportedFiles(String destinationStem,
com.compomics.util.experiment.identification.Identification identification)
Returns an ArrayList of all the files that will be written by the export.
|
public static ArrayList<File> deepLcExport(String destinationStem, 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)
destinationStem - The stem to use for the path.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.public static ArrayList<File> getExportedFiles(String destinationStem, com.compomics.util.experiment.identification.Identification identification)
destinationStem - The stem to use for the path.identification - The identification object containing the matches.public static File getDestinationFile(String destinationStem, String spectrumFile, boolean addSuffix)
destinationStem - The stem to use for the path.spectrumFile - The name of the spectrum file.addSuffix - A boolean indicating whehter the name of the spectrum
file should be appended to the stem.public static File getConfidentHitsDestinationFile(String destinationStem, String spectrumFile, boolean addSuffix)
destinationStem - The stem to use for the path.spectrumFile - The name of the spectrum file.addSuffix - A boolean indicating whehter the name of the spectrum
file should be appended to the stem.public static void deepLcExport(File destinationFile, File confidentHitsDestinationFile, HashSet<Long> keys, 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)
destinationFile - The file where to write the export.confidentHitsDestinationFile - The file where to write the export
for confident hits.keys - The keys of the spectrum matches.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.