eu.isas.peptideshaker.utils

Class DeepLcUtils

java.lang.Object

eu.isas.peptideshaker.utils.DeepLcUtils

public class DeepLcUtils
extends Object

Utils for the export and import of ms2pip results.

Author:

Marc Vaudel, Dafni Skiadopoulou

Constructor Summary

Constructors

Constructor and Description
DeepLcUtils()

Method Summary

Modifier and Type	Method and Description
static String	getModifications(com.compomics.util.experiment.biology.proteins.Peptide peptide, com.compomics.util.parameters.identification.search.ModificationParameters modificationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, com.compomics.util.experiment.biology.modifications.ModificationFactory modificationFactory) Returns the modifications of the peptides encoded as required by DeepLc.
static String	getPeptideData(com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption peptideAssumption, double retentionTime, com.compomics.util.parameters.identification.search.ModificationParameters modificationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, com.compomics.util.experiment.biology.modifications.ModificationFactory modificationFactory) Gets the peptide data to provide to ms2pip.
static long	getPeptideKey(String peptideData) Returns a unique key corresponding to the given peptide.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

DeepLcUtils

public DeepLcUtils()

Method Detail

getPeptideData

public static String getPeptideData(com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption peptideAssumption,
                                    double retentionTime,
                                    com.compomics.util.parameters.identification.search.ModificationParameters modificationParameters,
                                    com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
                                    com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters,
                                    com.compomics.util.experiment.biology.modifications.ModificationFactory modificationFactory)

Gets the peptide data to provide to ms2pip.

Parameters:

peptideAssumption - The peptide assumption.

retentionTime - The retention time when the peptide was measured.

modificationParameters - The modification parameters of the search.

sequenceMatchingParameters - The sequence matching parameters.

sequenceProvider - The sequence provider.

modificationFactory - The factory containing the modification details

Returns:

The peptide data as string.

getModifications

public static String getModifications(com.compomics.util.experiment.biology.proteins.Peptide peptide,
                                      com.compomics.util.parameters.identification.search.ModificationParameters modificationParameters,
                                      com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
                                      com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters,
                                      com.compomics.util.experiment.biology.modifications.ModificationFactory modificationFactory)

Returns the modifications of the peptides encoded as required by DeepLc.

Parameters:

peptide - The pepitde.

modificationParameters - The modification parameters of the search.

sequenceMatchingParameters - The sequence matching parameters.

sequenceProvider - The sequence provider.

modificationFactory - The factory containing the modification details

Returns:

the modifications of the peptides encoded as required by DeepLc.

getPeptideKey

public static long getPeptideKey(String peptideData)

Returns a unique key corresponding to the given peptide.

Parameters:

peptideData - The peptide data as string.

Returns:

The unique key corresponding to the peptide data.