eu.isas.peptideshaker.utils

Class Ms2PipUtils

java.lang.Object

eu.isas.peptideshaker.utils.Ms2PipUtils

public class Ms2PipUtils
extends Object

Utils for the export and import of ms2pip results.

Author:

Marc Vaudel, Dafni Skiadopoulou

Constructor Summary

Constructors

Constructor and Description
Ms2PipUtils()

Method Summary

Modifier and Type	Method and Description
static String	getPeptideData(com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption peptideAssumption, 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

Ms2PipUtils

public Ms2PipUtils()

Method Detail

getPeptideData

public static String getPeptideData(com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption peptideAssumption,
                                    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.

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.

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.