uk.ac.ebi.pride.utilities.data.controller

Class DataAccessUtilities

java.lang.Object

uk.ac.ebi.pride.utilities.data.controller.DataAccessUtilities

public final class DataAccessUtilities
extends Object

DataAccessUtilities provides methods for getting information out from the core objects.

Author:

Rui Wang, Yasset Perez-Riverol

Field Summary

Fields

Modifier and Type	Field and Description
static org.slf4j.Logger	logger

Method Summary

Methods

Modifier and Type	Method and Description
static List<CvParam>	getCvParam(ParamGroup paramGroup, String cvLabel, String accession) Get cv param by accession number and cv label.
static List<CvParam>	getCvParam(String name, String cvLabel, String accession, String value) Create a List of Cv Params
static int	getMsLevel(Spectrum spectrum) Get ms level of a spectrum
static int	getNumberOfPeaks(Spectrum spectrum) Count the number of peaks of a spectrum
static int	getNumberOfPeptides(Protein ident) Convenient method for number of peptides
static int	getNumberOfPTMs(Peptide peptide) Get the number of the modification of a peptide
static int	getNumberOfPTMs(Protein ident) Get the number of post translational modifications within a protein identification
static int	getNumberOfSubstitutionPTMs(Peptide peptide) Get the number of substitution modification of a peptide
static int	getNumberOfSubstitutionPTMs(Protein ident) Get the number of Substitution PTMs for an specific Protein Identification
static int	getNumberOfUniquePeptides(Protein ident) Convenient method for getting the number of unique peptides.
static List<Parameter>	getParamByName(ParamGroup paramGroup, String name) Get a list parameters using a given name.
static Peptide	getPeptide(Protein ident, int index) This is convenient method for accessing peptide.
static Map<PeptideEvidence,List<Peptide>>	getPeptideEvidence(List<Peptide> peptides) Get peptide Evidence for a Lis of Peptide Identifications
static Integer	getPrecursorCharge(List<Precursor> precursors)
static Integer	getPrecursorChargeParamGroup(ParamGroup paramGroup) Get precursor charge from param group
static double	getPrecursorIntensity(Spectrum spectrum) Get precursor intensity
static double	getPrecursorMz(ParamGroup paramGroup) Get precursor m/z value
static double	getPrecursorMz(Spectrum spectrum) Get precursor m/z value
static String	getProjectName(ExperimentMetaData metaData) Get the project of a experiment
static Integer	getProteinCoverage(Protein protein) Number of amino acids covered
static QuantPeptide	getQuantPeptide(Protein ident, int index) This is convenient method for accessing peptide.
static String	getRetentionTime(uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem oldSpectrumIdentification)
static Score	getScore(ParamGroup params)
static List<uk.ac.ebi.pride.utilities.term.SearchEngineCvTermReference>	getSearchEngineCvTermReference(ParamGroup paramGroup)
static List<uk.ac.ebi.pride.utilities.term.SearchEngineScoreCvTermReference>	getSearchEngineScoresCvTermReference(ParamGroup paramGroup)
static List<uk.ac.ebi.pride.utilities.term.SearchEngineCvTermReference>	getSearchEngineTypes(ParamGroup paramGroup) Deprecated.
static Double	getSelectedIonCharge(Precursor precursor, int index) Get the ion charge for a selected ion.
static Double	getSelectedIonIntensity(Precursor precursor, int index) Get the ion intensity value for a selected ion.
static Double	getSelectedIonMz(Precursor precursor, int index) Get the ion m/z value for a selected ion.
static double	getSumOfIntensity(Spectrum spectrum) Get the sum of all the peak intensities within a spectrum
static List<String>	getTaxonomy(ExperimentMetaData metaData) Get a list of taxonomy accessions based on a given metadata
static boolean	hasFragmentIon(Peptide peptide) Check whether peptide has fragment ion information
static boolean	hasFragmentIon(Spectrum spectrum) Check whether spectrum has fragment ion information

Methods inherited from class java.lang.Object

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

Field Detail

logger

public static final org.slf4j.Logger logger

Method Detail

getTaxonomy

public static List<String> getTaxonomy(ExperimentMetaData metaData)

Get a list of taxonomy accessions based on a given metadata

Parameters:

metaData - meta data

Returns:

List a list of taxonomy ids

getProjectName

public static String getProjectName(ExperimentMetaData metaData)

Get the project of a experiment

Parameters:

metaData - experiment metadata

Returns:

String project name

getNumberOfPeaks

public static int getNumberOfPeaks(Spectrum spectrum)

Count the number of peaks of a spectrum

Parameters:

spectrum - spectrum

Returns:

int number of peaks

getMsLevel

public static int getMsLevel(Spectrum spectrum)

Get ms level of a spectrum

Parameters:

spectrum - spectrum

Returns:

int ms level

getPrecursorChargeParamGroup

public static Integer getPrecursorChargeParamGroup(ParamGroup paramGroup)

Get precursor charge from param group

Parameters:

paramGroup - param group

Returns:

precursor charge

getPrecursorMz

public static double getPrecursorMz(Spectrum spectrum)

Get precursor m/z value

Parameters:

spectrum - spectrum

Returns:

double precursor m/z

getPrecursorMz

public static double getPrecursorMz(ParamGroup paramGroup)

Get precursor m/z value

Parameters:

paramGroup - param group

Returns:

precursor m/z

getPrecursorIntensity

public static double getPrecursorIntensity(Spectrum spectrum)

Get precursor intensity

Parameters:

spectrum - spectrum

Returns:

double precursor intensity

getSumOfIntensity

public static double getSumOfIntensity(Spectrum spectrum)

Get the sum of all the peak intensities within a spectrum

Parameters:

spectrum - spectrum

Returns:

double sum of intensities

getSelectedIonCharge

public static Double getSelectedIonCharge(Precursor precursor,
                          int index)

Get the ion charge for a selected ion.

Parameters:

precursor - precursor

index - index of the selected ion.

Returns:

Double selected ion charge.

getSelectedIonMz

public static Double getSelectedIonMz(Precursor precursor,
                      int index)

Get the ion m/z value for a selected ion.

Parameters:

precursor - precursor

index - index of the selected ion.

Returns:

Double selected ion m/z.

getSelectedIonIntensity

public static Double getSelectedIonIntensity(Precursor precursor,
                             int index)

Get the ion intensity value for a selected ion.

Parameters:

precursor - precursor

index - index of the selected ion.

Returns:

Double selected ion intensity.

getPeptide

public static Peptide getPeptide(Protein ident,
                 int index)

This is convenient method for accessing peptide.

Parameters:

ident - identification object

index - zero based index.

Returns:

Peptide peptide.

getQuantPeptide

public static QuantPeptide getQuantPeptide(Protein ident,
                           int index)

This is convenient method for accessing peptide.

Parameters:

ident - identification object

index - zero based index.

Returns:

Peptide peptide.

getNumberOfPeptides

public static int getNumberOfPeptides(Protein ident)

Convenient method for number of peptides

Parameters:

ident - identification object

Returns:

int number of peptides

getNumberOfUniquePeptides

public static int getNumberOfUniquePeptides(Protein ident)

Convenient method for getting the number of unique peptides.

Parameters:

ident - identification object

Returns:

int number of unique peptide sequences.

hasFragmentIon

public static boolean hasFragmentIon(Spectrum spectrum)

Check whether spectrum has fragment ion information

Parameters:

spectrum - spectrum

Returns:

boolean true if spectrum contains fragment ion information.

hasFragmentIon

public static boolean hasFragmentIon(Peptide peptide)

Check whether peptide has fragment ion information

Parameters:

peptide - peptide

Returns:

boolean true if peptide contains fragment ion information.

getNumberOfPTMs

public static int getNumberOfPTMs(Protein ident)

Get the number of post translational modifications within a protein identification

Parameters:

ident - protein identification

Returns:

int number of ptms

getNumberOfSubstitutionPTMs

public static int getNumberOfSubstitutionPTMs(Protein ident)

Get the number of Substitution PTMs for an specific Protein Identification

Parameters:

ident - ID of the Protein Identification

Returns:

Total number of Substitution PTMs

getNumberOfPTMs

public static int getNumberOfPTMs(Peptide peptide)

Get the number of the modification of a peptide

Parameters:

peptide - Peptide Object

Returns:

Total number of PTMs

getNumberOfSubstitutionPTMs

public static int getNumberOfSubstitutionPTMs(Peptide peptide)

Get the number of substitution modification of a peptide

Parameters:

peptide - Peptide

Returns:

Total number of Substitution PTMs

getSearchEngineTypes

@Deprecated
public static List<uk.ac.ebi.pride.utilities.term.SearchEngineCvTermReference> getSearchEngineTypes(ParamGroup paramGroup)

Deprecated.

Search and find a list of search engine types from input parameter group.

Parameters:

paramGroup - parameter group

Returns:

List a list of search engine

getScore

public static Score getScore(ParamGroup params)

getSearchEngineCvTermReference

public static List<uk.ac.ebi.pride.utilities.term.SearchEngineCvTermReference> getSearchEngineCvTermReference(ParamGroup paramGroup)

getSearchEngineScoresCvTermReference

public static List<uk.ac.ebi.pride.utilities.term.SearchEngineScoreCvTermReference> getSearchEngineScoresCvTermReference(ParamGroup paramGroup)

getCvParam

public static List<CvParam> getCvParam(ParamGroup paramGroup,
                       String cvLabel,
                       String accession)

Get cv param by accession number and cv label. This method tries to find the CvParam for the given accession and cvLabel. IMPORTANT NOTE: As the cvLabel may not always be present, the method will assume a valid match if the accession alone matches.

ToDo: perhaps separate method without cvLabel would be better (then this one could fail if no cvLabel was found)

Parameters:

paramGroup - parameter group

cvLabel - cv label.

accession - cv accession.

Returns:

CvParam cv param.

getCvParam

public static List<CvParam> getCvParam(String name,
                       String cvLabel,
                       String accession,
                       String value)

Create a List of Cv Params

Parameters:

value - Value of the CvParam

cvLabel - Label of the CvParam

accession - Accession of the CvParam

name - Name

Returns:

List

getParamByName

public static List<Parameter> getParamByName(ParamGroup paramGroup,
                             String name)

Get a list parameters using a given name.

Parameters:

paramGroup - parameter group

name - name string

Returns:

List a list of parameters

getPeptideEvidence

public static Map<PeptideEvidence,List<Peptide>> getPeptideEvidence(List<Peptide> peptides)

Get peptide Evidence for a Lis of Peptide Identifications

Parameters:

peptides - List of Peptide Identifications

Returns:

Map with Peptide Evidence an the List of Peptide Identifications related with this peptide Evidence

getPrecursorCharge

public static Integer getPrecursorCharge(List<Precursor> precursors)

getProteinCoverage

public static Integer getProteinCoverage(Protein protein)

Number of amino acids covered

Parameters:

protein - Protein to compute the Coverage

Returns:

Number of Amino acids Identified

getRetentionTime

public static String getRetentionTime(uk.ac.ebi.jmzidml.model.mzidml.SpectrumIdentificationItem oldSpectrumIdentification)