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

Class MzMLControllerImpl

java.lang.Object

uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzMLControllerImpl

All Implemented Interfaces:

MetaDataAccess, MzGraphDataAccess, PeptideDataAccess, ProteinDataAccess, ProteinGroupDataAccess, QuantDataAccess, DataAccessController

public class MzMLControllerImpl
extends CachedDataAccessController

MzMlControllerImpl provides methods to access mzML files.

Author:

Rui Wang, Yasset Perez-Riverol

Nested Class Summary

Nested classes/interfaces inherited from interface uk.ac.ebi.pride.utilities.data.controller.DataAccessController

DataAccessController.ContentCategory, DataAccessController.Type

Field Summary

Fields inherited from interface uk.ac.ebi.pride.utilities.data.controller.access.MzGraphDataAccess

CHROMATOGRAM_TYPE, MZGRAPH_TYPE, SPECTRUM_TYPE

Constructor Summary

Constructors

Constructor and Description
MzMLControllerImpl(File file) Construct a data access controller using a given mzML file

Method Summary

Methods

Modifier and Type	Method and Description
void	close() Close data access controller by resetting the data reader first
ParamGroup	getAdditional() In case of mzMl the additional parameters are related with the getFileContent This are a set of CVTerms related with the Content in the MzML File.
Chromatogram	getChromatogramById(Comparable id, boolean useCache) Get chromatogram using a chromatogram id, gives the option to choose whether to use cache.
List<CVLookup>	getCvLookups() Get a list of cvlookups, these are not cached
List<DataProcessing>	getDataProcessings() Get a list of data processings by checking the cache first
ExperimentMetaData	getExperimentMetaData() Get the Experiment Meta Data
ParamGroup	getFileContent() This summarizes the different types of spectra that can be expected in the file.
IdentificationMetaData	getIdentificationMetaData() The mzML do not contains Identification Metadata, just Spectrum Information
List<InstrumentConfiguration>	getInstrumentConfigurations() Get a list of instrument configurations by checking the cache first
MzGraphMetaData	getMzGraphMetaData() Get the Spectrum Metadata, the ScanSettings, The DataProcessing, and Instrument Configurations.
List<Organization>	getOrganizationContacts() Get a list of Organization contacts
List<Person>	getPersonContacts() Get a list of person contacts
ReferenceableParamGroup	getReferenceableParamGroup() Get referenceable paramgroup, this concept is only available in mzML It is a paramgroup with id and this is not cached
List<Sample>	getSamples() Get a list of samples by checking the cache first
List<ScanSetting>	getScanSettings() Get a list of scan settings by checking the cache first
List<Software>	getSoftwares() Get a List of Softwares
List<SourceFile>	getSourceFiles() Get a List of SourceFiles
String	getUid() Get the unique id for this data access controller It generates a MD5 hash using the absolute path of the file This will guarantee the same id if the file path is the same
MzMLUnmarshallerAdaptor	getUnmarshaller() Get the backend data reader
boolean	hasProtein() This method provide the way to know if the controller contain Identification Data and IdentificationMetadata.
static boolean	isValidFormat(File file) Check a file is mzML file

Methods inherited from class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.CachedDataAccessController

getAvailablePeptideLevelScores, getAvailableProteinLevelScores, getCache, getCachingStrategy, getChromatogramById, getChromatogramIds, getMode, getNumberOfFragmentIons, getNumberOfPeptides, getNumberOfPTMs, getNumberOfPTMs, getNumberOfSpectrumPeaks, getNumberOfUniquePeptides, getPeptideByIndex, getPeptideByIndex, getPeptideIds, getPeptidePrecursorCharge, getPeptidePrecursorMz, getPeptideQuantUnit, getPeptidesBySpectrum, getPeptideScore, getPeptideSequence, getPeptideSequenceEnd, getPeptideSequences, getPeptideSequenceStart, getPeptideSpectrumId, getProteinAccession, getProteinAccessionVersion, getProteinAmbiguityGroupById, getProteinAmbiguityGroupIds, getProteinById, getProteinIds, getProteinQuantUnit, getProteinScore, getProteinThreshold, getPTMs, getSearchDatabase, getSearchDatabaseVersion, getSearchEngineCvTermReferences, getSpectraDataBasedOnTitle, getSpectrumById, getSpectrumIdForPeptide, getSpectrumIds, getSpectrumMsLevel, getSpectrumPrecursorCharge, getSpectrumPrecursorIntensity, getSpectrumPrecursorMz, getSumOfIntensity, isSpectrumBasedOnTitle, populateCache, setCachingStrategy, setMode

Methods inherited from class uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.AbstractDataAccessController

getAvailableQuantPeptideLevelScores, getChromatogramByIndex, getChromatogramIndex, getContentCategories, getFragmentIons, getIsotopeLabellingQuantMethods, getLabelFreeQuantMethods, getName, getNumberOfChromatograms, getNumberOfIdentifiedSpectra, getNumberOfPeptides, getNumberOfPeptidesByRank, getNumberOfProteinAmbiguityGroups, getNumberOfProteins, getNumberOfQuantPeptides, getNumberOfQuantPeptides, getNumberOfQuantPTMs, getNumberOfQuantPTMs, getNumberOfReagents, getNumberOfSpectra, getNumberOfSubstitutionPTMs, getNumberOfSubstitutionPTMs, getNumberOfUniqueQuantPeptides, getPeptideEvidences, getPeptideIsotopeLabellingQuantMethods, getPeptideLabelFreeQuantMethods, getPeptideQuantData, getPeptideQuantStudyData, getPeptideRank, getPeptideTheoreticalMz, getProteinByIndex, getProteinCoverage, getProteinIsotopeLabellingQuantMethods, getProteinLabelFreeQuantMethods, getProteinQuantData, getProteinQuantStudyData, getProteinScores, getProteinSequence, getQuantMethods, getQuantPeptideByIndex, getQuantPeptideEvidences, getQuantPeptideIds, getQuantPeptideQuantScore, getQuantPeptideScore, getQuantPeptideSequence, getQuantPeptideSequences, getQuantPeptideSpectrumId, getQuantPTMs, getQuantSample, getReferenceSubSampleIndex, getSource, getSpectraByIndex, getSpectrumIndex, getStudyVariables, getSubstitutionPTMs, getType, hasChromatogram, hasDecoyInformation, hasIsotopeLabellingQuantMethods, hasLabelFreeQuantMethods, hasMetaDataInformation, hasPeptide, hasPeptideQuantData, hasPeptideTotalIntensities, hasProteinAmbiguityGroup, hasProteinQuantData, hasProteinSequence, hasProteinTotalIntensities, hasQuantData, hasQuantPeptide, hasSpectrum, indexOfProtein, isIdentifiedSpectrum, proteinsAreInferred, setContentCategories, setInferredProteinGroups, setName, setSource, setType, setUid

Methods inherited from class java.lang.Object

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

Constructor Detail

MzMLControllerImpl

public MzMLControllerImpl(File file)

Construct a data access controller using a given mzML file

Parameters:

file - mzML file

Method Detail

getUnmarshaller

public MzMLUnmarshallerAdaptor getUnmarshaller()

Get the backend data reader

Returns:

MzMLUnmarshallerAdaptor mzML reader

getUid

public String getUid()

Get the unique id for this data access controller It generates a MD5 hash using the absolute path of the file This will guarantee the same id if the file path is the same

Specified by:

getUid in interface DataAccessController

Overrides:

getUid in class AbstractDataAccessController

Returns:

String unique id

getCvLookups

public List<CVLookup> getCvLookups()

Get a list of cvlookups, these are not cached

Returns:

List a list of cvlookups

getReferenceableParamGroup

public ReferenceableParamGroup getReferenceableParamGroup()

Get referenceable paramgroup, this concept is only available in mzML It is a paramgroup with id and this is not cached

Returns:

ReferenceableParamGroup param group

getSamples

public List<Sample> getSamples()

Get a list of samples by checking the cache first

Overrides:

getSamples in class AbstractDataAccessController

Returns:

List a list of samples

getPersonContacts

public List<Person> getPersonContacts()

Get a list of person contacts

Returns:

List list of persons

getOrganizationContacts

public List<Organization> getOrganizationContacts()

Get a list of Organization contacts

Returns:

List list of persons

getSourceFiles

public List<SourceFile> getSourceFiles()

Get a List of SourceFiles

Returns:

List List of SourceFile

getFileContent

public ParamGroup getFileContent()

This summarizes the different types of spectra that can be expected in the file. This is expected to aid processing software in skipping files that do not contain appropriate spectrum types for it. It should also describe the nativeID format used in the file by referring to an appropriate CV term.

Returns:

ParamGroup A list of CvTerms Related with the File Content

getSoftwares

public List<Software> getSoftwares()

Get a List of Softwares

Returns:

List List of Softwares

getScanSettings

public List<ScanSetting> getScanSettings()

Get a list of scan settings by checking the cache first

Returns:

List a list of scan settings

getInstrumentConfigurations

public List<InstrumentConfiguration> getInstrumentConfigurations()

Get a list of instrument configurations by checking the cache first

Returns:

List a list of instrument configurations

getDataProcessings

public List<DataProcessing> getDataProcessings()

Get a list of data processings by checking the cache first

Returns:

List a list of data processings

getAdditional

public ParamGroup getAdditional()

In case of mzMl the additional parameters are related with the getFileContent This are a set of CVTerms related with the Content in the MzML File. Also we add the the Date of the Run as a CvParam, it is very important to know when this information was generated.

Overrides:

getAdditional in class AbstractDataAccessController

Returns:

ParamGroup param group

getChromatogramById

public Chromatogram getChromatogramById(Comparable id,
                               boolean useCache)

Get chromatogram using a chromatogram id, gives the option to choose whether to use cache. This implementation provides a way of by passing the cache.

Overrides:

getChromatogramById in class CachedDataAccessController

Parameters:

id - chromatogram id

useCache - true means to use cache

Returns:

Chromatogram chromatogram object

close

public void close()

Close data access controller by resetting the data reader first

Specified by:

close in interface DataAccessController

Overrides:

close in class CachedDataAccessController

getExperimentMetaData

public ExperimentMetaData getExperimentMetaData()

Description copied from class: CachedDataAccessController

Get the Experiment Meta Data

Specified by:

getExperimentMetaData in interface MetaDataAccess

Overrides:

getExperimentMetaData in class CachedDataAccessController

Returns:

ExperimentMetaData

getMzGraphMetaData

public MzGraphMetaData getMzGraphMetaData()

Get the Spectrum Metadata, the ScanSettings, The DataProcessing, and Instrument Configurations.

Specified by:

getMzGraphMetaData in interface MetaDataAccess

Overrides:

getMzGraphMetaData in class CachedDataAccessController

Returns:

MzGraphMetaData is the Metadata related with Spectrum Information

getIdentificationMetaData

public IdentificationMetaData getIdentificationMetaData()

The mzML do not contains Identification Metadata, just Spectrum Information

Specified by:

getIdentificationMetaData in interface MetaDataAccess

Overrides:

getIdentificationMetaData in class CachedDataAccessController

Returns:

The MzML do not support Identification Metadata

hasProtein

public boolean hasProtein()

This method provide the way to know if the controller contain Identification Data and IdentificationMetadata.

Specified by:

hasProtein in interface ProteinDataAccess

Overrides:

hasProtein in class AbstractDataAccessController

Returns:

True if the DataAccessController contains Proteins

isValidFormat

public static boolean isValidFormat(File file)

Check a file is mzML file

Parameters:

file - input file

Returns:

boolean true means mzML