io.github.bigbio.pgatk.io.pride

Class ArchiveSpectrum

java.lang.Object

io.github.bigbio.pgatk.io.pride.ArchiveSpectrum

All Implemented Interfaces:

Spectrum, Serializable

public class ArchiveSpectrum
extends Object
implements Spectrum

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
ArchiveSpectrum()
ArchiveSpectrum(String usi, String projectAccession, String assayAccession, String spectrumFile, String sourceID, String spectrumTitle, Double[] masses, Double[] intensities, Integer numPeaks, Integer msLevel, Integer precursorCharge, Double precursorMz, Double retentionTime, Set<CvParam> properties, String peptideSequence, Integer missedCleavages, Collection<IdentifiedModification> modifications, List<String> annotations, Boolean isDecoy, Set<CvParam> qualityEstimationMethods, Boolean isValid, List<String> proteinAccessions, List<String> geneAccessions)

Method Summary

Modifier and Type	Method and Description
Collection<? extends Param>	getAdditional() Retrieves file format specific variables as parameters.
Collection<? extends String>	getAdditionalAttributesStrings()
Collection<? extends CvParam>	getAttributes()
String	getId() The textual representation of an ID of a scan.
Long	getIndex() Internal Spectrum in the corresponding file MGF or mzXML or mzML, starting from 1, incrementing by one for each consecutive spectrum.
Collection<String>	getModificationNames()
Integer	getNumberModifiedSites()
Map<Double,Double>	getPeakList() Returns the spectrum's peak list as a HashMap with the m/z values as keys and the corresponding intensities as values.
Double	getPrecursorIntensity() Returns the precursor's intensity or null in case it it not available.
Double	getPrecursorMZ() Returns the precursor's m/z or null in case the precursor's m/z is not available.
Boolean	isDecoy()
Boolean	isValid()

Methods inherited from class java.lang.Object

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

Methods inherited from interface io.github.bigbio.pgatk.io.common.spectra.Spectrum

getMsLevel, getPrecursorCharge

Constructor Detail

ArchiveSpectrum

public ArchiveSpectrum()

ArchiveSpectrum

public ArchiveSpectrum(String usi,
                       String projectAccession,
                       String assayAccession,
                       String spectrumFile,
                       String sourceID,
                       String spectrumTitle,
                       Double[] masses,
                       Double[] intensities,
                       Integer numPeaks,
                       Integer msLevel,
                       Integer precursorCharge,
                       Double precursorMz,
                       Double retentionTime,
                       Set<CvParam> properties,
                       String peptideSequence,
                       Integer missedCleavages,
                       Collection<IdentifiedModification> modifications,
                       List<String> annotations,
                       Boolean isDecoy,
                       Set<CvParam> qualityEstimationMethods,
                       Boolean isValid,
                       List<String> proteinAccessions,
                       List<String> geneAccessions)

Method Detail

getAdditionalAttributesStrings

public Collection<? extends String> getAdditionalAttributesStrings()

getModificationNames

public Collection<String> getModificationNames()

getNumberModifiedSites

public Integer getNumberModifiedSites()

isDecoy

public Boolean isDecoy()

getAttributes

public Collection<? extends CvParam> getAttributes()

isValid

public Boolean isValid()

getIndex

public Long getIndex()

Description copied from interface: Spectrum

Internal Spectrum in the corresponding file MGF or mzXML or mzML, starting from 1, incrementing by one for each consecutive spectrum. This is the number is used in the mzIdentML and mzTab files to reference the Spectrum.

Specified by:

getIndex in interface Spectrum

getId

public String getId()

Description copied from interface: Spectrum

The textual representation of an ID of a scan. mzML provides those IDs by default, in mzXML there is no such element, so this will return the same as Spectrum.getIndex()}.

Specified by:

getId in interface Spectrum

getPrecursorMZ

public Double getPrecursorMZ()

Description copied from interface: Spectrum

Returns the precursor's m/z or null in case the precursor's m/z is not available.

Specified by:

getPrecursorMZ in interface Spectrum

Returns:

getPrecursorIntensity

public Double getPrecursorIntensity()

Description copied from interface: Spectrum

Returns the precursor's intensity or null in case it it not available.

Specified by:

getPrecursorIntensity in interface Spectrum

Returns:

getPeakList

public Map<Double,Double> getPeakList()

Description copied from interface: Spectrum

Returns the spectrum's peak list as a HashMap with the m/z values as keys and the corresponding intensities as values.

Specified by:

getPeakList in interface Spectrum

Returns:

getAdditional

public Collection<? extends Param> getAdditional()

Description copied from interface: Spectrum

Retrieves file format specific variables as parameters. Whenever possible cvParams from the MS ontology will be used to report these additional fields.

Specified by:

getAdditional in interface Spectrum

Returns:

A ParamGroup containing the additional fields as parameters.