io.github.bigbio.pgatk.io.pride

Class AnnotatedSpectrum

java.lang.Object

io.github.bigbio.pgatk.io.pride.AnnotatedSpectrum

All Implemented Interfaces:

Spectrum, Serializable

public class AnnotatedSpectrum
extends Object
implements Spectrum

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
AnnotatedSpectrum()
AnnotatedSpectrum(String usi, String pepSequence, String peptidoform, List<String> proteinAccessions, List<String> geneAccessions, List<AccessionLocalization> proteinLocalizations, List<GeneCoordinates> geneLocalizations, String sampleAccession, String organism, List<AvroTuple> sample, List<AvroTuple> biologicalAnnotations, double precursorMz, Integer precursorCharge, List<AvroModification> modifications, List<Double> masses, List<Double> intensities, Double retentionTime, Integer msLevel, Integer missedCleavages, List<AvroTerm> qualityScores, List<AvroTuple> msAnnotations, String pxAccession, Boolean isDecoy, Double peptideIntensity)

Method Summary

Modifier and Type	Method and Description
Collection<? extends Param>	getAdditional() Retrieves file format specific variables as parameters.
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.
List<Double>	getIntensities()
List<Double>	getMasses()
Integer	getMsLevel() Returns the msLevel of the spectrum.
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.
Integer	getPrecursorCharge() Returns the spectrum's charge or null in case the charge is not available.
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.
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

AnnotatedSpectrum

public AnnotatedSpectrum()

AnnotatedSpectrum

public AnnotatedSpectrum(String usi,
                         String pepSequence,
                         String peptidoform,
                         List<String> proteinAccessions,
                         List<String> geneAccessions,
                         List<AccessionLocalization> proteinLocalizations,
                         List<GeneCoordinates> geneLocalizations,
                         String sampleAccession,
                         String organism,
                         List<AvroTuple> sample,
                         List<AvroTuple> biologicalAnnotations,
                         double precursorMz,
                         Integer precursorCharge,
                         List<AvroModification> modifications,
                         List<Double> masses,
                         List<Double> intensities,
                         Double retentionTime,
                         Integer msLevel,
                         Integer missedCleavages,
                         List<AvroTerm> qualityScores,
                         List<AvroTuple> msAnnotations,
                         String pxAccession,
                         Boolean isDecoy,
                         Double peptideIntensity)

Method Detail

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

getPrecursorCharge

public Integer getPrecursorCharge()

Description copied from interface: Spectrum

Returns the spectrum's charge or null in case the charge is not available.

Specified by:

getPrecursorCharge in interface Spectrum

Returns:

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:

getMsLevel

public Integer getMsLevel()

Description copied from interface: Spectrum

Returns the msLevel of the spectrum. NULL in case the MS level is not available or unknown.

Specified by:

getMsLevel 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.

toString

public String toString()

Overrides:

toString in class Object

getMasses

public List<Double> getMasses()

getIntensities

public List<Double> getIntensities()