org.expasy.mzjava.proteomics.ms.consensus

Class PeptideConsensusSpectrum

java.lang.Object

org.expasy.mzjava.core.ms.spectrum.Spectrum<A>

org.expasy.mzjava.core.ms.consensus.ConsensusSpectrum<PepLibPeakAnnotation>

org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum

All Implemented Interfaces:

PeakList<PepLibPeakAnnotation>

public class PeptideConsensusSpectrum
extends ConsensusSpectrum<PepLibPeakAnnotation>

Version:

1.0

Author:

Oliver Horlacher

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static interface	PeptideConsensusSpectrum.AnnotationParametersSetter
static class	PeptideConsensusSpectrum.Builder
static class	PeptideConsensusSpectrum.BuilderOld
static interface	PeptideConsensusSpectrum.ConsensusParametersSetter
static interface	PeptideConsensusSpectrum.FilterParametersSetter
static class	PeptideConsensusSpectrum.Status

Nested classes/interfaces inherited from interface org.expasy.mzjava.core.ms.peaklist.PeakList

PeakList.Precision

Field Summary

Fields inherited from class org.expasy.mzjava.core.ms.consensus.ConsensusSpectrum

memberIds, name, precursorMzMean, precursorMzStdev, simScoreMean, simScoreStdev

Constructor Summary

Constructors

Modifier	Constructor and Description
	PeptideConsensusSpectrum(Peptide peptide) Construct a LibrarySpectrum for the peptide
protected	PeptideConsensusSpectrum(PeptideConsensusSpectrum src, PeakProcessor<PepLibPeakAnnotation,PepLibPeakAnnotation> peakProcessor) Copy constructor
protected	PeptideConsensusSpectrum(PeptideConsensusSpectrum src, PeakProcessorChain<PepLibPeakAnnotation> peakProcessorChain)
	PeptideConsensusSpectrum(Peptide peptide, int initialCapacity, PeakList.Precision precision) Construct a Spectrum that has an initial capacity of initialCapacity and a precision of precision
	PeptideConsensusSpectrum(Peptide peptide, int initialCapacity, PeakList.Precision precision, Set<UUID> memberIds) Construct a Spectrum that has an initial capacity of initialCapacity and a precision of precision
	PeptideConsensusSpectrum(Peptide peptide, PeakList.Precision precision) Construct a Spectrum that has a precision of precision
	PeptideConsensusSpectrum(Peptide peptide, PeakList.Precision precision, Set<UUID> memberIds) Construct a Spectrum that has a precision of precision
	PeptideConsensusSpectrum(Peptide peptide, PeakList.Precision precision, Set<UUID> memberIDs, Set<String> proteinAccessionNumbers)
	PeptideConsensusSpectrum(Peptide peptide, PeakList.Precision precision, Set<UUID> memberIDs, Set<String> proteinAccessionNumbers, RetentionTimeDiscrete retentionTimeDiscrete)
	PeptideConsensusSpectrum(Peptide peptide, Set<UUID> memberIds) Construct a LibrarySpectrum for the peptide

Method Summary

Methods

Modifier and Type	Method and Description
void	addProteinAccessionNumbers(Collection<String> accessionNumbers) Add all the accession numbers from accessionNumbers to the accession number list of this LibrarySpectrum
void	addProteinAccessionNumbers(String... acc) Add a protein accession number to the accession number list of this LibrarySpectrum
static PeptideConsensusSpectrum.BuilderOld	builder()
static PeptideConsensusSpectrum.ConsensusParametersSetter	builder(PeakList.Precision precision, URI spectrumSource)
void	clearProteinAccessionNumber() Clear the accession number list //review should this class be mutable?
PeptideConsensusSpectrum	copy(PeakProcessor<PepLibPeakAnnotation,PepLibPeakAnnotation> peakProcessor) Return PeakList copy processed with PeakProcessor
PeptideConsensusSpectrum	copy(PeakProcessorChain<PepLibPeakAnnotation> peakProcessorChain) Return PeakList copy processed with PeakProcessorChain
boolean	equals(Object o)
String	getComment() Return the comment
Peptide	getPeptide() Return the peptide
Set<String>	getProteinAccessionNumbers() Return an unmodifiable list containing the protein accession numbers associated with the peptide tha this LibrarySpectrum represents.
com.google.common.base.Optional<RetentionTimeDiscrete>	getRetentionTime()
URI	getSpectrumSource()
PeptideConsensusSpectrum.Status	getStatus() Returns this LibrarySpectrum's status.
int	hashCode()
void	setComment(String comment) Set the comment
void	setPeptide(Peptide peptide)
void	setRetentionTime(com.google.common.base.Optional<RetentionTimeDiscrete> retentionTime)
void	setSpectrumSource(URI spectrumSource)
void	setStatus(PeptideConsensusSpectrum.Status status) Set the status
String	toString()

Methods inherited from class org.expasy.mzjava.core.ms.consensus.ConsensusSpectrum

addMemberIds, getMemberIds, getName, getPrecursorMzMean, getPrecursorMzStdev, getSimScoreMean, getSimScoreStdev, nrOfMembers, setName, setPrecursorStats, setScoreStats

Methods inherited from class org.expasy.mzjava.core.ms.spectrum.Spectrum

add, add, add, addAnnotation, addAnnotations, addPeaks, addPeaks, addPeaksNoAnnotations, addSorted, addSorted, apply, apply, calcVectorLength, clear, clearAnnotations, clearAnnotationsAt, cursor, ensureCapacity, getAnnotationIndexes, getAnnotations, getBasePeakIntensity, getBasePeakMz, getClosestIndex, getFirstAnnotation, getId, getIntensities, getIntensities, getIntensities, getIntensity, getMostIntenseIndex, getMostIntenseIndex, getMsLevel, getMz, getMzs, getMzs, getMzs, getPrecision, getPrecursor, getTotalIonCurrent, hasAnnotations, hasAnnotationsAt, indexOf, indexOf, isEmpty, removeAnnotation, setId, setIntensityAt, setMsLevel, setPrecursor, size, sortAnnotations, trimToSize

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

PeptideConsensusSpectrum

public PeptideConsensusSpectrum(Peptide peptide)

Construct a LibrarySpectrum for the peptide

Parameters:

peptide - the peptide

PeptideConsensusSpectrum

public PeptideConsensusSpectrum(Peptide peptide,
                        Set<UUID> memberIds)

Construct a LibrarySpectrum for the peptide

Parameters:

peptide - the peptide

memberIds - UUIDs of member spectra

PeptideConsensusSpectrum

public PeptideConsensusSpectrum(Peptide peptide,
                        PeakList.Precision precision,
                        Set<UUID> memberIds)

Construct a Spectrum that has a precision of precision

Parameters:

peptide - the peptide

precision - the precision

PeptideConsensusSpectrum

public PeptideConsensusSpectrum(Peptide peptide,
                        PeakList.Precision precision)

Construct a Spectrum that has a precision of precision

Parameters:

peptide - the peptide

precision - the precision

PeptideConsensusSpectrum

public PeptideConsensusSpectrum(Peptide peptide,
                        int initialCapacity,
                        PeakList.Precision precision,
                        Set<UUID> memberIds)

Construct a Spectrum that has an initial capacity of initialCapacity and a precision of precision

Parameters:

peptide - the peptide

initialCapacity - the initial capacity

precision - the precision

PeptideConsensusSpectrum

public PeptideConsensusSpectrum(Peptide peptide,
                        PeakList.Precision precision,
                        Set<UUID> memberIDs,
                        Set<String> proteinAccessionNumbers)

PeptideConsensusSpectrum

public PeptideConsensusSpectrum(Peptide peptide,
                        PeakList.Precision precision,
                        Set<UUID> memberIDs,
                        Set<String> proteinAccessionNumbers,
                        RetentionTimeDiscrete retentionTimeDiscrete)

PeptideConsensusSpectrum

public PeptideConsensusSpectrum(Peptide peptide,
                        int initialCapacity,
                        PeakList.Precision precision)

Construct a Spectrum that has an initial capacity of initialCapacity and a precision of precision

Parameters:

peptide - the peptide

initialCapacity - the initial capacity

precision - the precision

PeptideConsensusSpectrum

protected PeptideConsensusSpectrum(PeptideConsensusSpectrum src,
                        PeakProcessor<PepLibPeakAnnotation,PepLibPeakAnnotation> peakProcessor)

Copy constructor

Parameters:

src - the LibrarySpectrum to copy

PeptideConsensusSpectrum

protected PeptideConsensusSpectrum(PeptideConsensusSpectrum src,
                        PeakProcessorChain<PepLibPeakAnnotation> peakProcessorChain)

Method Detail

builder

public static PeptideConsensusSpectrum.BuilderOld builder()

equals

public boolean equals(Object o)

Overrides:

equals in class ConsensusSpectrum<PepLibPeakAnnotation>

hashCode

public int hashCode()

Overrides:

hashCode in class ConsensusSpectrum<PepLibPeakAnnotation>

copy

public PeptideConsensusSpectrum copy(PeakProcessor<PepLibPeakAnnotation,PepLibPeakAnnotation> peakProcessor)

Description copied from interface: PeakList

Return PeakList copy processed with PeakProcessor

Specified by:

copy in interface PeakList<PepLibPeakAnnotation>

Overrides:

copy in class ConsensusSpectrum<PepLibPeakAnnotation>

Parameters:

peakProcessor - the processor to process the peaks

Returns:

the copy of this with the peaks processed by peakProcessor

copy

public PeptideConsensusSpectrum copy(PeakProcessorChain<PepLibPeakAnnotation> peakProcessorChain)

Description copied from interface: PeakList

Return PeakList copy processed with PeakProcessorChain

Specified by:

copy in interface PeakList<PepLibPeakAnnotation>

Overrides:

copy in class ConsensusSpectrum<PepLibPeakAnnotation>

Parameters:

peakProcessorChain - the processor chain to process the peaks

Returns:

the copy of this with the peaks processed by peakProcessorChain

getPeptide

public Peptide getPeptide()

Return the peptide

Returns:

the peptide

setPeptide

public void setPeptide(Peptide peptide)

addProteinAccessionNumbers

public void addProteinAccessionNumbers(String... acc)

Add a protein accession number to the accession number list of this LibrarySpectrum

Parameters:

acc - the protein accession number

addProteinAccessionNumbers

public void addProteinAccessionNumbers(Collection<String> accessionNumbers)

Add all the accession numbers from accessionNumbers to the accession number list of this LibrarySpectrum

Parameters:

accessionNumbers - the collection containing the accession numbers to add

clearProteinAccessionNumber

public void clearProteinAccessionNumber()

Clear the accession number list //review should this class be mutable?

getProteinAccessionNumbers

public Set<String> getProteinAccessionNumbers()

Return an unmodifiable list containing the protein accession numbers associated with the peptide tha this LibrarySpectrum represents.

Returns:

an unmodifiable list containing the protein accession numbers associated with the peptide tha this LibrarySpectrum represents

toString

public String toString()

Overrides:

toString in class Object

setStatus

public void setStatus(PeptideConsensusSpectrum.Status status)

Set the status

Parameters:

status - the status

getComment

public String getComment()

Return the comment

Returns:

the comment

setComment

public void setComment(String comment)

Set the comment

Parameters:

comment - the comment //review make immutable?

getStatus

public PeptideConsensusSpectrum.Status getStatus()

Returns this LibrarySpectrum's status.

Returns:

this LibrarySpectrum's status

getSpectrumSource

public URI getSpectrumSource()

setSpectrumSource

public void setSpectrumSource(URI spectrumSource)

setRetentionTime

public void setRetentionTime(com.google.common.base.Optional<RetentionTimeDiscrete> retentionTime)

getRetentionTime

public com.google.common.base.Optional<RetentionTimeDiscrete> getRetentionTime()

builder

public static PeptideConsensusSpectrum.ConsensusParametersSetter builder(PeakList.Precision precision,
                                                         URI spectrumSource)