uk.ac.ebi.pride.utilities.data.core

Class Spectrum

java.lang.Object

uk.ac.ebi.pride.utilities.data.core.ParamGroup

uk.ac.ebi.pride.utilities.data.core.IdentifiableParamGroup

uk.ac.ebi.pride.utilities.data.core.MzGraph

uk.ac.ebi.pride.utilities.data.core.Spectrum

All Implemented Interfaces:

Serializable, Cloneable, MassSpecObject

public class Spectrum
extends MzGraph
implements Cloneable

A peak list including the underlying acquisitions.

In mzML 1.1.0.1, it should the following cv terms:

1. It may have only one "scan polarity" (negative scan, positive scan).

2. It must have only one "spectrum type" (charge inversion mass spectrum, constant neutral gain spectrum and et al)

3. It must have only one "spectrum representation" or any of its children. (centroid spectrum, profile spectrum)

4. It may have one or more "spectrum attribute" (total ion current, zoom scan, base peak m/z, ms level, spectrum title and etc al)

Author:

Yasset Perez-Riverol, Rui Wang Date: 03-Feb-2010 Time: 08:46:05

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
Spectrum(Comparable id, String name, int index, DataProcessing defaultDataProcessing, int defaultArrayLength, List<BinaryDataArray> binaryDataArrays, String spotID, SourceFile sourceFile, ScanList scanList, List<Precursor> precursors, List<ParamGroup> products, List<Peptide> peptide)
Spectrum(ParamGroup params, Comparable id, String name, int index, DataProcessing defaultDataProcessing, int defaultArrayLength, List<BinaryDataArray> binaryDataArrays, String spotID, SourceFile sourceFile, ScanList scanList, List<Precursor> precursors, List<ParamGroup> products)
Spectrum(ParamGroup params, Comparable id, String name, int index, DataProcessing defaultDataProcessing, int defaultArrayLength, List<BinaryDataArray> binaryDataArrays, String spotID, SourceFile sourceFile, ScanList scanList, List<Precursor> precursors, List<ParamGroup> products, List<Peptide> peptide)
Spectrum(Spectrum spectrum)

Method Summary

Methods

Modifier and Type	Method and Description
Object	clone()
boolean	equals(Object o)
BinaryDataArray	getIntensityBinaryDataArray()
double[][]	getMassIntensityMap()
BinaryDataArray	getMzBinaryDataArray()
List<Peptide>	getPeptide()
List<Precursor>	getPrecursors()
List<ParamGroup>	getProducts()
ScanList	getScanList()
SourceFile	getSourceFile()
String	getSpotID()
int	hashCode()
void	setMassIntensityMap(double[][] peakMap)
void	setPeptide(List<Peptide> peptide)
void	setPrecursors(List<Precursor> precursors)
void	setProducts(List<ParamGroup> products)
void	setScanList(ScanList scanList)
void	setSourceFile(SourceFile sourceFile)
void	setSpotID(String spotID)

Methods inherited from class uk.ac.ebi.pride.utilities.data.core.MzGraph

getBinaryDataArray, getBinaryDataArrays, getDataProcessing, getDefaultArrayLength, getIndex, setBinaryDataArrays, setDataProcessing, setDefaultArrayLength, setIndex

Methods inherited from class uk.ac.ebi.pride.utilities.data.core.IdentifiableParamGroup

getId, getName, setId, setName, toString

Methods inherited from class uk.ac.ebi.pride.utilities.data.core.ParamGroup

addCvParam, addCvParams, addUserParam, addUserParams, getCvParams, getUserParams, isEmpty, removeCvParam, removeCvParams, removeUserParam, removeUserParams, setCvParams, setUserParams

Methods inherited from class java.lang.Object

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

Constructor Detail

Spectrum

public Spectrum(Comparable id,
        String name,
        int index,
        DataProcessing defaultDataProcessing,
        int defaultArrayLength,
        List<BinaryDataArray> binaryDataArrays,
        String spotID,
        SourceFile sourceFile,
        ScanList scanList,
        List<Precursor> precursors,
        List<ParamGroup> products,
        List<Peptide> peptide)

Spectrum

public Spectrum(ParamGroup params,
        Comparable id,
        String name,
        int index,
        DataProcessing defaultDataProcessing,
        int defaultArrayLength,
        List<BinaryDataArray> binaryDataArrays,
        String spotID,
        SourceFile sourceFile,
        ScanList scanList,
        List<Precursor> precursors,
        List<ParamGroup> products)

Spectrum

public Spectrum(ParamGroup params,
        Comparable id,
        String name,
        int index,
        DataProcessing defaultDataProcessing,
        int defaultArrayLength,
        List<BinaryDataArray> binaryDataArrays,
        String spotID,
        SourceFile sourceFile,
        ScanList scanList,
        List<Precursor> precursors,
        List<ParamGroup> products,
        List<Peptide> peptide)

Spectrum

public Spectrum(Spectrum spectrum)

Method Detail

getSpotID

public String getSpotID()

setSpotID

public void setSpotID(String spotID)

getSourceFile

public SourceFile getSourceFile()

setSourceFile

public void setSourceFile(SourceFile sourceFile)

getScanList

public ScanList getScanList()

setScanList

public void setScanList(ScanList scanList)

getPrecursors

public List<Precursor> getPrecursors()

setPrecursors

public void setPrecursors(List<Precursor> precursors)

getProducts

public List<ParamGroup> getProducts()

setProducts

public void setProducts(List<ParamGroup> products)

getMzBinaryDataArray

public BinaryDataArray getMzBinaryDataArray()

getIntensityBinaryDataArray

public BinaryDataArray getIntensityBinaryDataArray()

getPeptide

public List<Peptide> getPeptide()

setPeptide

public void setPeptide(List<Peptide> peptide)

getMassIntensityMap

public double[][] getMassIntensityMap()

setMassIntensityMap

public void setMassIntensityMap(double[][] peakMap)

equals

public boolean equals(Object o)

Overrides:

equals in class MzGraph

hashCode

public int hashCode()

Overrides:

hashCode in class MzGraph

clone

public Object clone()
             throws CloneNotSupportedException

Overrides:

clone in class Object

Throws:

CloneNotSupportedException