io.github.msdk.datamodel

Class SimpleChromatogram

java.lang.Object

io.github.msdk.datamodel.SimpleChromatogram

All Implemented Interfaces:

Chromatogram

public class SimpleChromatogram
extends Object
implements Chromatogram

Simple implementation of the Chromatogram interface.

Constructor Summary

Constructors

Constructor and Description
SimpleChromatogram()

Method Summary

Modifier and Type	Method and Description
void	addDataPoint(Float rt, Double mz, Float intensity) Adds a data point to the end of the chromatogram
Integer	getChromatogramNumber() Returns the number of this chromatogram, represented by an integer, typically positive.
ChromatogramType	getChromatogramType() Returns the type of the chromatogram.
float[]	getIntensityValues() getIntensityValues.
float[]	getIntensityValues(float[] array) getIntensityValues.
IonAnnotation	getIonAnnotation() Returns the ion annotation for this chromatogram.
List<IsolationInfo>	getIsolations() Returns a list of isolations performed for this chromatogram.
Double	getMz() Returns the m/z value of this chromatogram, or null if no m/z value is set for the chromatogram.
double[]	getMzValues() getMzValues.
double[]	getMzValues(double[] array)
Integer	getNumberOfDataPoints() getNumberOfDataPoints.
RawDataFile	getRawDataFile() Returns the raw data file that contains this chromatogram.
float[]	getRetentionTimes() Returns the info of this chromatogram.
float[]	getRetentionTimes(float[] array)
com.google.common.collect.Range<Float>	getRtRange() Returns the range of retention times.
SeparationType	getSeparationType() Returns the separation type used for separation of molecules.
void	setChromatogramNumber(Integer chromatogramNumber)
void	setChromatogramType(ChromatogramType newChromatogramType)
void	setDataPoints(float[] rtValues, double[] mzValues, float[] intensityValues, Integer size)
void	setIonAnnotation(IonAnnotation ionAnnotation)
void	setMz(Double newMz)
void	setRawDataFile(RawDataFile newRawDataFile)
void	setSeparationType(SeparationType separationType)

Methods inherited from class java.lang.Object

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

Constructor Detail

SimpleChromatogram

public SimpleChromatogram()

Method Detail

getRawDataFile

@Nullable
public RawDataFile getRawDataFile()

Returns the raw data file that contains this chromatogram. This might return null when the chromatogram is created, but once the chromatogram is added to the raw data file by calling RawDataFile.addChromatogram(), the RawDataFile automatically calls the Chromatogram.setRawDataFile() method to update this reference.

Specified by:

getRawDataFile in interface Chromatogram

Returns:

RawDataFile containing this chromatogram, or null.

setRawDataFile

public void setRawDataFile(@Nonnull
                           RawDataFile newRawDataFile)

Parameters:

newRawDataFile - a RawDataFile object.

getChromatogramNumber

@Nonnull
public Integer getChromatogramNumber()

Returns the number of this chromatogram, represented by an integer, typically positive. Typically, the chromatogram number will be unique within the file. However, the data model does not guarantee that, and in some cases multiple chromatogram with the same number may be present in the file.

Specified by:

getChromatogramNumber in interface Chromatogram

Returns:

Chromatogram number

setChromatogramNumber

public void setChromatogramNumber(@Nonnull
                                  Integer chromatogramNumber)

Parameters:

chromatogramNumber - a Integer object.

getChromatogramType

@Nonnull
public ChromatogramType getChromatogramType()

Returns the type of the chromatogram. If unknown, ChromatogramType.UNKNOWN is returned.

Specified by:

getChromatogramType in interface Chromatogram

Returns:

Chromatogram type

setChromatogramType

public void setChromatogramType(@Nonnull
                                ChromatogramType newChromatogramType)

Parameters:

newChromatogramType - a ChromatogramType object.

getNumberOfDataPoints

@Nonnull
public Integer getNumberOfDataPoints()

getNumberOfDataPoints.

Specified by:

getNumberOfDataPoints in interface Chromatogram

Returns:

a Integer object.

getRetentionTimes

@Nonnull
public float[] getRetentionTimes()

Returns the info of this chromatogram. Generally, this method should pass null to the method that takes an array as a parameter. Note: this method may need to read data from disk, therefore it may be quite slow.

Specified by:

getRetentionTimes in interface Chromatogram

Returns:

an array of

getRetentionTimes

@Nonnull
public float[] getRetentionTimes(@Nullable
                                          float[] array)

Specified by:

getRetentionTimes in interface Chromatogram

Parameters:

array - an array of float.

Returns:

an array of float.

getMzValues

@Nonnull
public double[] getMzValues()

getMzValues.

Specified by:

getMzValues in interface Chromatogram

Returns:

an array of double.

getMzValues

@Nonnull
public double[] getMzValues(@Nullable
                                     double[] array)

Specified by:

getMzValues in interface Chromatogram

Parameters:

array - an array of float.

Returns:

an array of float.

getIntensityValues

@Nonnull
public float[] getIntensityValues()

getIntensityValues.

Specified by:

getIntensityValues in interface Chromatogram

Returns:

an array of float.

getIntensityValues

@Nonnull
public float[] getIntensityValues(@Nullable
                                           float[] array)

getIntensityValues.

Specified by:

getIntensityValues in interface Chromatogram

Parameters:

array - an array of float.

Returns:

an array of float.

setDataPoints

public void setDataPoints(@Nonnull
                          float[] rtValues,
                          @Nullable
                          double[] mzValues,
                          @Nonnull
                          float[] intensityValues,
                          @Nonnull
                          Integer size)

Parameters:

rtValues - an array of float.

mzValues - an array of double.

intensityValues - an array of float.

size - a Integer object.

getIsolations

@Nonnull
public List<IsolationInfo> getIsolations()

Returns a list of isolations performed for this chromatogram. These isolations may also include fragmentations (tandem MS).

Specified by:

getIsolations in interface Chromatogram

Returns:

A mutable list of isolations. New isolation items can be added to this list.

getSeparationType

@Nonnull
public SeparationType getSeparationType()

Returns the separation type used for separation of molecules.

Specified by:

getSeparationType in interface Chromatogram

Returns:

the seperation type. Returns SeparationType.UNKNOWN for unknown separations.

setSeparationType

public void setSeparationType(@Nonnull
                              SeparationType separationType)

Parameters:

separationType - a SeparationType object.

getMz

@Nullable
public Double getMz()

Returns the m/z value of this chromatogram, or null if no m/z value is set for the chromatogram.

Specified by:

getMz in interface Chromatogram

Returns:

a Double object.

setMz

public void setMz(@Nullable
                  Double newMz)

Parameters:

newMz - a Double object.

setIonAnnotation

public void setIonAnnotation(@Nonnull
                             IonAnnotation ionAnnotation)

Parameters:

ionAnnotation - a IonAnnotation object.

getIonAnnotation

public IonAnnotation getIonAnnotation()

Returns the ion annotation for this chromatogram.

Specified by:

getIonAnnotation in interface Chromatogram

Returns:

the ion annotation.

getRtRange

@Nullable
public com.google.common.collect.Range<Float> getRtRange()

Returns the range of retention times. This can return null if the chromatogram has no data points.

Specified by:

getRtRange in interface Chromatogram

Returns:

RT range

addDataPoint

public void addDataPoint(@Nonnull
                         Float rt,
                         @Nullable
                         Double mz,
                         @Nonnull
                         Float intensity)

Adds a data point to the end of the chromatogram

Parameters:

rt - a Float object.

mz - a Double object.

intensity - a Float object.