io.github.msdk.datamodel

Interface Chromatogram

All Known Implementing Classes:

SimpleChromatogram

public interface Chromatogram

Represents a single chromatogram.

Method Summary

Modifier and Type	Method and Description
Integer	getChromatogramNumber() Returns the number of this chromatogram, represented by an integer, typically positive.
ChromatogramType	getChromatogramType() Returns the type of the chromatogram.
default 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.
default double[]	getMzValues() getMzValues.
double[]	getMzValues(double[] array)
Integer	getNumberOfDataPoints() getNumberOfDataPoints.
RawDataFile	getRawDataFile() Returns the raw data file that contains this chromatogram.
default 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.

Method Detail

getRawDataFile

@Nullable
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.

Returns:

RawDataFile containing this chromatogram, or null.

getChromatogramNumber

@Nonnull
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.

Returns:

Chromatogram number

getChromatogramType

@Nonnull
ChromatogramType getChromatogramType()

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

Returns:

Chromatogram type

getNumberOfDataPoints

@Nonnull
Integer getNumberOfDataPoints()

getNumberOfDataPoints.

Returns:

a Integer object.

getRetentionTimes

@Nonnull
default 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.

Returns:

an array of

getRetentionTimes

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

getIntensityValues

@Nonnull
default float[] getIntensityValues()

getIntensityValues.

Returns:

an array of float.

getIntensityValues

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

getIntensityValues.

Parameters:

array - an array of float.

Returns:

an array of float.

getMzValues

@Nullable
default double[] getMzValues()

getMzValues.

Returns:

an array of double.

getMzValues

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

Parameters:

array -

Returns:

getMz

@Nullable
Double getMz()

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

Returns:

a Double object.

getIsolations

@Nonnull
List<IsolationInfo> getIsolations()

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

Returns:

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

getSeparationType

@Nonnull
SeparationType getSeparationType()

Returns the separation type used for separation of molecules.

Returns:

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

getIonAnnotation

IonAnnotation getIonAnnotation()

Returns the ion annotation for this chromatogram.

Returns:

the ion annotation.

getRtRange

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

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

Returns:

RT range