io.github.msdk.id.sirius

Class SiriusIdentificationMethod

java.lang.Object

io.github.msdk.id.sirius.SiriusIdentificationMethod

All Implemented Interfaces:

MSDKMethod<List<IonAnnotation>>

public class SiriusIdentificationMethod
extends Object
implements MSDKMethod<List<IonAnnotation>>

SiriusIdentificationMethod class.

This class wraps the Sirius module and transforms its results into MSDK data structures Transformation of IdentificationResult (Sirius) into IonAnnatation (MSDK)

Constructor Summary

Constructors

Constructor and Description
SiriusIdentificationMethod(List<MsSpectrum> ms1, List<MsSpectrum> ms2, Double parentMass, IonType ion, Integer numberOfCandidates, de.unijena.bioinf.ChemistryBase.chem.FormulaConstraints constraints, Double deviation) Constructor for SiriusIdentificationMethod class.

Method Summary

Modifier and Type	Method and Description
void	cancel() Cancel a running algorithm.
List<IonAnnotation>	execute() Performs the algorithm.
de.unijena.bioinf.ChemistryBase.ms.Ms2Experiment	getExperiment()
Float	getFinishedPercentage() Returns a number in the interval 0 to 1.0, representing the portion of the task that has completed, or null if the algorithm has not yet started.
IonType	getIonization()
List<MsSpectrum>	getMs2Spectra()
List<MsSpectrum>	getMsSpectra()
int	getNumberOfCandidates()
double	getParentMass()
List<IonAnnotation>	getResult() Returns the result of this algorithm, or null.
protected List<de.unijena.bioinf.sirius.IdentificationResult>	siriusProcessSpectra() Method for processing spectra by Sirius module

Methods inherited from class java.lang.Object

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

Constructor Detail

SiriusIdentificationMethod

public SiriusIdentificationMethod(@Nullable
                                  List<MsSpectrum> ms1,
                                  @Nullable
                                  List<MsSpectrum> ms2,
                                  @Nonnull
                                  Double parentMass,
                                  @Nonnull
                                  IonType ion,
                                  @Nullable
                                  Integer numberOfCandidates,
                                  @Nullable
                                  de.unijena.bioinf.ChemistryBase.chem.FormulaConstraints constraints,
                                  @Nullable
                                  Double deviation)

Constructor for SiriusIdentificationMethod class.

Parameters:

ms1 - - can be null! MsSpectrum level 1

ms2 - - MsSpectrum level 2

parentMass - - Most intensive usually or specified

ion - - Ionization

numberOfCandidates - - amount of IdentificationResults to be returned from Sirius

constraints - - FormulaConstraints provided by the end user. Can be created using ConstraintsGenerator

deviation - - float value of possible mass deviation in ppm

Method Detail

getParentMass

public double getParentMass()

getIonization

public IonType getIonization()

getMsSpectra

public List<MsSpectrum> getMsSpectra()

getMs2Spectra

public List<MsSpectrum> getMs2Spectra()

getNumberOfCandidates

public int getNumberOfCandidates()

siriusProcessSpectra

protected List<de.unijena.bioinf.sirius.IdentificationResult> siriusProcessSpectra()
                                                                            throws MSDKException

Method for processing spectra by Sirius module

Transformation of MSDK data structures into Sirius structures and processing by Sirius Method is left to be protected for test coverage

Throws:

MSDKException

getFinishedPercentage

@Nullable
public Float getFinishedPercentage()

Description copied from interface: MSDKMethod

Returns a number in the interval 0 to 1.0, representing the portion of the task that has completed, or null if the algorithm has not yet started.

Specified by:

getFinishedPercentage in interface MSDKMethod<List<IonAnnotation>>

Returns:

Finished percentage (0.0 to 1.0, inclusive), or null.

execute

@Nullable
public List<IonAnnotation> execute()
                                      throws MSDKException

Description copied from interface: MSDKMethod

Performs the algorithm. This method may throw MSDKException or MSDKRuntimeException if error occurs.

Specified by:

execute in interface MSDKMethod<List<IonAnnotation>>

Returns:

the result of this algorithm, or null

Throws:

MSDKException - On any error

getResult

@Nullable
public List<IonAnnotation> getResult()

Description copied from interface: MSDKMethod

Returns the result of this algorithm, or null.

Specified by:

getResult in interface MSDKMethod<List<IonAnnotation>>

Returns:

a ResultType object.

cancel

public void cancel()

Description copied from interface: MSDKMethod

Cancel a running algorithm. This method can be called from any thread.

Specified by:

cancel in interface MSDKMethod<List<IonAnnotation>>

getExperiment

public de.unijena.bioinf.ChemistryBase.ms.Ms2Experiment getExperiment()