io.github.msdk.id.sirius

Class FingerIdWebMethod

java.lang.Object

io.github.msdk.id.sirius.FingerIdWebMethod

All Implemented Interfaces:

MSDKMethod<List<IonAnnotation>>

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

Class FingerIdWebMethod

This class wraps the FingerId API provided by boecker-labs Uses the results of SiriusIdentificationMethod and returns exteneded IonAnnotations

Constructor Summary

Constructors

Constructor and Description
FingerIdWebMethod(de.unijena.bioinf.ChemistryBase.ms.Ms2Experiment experiment, SiriusIonAnnotation ionAnnotation) Simplified FingerIdWebMethod constructor
FingerIdWebMethod(de.unijena.bioinf.ChemistryBase.ms.Ms2Experiment experiment, SiriusIonAnnotation ionAnnotation, Integer candidatesAmount) Constructor for a FingerIdWebMethod

Method Summary

Modifier and Type	Method and Description
void	cancel() Cancel a running algorithm.
List<IonAnnotation>	execute() Performs the algorithm.
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.
List<IonAnnotation>	getResult() Returns the result of this algorithm, or null.

Methods inherited from class java.lang.Object

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

Constructor Detail

FingerIdWebMethod

public FingerIdWebMethod(@Nonnull
                         de.unijena.bioinf.ChemistryBase.ms.Ms2Experiment experiment,
                         @Nonnull
                         SiriusIonAnnotation ionAnnotation,
                         @Nonnull
                         Integer candidatesAmount)
                  throws MSDKException

Constructor for a FingerIdWebMethod

Parameters:

experiment - - Ms2Experiment that was used to get ionAnnotation

ionAnnotation - - SiriusIonAnnotation returned from SiriusIdentificationMethod with FTree field specified

candidatesAmount - - amount of candidates to be returned from this method

Throws:

MSDKException - if any

FingerIdWebMethod

public FingerIdWebMethod(@Nonnull
                         de.unijena.bioinf.ChemistryBase.ms.Ms2Experiment experiment,
                         @Nonnull
                         SiriusIonAnnotation ionAnnotation)
                  throws MSDKException

Simplified FingerIdWebMethod constructor

In this case, FingerId will return unspecified amount of compounds (500-7000)

Parameters:

experiment - - Ms2Experiment object

ionAnnotation - - SiriusIonAnnotation with FTree specified

Throws:

MSDKException - if any

Method Detail

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>>