io.github.msdk.featuredetection.msmsdetection

Class MsMsDetectionMethod

java.lang.Object

io.github.msdk.featuredetection.msmsdetection.MsMsDetectionMethod

All Implemented Interfaces:

MSDKMethod<List<IonAnnotation>>

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

This class creates a list of IonAnnotations for a RawDataFile based the MS2 scans.

Constructor Summary

Constructors

Constructor and Description
MsMsDetectionMethod(RawDataFile rawDataFile, List<MsScan> msScans, MzTolerance mzTolerance, RTTolerance rtTolerance, Double intensityTolerance) Constructor for MsMsDetectionMethod.

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

MsMsDetectionMethod

public MsMsDetectionMethod(@Nonnull
                           RawDataFile rawDataFile,
                           @Nonnull
                           List<MsScan> msScans,
                           @Nonnull
                           MzTolerance mzTolerance,
                           @Nonnull
                           RTTolerance rtTolerance,
                           @Nonnull
                           Double intensityTolerance)

Constructor for MsMsDetectionMethod.

Parameters:

rawDataFile - a RawDataFile object.

msScans - a list of MsScan objects.

mzTolerance - a MzTolerance object.

rtTolerance - a RTTolerance object.

intensityTolerance - a Double object.

Method Detail

execute

public List<IonAnnotation> execute()
                            throws MSDKException

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

getFinishedPercentage

@Nullable
public 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.

Specified by:

getFinishedPercentage in interface MSDKMethod<List<IonAnnotation>>

Returns:

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

getResult

@Nullable
public List<IonAnnotation> getResult()

Returns the result of this algorithm, or null.

Specified by:

getResult in interface MSDKMethod<List<IonAnnotation>>

Returns:

a ResultType object.

cancel

public void cancel()

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

Specified by:

cancel in interface MSDKMethod<List<IonAnnotation>>