io.github.msdk.featuredetection.chromatogrambuilder

Class ChromatogramBuilderMethod

java.lang.Object

io.github.msdk.featuredetection.chromatogrambuilder.ChromatogramBuilderMethod

All Implemented Interfaces:

MSDKMethod<List<Chromatogram>>

public class ChromatogramBuilderMethod
extends Object
implements MSDKMethod<List<Chromatogram>>

ChromatogramBuilderMethod class.

Constructor Summary

Constructors

Constructor and Description
ChromatogramBuilderMethod(RawDataFile inputFile, double noiseLevel, double minimumTimeSpan, double minimumHeight, MzTolerance mzTolerance) Constructor for ChromatogramBuilderMethod.
ChromatogramBuilderMethod(RawDataFile inputFile, List<MsScan> inputScans, Double noiseLevel, Double minimumTimeSpan, Double minimumHeight, MzTolerance mzTolerance) Constructor for ChromatogramBuilderMethod.

Method Summary

Modifier and Type	Method and Description
void	cancel() Cancel a running algorithm.
List<Chromatogram>	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<Chromatogram>	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

ChromatogramBuilderMethod

public ChromatogramBuilderMethod(RawDataFile inputFile,
                                 double noiseLevel,
                                 double minimumTimeSpan,
                                 double minimumHeight,
                                 MzTolerance mzTolerance)

Constructor for ChromatogramBuilderMethod. This version uses the same MzTolerance for every scan that does not provide its own MzTolerance.

Parameters:

inputFile - a RawDataFile object.

minimumTimeSpan - a Double object.

minimumHeight - a Double object.

mzTolerance - an object that implements the MZTolerance interface.

noiseLevel - a Float object.

ChromatogramBuilderMethod

public ChromatogramBuilderMethod(@Nonnull
                                 RawDataFile inputFile,
                                 @Nonnull
                                 List<MsScan> inputScans,
                                 @Nonnull
                                 Double noiseLevel,
                                 @Nonnull
                                 Double minimumTimeSpan,
                                 @Nonnull
                                 Double minimumHeight,
                                 @Nonnull
                                 MzTolerance mzTolerance)

Constructor for ChromatogramBuilderMethod. This version uses the same MzTolerance for every scan that does not provide its own MzTolerance.

Parameters:

inputFile - a RawDataFile object.

inputScans - a List object.

minimumTimeSpan - a Double object.

minimumHeight - a Double object.

mzTolerance - an object that implements the MZTolerance interface.

noiseLevel - a Float object.

Method Detail

execute

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

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

Specified by:

execute in interface MSDKMethod<List<Chromatogram>>

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<Chromatogram>>

Returns:

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

getResult

@Nullable
public List<Chromatogram> getResult()

Returns the result of this algorithm, or null.

Specified by:

getResult in interface MSDKMethod<List<Chromatogram>>

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<Chromatogram>>