io.github.msdk.featuredetection.adap3d

Class ADAP3DFeatureDetectionMethod

java.lang.Object

io.github.msdk.featuredetection.adap3d.ADAP3DFeatureDetectionMethod

All Implemented Interfaces:

MSDKMethod<List<Feature>>

public class ADAP3DFeatureDetectionMethod
extends Object
implements MSDKMethod<List<Feature>>

This class is used to run the whole ADAP3D algorithm and get peaks.

Constructor Summary

Constructors

Constructor and Description
ADAP3DFeatureDetectionMethod(RawDataFile rawFile) Constructor
ADAP3DFeatureDetectionMethod(RawDataFile rawFile, ADAP3DFeatureDetectionParameters params) Constructor
ADAP3DFeatureDetectionMethod(RawDataFile rawFile, Predicate<MsScan> msScanPredicate) Constructor
ADAP3DFeatureDetectionMethod(RawDataFile rawFile, Predicate<MsScan> msScanPredicate, ADAP3DFeatureDetectionParameters parameters) Constructor

Method Summary

Modifier and Type	Method and Description
void	cancel() Cancel a running algorithm.
List<Feature>	execute() This method performs 3 steps: Step 1.
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<Feature>	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

ADAP3DFeatureDetectionMethod

public ADAP3DFeatureDetectionMethod(@Nonnull
                                    RawDataFile rawFile)

Constructor

Parameters:

rawFile - RawDataFile object.

ADAP3DFeatureDetectionMethod

public ADAP3DFeatureDetectionMethod(@Nonnull
                                    RawDataFile rawFile,
                                    @Nullable
                                    Predicate<MsScan> msScanPredicate)

Constructor

Parameters:

rawFile - RawDataFile object.

msScanPredicate - a Predicate object. Only MsScan which pass this predicate will be processed.

ADAP3DFeatureDetectionMethod

public ADAP3DFeatureDetectionMethod(@Nonnull
                                    RawDataFile rawFile,
                                    @Nonnull
                                    ADAP3DFeatureDetectionParameters params)

Constructor

Parameters:

rawFile - RawDataFile object.

ADAP3DFeatureDetectionMethod

public ADAP3DFeatureDetectionMethod(@Nonnull
                                    RawDataFile rawFile,
                                    @Nullable
                                    Predicate<MsScan> msScanPredicate,
                                    @Nonnull
                                    ADAP3DFeatureDetectionParameters parameters)

Constructor

Parameters:

rawFile - RawDataFile object.

msScanPredicate - a Predicate object. Only MsScan which pass this predicate will be processed.

Method Detail

execute

public List<Feature> execute()

This method performs 3 steps:
Step 1. Run ADAP3DPeakDetectionAlgorithm.execute with the default parameters and detect 20 highest peaks.
Step 2. Estimate new parameters for ADAP3DPeakDetectionAlgorithm from those 20 peaks.
Step 3. Run ADAP3DPeakDetectionAlgorithm.execute with the new parameters and detect all other peaks.

Specified by:

execute in interface MSDKMethod<List<Feature>>

Returns:

newFeatureList a list of Feature

getFinishedPercentage

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<Feature>>

Returns:

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

getResult

public List<Feature> getResult()

Returns the result of this algorithm, or null.

Specified by:

getResult in interface MSDKMethod<List<Feature>>

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<Feature>>