io.github.msdk.alignment.joinaligner

Class JoinAlignerMethod

java.lang.Object

io.github.msdk.alignment.joinaligner.JoinAlignerMethod

All Implemented Interfaces:

MSDKMethod<FeatureTable>

public class JoinAlignerMethod
extends Object
implements MSDKMethod<FeatureTable>

This class aligns feature tables based on a match score. The score is calculated based on the mass and retention time of each peak using a set of tolerances.

Constructor Summary

Constructors

Constructor and Description
JoinAlignerMethod(List<FeatureTable> featureTables, MzTolerance mzTolerance, RTTolerance rtTolerance) Constructor for MatchAlignerMethod.

Method Summary

Modifier and Type	Method and Description
void	cancel() Cancel a running algorithm.
FeatureTable	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.
FeatureTable	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

JoinAlignerMethod

public JoinAlignerMethod(@Nonnull
                         List<FeatureTable> featureTables,
                         @Nonnull
                         MzTolerance mzTolerance,
                         @Nonnull
                         RTTolerance rtTolerance)

Constructor for MatchAlignerMethod.

Parameters:

featureTables - a List object.

mzTolerance - an objectt

rtTolerance - a RTTolerance object.

Method Detail

execute

public FeatureTable execute()
                     throws MSDKException

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

Specified by:

execute in interface MSDKMethod<FeatureTable>

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<FeatureTable>

Returns:

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

getResult

@Nullable
public FeatureTable getResult()

Returns the result of this algorithm, or null.

Specified by:

getResult in interface MSDKMethod<FeatureTable>

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<FeatureTable>