io.github.msdk.spectra.peakinvestigator

Class PeakInvestigatorScanExtractingMethod

java.lang.Object

io.github.msdk.spectra.peakinvestigator.PeakInvestigatorScanExtractingMethod

All Implemented Interfaces:

MSDKMethod<List<MsSpectrum>>

public class PeakInvestigatorScanExtractingMethod
extends Object
implements MSDKMethod<List<MsSpectrum>>

This class extracts scans from the results returned from PeakInvestigator. Internally, it returns a SimpleMsSpectrum object if no error bars are present. Otherwise, it returns a PeakInvestigatorMsSpectrum, which decorates a SimpleMsSpectrum.

Method Summary

Modifier and Type	Method and Description
void	cancel() Cancel a running algorithm.
List<MsSpectrum>	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<MsSpectrum>	getResult() Returns the result of this algorithm, or null.
protected MsSpectrum	parseMsSpectrum(BufferedReader reader) This function assumes that the data is either formatted as two columns or five columns, separated by whitespace.

Methods inherited from class java.lang.Object

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

Method Detail

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<MsSpectrum>>

Returns:

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

execute

public List<MsSpectrum> execute()
                         throws MSDKException

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

Specified by:

execute in interface MSDKMethod<List<MsSpectrum>>

Returns:

the result of this algorithm, or null

Throws:

MSDKException - On any error

getResult

public List<MsSpectrum> getResult()

Returns the result of this algorithm, or null.

Specified by:

getResult in interface MSDKMethod<List<MsSpectrum>>

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<MsSpectrum>>

parseMsSpectrum

protected MsSpectrum parseMsSpectrum(BufferedReader reader)
                              throws IOException

This function assumes that the data is either formatted as two columns or five columns, separated by whitespace. If two columns, a MsSpectrum is returned via MSDKObjectBuilder.getMsSpectrum(). If five columns, the simple MsSpectrum is decorated using the PeakInvestigatorMsSpectrum.

Parameters:

reader - a BufferedReader object.

Returns:

a MsSpectrum object.

Throws:

IOException - if any.