org.expasy.mzjava.external.io.ms.spectrum

Interface ConsistencyCheck

All Known Implementing Classes:

FirstMzCheck, LastMzCheck, MzmlConsistencyCheck, MzmlSpectrumCheck, TicCheck

public interface ConsistencyCheck

A consistency check interface

Author:

fnikitin

Method Summary

Methods

Modifier and Type	Method and Description
boolean	checkConsistency(MsnSpectrum observedValueContainer, uk.ac.ebi.jmzml.model.mzml.Spectrum expectedValueContainer, float delta) Check consistency
com.google.common.base.Optional<Double>	getExpectedValue(uk.ac.ebi.jmzml.model.mzml.Spectrum expectedValueContainer) Get expected value from a container
com.google.common.base.Optional<Double>	getObservedValue(MsnSpectrum spectrum) Get observed value from an MsnSpectrum
String	onFailSendWarning(MsnSpectrum observedValueContainer, uk.ac.ebi.jmzml.model.mzml.Spectrum expectedValueContainer) Send warning when check fails
ConsistencyCheckException	onFailThrowException(MsnSpectrum observedValueContainer, uk.ac.ebi.jmzml.model.mzml.Spectrum expectedValueContainer) Throw a ConsistencyCheckException when check fails

Method Detail

checkConsistency

boolean checkConsistency(MsnSpectrum observedValueContainer,
                       uk.ac.ebi.jmzml.model.mzml.Spectrum expectedValueContainer,
                       float delta)

Check consistency

Parameters:

observedValueContainer - spectrum mscheck value from

expectedValueContainer - container to mscheck value with

delta - the maximum delta between expected and actual for which both numbers are still considered equal.

Returns:

false if failed

getExpectedValue

com.google.common.base.Optional<Double> getExpectedValue(uk.ac.ebi.jmzml.model.mzml.Spectrum expectedValueContainer)

Get expected value from a container

Parameters:

expectedValueContainer - potentially contains expected value

Returns:

an optional value

getObservedValue

com.google.common.base.Optional<Double> getObservedValue(MsnSpectrum spectrum)

Get observed value from an MsnSpectrum

Parameters:

spectrum - the spectrum container

Returns:

the optional observed value to check for consistency

onFailSendWarning

String onFailSendWarning(MsnSpectrum observedValueContainer,
                       uk.ac.ebi.jmzml.model.mzml.Spectrum expectedValueContainer)

Send warning when check fails

Returns:

a warning message

onFailThrowException

ConsistencyCheckException onFailThrowException(MsnSpectrum observedValueContainer,
                                             uk.ac.ebi.jmzml.model.mzml.Spectrum expectedValueContainer)

Throw a ConsistencyCheckException when check fails

Returns:

a ConsistencyCheckException