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

Class MzmlSpectrumCheck

java.lang.Object

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

All Implemented Interfaces:

ConsistencyCheck

Direct Known Subclasses:

FirstMzCheck, LastMzCheck, TicCheck

public abstract class MzmlSpectrumCheck
extends Object
implements ConsistencyCheck

The base object to define a consistency check between a MsnSpectrum and a ebi mzml Spectrum for a specific target value.

Constructor Summary

Constructors

Constructor and Description
MzmlSpectrumCheck()

Method Summary

Methods

Modifier and Type	Method and Description
boolean	assertConsistent(double expected, double observed, float delta)
boolean	checkConsistency(MsnSpectrum msnSpectrum, uk.ac.ebi.jmzml.model.mzml.Spectrum mzXmlSpectrum, float delta) Check consistency
protected com.google.common.base.Optional<Double>	getExpectedValue(uk.ac.ebi.jmzml.model.mzml.Spectrum mzmlSpectrum, String param)
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
void	setName(String name)

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.expasy.mzjava.external.io.ms.spectrum.ConsistencyCheck

getExpectedValue, getObservedValue

Constructor Detail

MzmlSpectrumCheck

public MzmlSpectrumCheck()

Method Detail

setName

public void setName(String name)

checkConsistency

public boolean checkConsistency(MsnSpectrum msnSpectrum,
                       uk.ac.ebi.jmzml.model.mzml.Spectrum mzXmlSpectrum,
                       float delta)

Description copied from interface: ConsistencyCheck

Check consistency

Specified by:

checkConsistency in interface ConsistencyCheck

Parameters:

msnSpectrum - spectrum mscheck value from

mzXmlSpectrum - 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

assertConsistent

public boolean assertConsistent(double expected,
                       double observed,
                       float delta)

onFailSendWarning

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

Description copied from interface: ConsistencyCheck

Send warning when check fails

Specified by:

onFailSendWarning in interface ConsistencyCheck

Returns:

a warning message

onFailThrowException

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

Description copied from interface: ConsistencyCheck

Throw a ConsistencyCheckException when check fails

Specified by:

onFailThrowException in interface ConsistencyCheck

Returns:

a ConsistencyCheckException

getExpectedValue

protected com.google.common.base.Optional<Double> getExpectedValue(uk.ac.ebi.jmzml.model.mzml.Spectrum mzmlSpectrum,
                                                       String param)