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

Class ConsistencyChecker<C extends ConsistencyCheck>

java.lang.Object

org.expasy.mzjava.external.io.ms.spectrum.ConsistencyChecker<C>

Type Parameters:

C - the type of ConsistencyCheck handled by this object.

All Implemented Interfaces:

ConsistencyCheckHandler<C>

public class ConsistencyChecker<C extends ConsistencyCheck>
extends Object
implements ConsistencyCheckHandler<C>

ConsistencyChecker checks for consistencies on MsnSpectrum. This object handles a set of ConsistencyChecks in 2 sets: one strict and another tolerant. A ConsistencyCheck is strict if its failure cause a ConsistencyCheckException to be thrown. A ConsistencyCheck is tolerant if its failure cause a warning to be optionally logged.

Constructor Summary

Constructors

Constructor and Description
ConsistencyChecker(Set<C> consistencies) Create an instance of ConsistencyChecker composed of a given strict consistencies

Method Summary

Methods

Modifier and Type	Method and Description
void	checkConsistencies(MsnSpectrum spectrum, uk.ac.ebi.jmzml.model.mzml.Spectrum expectedValueContainer) Check strict and tolerant consistencies on spectrum
void	setDelta(float delta) Set delta value
void	turnStrict(Set<C> ccs) Set the given checks as strict
void	turnTolerant() All strict checks become tolerant
void	turnTolerant(Set<C> ccs) Set the given checks as tolerant

Methods inherited from class java.lang.Object

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

Constructor Detail

ConsistencyChecker

public ConsistencyChecker(Set<C> consistencies)

Create an instance of ConsistencyChecker composed of a given strict consistencies

Parameters:

consistencies - strict consistency checks

Method Detail

setDelta

public void setDelta(float delta)

Description copied from interface: ConsistencyCheckHandler

Set delta value

Specified by:

setDelta in interface ConsistencyCheckHandler<C extends ConsistencyCheck>

Parameters:

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

turnTolerant

public void turnTolerant()

All strict checks become tolerant

checkConsistencies

public void checkConsistencies(MsnSpectrum spectrum,
                      uk.ac.ebi.jmzml.model.mzml.Spectrum expectedValueContainer)

Check strict and tolerant consistencies on spectrum

Parameters:

spectrum - the spectrum to check for consistencies

expectedValueContainer - contains expected values

turnTolerant

public void turnTolerant(Set<C> ccs)

Set the given checks as tolerant

Specified by:

turnTolerant in interface ConsistencyCheckHandler<C extends ConsistencyCheck>

Parameters:

ccs - consistency checks

turnStrict

public void turnStrict(Set<C> ccs)

Set the given checks as strict

Specified by:

turnStrict in interface ConsistencyCheckHandler<C extends ConsistencyCheck>

Parameters:

ccs - consistency checks