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

Enum MzmlConsistencyCheck

java.lang.Object

java.lang.Enum<MzmlConsistencyCheck>

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

All Implemented Interfaces:

Serializable, Comparable<MzmlConsistencyCheck>, ConsistencyCheck

public enum MzmlConsistencyCheck
extends Enum<MzmlConsistencyCheck>
implements ConsistencyCheck

An enumeration of all consistency to check in mzml.

Author:

fnikitin

Enum Constant Summary

Enum Constants

Enum Constant and Description
HIGHEST_MZ
LOWEST_MZ
TOTAL_ION_CURRENT

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 observedValueContainer) 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
static MzmlConsistencyCheck	valueOf(String name) Returns the enum constant of this type with the specified name.
static MzmlConsistencyCheck[]	values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods inherited from class java.lang.Enum

clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Detail

LOWEST_MZ

public static final MzmlConsistencyCheck LOWEST_MZ

HIGHEST_MZ

public static final MzmlConsistencyCheck HIGHEST_MZ

TOTAL_ION_CURRENT

public static final MzmlConsistencyCheck TOTAL_ION_CURRENT

Method Detail

values

public static MzmlConsistencyCheck[] values()

Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:

for (MzmlConsistencyCheck c : MzmlConsistencyCheck.values())
    System.out.println(c);

Returns:

an array containing the constants of this enum type, in the order they are declared

valueOf

public static MzmlConsistencyCheck valueOf(String name)

Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)

Parameters:

name - the name of the enum constant to be returned.

Returns:

the enum constant with the specified name

Throws:

IllegalArgumentException - if this enum type has no constant with the specified name

NullPointerException - if the argument is null

checkConsistency

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

Description copied from interface: ConsistencyCheck

Check consistency

Specified by:

checkConsistency in interface ConsistencyCheck

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

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

Description copied from interface: ConsistencyCheck

Get expected value from a container

Specified by:

getExpectedValue in interface ConsistencyCheck

Parameters:

expectedValueContainer - potentially contains expected value

Returns:

an optional value

getObservedValue

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

Description copied from interface: ConsistencyCheck

Get observed value from an MsnSpectrum

Specified by:

getObservedValue in interface ConsistencyCheck

Parameters:

observedValueContainer - the spectrum container

Returns:

the optional observed value to check for consistency

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