Package uk.ac.ebi.pride.jmztab2.utils.errors

Class LogicalErrorType

java.lang.Object

uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType

uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

All Implemented Interfaces:

java.io.Serializable

public final class LogicalErrorType
extends MZTabErrorType

Reporting errors related to the logical relationships among the different sections in a file. Reference: http://code.google.com/p/mztab/wiki/jmzTab_message for details.

Since:

29/01/13

Author:

qingwei

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType

MZTabErrorType.Category, MZTabErrorType.Level

Field Summary

Fields

Modifier and Type	Field	Description
static MZTabErrorType	AbundanceColumnSameId	Constant AbundanceColumnSameId
static MZTabErrorType	AbundanceColumnTogether	Constant AbundanceColumnTogether
static MZTabErrorType	AmbiguityMod	Constant AmbiguityMod
static MZTabErrorType	AssayNotDefined	Constant AssayNotDefined
static MZTabErrorType	AssayRefs	Constant AssayRefs
static MZTabErrorType	CHEMMODS	Constant CHEMMODS
static MZTabErrorType	ColumnNotValid	Constant ColumnNotValid
static MZTabErrorType	DuplicationAccession	Constant DuplicationAccession
static MZTabErrorType	DuplicationDefine	Constant DuplicationDefine
static MZTabErrorType	DuplicationID	Constant DuplicationID
static MZTabErrorType	ExternalStudyFormatNotDefined	Constant ExternalStudyFormatNotDefined
static MZTabErrorType	ExternalStudyIdFormatNotDefined	Constant ExternalStudyIdFormatNotDefined
static MZTabErrorType	FixedMod	Constant FixedMod
static MZTabErrorType	HeaderLine	Constant HeaderLine
static MZTabErrorType	HeaderNotValid	Constant HeaderNotValid
static MZTabErrorType	IdNumber	Constant IdNumber
static MZTabErrorType	ItemNumberMismatch	Constant ItemNumberMismatch
static MZTabErrorType	LineOrder	Constant LineOrder
static MZTabErrorType	ModificationPosition	Constant ModificationPosition
static MZTabErrorType	MsRunHashMethodNotDefined	Constant MsRunHashMethodNotDefined
static MZTabErrorType	MsRunLocation	Constant MsRunLocation
static MZTabErrorType	MsRunNotDefined	Constant MsRunNotDefined
static MZTabErrorType	NoDatabaseMustHaveNullPrefix	Constant NoDatabaseMustHaveNullPrefix
static MZTabErrorType	NoHeaderLine	Constant NoHeaderLine
static MZTabErrorType	NoMetadataSection	Constant NoMetadataSection
static MZTabErrorType	NoSmallMoleculeEvidenceSection	Constant NoSmallMoleculeEvidenceSection
static MZTabErrorType	NoSmallMoleculeFeatureQuantificationUnit	Constant NoSmallMoleculeFeatureQuantificationUnit
static MZTabErrorType	NoSmallMoleculeFeatureSection	Constant NoSmallMoleculeFeatureSection
static MZTabErrorType	NoSmallMoleculeIdentificationReliability	Constant NoSmallMoleculeIdentificationReliability
static MZTabErrorType	NoSmallMoleculeQuantificationUnit	Constant NoSmallMoleculeQuantificationUnit
static MZTabErrorType	NoSmallMoleculeSummarySection	Constant NoSmallMoleculeSummarySection
static MZTabErrorType	NotDefineInHeader	Constant NotDefineInHeader
static MZTabErrorType	NotDefineInMetadata	Constant NotDefineInMetadata
static MZTabErrorType	NotNULL	Constant NotNULL
static MZTabErrorType	NULL	Constant NULL
static MZTabErrorType	PeptideSearchEngineScoreNotDefined	Constant PeptideSearchEngineScoreNotDefined
static MZTabErrorType	PeptideSection	Constant PeptideSection
static MZTabErrorType	ProteinCoverage	Constant ProteinCoverage
static MZTabErrorType	ProteinSearchEngineScoreNotDefined	Constant ProteinSearchEngineScoreNotDefined
static MZTabErrorType	PSMSearchEngineScoreNotDefined	Constant PSMSearchEngineScoreNotDefined
static MZTabErrorType	QuantificationAbundance	Constant QuantificationAbundance
static MZTabErrorType	SingleStudyVariableName	Constant SingleStudyVariableName
static MZTabErrorType	SmallMoleculeSearchEngineScoreNotDefined	Constant SmallMoleculeSearchEngineScoreNotDefined
static MZTabErrorType	SoftwareVersion	Constant SoftwareVersion
static MZTabErrorType	SpectraRef	Constant SpectraRef
static MZTabErrorType	StudyVariableNotDefined	Constant StudyVariableNotDefined
static MZTabErrorType	SubstituteIdentifier	Constant SubstituteIdentifier
static MZTabErrorType	UndefinedStudyVariableNameOnceOnly	Constant UndefinedStudyVariableNameOnceOnly
static MZTabErrorType	UnknownRefId	Constant UnknownRefId
static MZTabErrorType	VariableMod	Constant VariableMod

Method Summary

Modifier and Type	Method	Description
static MZTabErrorType[]	getValues()

Methods inherited from class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType

createError, createInfo, createWarn, equals, findLevel, forLevel, getCategory, getCause, getCode, getLevel, getOriginal, hashCode, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

NULL

public static final MZTabErrorType NULL

Constant NULL

NotNULL

public static final MZTabErrorType NotNULL

Constant NotNULL

LineOrder

public static final MZTabErrorType LineOrder

Constant LineOrder

HeaderLine

public static final MZTabErrorType HeaderLine

Constant HeaderLine

NoHeaderLine

public static final MZTabErrorType NoHeaderLine

Constant NoHeaderLine

MsRunNotDefined

public static final MZTabErrorType MsRunNotDefined

Constant MsRunNotDefined

AssayNotDefined

public static final MZTabErrorType AssayNotDefined

Constant AssayNotDefined

StudyVariableNotDefined

public static final MZTabErrorType StudyVariableNotDefined

Constant StudyVariableNotDefined

ProteinSearchEngineScoreNotDefined

public static final MZTabErrorType ProteinSearchEngineScoreNotDefined

Constant ProteinSearchEngineScoreNotDefined

PeptideSearchEngineScoreNotDefined

public static final MZTabErrorType PeptideSearchEngineScoreNotDefined

Constant PeptideSearchEngineScoreNotDefined

PSMSearchEngineScoreNotDefined

public static final MZTabErrorType PSMSearchEngineScoreNotDefined

Constant PSMSearchEngineScoreNotDefined

SmallMoleculeSearchEngineScoreNotDefined

public static final MZTabErrorType SmallMoleculeSearchEngineScoreNotDefined

Constant SmallMoleculeSearchEngineScoreNotDefined

MsRunHashMethodNotDefined

public static final MZTabErrorType MsRunHashMethodNotDefined

Constant MsRunHashMethodNotDefined

NotDefineInMetadata

public static final MZTabErrorType NotDefineInMetadata

Constant NotDefineInMetadata

NotDefineInHeader

public static final MZTabErrorType NotDefineInHeader

Constant NotDefineInHeader

DuplicationDefine

public static final MZTabErrorType DuplicationDefine

Constant DuplicationDefine

DuplicationAccession

public static final MZTabErrorType DuplicationAccession

Constant DuplicationAccession

AssayRefs

public static final MZTabErrorType AssayRefs

Constant AssayRefs

ProteinCoverage

public static final MZTabErrorType ProteinCoverage

Constant ProteinCoverage

IdNumber

public static final MZTabErrorType IdNumber

Constant IdNumber

ModificationPosition

public static final MZTabErrorType ModificationPosition

Constant ModificationPosition

CHEMMODS

public static final MZTabErrorType CHEMMODS

Constant CHEMMODS

SubstituteIdentifier

public static final MZTabErrorType SubstituteIdentifier

Constant SubstituteIdentifier

SoftwareVersion

public static final MZTabErrorType SoftwareVersion

Constant SoftwareVersion

AbundanceColumnTogether

public static final MZTabErrorType AbundanceColumnTogether

Constant AbundanceColumnTogether

AbundanceColumnSameId

public static final MZTabErrorType AbundanceColumnSameId

Constant AbundanceColumnSameId

SpectraRef

public static final MZTabErrorType SpectraRef

Constant SpectraRef

AmbiguityMod

public static final MZTabErrorType AmbiguityMod

Constant AmbiguityMod

MsRunLocation

public static final MZTabErrorType MsRunLocation

Constant MsRunLocation

FixedMod

public static final MZTabErrorType FixedMod

Constant FixedMod

VariableMod

public static final MZTabErrorType VariableMod

Constant VariableMod

PeptideSection

public static final MZTabErrorType PeptideSection

Constant PeptideSection

QuantificationAbundance

public static final MZTabErrorType QuantificationAbundance

Constant QuantificationAbundance

DuplicationID

public static final MZTabErrorType DuplicationID

Constant DuplicationID

ColumnNotValid

public static final MZTabErrorType ColumnNotValid

Constant ColumnNotValid

HeaderNotValid

public static final MZTabErrorType HeaderNotValid

Constant HeaderNotValid

NoMetadataSection

public static final MZTabErrorType NoMetadataSection

Constant NoMetadataSection

NoSmallMoleculeEvidenceSection

public static final MZTabErrorType NoSmallMoleculeEvidenceSection

Constant NoSmallMoleculeEvidenceSection

NoSmallMoleculeFeatureSection

public static final MZTabErrorType NoSmallMoleculeFeatureSection

Constant NoSmallMoleculeFeatureSection

NoSmallMoleculeSummarySection

public static final MZTabErrorType NoSmallMoleculeSummarySection

Constant NoSmallMoleculeSummarySection

NoSmallMoleculeQuantificationUnit

public static final MZTabErrorType NoSmallMoleculeQuantificationUnit

Constant NoSmallMoleculeQuantificationUnit

NoSmallMoleculeFeatureQuantificationUnit

public static final MZTabErrorType NoSmallMoleculeFeatureQuantificationUnit

Constant NoSmallMoleculeFeatureQuantificationUnit

NoSmallMoleculeIdentificationReliability

public static final MZTabErrorType NoSmallMoleculeIdentificationReliability

Constant NoSmallMoleculeIdentificationReliability

ExternalStudyIdFormatNotDefined

public static final MZTabErrorType ExternalStudyIdFormatNotDefined

Constant ExternalStudyIdFormatNotDefined

ExternalStudyFormatNotDefined

public static final MZTabErrorType ExternalStudyFormatNotDefined

Constant ExternalStudyFormatNotDefined

NoDatabaseMustHaveNullPrefix

public static final MZTabErrorType NoDatabaseMustHaveNullPrefix

Constant NoDatabaseMustHaveNullPrefix

ItemNumberMismatch

public static final MZTabErrorType ItemNumberMismatch

Constant ItemNumberMismatch

UnknownRefId

public static final MZTabErrorType UnknownRefId

Constant UnknownRefId

SingleStudyVariableName

public static final MZTabErrorType SingleStudyVariableName

Constant SingleStudyVariableName

UndefinedStudyVariableNameOnceOnly

public static final MZTabErrorType UndefinedStudyVariableNameOnceOnly

Constant UndefinedStudyVariableNameOnceOnly

Method Detail

getValues

public static MZTabErrorType[] getValues()