Uses of Class
uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType

Packages that use MZTabErrorType

Package	Description
uk.ac.ebi.pride.jmztab2.utils.errors	This package contains error type definitions and related classes used during mzTab validation.

Uses of MZTabErrorType in uk.ac.ebi.pride.jmztab2.utils.errors

Subclasses of MZTabErrorType in uk.ac.ebi.pride.jmztab2.utils.errors

Modifier and Type	Class	Description
class	CrossCheckErrorType	Provide crosscheck service, that is parse the consistent between current mztab file and some other resource (eg, database, xml file and so on).
class	FormatErrorType	Diagnose different types of format-related (reporting format problems).
class	LogicalErrorType	Reporting errors related to the logical relationships among the different sections in a file.

Fields in uk.ac.ebi.pride.jmztab2.utils.errors declared as MZTabErrorType

Modifier and Type	Field	Description
static MZTabErrorType	FormatErrorType.AbundanceColumn	Constant AbundanceColumn
static MZTabErrorType	LogicalErrorType.AbundanceColumnSameId	Constant AbundanceColumnSameId
static MZTabErrorType	LogicalErrorType.AbundanceColumnTogether	Constant AbundanceColumnTogether
static MZTabErrorType	LogicalErrorType.AmbiguityMod	Constant AmbiguityMod
static MZTabErrorType	LogicalErrorType.AssayNotDefined	Constant AssayNotDefined
static MZTabErrorType	LogicalErrorType.AssayRefs	Constant AssayRefs
static MZTabErrorType	LogicalErrorType.CHEMMODS	Constant CHEMMODS
static MZTabErrorType	FormatErrorType.CHEMMODSAccession	Constant CHEMMODSAccession
static MZTabErrorType	LogicalErrorType.ColumnNotValid	Constant ColumnNotValid
static MZTabErrorType	FormatErrorType.ColUnit	Constant ColUnit
static MZTabErrorType	FormatErrorType.CountMatch	Constant CountMatch
static MZTabErrorType	CrossCheckErrorType.CvTermMalformed	Constant CvTermMalformed
static MZTabErrorType	CrossCheckErrorType.CvTermNotAllowed	Constant CvTermNotAllowed
static MZTabErrorType	CrossCheckErrorType.CvTermNotInRule	Constant CvTermNotInRule
static MZTabErrorType	CrossCheckErrorType.CvTermOptional	Constant CvTermOptional
static MZTabErrorType	CrossCheckErrorType.CvTermRecommended	Constant CvTermRecommended
static MZTabErrorType	CrossCheckErrorType.CvTermRequired	Constant CvTermRequired
static MZTabErrorType	CrossCheckErrorType.CvTermXor	Constant CvTermXor
static MZTabErrorType	CrossCheckErrorType.CvUndefinedInMetadata	Constant CvUndefinedInMetadata
static MZTabErrorType	CrossCheckErrorType.CvUnused	Constant CvUnused
static MZTabErrorType	FormatErrorType.Double	Constant Double
static MZTabErrorType	FormatErrorType.DoubleList	Constant DoubleList
static MZTabErrorType	LogicalErrorType.DuplicationAccession	Constant DuplicationAccession
static MZTabErrorType	LogicalErrorType.DuplicationDefine	Constant DuplicationDefine
static MZTabErrorType	LogicalErrorType.DuplicationID	Constant DuplicationID
static MZTabErrorType	FormatErrorType.Email	Constant Email
static MZTabErrorType	LogicalErrorType.ExternalStudyFormatNotDefined	Constant ExternalStudyFormatNotDefined
static MZTabErrorType	LogicalErrorType.ExternalStudyIdFormatNotDefined	Constant ExternalStudyIdFormatNotDefined
static MZTabErrorType	LogicalErrorType.FixedMod	Constant FixedMod
static MZTabErrorType	FormatErrorType.GOTermList	Constant GOTermList
static MZTabErrorType	LogicalErrorType.HeaderLine	Constant HeaderLine
static MZTabErrorType	LogicalErrorType.HeaderNotValid	Constant HeaderNotValid
static MZTabErrorType	LogicalErrorType.IdNumber	Constant IdNumber
static MZTabErrorType	FormatErrorType.IndexedElement	Constant IndexedElement
static MZTabErrorType	FormatErrorType.Integer	Constant Integer
static MZTabErrorType	FormatErrorType.IntegerList	Constant IntegerList
static MZTabErrorType	FormatErrorType.InvalidColunitFormat	Constant InvalidColunitFormat
static MZTabErrorType	LogicalErrorType.ItemNumberMismatch	Constant ItemNumberMismatch
static MZTabErrorType	LogicalErrorType.LineOrder	Constant LineOrder
static MZTabErrorType	FormatErrorType.LinePrefix	Constant LinePrefix
static MZTabErrorType	FormatErrorType.ModificationList	Constant ModificationList
static MZTabErrorType	LogicalErrorType.ModificationPosition	Constant ModificationPosition
static MZTabErrorType	LogicalErrorType.MsRunHashMethodNotDefined	Constant MsRunHashMethodNotDefined
static MZTabErrorType	LogicalErrorType.MsRunLocation	Constant MsRunLocation
static MZTabErrorType	LogicalErrorType.MsRunNotDefined	Constant MsRunNotDefined
static MZTabErrorType	FormatErrorType.MsRunOptionalColumn	Constant MsRunOptionalColumn
static MZTabErrorType	FormatErrorType.MTDDefineLabel	Constant MTDDefineLabel
static MZTabErrorType	FormatErrorType.MTDLine	Constant MTDLine
static MZTabErrorType	FormatErrorType.MZBoolean	Constant MZBoolean
static MZTabErrorType	FormatErrorType.MZTabId	Constant MZTabType
static MZTabErrorType	FormatErrorType.MZTabMode	Constant MZTabMode
static MZTabErrorType	FormatErrorType.MZTabType	Constant MZTabType
static MZTabErrorType	FormatErrorType.MZTabVersion	Constant MZTabVersion
static MZTabErrorType	LogicalErrorType.NoDatabaseMustHaveNullPrefix	Constant NoDatabaseMustHaveNullPrefix
static MZTabErrorType	LogicalErrorType.NoHeaderLine	Constant NoHeaderLine
static MZTabErrorType	LogicalErrorType.NoMetadataSection	Constant NoMetadataSection
static MZTabErrorType	LogicalErrorType.NoSmallMoleculeEvidenceSection	Constant NoSmallMoleculeEvidenceSection
static MZTabErrorType	LogicalErrorType.NoSmallMoleculeFeatureQuantificationUnit	Constant NoSmallMoleculeFeatureQuantificationUnit
static MZTabErrorType	LogicalErrorType.NoSmallMoleculeFeatureSection	Constant NoSmallMoleculeFeatureSection
static MZTabErrorType	LogicalErrorType.NoSmallMoleculeIdentificationReliability	Constant NoSmallMoleculeIdentificationReliability
static MZTabErrorType	LogicalErrorType.NoSmallMoleculeQuantificationUnit	Constant NoSmallMoleculeQuantificationUnit
static MZTabErrorType	LogicalErrorType.NoSmallMoleculeSummarySection	Constant NoSmallMoleculeSummarySection
static MZTabErrorType	LogicalErrorType.NotDefineInHeader	Constant NotDefineInHeader
static MZTabErrorType	LogicalErrorType.NotDefineInMetadata	Constant NotDefineInMetadata
static MZTabErrorType	LogicalErrorType.NotNULL	Constant NotNULL
static MZTabErrorType	LogicalErrorType.NULL	Constant NULL
static MZTabErrorType	FormatErrorType.OptionalCVParamColumn	Constant OptionalCVParamColumn
static MZTabErrorType	FormatErrorType.Param	Constant Param
static MZTabErrorType	FormatErrorType.ParamAccessionNotNamespaced	Constant ParamAccessionNotNamespaced
static MZTabErrorType	FormatErrorType.ParamList	Constant ParamList
static MZTabErrorType	LogicalErrorType.PeptideSearchEngineScoreNotDefined	Constant PeptideSearchEngineScoreNotDefined
static MZTabErrorType	LogicalErrorType.PeptideSection	Constant PeptideSection
static MZTabErrorType	LogicalErrorType.ProteinCoverage	Constant ProteinCoverage
static MZTabErrorType	LogicalErrorType.ProteinSearchEngineScoreNotDefined	Constant ProteinSearchEngineScoreNotDefined
static MZTabErrorType	LogicalErrorType.PSMSearchEngineScoreNotDefined	Constant PSMSearchEngineScoreNotDefined
static MZTabErrorType	FormatErrorType.Publication	Constant Publication
static MZTabErrorType	LogicalErrorType.QuantificationAbundance	Constant QuantificationAbundance
static MZTabErrorType	FormatErrorType.RegexMismatch	Constant RegexMismatch
static MZTabErrorType	FormatErrorType.Reliability	Constant Reliability
static MZTabErrorType	CrossCheckErrorType.RulePointerObjectNullOptional	Constant RulePointerObjectNullOptional
static MZTabErrorType	CrossCheckErrorType.RulePointerObjectNullRecommended	Constant RulePointerObjectNullRecommended
static MZTabErrorType	CrossCheckErrorType.RulePointerObjectNullRequired	Constant RulePointerObjectNullRequired
static MZTabErrorType	FormatErrorType.SearchEngineScore	Constant SearchEngineScore
static MZTabErrorType	CrossCheckErrorType.SemanticValidationException	Constant SemanticValidationException
static MZTabErrorType	FormatErrorType.Sequence	Constant Sequence
static MZTabErrorType	LogicalErrorType.SingleStudyVariableName	Constant SingleStudyVariableName
static MZTabErrorType	LogicalErrorType.SmallMoleculeSearchEngineScoreNotDefined	Constant SmallMoleculeSearchEngineScoreNotDefined
static MZTabErrorType	LogicalErrorType.SoftwareVersion	Constant SoftwareVersion
static MZTabErrorType	CrossCheckErrorType.Species	Constant Species
static MZTabErrorType	FormatErrorType.SpectraRef	Constant SpectraRef
static MZTabErrorType	LogicalErrorType.SpectraRef	Constant SpectraRef
static MZTabErrorType	FormatErrorType.StableColumn	Constant StableColumn
static MZTabErrorType	FormatErrorType.StringList	Constant StringList
static MZTabErrorType	LogicalErrorType.StudyVariableNotDefined	Constant StudyVariableNotDefined
static MZTabErrorType	LogicalErrorType.SubstituteIdentifier	Constant SubstituteIdentifier
static MZTabErrorType	LogicalErrorType.UndefinedStudyVariableNameOnceOnly	Constant UndefinedStudyVariableNameOnceOnly
static MZTabErrorType	LogicalErrorType.UnknownRefId	Constant UnknownRefId
static MZTabErrorType	FormatErrorType.URI	Constant URI
static MZTabErrorType	FormatErrorType.URL	Constant URL
static MZTabErrorType	LogicalErrorType.VariableMod	Constant VariableMod

Methods in uk.ac.ebi.pride.jmztab2.utils.errors that return MZTabErrorType

Modifier and Type	Method	Description
protected static MZTabErrorType	MZTabErrorType.createError(MZTabErrorType.Category category, java.lang.String keyword)	Generate a MZTabErrorType.Level.Error by parse keyword.
protected static MZTabErrorType	MZTabErrorType.createInfo(MZTabErrorType.Category category, java.lang.String keyword)	Generate a MZTabErrorType.Level.Info by parse keyword.
protected static MZTabErrorType	MZTabErrorType.createWarn(MZTabErrorType.Category category, java.lang.String keyword)	Generate a MZTabErrorType.Level.Warn by parse keyword.
static MZTabErrorType	MZTabErrorType.forLevel(MZTabErrorType.Category category, MZTabErrorType.Level level, java.lang.String keyword)
MZTabErrorType	MZTabError.getType()	Getter for the field type.
MZTabErrorType	MZTabErrorTypeMap.getType(int code)	getType.
static MZTabErrorType[]	CrossCheckErrorType.getValues()
static MZTabErrorType[]	FormatErrorType.getValues()
static MZTabErrorType[]	LogicalErrorType.getValues()

Methods in uk.ac.ebi.pride.jmztab2.utils.errors that return types with arguments of type MZTabErrorType

Modifier and Type	Method	Description
java.util.Map<java.lang.Integer,MZTabErrorType>	MZTabErrorTypeMap.getTypeMap()	Getter for the field typeMap.

Constructors in uk.ac.ebi.pride.jmztab2.utils.errors with parameters of type MZTabErrorType

Constructor	Description
MZTabError(MZTabErrorType type, int lineNumber, java.lang.String... values)	System will fill a couple of values one by one, and generate a concrete error message during parse MZTabError.lineNumber line in mzTab file.