All Classes Interface Summary Class Summary Enum Summary Exception Summary Annotation Types Summary
Class |
Description |
AbundanceColumn |
If the data exporter wishes to report only final results for 'Summary' files (i.e. following averaging over replicates),
then these MUST be reported as quantitative values in the columns associated with the study_variable[1-n] (e.g.
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AbundanceColumn.Field |
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AndValidationHandler |
Implements 'AND' logic, meaning all alternative possible terms or term roots for
an object must occur.
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Assay |
Specification of assay.
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Assay.Properties |
Property enumeration for Assay.
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AssayFormat |
Format specification for Assay .
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AssaySerializer |
AssaySerializer implementation for Assay .
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AssayValidator |
Validates that the quantification method section is present in metadata.
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CheckParameter |
JAVAX validation compliant annotation.
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ClassPathFile |
Test files enum to configure test files.
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ColumnParameterMapping |
Defines the used unit for a column in the mzTab-M file.
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ColumnParameterMapping.Properties |
Property enumeration for ColumnParameterMapping.
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COMLineParser |
Comment line parser.
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Comment |
Comment lines can be placed anywhere in an mzTab file.
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Comment.PrefixEnum |
Gets or Sets prefix
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Comment.Properties |
Property enumeration for Comment.
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Contact |
The contact’s name, affiliation and e-mail.
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Contact.Properties |
Property enumeration for Contact.
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ContactFormat |
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ContactSerializer |
ContactSerializer implementation for Contact .
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CrossCheckErrorType |
Provide crosscheck service, that is parse the consistent between current mztab file and
some other resource (eg, database, xml file and so on).
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CV |
Specification of controlled vocabularies.
label: A string describing the labels of the controlled vocabularies/ontologies used in the mzTab file as a short-hand e.g.
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CV.Properties |
Property enumeration for CV.
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CvDefinitionValidationHandler |
Validates that controlled vocabularies used by parameters are defined in the
metadata CV section.
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CvFormat |
Format specification for CV .
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CvMapping |
Java-Klasse für anonymous complex type.
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CvMapping.CvMappingRuleList |
Java-Klasse für anonymous complex type.
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CvMapping.CvReferenceList |
Java-Klasse für anonymous complex type.
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CvMappingRule |
Java-Klasse für anonymous complex type.
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CvMappingRule.CvTermsCombinationLogic |
Java-Klasse für null.
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CvMappingRule.RequirementLevel |
Java-Klasse für null.
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CvMappingUtils |
Utility methods for conversion between the mapping file domain and the mzTab
domain.
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CvMappingValidator |
Validator implementation that uses a provided xml mapping file with rules for
required, recommended and optional CV parameters to assert that an mzTab
follows these rules.
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CvParameterLookupService |
Abstraction over OLSClient to autoconvert Terms to Parameters and to allow
easy matching of Parameters against parent terms and their children.
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CvReference |
Java-Klasse für anonymous complex type.
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CvRuleHandler |
Interface for rule logic handling implementations.
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CvSerializer |
CvSerializer implementation for CV .
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CvTerm |
Java-Klasse für anonymous complex type.
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CvTermSelectionHandler |
Interface for JxPath subtree selection handling.
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CvTermValidationHandler |
Interface for handling of rule evaluation results.
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CvValidator |
Validates that the controlled vocabulary section is present in metadata and
that it is correctly populated.
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Database |
Specification of databases.
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Database.Properties |
Property enumeration for Database.
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DatabaseFormat |
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DatabaseSerializer |
DatabaseSerializer implementation for Database .
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DatabaseValidator |
Validates that the database section is present and correctly populated in
metadata.
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ElementNameMappingException |
ElementNameMappingException should be thrown to indicate that the state of
the passed in element did not allow mapping to a proper mzTab name.
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EmptyRuleHandler |
Implements handling of rules that have no cv parameter match.
|
Error |
Error
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Error.Properties |
Property enumeration for Error.
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ExtractClassPathFiles |
ExtractClassPathFiles class.
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ExtraParametersValidationHandler |
Implements handling of cv parameters (not user params) that are found at the object.
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FieldValidator<T> |
Implementations of the field validator are applied to the type object (usually a parsed string element)
during the parsing process.
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FormatErrorType |
Diagnose different types of format-related (reporting format problems).
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IMZTabColumn |
IMZTabColumn interface.
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IndexedElement |
Indexed elements (IDs) define a unique ID for a collection of multiple
metadata elements of the same type within the mzTab-M document, e.g. for
sample, assay, study variable etc.
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IndexedElementImpl |
Implementation of IndexedElement where more information is required than just
the id.
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Instrument |
The name, source, analyzer and detector of the instruments used in the experiment.
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Instrument.Properties |
Property enumeration for Instrument.
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InstrumentFormat |
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InstrumentSerializer |
InstrumentSerializer implementation for Instrument .
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IOptColumnMappingBuilder |
Interface for optional column mapping builders.
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ISmallMoleculeColumn |
ISmallMoleculeColumn interface.
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ISmallMoleculeEvidenceColumn |
ISmallMoleculeEvidenceColumn interface.
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ISmallMoleculeFeatureColumn |
ISmallMoleculeFeatureColumn interface.
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JxPathElement |
Utility methods for simpler Java 8 compatible handling of JXPath selections
and pointers.
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LogicalErrorType |
Reporting errors related to the logical relationships among the different
sections in a file.
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LogMethodName |
JUnit TestWatcher to LOGGER the executed test method name.
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Metadata |
The metadata section provides additional information about the dataset(s) reported in the mzTab file.
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Metadata.PrefixEnum |
The metadata section prefix.
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Metadata.Properties |
Property enumeration for Metadata.
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MetadataElement |
Define all elements used in metadata.
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MetadataFormat |
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MetadataProperty |
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MetadataSerializer |
MetadataSerializer class.
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MsRun |
Specification of ms_run.
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MsRun.Properties |
Property enumeration for MsRun.
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MsRunFormat |
Format specification for MsRun .
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MsRunSerializer |
MsRunSerializer implementation for MsRun .
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MsRunValidator |
Validates that the ms run section is present in metadata.
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MTDLineParser |
Parse a metadata line into a element.
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MZBoolean |
In mzTab, using 0-false, 1-true to express the boolean value.
|
MzTab |
mzTab-M is intended as a reporting standard for quantitative results from metabolomics/lipodomics approaches.
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MzTab.Properties |
Property enumeration for MzTab.
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MzTabAccess |
Utility class for easier access to linked information within an mztab-M data
object.
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MzTabBeanValidator |
This validator used the HibernateValidator bean validation reference
implementation.
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MZTabColumn |
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MZTabColumnFactory |
This is a static factory class which used to generate a couple of MZTabColumn
objects, and organizes them into "logicalPosition, MZTabColumn" pairs.
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MZTabCommandLine |
MZTabCommandLine class.
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MZTabConstants |
Define a couple of constants used in the jmzTab API.
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MZTabConversionException |
Runtime exception for mzTab conversion
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MZTabDataLineParser<T> |
This class allows the validation and loading of the data into mzTab domain
objects.
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MZTabError |
mzTab files can be validated to ensure that they comply with the latest
version of the format specification.
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MZTabErrorList |
A limit max capacity list, if contains a couple of
MZTabError objects.
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MZTabErrorOverflowException |
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MZTabErrorType |
MZTabErrorType class.
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MZTabErrorType.Category |
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MZTabErrorType.Level |
We classify diagnosis message types into three levels: Info, Warn and Error, all of them coming from
the notational conventions of the specification.
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MZTabErrorTypeMap |
This list class used to storage all types of MZTabError, and provide query service based on
the error/warn code.
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MZTabException |
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MzTabFileParser |
MZTabFileParser provides reading functionality of the mzTab file.
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MZTabHeaderLineParser |
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MzTabIdValidator |
Validates that mzTab-ID is neither null nor empty.
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MZTabLineParser |
Common tab split line parser.
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MzTabNonValidatingWriter |
MzTabNonValidatingWriter allows to write MzTab objects without additional
validation checks.
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MZTabParserContext |
MZTabParserContext is used to keep track of indexed elements and interrelations during parsing.
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MZTabProperties |
This class will load the properties used by the mzTab-M library for message formatting during validation.
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MZTabStringUtils |
Provide a couple of functions for translate, parse and print formatted string defined in the mzTab specification.
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MZTabUtils |
Provide a couple of functions for translating, parsing and printing formatted strings
defined in the mzTab specification.
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MzTabValidatingWriter |
MzTabValidatingWriter allows to write MzTab objects after validation with a
custom or default validator.
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MzTabValidatingWriter.WriteAndParseValidator |
A default validator implemenation that first writes and then parses the
created temporary file, performing the parser checks.
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MzTabValidator |
Delegating validator implementation that forwards validation to the provided
validator implementations.
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MzTabVersionValidator |
Validates that mzTab-version is neither null nor empty.
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MzTabWriter<T> |
Interface for mztab writer implementors.
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MzTabWriterDefaults |
Default mapper and schema definitions for writing of mzTab files using the
Jackson CSV mapper.
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ObjectFactory |
This object contains factory methods for each
Java content interface and Java element interface
generated in the info.psidev.cvmapping package.
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OptColumnMapping |
Additional columns can be added to the end of the small molecule table.
|
OptColumnMapping.Properties |
Property enumeration for OptColumnMapping.
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OptColumnMappingBuilder |
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OptColumnMappingBuilder.GlobalOptColumnMappingBuilder |
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OptColumnMappingBuilder.IndexedElementOptColumnMappingBuilder |
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OptionColumn |
Additional columns can be added to the end of the protein table.
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OrValidationHandler |
Implements 'OR' logic, meaning alternative possible terms or term roots for
an object may be present.
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Parameter |
mzTab makes use of CV parameters.
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Parameter.Properties |
Property enumeration for Parameter.
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ParameterComparisonResult |
Result of a comparison of a CvTerm T defined in a CvRule against the parameter P
found via JXPath.
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ParameterConverter |
Parameter to String converter implementation for
Parameter .
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ParameterFormat |
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ParameterOptionColumn |
An kind of OptionColumn which use CV parameter accessions in following the format:
opt_{OBJECT_ID}_cv_{accession}_{parameter name}.
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ParameterValidator |
Base interface for parameter validation with default validation method.
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PositionMapping |
Create and maintain a couple of mappings between physical position and logical position.
|
Publication |
A publication associated with this file.
|
Publication.Properties |
Property enumeration for Publication.
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PublicationFormat |
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PublicationItem |
A publication item, defined by a qualifier and a native accession, e.g. pubmed id.
|
PublicationItem.Properties |
Property enumeration for PublicationItem.
|
PublicationItem.TypeEnum |
The type qualifier of this publication item.
|
PublicationSerializer |
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QuantificationMethodValidator |
Validates that the quantification method section is present in metadata.
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RefiningValidator<T> |
Implementations of the refining validator are applied to the type object
after the actual line parsing process, for post-hoc validation.
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RemoveUserParams |
Removes user parameters from the provided selection.
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ResolvingCvRuleHandler |
Implements resolution of cv parameters using the provided lookup service.
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RuleEvaluationResult |
Captures results of applying a rule to a parameter selection.
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Sample |
Specification of sample.
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Sample.Properties |
Property enumeration for Sample.
|
SampleFormat |
Format specification for Sample .
|
SampleProcessing |
A list of parameters describing a sample processing, preparation or handling step similar to a biological or analytical methods report.
|
SampleProcessing.Properties |
Property enumeration for SampleProcessing.
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SampleProcessingFormat |
|
SampleProcessingSerializer |
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SampleSerializer |
SampleSerializer implementation for Sample .
|
Section |
Every line in an mzTab file MUST start with a three letter code identifying the type of line delimited by
a Tab character.
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SEHLineParser |
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Serializers |
Utility class providing helper methods for other serializers.
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SetOperations |
Utility methods for sets with common names.
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SFHLineParser |
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SharedParametersValidationHandler |
Implements support for validating multiple parameters and the intersection
between terms as described by the rule and the actually found ones.
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SmallMoleculeColumn |
Define the stable columns which have stable order in the small molecule header
line
|
SmallMoleculeColumn.Stable |
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SmallMoleculeEvidence |
The small molecule evidence section is table-based, representing evidence for identifications of small molecules/features, from database search or any other process used to give putative identifications to molecules.
|
SmallMoleculeEvidence.HeaderPrefixEnum |
The small molecule evidence table header prefix.
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SmallMoleculeEvidence.PrefixEnum |
The small molecule evidence table row prefix.
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SmallMoleculeEvidence.Properties |
Property enumeration for SmallMoleculeEvidence.
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SmallMoleculeEvidenceColumn |
Define the stable columns which have stable order in the small molecule
evidence header line.
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SmallMoleculeEvidenceColumn.Stable |
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SmallMoleculeEvidenceFormat |
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SmallMoleculeEvidenceSerializer |
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SmallMoleculeFeature |
The small molecule feature section is table-based, representing individual MS regions (generally considered to be the elution profile for all isotopomers formed from a single charge state of a molecule), that have been measured/quantified.
|
SmallMoleculeFeature.HeaderPrefixEnum |
The small molecule feature table header prefix.
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SmallMoleculeFeature.PrefixEnum |
The small molecule feature table row prefix.
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SmallMoleculeFeature.Properties |
Property enumeration for SmallMoleculeFeature.
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SmallMoleculeFeatureColumn |
Define the stable columns which have stable order in the small molecule
feature header line.
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SmallMoleculeFeatureColumn.Stable |
|
SmallMoleculeFeatureFormat |
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SmallMoleculeFeatureQuantificationUnitValidator |
Validates that smallMoleculeFeatureQuantificationUnit is neither null nor
empty.
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SmallMoleculeFeatureSerializer |
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SmallMoleculeIdConfidenceMeasureValidator |
Validates that smallMolecule identification confidence measure is neither
null nor empty.
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SmallMoleculeQuantificationUnitValidator |
Validates that smallMoleculeQuantificationUnit is neither null nor empty.
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SmallMoleculeSummary |
The small molecule summary section is table-based, represented summarized quantitative information across assays and study variables, grouped by identification in rows.
|
SmallMoleculeSummary.HeaderPrefixEnum |
The small molecule table header prefix.
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SmallMoleculeSummary.PrefixEnum |
The small molecule table row prefix.
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SmallMoleculeSummary.Properties |
Property enumeration for SmallMoleculeSummary.
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SmallMoleculeSummaryFormat |
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SmallMoleculeSummarySerializer |
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SMELineParser |
SMELineParser class.
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SMFLineParser |
SMFLineParser class.
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SMHLineParser |
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SMLLineParser |
SMLLineParser class.
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Software |
Software used to analyze the data and obtain the reported results.
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Software.Properties |
Property enumeration for Software.
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SoftwareFormat |
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SoftwareSerializer |
SoftwareSerializer implementation for Software .
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SoftwareValidator |
Validates that the software section is present in metadata and contains at
least one item.
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SpectraRef |
Reference to a spectrum in a spectrum file, for example a fragmentation spectrum has been used to support the identification.
|
SpectraRef.Properties |
Property enumeration for SpectraRef.
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SpectraRefValidator |
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SplitList<E> |
This is list which each item split by a split char.
|
StringList |
A typed list of strings.
|
StudyVariable |
Specification of study_variable.
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StudyVariable.Properties |
Property enumeration for StudyVariable.
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StudyVariableFormat |
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StudyVariableSerializer |
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StudyVariableValidator |
Validates that the study variable section is present in metadata and is
linked to all assays and ms runs.
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Uri |
A URI pointing to the file’s source data (e.g., a MetaboLights records) or an external file with more details about the study design.
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Uri.Properties |
Property enumeration for Uri.
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UriConverter |
Converter from Uri to String.
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UriFormat |
Format specification for Uri .
|
UriSerializer |
UriSerializer implementation for Uri .
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ValidationMessage |
ValidationMessage
|
ValidationMessage.CategoryEnum |
Gets or Sets category
|
ValidationMessage.MessageTypeEnum |
Gets or Sets messageType
|
ValidationMessage.Properties |
Property enumeration for ValidationMessage.
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Validator<T> |
Validator interface.
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XorValidationHandler |
Implements 'XOR' logic, meaning mutually exclusive alternative possible terms or term roots for
an object are allowed.
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ZipResourceExtractionException |
This runtime exception is thrown when IO exceptions are encountered within
the ZipResourceExtractor test rule.
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ZipResourceExtractor |
ZipResourceExtractor class.
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