| Package | Description | 
|---|---|
| uk.ac.ebi.arrayexpress2.magetab.datamodel | 
 Classes for constructing an in-memory datamodel of the data contained in IDF and
SDRF files, as specified by the MAGE-TAB specification. 
 | 
| uk.ac.ebi.arrayexpress2.magetab.datamodel.graph | 
 Some high-level graph modelling classes, for representing abstract graphs. 
 | 
| uk.ac.ebi.arrayexpress2.magetab.exception | 
 All defined exceptions thrown anywhere in the suite of tools and utilities for
working with MAGE-TAB documents and datastructures. 
 | 
| uk.ac.ebi.arrayexpress2.magetab.handler | 
 Handler classes, interfaces and utilities for interpreting MAGE-TAB documents
and converting to objects in the datamodel and ArrayExpress 2 domain model. 
 | 
| uk.ac.ebi.arrayexpress2.magetab.handler.adf | 
 ADF specific handler classes. 
 | 
| uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl | 
 Specific, concrete ADF header handler implementations. 
 | 
| uk.ac.ebi.arrayexpress2.magetab.handler.adf.node | 
 ADF "graph part" specific handler classes. 
 | 
| uk.ac.ebi.arrayexpress2.magetab.handler.adf.node.attribute | 
 ADF graph handler implementations that are capable of handling data items that
represent attributes attached to a node in the ADF, as defined by the MAGE-TAB
specification. 
 | 
| uk.ac.ebi.arrayexpress2.magetab.handler.idf | 
 IDF specific handler classes. 
 | 
| uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl | 
 Specific, concrete IDF handler implementations. 
 | 
| uk.ac.ebi.arrayexpress2.magetab.handler.sdrf | 
 SDRF specific handler classes. 
 | 
| uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node | 
 Specific handlers for SDRF node data items, as defined in the MAGE-TAB
specification. 
 | 
| uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute | 
 SDRF Handler implementations that are capable of handling data items that
represent attributes attached to a node, as defined by the MAGE-TAB
specification. 
 | 
| uk.ac.ebi.arrayexpress2.magetab.parser | 
 Parser classes for parsing MAGE-TAB aspects. 
 | 
| Modifier and Type | Method and Description | 
|---|---|
void | 
ADF.storeNode(ADFNode node)
Deprecated. 
 
since version 1.1, use  
AbstractGraph.addNode(uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.Node)
             instead | 
void | 
SDRF.storeNode(SDRFNode node)
Deprecated. 
 
since version 1.1, use  
AbstractGraph.addNode(uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.Node)
             instead | 
| Modifier and Type | Method and Description | 
|---|---|
void | 
AbstractGraph.addNode(S node)  | 
void | 
Graph.addNode(S node)
Store a node in the  
Graph. | 
void | 
AbstractGraph.checkForCycles(Node node,
              Node childNode)  | 
void | 
Graph.checkForCycles(Node node,
              Node childNode)
Assertain whether this graph contains any cycles. 
 | 
void | 
AbstractGraph.resolveGraphStructure(S node)  | 
void | 
Graph.resolveGraphStructure(S node)
Update this node being stored with appropriate references to it's parents and update any child node references
 that are already present in the graph. 
 | 
void | 
AbstractGraph.updateNode(S node)  | 
void | 
Graph.updateNode(S node)
Updates an node in the SDRF graph, on the assumption that its position in the graph, or its children, have been
 altered. 
 | 
| Modifier and Type | Class and Description | 
|---|---|
class  | 
ConversionException
A  
ParseException that gets thrown whenever part of a MAGETABInvestigation
 or a MAGETABInvestigation fails a conversion process. | 
class  | 
IllegalLineLengthException
A  
ParseException that is thrown whenever a line parsed from a TDT file is an illegal length. | 
class  | 
InconsistentEntryCountException
A  
ParseException that is thrown when the number of entries in a spreadsheet is not consistent, for example
 when an fixed size matrix is expected but column lengths are variable. | 
class  | 
UnmatchedTagException
A  
ParseException that gets thrown whenever a tag in a TDT file is mismatched when compared to the expected
 one, or if the content type is wrong for the header. | 
class  | 
ValidateException
A  
ParseException that gets thrown whenever part of a MAGETABInvestigation
 or a MAGETABInvestigation fails a validation process. | 
| Modifier and Type | Method and Description | 
|---|---|
void | 
ReadHandler.read(H header,
    D data,
    T target,
    int lineNumber,
    int columnNumber)
Cause the handler to read the supplied data into the supplied target object. 
 | 
| Modifier and Type | Method and Description | 
|---|---|
void | 
ADFGraphReadHandler.read(String[] header,
    String[] data,
    ADF adf,
    int lineNumber,
    int columnNumber)  | 
void | 
ADFHeaderReadHandler.read(String header,
    String[] data,
    ADF adf,
    int lineNumber,
    int columnNumber)
Invoke this read handler. 
 | 
protected int | 
ADFGraphReadHandler.readAttribute(ADFAttributeReader reader,
             String[] header,
             String[] data,
             ADFNode parentNode,
             int startIndex)  | 
protected abstract void | 
ADFGraphReadHandler.readData(String[] header,
        String[] data,
        ADF adf,
        int lineNumber,
        int columnNumber)
Performs the unit of work to read the data into the internal datamodel. 
 | 
protected abstract void | 
ADFHeaderReadHandler.readValue(ADF adf,
         String value,
         int lineNumber,
         String... types)
Performs the unit of work to read the data into the internal MAGE-TAB investigation. 
 | 
| Modifier and Type | Method and Description | 
|---|---|
protected void | 
ProviderHandler.readValue(ADF adf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
SurfaceTypeTermSourceRefHandler.readValue(ADF adf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
SequencePolymerTypeHandler.readValue(ADF adf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
SurfaceTypeHandler.readValue(ADF adf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
AccessionHandler.readValue(ADF adf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
TechnologyTypeHandler.readValue(ADF adf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
TermSourceNameHandler.readValue(ADF adf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
TechnologyTypeTermAccessionHandler.readValue(ADF adf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
SurfaceTypeTermAccessionHandler.readValue(ADF adf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
CommentHandler.readValue(ADF adf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
SequencePolymerTypeTermSourceRefHandler.readValue(ADF adf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
VersionHandler.readValue(ADF adf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
SubstrateTypeTermAccessionHandler.readValue(ADF adf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
SequencePolymerTypeTermAccessionHandler.readValue(ADF adf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
TermSourceVersionHandler.readValue(ADF adf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
SubstrateTypeHandler.readValue(ADF adf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
ArrayDesignNameHandler.readValue(ADF adf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
SubstrateTypeTermSourceRefHandler.readValue(ADF adf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
PrintingProtocolHandler.readValue(ADF adf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
TechnologyTypeTermSourceRefHandler.readValue(ADF adf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
TermSourceFileHandler.readValue(ADF adf,
         String value,
         int lineNumber,
         String... types)  | 
| Modifier and Type | Method and Description | 
|---|---|
protected void | 
CompositeElementHandler.readData(String[] header,
        String[] data,
        ADF adf,
        int lineNumber,
        int columnNumber)  | 
protected void | 
FeatureHandler.readData(String[] header,
        String[] value,
        ADF adf,
        int lineNumber,
        int columnNumber)  | 
protected void | 
ReporterHandler.readData(String[] header,
        String[] data,
        ADF adf,
        int lineNumber,
        int columnNumber)  | 
| Modifier and Type | Method and Description | 
|---|---|
void | 
ControlTypeAttributeReader.readAttributes(String[] header,
              String[] data,
              ADFNode adfNode)  | 
void | 
ReporterGroupAttributeReader.readAttributes(String[] header,
              String[] data,
              ADFNode adfNode)  | 
void | 
ADFAttributeReader.readAttributes(String[] header,
              String[] data,
              ADFNode adfNode)
Reads the attributes from the data and sets them on the supplied SDRFNode 
 | 
| Modifier and Type | Method and Description | 
|---|---|
void | 
IDFReadHandler.read(String header,
    String[] data,
    IDF idf,
    int lineNumber,
    int columnNumber)
Invoke this read handler. 
 | 
protected abstract void | 
IDFReadHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)
Performs the unit of work to read the data into the internal MAGE-TAB investigation. 
 | 
| Modifier and Type | Method and Description | 
|---|---|
protected void | 
ExperimentalDesignTermAccessionHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
ProtocolSoftwareHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
PublicationStatusTermSourceRefHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
ExperimentalFactorTypeHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
ProtocolHardwareHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
QualityControlTypeHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
void | 
AccessionHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
PersonRolesTermSourceRefHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
ReplicateTermSourceRefHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
PublicationDoiHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
TermSourceNameHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
PublicReleaseDateHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
PersonMidInitialsHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
ProtocolDescriptionHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
PublicationAuthorListHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
ExperimentalFactorTermSourceRefHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
PersonAddressHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
PersonFirstNameHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
void | 
CommentHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
PersonEmailHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
ProtocolNameHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
NormalizationTermAccessionHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
ReplicateTermAccessionHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
ProtocolContactHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
QualityControlTermAccessionHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
PublicationStatusTermAccessionHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
ExperimentalDesignTermSourceRefHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
PersonLastNameHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
TermSourceVersionHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
SDRFFileHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
PubMedIdHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
ProtocolTermAccessionHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
ProtocolTypeHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
InvestigationTitleHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
ReplicateTypeHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
NormalizationTypeHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
DateOfExperimentHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
ExperimentDescriptionHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
ExperimentalFactorTermAccessionHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
ProtocolTermSourceRefHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
NormalizationTermSourceRefHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
PersonFaxHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
PersonAffiliationHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
ExperimentalFactorNameHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
ProtocolParametersHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
ExperimentalDesignHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
PersonRolesTermAccessionHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
QualityControlTermSourceRefHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
PublicationStatusHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
PersonRolesHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
TermSourceFileHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
PersonPhoneHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
MAGETABVersionHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
protected void | 
PublicationTitleHandler.readValue(IDF idf,
         String value,
         int lineNumber,
         String... types)  | 
| Modifier and Type | Method and Description | 
|---|---|
protected <T extends SDRFNode>  | 
SDRFReadInContextHandler.fetchUpstreamNode(SDRF sdrf,
                 String nodeName,
                 Class<T> nodeClass)
Used for adding nodes that are upstream of the current node in the SDRF graph. 
 | 
protected SDRFNode | 
SDRFReadInContextHandler.handleUpstreamNode(SDRF sdrf,
                  String nodeName,
                  String nodeType,
                  int lineNumber,
                  int columnNumber)
Used for adding nodes that are upstream of the current node in the SDRF graph. 
 | 
void | 
SDRFReadInContextHandler.read(String[] header,
    String[] data,
    SDRF sdrf,
    int lineNumber,
    int columnNumber)  | 
void | 
SDRFReadHandler.read(String[] header,
    String[] data,
    SDRF sdrf,
    int lineNumber,
    int columnNumber)  | 
protected int | 
SDRFReadHandler.readAttribute(SDRFAttributeReader reader,
             String[] header,
             String[] data,
             SDRF sdrf,
             SDRFNode parentNode,
             int lineNumber,
             int columnNumber,
             int startIndex)  | 
protected abstract void | 
SDRFReadHandler.readData(String[] header,
        String[] data,
        SDRF sdrf,
        int lineNumber,
        int columnNumber)
Performs the unit of work to read the data into the internal datamodel. 
 | 
abstract void | 
SDRFReadInContextHandler.readDataFrom(String[] header,
            String[] data,
            SDRF sdrf,
            int lineNumber,
            int columnNumber)
Performs the unit of work to read the data into the internal datamodel. 
 | 
void | 
SDRFReadInContextHandler.readFrom(String[] header,
        String[] data,
        SDRF sdrf,
        int lineNumber,
        int columnNumber)
Cause the handler to read some of the supplied data (usually starting from startIndex) into the supplied target
 object, using additional context information where appropriate. 
 | 
| Modifier and Type | Method and Description | 
|---|---|
void | 
DerivedArrayDataHandler.readData(String[] header,
        String[] data,
        SDRF sdrf,
        int lineNumber,
        int columnNumber)  | 
void | 
LabeledExtractHandler.readData(String[] header,
        String[] data,
        SDRF sdrf,
        int lineNumber,
        int columnNumber)  | 
void | 
NormalizationHandler.readData(String[] header,
        String[] data,
        SDRF sdrf,
        int lineNumber,
        int columnNumber)  | 
void | 
ScanHandler.readData(String[] header,
        String[] data,
        SDRF sdrf,
        int lineNumber,
        int columnNumber)  | 
void | 
ImageHandler.readData(String[] header,
        String[] data,
        SDRF sdrf,
        int lineNumber,
        int columnNumber)  | 
void | 
ArrayDataMatrixHandler.readData(String[] header,
        String[] data,
        SDRF sdrf,
        int lineNumber,
        int columnNumber)  | 
void | 
ProtocolHandler.readData(String[] header,
        String[] data,
        SDRF sdrf,
        int lineNumber,
        int columnNumber)  | 
void | 
AssayHandler.readData(String[] header,
        String[] data,
        SDRF sdrf,
        int lineNumber,
        int columnNumber)  | 
void | 
FactorValueNodeHandler.readData(String[] header,
        String[] data,
        SDRF sdrf,
        int lineNumber,
        int columnNumber)  | 
void | 
ExtractHandler.readData(String[] header,
        String[] data,
        SDRF sdrf,
        int lineNumber,
        int columnNumber)  | 
void | 
DerivedArrayDataMatrixHandler.readData(String[] header,
        String[] data,
        SDRF sdrf,
        int lineNumber,
        int columnNumber)  | 
protected void | 
ArrayDataHandler.readData(String[] header,
        String[] data,
        SDRF sdrf,
        int lineNumber,
        int columnNumber)  | 
protected void | 
UnknownHeaderHandler.readData(String[] header,
        String[] data,
        SDRF sdrf,
        int lineNumber,
        int columnNumber)  | 
void | 
SourceHandler.readData(String[] header,
        String[] data,
        SDRF sdrf,
        int lineNumber,
        int columnNumber)  | 
void | 
SampleHandler.readData(String[] header,
        String[] data,
        SDRF sdrf,
        int lineNumber,
        int columnNumber)  | 
void | 
HybridizationHandler.readData(String[] header,
        String[] data,
        SDRF sdrf,
        int lineNumber,
        int columnNumber)  | 
void | 
ProtocolHandler.readDataFrom(String[] header,
            String[] data,
            SDRF sdrf,
            int lineNumber,
            int columnNumber)
A specialised alternate form of the  
SDRFReadInContextHandler.canReadHeader(String[]) method for handling Protocol Application
 Nodes. | 
void | 
FactorValueNodeHandler.readDataFrom(String[] header,
            String[] data,
            SDRF sdrf,
            int lineNumber,
            int columnNumber)
A specialised alternate form of the  
SDRFReadHandler.readData(String[],
 String[], uk.ac.ebi.arrayexpress2.magetab.datamodel.SDRF, int, int) method, specialised for handling Factor
 Value "floating" nodes. | 
| Modifier and Type | Method and Description | 
|---|---|
void | 
PerformerAttributeReader.readAttributes(String[] header,
              String[] data,
              SDRF sdrf,
              SDRFNode sdrfNode,
              int lineNumber,
              int columnNumber)  | 
void | 
MaterialTypeAttributeReader.readAttributes(String[] header,
              String[] data,
              SDRF sdrf,
              SDRFNode sdrfNode,
              int lineNumber,
              int columnNumber)  | 
void | 
TechnologyTypeAttributeReader.readAttributes(String[] header,
              String[] data,
              SDRF sdrf,
              SDRFNode sdrfNode,
              int lineNumber,
              int columnNumber)  | 
void | 
LabelAttributeReader.readAttributes(String[] header,
              String[] data,
              SDRF sdrf,
              SDRFNode sdrfNode,
              int lineNumber,
              int columnNumber)  | 
void | 
ArrayDesignAttributeReader.readAttributes(String[] header,
              String[] data,
              SDRF sdrf,
              SDRFNode parentNode,
              int lineNumber,
              int columnNumber)  | 
void | 
ParameterValueAttributeReader.readAttributes(String[] header,
              String[] data,
              SDRF sdrf,
              SDRFNode sdrfNode,
              int lineNumber,
              int columnNumber)  | 
void | 
ProviderAttributeReader.readAttributes(String[] header,
              String[] data,
              SDRF sdrf,
              SDRFNode sdrfNode,
              int lineNumber,
              int columnNumber)  | 
void | 
SDRFAttributeReader.readAttributes(String[] header,
              String[] data,
              SDRF sdrf,
              SDRFNode sdrfNode,
              int lineNumber,
              int columnNumber)
Reads the attributes from the data and sets them on the supplied SDRFNode 
 | 
void | 
FactorValueAttributeReader.readAttributes(String[] header,
              String[] data,
              SDRF sdrf,
              SDRFNode sdrfNode,
              int lineNumber,
              int columnNumber)  | 
void | 
CharacteristicsAttributeReader.readAttributes(String[] header,
              String[] data,
              SDRF sdrf,
              SDRFNode parentNode,
              int lineNumber,
              int columnNumber)  | 
| Modifier and Type | Method and Description | 
|---|---|
MAGETABInvestigation | 
MAGETABParser.parse(File idfFile)  | 
MAGETABArrayDesign | 
MAGETABArrayParser.parse(File adfFile)  | 
IDF | 
IDFParser.parse(File idfFile)  | 
SDRF | 
SDRFParser.parse(File sdrfFile)  | 
ADF | 
ADFParser.parse(InputStream adfIn)
Performs parsing from the specified input stream source, populating an  
ADF object which is returned. | 
MAGETABInvestigation | 
MAGETABParser.parse(InputStream idfIn)  | 
T | 
Parser.parse(InputStream dataIn)
Perform parsing from the supplied input stream to a new data model instance. 
 | 
MAGETABArrayDesign | 
MAGETABArrayParser.parse(InputStream adfIn)  | 
IDF | 
IDFParser.parse(InputStream idfIn)
Performs parsing from the specified input stream source, populating an  
IDF object which is returned. | 
SDRF | 
SDRFParser.parse(InputStream sdrfIn)
Performs parsing from the specified input stream source, populating an  
SDRF object which is returned. | 
ADF | 
ADFParser.parse(InputStream adfIn,
     ADF adf)  | 
ADF | 
ADFParser.parse(InputStream adfIn,
     ADF adf,
     ExecutorService service)  | 
IDF | 
IDFParser.parse(InputStream idfIn,
     IDF idf)
Alternate form of the  
IDFParser.parse(java.io.InputStream) method that allows callers to specify the IDF object
 they want to be populated. | 
IDF | 
IDFParser.parse(InputStream idfIn,
     IDF idf,
     ExecutorService service)
Alternate form of the  
IDFParser.parse(java.io.InputStream) method that allows callers to specify both the IDF
 object they wish to be populated and an executor service that should be used to execute all IDF handler tasks. | 
MAGETABArrayDesign | 
MAGETABArrayParser.parse(InputStream adfIn,
     MAGETABArrayDesign arrayDesign)  | 
MAGETABArrayDesign | 
MAGETABArrayParser.parse(InputStream adfIn,
     MAGETABArrayDesign arrayDesign,
     ExecutorService service)  | 
MAGETABInvestigation | 
MAGETABParser.parse(InputStream idfIn,
     MAGETABInvestigation investigation)  | 
MAGETABInvestigation | 
MAGETABParser.parse(InputStream idfIn,
     MAGETABInvestigation investigation,
     ExecutorService service)  | 
SDRF | 
SDRFParser.parse(InputStream sdrfIn,
     SDRF sdrf)
Alternate form of the  
SDRFParser.parse(java.io.InputStream) method that allows callers to specify the SDRF object
 they want to be populated. | 
SDRF | 
SDRFParser.parse(InputStream sdrfIn,
     SDRF sdrf,
     ExecutorService service)
Alternate form of the  
SDRFParser.parse(java.io.InputStream) method that allows callers to specify both the SDRF
 object they wish to be populated and an executor service that should be used to execute all SDRF handler tasks. | 
T | 
Parser.parse(InputStream dataIn,
     T target)
Perform parsing from the supplied input stream to a new data model instance. 
 | 
T | 
Parser.parse(InputStream dataIn,
     T target,
     ExecutorService service)
Perform parsing from the supplied input stream to a new data model instance, delegating all work to the supplied
 Executor Service to enable parsing in parallel. 
 | 
MAGETABInvestigation | 
MAGETABParser.parse(URL idfURL)  | 
MAGETABArrayDesign | 
MAGETABArrayParser.parse(URL adfURL)  | 
IDF | 
IDFParser.parse(URL idfURL)  | 
SDRF | 
SDRFParser.parse(URL sdrfURL)  | 
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