java.lang.Object
- psidev.psi.mi.jami.tab.extension.datasource.AbstractMitabSource<T,P,F>

All Implemented Interfaces:

InteractionSource<T>, InteractionStream<T>, MIDataSource, MIFileDataSource, MIFileParserListener, MitabSource<T>, MitabStreamSource<T>, MitabParserListener

Direct Known Subclasses:

LightMitabBinarySource, LightMitabSource, MitabBinaryEvidenceSource, MitabEvidenceSource, MitabModelledBinarySource, MitabModelledSource
```
public abstract class AbstractMitabSource<T extends Interaction,P extends Participant,F extends Feature>
extends Object
implements MitabSource<T>
```
Abstract class for an InteractionSource coming from a MITAB file. This datasource provides interaction iterator and collection
Since:
```
08/11/13
```
Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Field Summary
- Fields inherited from interface psidev.psi.mi.jami.datasource.MIFileDataSource
  FILE_URI_PREFIX, URL_PREFIX_REGEXP

Constructor Summary

Constructors
Constructor Description

AbstractMitabSource(AbstractMitabStreamSource<T,P,F> delegatedSource)
Constructor for AbstractMitabSource.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`close()`	close.
`MIFileParserListener`	`getFileParserListener()`	getFileParserListener.
`Collection<T>`	`getInteractions()`	getInteractions.
`Iterator<T>`	`getInteractionsIterator()`	getInteractionsIterator.
`long`	`getNumberOfInteractions()`	getNumberOfInteractions.
`void`	`initialiseContext(Map<String,Object> options)`	Initialise the context of the MIDataSource given a map of options
`void`	`onAliasWithoutDbSource(MitabAlias alias)`	onAliasWithoutDbSource.
`void`	`onAliasWithoutName(FileSourceContext context)`	Listen to an event fired when an alias does not have a name
`void`	`onAnnotationWithoutTopic(FileSourceContext context)`	Listen to an event fired when an annotation does not have a topic
`void`	`onEmptyUniqueIdentifiers(int line, int column, int mitabColumn)`	onEmptyUniqueIdentifiers.
`void`	`onInteractionWithoutParticipants(Interaction interaction, FileSourceContext context)`	Listen to an event fired when an interaction is read and does not have any participants.
`void`	`onInvalidOrganismTaxid(String taxid, FileSourceContext context)`	Listen to an event fired when an organism does not have a valid taxid (positive integer or -1, -2, -3, -4, -5)
`void`	`onInvalidPosition(String message, FileSourceContext context)`	Listen to an event fired when a position is not valid
`void`	`onInvalidRange(String message, FileSourceContext context)`	Listen to an event fired when a range is not valid
`void`	`onInvalidStoichiometry(String message, FileSourceContext context)`	Listen to an event fired when a stoichiometry is not valid
`void`	`onInvalidSyntax(FileSourceContext context, Exception e)`	Listen to an invalid syntax causing an Exception
`void`	`onMissingChecksumMethod(FileSourceContext context)`	Listen to an event fired when a checksum does not have a method
`void`	`onMissingChecksumValue(FileSourceContext context)`	Listen to an event fired when a checksum does not have a value
`void`	`onMissingConfidenceType(FileSourceContext context)`	Listen to an event fired when a confidence does not have a confidence type
`void`	`onMissingConfidenceValue(FileSourceContext context)`	Listen to an event fired when a confidence does not have a value
`void`	`onMissingCvTermName(CvTerm term, FileSourceContext context, String message)`	Listen to an event fired when a CvTerm is read and does not have any names.
`void`	`onMissingExpansionId(MitabCvTerm expansion)`	onMissingExpansionId.
`void`	`onMissingInteractorIdentifierColumns(int line, int column, int mitabColumn)`	onMissingInteractorIdentifierColumns.
`void`	`onMissingInteractorName(Interactor interactor, FileSourceContext context)`	Listen to an event fired when an interactor is read and does not have any names.
`void`	`onMissingParameterType(FileSourceContext context)`	Listen to an event fired when a parameter does not have a type
`void`	`onMissingParameterValue(FileSourceContext context)`	Listen to an event fired when a parameter does not have a value
`void`	`onParticipantWithoutInteractor(Participant participant, FileSourceContext context)`	Listen to en event fired when a Participant is read and no interactor details has been provided.
`void`	`onSeveralCreatedDateFound(Collection<MitabDate> dates)`	onSeveralCreatedDateFound.
`void`	`onSeveralCvTermsFound(Collection<MitabCvTerm> terms, FileSourceContext context, String message)`	Listen to an event where several CvTerms were found and only one was expected.
`void`	`onSeveralFirstAuthorFound(Collection<MitabAuthor> authors)`	onSeveralFirstAuthorFound.
`void`	`onSeveralHostOrganismFound(Collection<MitabOrganism> organisms, FileSourceContext context)`	Listen to an event where several host organisms were found in a single experiment and only one was expected.
`void`	`onSeveralOrganismFound(Collection<MitabOrganism> organisms)`	onSeveralOrganismFound.
`void`	`onSeveralSourceFound(Collection<MitabSource> sources)`	onSeveralSourceFound.
`void`	`onSeveralStoichiometryFound(Collection<MitabStoichiometry> stoichiometry)`	onSeveralStoichiometryFound.
`void`	`onSeveralUniqueIdentifiers(Collection<MitabXref> ids)`	onSeveralUniqueIdentifiers.
`void`	`onSeveralUpdatedDateFound(Collection<MitabDate> dates)`	onSeveralUpdatedDateFound.
`void`	`onSyntaxWarning(FileSourceContext context, String message)`	Listen to an event fired when the syntax of the file is valid but the content is not expected or some information may be lost.
`void`	`onTextFoundInConfidence(MitabConfidence conf)`	onTextFoundInConfidence.
`void`	`onTextFoundInIdentifier(MitabXref xref)`	onTextFoundInIdentifier.
`void`	`onXrefWithoutDatabase(FileSourceContext context)`	Listen to an event fired when a xref does not have a database
`void`	`onXrefWithoutId(FileSourceContext context)`	Listen to an event fired when a xref does not have an id
`void`	`reset()`	reset.
`void`	`setFileParserListener(MIFileParserListener listener)`	setFileParserListener
`boolean`	`validateSyntax()`	validateSyntax.
`boolean`	`validateSyntax(MIFileParserListener listener)`	Validate the syntax of this MIFileDataSource and uses the provided MIFileParserListener to listen to the events.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - AbstractMitabSource
```
public AbstractMitabSource(AbstractMitabStreamSource<T,P,F> delegatedSource)
```
    Constructor for AbstractMitabSource.
    
    Parameters:
    
    delegatedSource - a AbstractMitabStreamSource object.
- Method Detail
  - getInteractions
```
public Collection<T> getInteractions()
                              throws MIIOException
```
    getInteractions.
    
    Specified by:
    
    getInteractions in interface InteractionSource<T extends Interaction>
    
    Returns:
    
    a Collection object.
    
    Throws:
    
    MIIOException - if any.
  - getNumberOfInteractions
```
public long getNumberOfInteractions()
```
    getNumberOfInteractions.
    
    Specified by:
    
    getNumberOfInteractions in interface InteractionSource<T extends Interaction>
    
    Returns:
    
    a long.
  - getInteractionsIterator
```
public Iterator<T> getInteractionsIterator()
                                    throws MIIOException
```
    getInteractionsIterator.
    
    Specified by:
    
    getInteractionsIterator in interface InteractionStream<T extends Interaction>
    
    Returns:
    
    a Iterator object.
    
    Throws:
    
    MIIOException - if any.
  - getFileParserListener
```
public MIFileParserListener getFileParserListener()
```
    getFileParserListener.
    
    Specified by:
    
    getFileParserListener in interface MIFileDataSource
    
    Returns:
    
    a MIFileParserListener object.
  - setFileParserListener
```
public void setFileParserListener(MIFileParserListener listener)
```
    setFileParserListener
    
    Specified by:
    
    setFileParserListener in interface MIFileDataSource
    
    Parameters:
    
    listener - a MIFileParserListener object.
  - validateSyntax
```
public boolean validateSyntax()
                       throws MIIOException
```
    validateSyntax.
    
    Specified by:
    
    validateSyntax in interface MIFileDataSource
    
    Returns:
    
    a boolean.
    
    Throws:
    
    MIIOException - if any.
  - validateSyntax
```
public boolean validateSyntax(MIFileParserListener listener)
                       throws MIIOException
```
    Validate the syntax of this MIFileDataSource and uses the provided MIFileParserListener to listen to the events. The provided listener will be set as the MIFileParserListener of this datasource
    
    Specified by:
    
    validateSyntax in interface MIFileDataSource
    
    Parameters:
    
    listener - : the listener for parsing events
    
    Returns:
    
    true if the file syntax is valid
    
    Throws:
    
    MIIOException - : if some severe syntax errors are found in the file and it stops the parsing
  - initialiseContext
```
public void initialiseContext(Map<String,Object> options)
```
    Initialise the context of the MIDataSource given a map of options
    
    Specified by:
    
    initialiseContext in interface MIDataSource
    
    Parameters:
    
    options - : the options provided by the user
  - close
```
public void close()
           throws MIIOException
```
    close.
    
    Specified by:
    
    close in interface MIDataSource
    
    Throws:
    
    MIIOException - if any.
  - reset
```
public void reset()
           throws MIIOException
```
    reset.
    
    Specified by:
    
    reset in interface MIDataSource
    
    Throws:
    
    MIIOException - if any.
  - onTextFoundInIdentifier
```
public void onTextFoundInIdentifier(MitabXref xref)
```
    onTextFoundInIdentifier.
    
    Specified by:
    
    onTextFoundInIdentifier in interface MitabParserListener
    
    Parameters:
    
    xref - a MitabXref object.
  - onTextFoundInConfidence
```
public void onTextFoundInConfidence(MitabConfidence conf)
```
    onTextFoundInConfidence.
    
    Specified by:
    
    onTextFoundInConfidence in interface MitabParserListener
    
    Parameters:
    
    conf - a MitabConfidence object.
  - onMissingExpansionId
```
public void onMissingExpansionId(MitabCvTerm expansion)
```
    onMissingExpansionId.
    
    Specified by:
    
    onMissingExpansionId in interface MitabParserListener
    
    Parameters:
    
    expansion - a MitabCvTerm object.
  - onSeveralUniqueIdentifiers
```
public void onSeveralUniqueIdentifiers(Collection<MitabXref> ids)
```
    onSeveralUniqueIdentifiers.
    
    Specified by:
    
    onSeveralUniqueIdentifiers in interface MitabParserListener
    
    Parameters:
    
    ids - a Collection object.
  - onEmptyUniqueIdentifiers
```
public void onEmptyUniqueIdentifiers(int line,
                                     int column,
                                     int mitabColumn)
```
    onEmptyUniqueIdentifiers.
    
    Specified by:
    
    onEmptyUniqueIdentifiers in interface MitabParserListener
    
    Parameters:
    
    line - a int.
    
    column - a int.
    
    mitabColumn - a int.
  - onMissingInteractorIdentifierColumns
```
public void onMissingInteractorIdentifierColumns(int line,
                                                 int column,
                                                 int mitabColumn)
```
    onMissingInteractorIdentifierColumns.
    
    Specified by:
    
    onMissingInteractorIdentifierColumns in interface MitabParserListener
    
    Parameters:
    
    line - a int.
    
    column - a int.
    
    mitabColumn - a int.
  - onSeveralOrganismFound
```
public void onSeveralOrganismFound(Collection<MitabOrganism> organisms)
```
    onSeveralOrganismFound.
    
    Specified by:
    
    onSeveralOrganismFound in interface MitabParserListener
    
    Parameters:
    
    organisms - a Collection object.
  - onSeveralStoichiometryFound
```
public void onSeveralStoichiometryFound(Collection<MitabStoichiometry> stoichiometry)
```
    onSeveralStoichiometryFound.
    
    Specified by:
    
    onSeveralStoichiometryFound in interface MitabParserListener
    
    Parameters:
    
    stoichiometry - a Collection object.
  - onSeveralFirstAuthorFound
```
public void onSeveralFirstAuthorFound(Collection<MitabAuthor> authors)
```
    onSeveralFirstAuthorFound.
    
    Specified by:
    
    onSeveralFirstAuthorFound in interface MitabParserListener
    
    Parameters:
    
    authors - a Collection object.
  - onSeveralSourceFound
```
public void onSeveralSourceFound(Collection<MitabSource> sources)
```
    onSeveralSourceFound.
    
    Specified by:
    
    onSeveralSourceFound in interface MitabParserListener
    
    Parameters:
    
    sources - a Collection object.
  - onSeveralCreatedDateFound
```
public void onSeveralCreatedDateFound(Collection<MitabDate> dates)
```
    onSeveralCreatedDateFound.
    
    Specified by:
    
    onSeveralCreatedDateFound in interface MitabParserListener
    
    Parameters:
    
    dates - a Collection object.
  - onSeveralUpdatedDateFound
```
public void onSeveralUpdatedDateFound(Collection<MitabDate> dates)
```
    onSeveralUpdatedDateFound.
    
    Specified by:
    
    onSeveralUpdatedDateFound in interface MitabParserListener
    
    Parameters:
    
    dates - a Collection object.
  - onAliasWithoutDbSource
```
public void onAliasWithoutDbSource(MitabAlias alias)
```
    onAliasWithoutDbSource.
    
    Specified by:
    
    onAliasWithoutDbSource in interface MitabParserListener
    
    Parameters:
    
    alias - a MitabAlias object.
  - onSeveralCvTermsFound
```
public void onSeveralCvTermsFound(Collection<MitabCvTerm> terms,
                                  FileSourceContext context,
                                  String message)
```
    Listen to an event where several CvTerms were found and only one was expected. Can happen when reading a clustered interaction evidence for instance
    
    Specified by:
    
    onSeveralCvTermsFound in interface MitabParserListener
    
    Parameters:
    
    terms - a Collection object.
    
    context - a FileSourceContext object.
    
    message - a String object.
  - onSeveralHostOrganismFound
```
public void onSeveralHostOrganismFound(Collection<MitabOrganism> organisms,
                                       FileSourceContext context)
```
    Listen to an event where several host organisms were found in a single experiment and only one was expected. Can happen when reading a clustered interaction evidence for instance
    
    Specified by:
    
    onSeveralHostOrganismFound in interface MitabParserListener
    
    Parameters:
    
    organisms - a Collection object.
    
    context - a FileSourceContext object.
  - onInvalidSyntax
```
public void onInvalidSyntax(FileSourceContext context,
                            Exception e)
```
    Listen to an invalid syntax causing an Exception
    
    Specified by:
    
    onInvalidSyntax in interface MIFileParserListener
    
    Parameters:
    
    context - : file context
    
    e - a Exception object.
  - onSyntaxWarning
```
public void onSyntaxWarning(FileSourceContext context,
                            String message)
```
    Listen to an event fired when the syntax of the file is valid but the content is not expected or some information may be lost.
    
    Specified by:
    
    onSyntaxWarning in interface MIFileParserListener
    
    Parameters:
    
    context - : file context
    
    message - : warning message
  - onMissingCvTermName
```
public void onMissingCvTermName(CvTerm term,
                                FileSourceContext context,
                                String message)
```
    Listen to an event fired when a CvTerm is read and does not have any names. At least a shortname is expected for each CvTerm so such a term may be loaded with an automatically generated shortname.
    
    Specified by:
    
    onMissingCvTermName in interface MIFileParserListener
    
    Parameters:
    
    term - : cv without name
    
    context - : file context
    
    message - : error message
  - onMissingInteractorName
```
public void onMissingInteractorName(Interactor interactor,
                                    FileSourceContext context)
```
    Listen to an event fired when an interactor is read and does not have any names. At least a shortname is expected for each interactor so such an interactor may be loaded with an automatically generated shortname.
    
    Specified by:
    
    onMissingInteractorName in interface MIFileParserListener
    
    Parameters:
    
    interactor - : interactor without name
    
    context - : file context
  - onParticipantWithoutInteractor
```
public void onParticipantWithoutInteractor(Participant participant,
                                           FileSourceContext context)
```
    Listen to en event fired when a Participant is read and no interactor details has been provided. In such a case, the interactor can be automatically generated as an unknown interactor
    
    Specified by:
    
    onParticipantWithoutInteractor in interface MIFileParserListener
    
    Parameters:
    
    participant - : participant without interactor
    
    context - : file context
  - onInteractionWithoutParticipants
```
public void onInteractionWithoutParticipants(Interaction interaction,
                                             FileSourceContext context)
```
    Listen to an event fired when an interaction is read and does not have any participants. The interaction may be loaded as an empty interaction.
    
    Specified by:
    
    onInteractionWithoutParticipants in interface MIFileParserListener
    
    Parameters:
    
    interaction - : interaction without participants
    
    context - : file context
  - onInvalidOrganismTaxid
```
public void onInvalidOrganismTaxid(String taxid,
                                   FileSourceContext context)
```
    Listen to an event fired when an organism does not have a valid taxid (positive integer or -1, -2, -3, -4, -5)
    
    Specified by:
    
    onInvalidOrganismTaxid in interface MIFileParserListener
    
    Parameters:
    
    taxid - : invalid taxid
    
    context - : file context
  - onMissingParameterValue
```
public void onMissingParameterValue(FileSourceContext context)
```
    Listen to an event fired when a parameter does not have a value
    
    Specified by:
    
    onMissingParameterValue in interface MIFileParserListener
    
    Parameters:
    
    context - : file context
  - onMissingParameterType
```
public void onMissingParameterType(FileSourceContext context)
```
    Listen to an event fired when a parameter does not have a type
    
    Specified by:
    
    onMissingParameterType in interface MIFileParserListener
    
    Parameters:
    
    context - : file context
  - onMissingConfidenceValue
```
public void onMissingConfidenceValue(FileSourceContext context)
```
    Listen to an event fired when a confidence does not have a value
    
    Specified by:
    
    onMissingConfidenceValue in interface MIFileParserListener
    
    Parameters:
    
    context - : file context
  - onMissingConfidenceType
```
public void onMissingConfidenceType(FileSourceContext context)
```
    Listen to an event fired when a confidence does not have a confidence type
    
    Specified by:
    
    onMissingConfidenceType in interface MIFileParserListener
    
    Parameters:
    
    context - : file context
  - onMissingChecksumValue
```
public void onMissingChecksumValue(FileSourceContext context)
```
    Listen to an event fired when a checksum does not have a value
    
    Specified by:
    
    onMissingChecksumValue in interface MIFileParserListener
    
    Parameters:
    
    context - : file context
  - onMissingChecksumMethod
```
public void onMissingChecksumMethod(FileSourceContext context)
```
    Listen to an event fired when a checksum does not have a method
    
    Specified by:
    
    onMissingChecksumMethod in interface MIFileParserListener
    
    Parameters:
    
    context - : file context
  - onInvalidPosition
```
public void onInvalidPosition(String message,
                              FileSourceContext context)
```
    Listen to an event fired when a position is not valid
    
    Specified by:
    
    onInvalidPosition in interface MIFileParserListener
    
    Parameters:
    
    message - : error message
    
    context - : file context
  - onInvalidRange
```
public void onInvalidRange(String message,
                           FileSourceContext context)
```
    Listen to an event fired when a range is not valid
    
    Specified by:
    
    onInvalidRange in interface MIFileParserListener
    
    Parameters:
    
    message - : error message
    
    context - : file context
  - onInvalidStoichiometry
```
public void onInvalidStoichiometry(String message,
                                   FileSourceContext context)
```
    Listen to an event fired when a stoichiometry is not valid
    
    Specified by:
    
    onInvalidStoichiometry in interface MIFileParserListener
    
    Parameters:
    
    message - : : error message
    
    context - : file context
  - onXrefWithoutDatabase
```
public void onXrefWithoutDatabase(FileSourceContext context)
```
    Listen to an event fired when a xref does not have a database
    
    Specified by:
    
    onXrefWithoutDatabase in interface MIFileParserListener
    
    Parameters:
    
    context - : file context
  - onXrefWithoutId
```
public void onXrefWithoutId(FileSourceContext context)
```
    Listen to an event fired when a xref does not have an id
    
    Specified by:
    
    onXrefWithoutId in interface MIFileParserListener
    
    Parameters:
    
    context - : file context
  - onAnnotationWithoutTopic
```
public void onAnnotationWithoutTopic(FileSourceContext context)
```
    Listen to an event fired when an annotation does not have a topic
    
    Specified by:
    
    onAnnotationWithoutTopic in interface MIFileParserListener
    
    Parameters:
    
    context - : file context
  - onAliasWithoutName
```
public void onAliasWithoutName(FileSourceContext context)
```
    Listen to an event fired when an alias does not have a name
    
    Specified by:
    
    onAliasWithoutName in interface MIFileParserListener
    
    Parameters:
    
    context - : file context

Class AbstractMitabSource<T extends Interaction,​P extends Participant,​F extends Feature>

Field Summary

Fields inherited from interface psidev.psi.mi.jami.datasource.MIFileDataSource

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

AbstractMitabSource

Method Detail

getInteractions

getNumberOfInteractions

getInteractionsIterator

getFileParserListener

setFileParserListener

validateSyntax

validateSyntax

initialiseContext

close

reset

onTextFoundInIdentifier

onTextFoundInConfidence

onMissingExpansionId

onSeveralUniqueIdentifiers

onEmptyUniqueIdentifiers

onMissingInteractorIdentifierColumns

onSeveralOrganismFound

onSeveralStoichiometryFound

onSeveralFirstAuthorFound

onSeveralSourceFound

onSeveralCreatedDateFound

onSeveralUpdatedDateFound

onAliasWithoutDbSource

onSeveralCvTermsFound

onSeveralHostOrganismFound

onInvalidSyntax

onSyntaxWarning

onMissingCvTermName

onMissingInteractorName

onParticipantWithoutInteractor

onInteractionWithoutParticipants

onInvalidOrganismTaxid

onMissingParameterValue

onMissingParameterType

onMissingConfidenceValue

onMissingConfidenceType

onMissingChecksumValue

onMissingChecksumMethod

onInvalidPosition

onInvalidRange

onInvalidStoichiometry

onXrefWithoutDatabase

onXrefWithoutId

onAnnotationWithoutTopic

onAliasWithoutName

Class AbstractMitabSource<T extends Interaction,P extends Participant,F extends Feature>