Package psidev.psi.mi.jami.tab.extension.datasource

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

java.lang.Object

psidev.psi.mi.jami.tab.extension.datasource.AbstractMitabStreamSource<T,P,F>

All Implemented Interfaces:

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

Direct Known Subclasses:

LightMitabBinaryStreamSource, LightMitabStreamSource, MitabBinaryEvidenceStreamSource, MitabEvidenceStreamSource, MitabModelledBinaryStreamSource, MitabModelledStreamSource

public abstract class AbstractMitabStreamSource<T extends Interaction,P extends Participant,F extends Feature>
extends Object
implements MitabStreamSource<T>

abstract class for Mitab datasource. This datasource loads all the interactions from a MITAB file

Since:

21/06/13

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
AbstractMitabStreamSource()	Empty constructor for the factory
AbstractMitabStreamSource(File file)	Constructor for AbstractMitabStreamSource.
AbstractMitabStreamSource(InputStream input)	Constructor for AbstractMitabStreamSource.
AbstractMitabStreamSource(Reader reader)	Constructor for AbstractMitabStreamSource.
AbstractMitabStreamSource(URL url)	Constructor for AbstractMitabStreamSource.

Method Summary

Modifier and Type	Method	Description
void	close()	close.
protected abstract Iterator<T>	createMitabIterator()	createMitabIterator.
MIFileParserListener	getFileParserListener()	getFileParserListener.
Iterator<T>	getInteractionsIterator()	getInteractionsIterator.
InteractorFactory	getInteractorFactory()	Getter for the field interactorFactory.
protected MitabLineParser<T,P,F>	getLineParser()	Getter for the field lineParser.
void	initialiseContext(Map<String,Object> options)	Initialise the context of the MIDataSource given a map of options
protected abstract void	initialiseMitabLineParser(File file)	initialiseMitabLineParser.
protected abstract void	initialiseMitabLineParser(InputStream input)	initialiseMitabLineParser.
protected abstract void	initialiseMitabLineParser(Reader reader)	initialiseMitabLineParser.
protected abstract void	initialiseMitabLineParser(URL url)	initialiseMitabLineParser.
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
protected void	reInit()	reInit.
void	reset()	reset.
void	setFileParserListener(MIFileParserListener listener)	setFileParserListener
void	setInteractorFactory(InteractorFactory interactorFactory)	Setter for the field interactorFactory.
protected void	setLineParser(AbstractInteractionLineParser<T,P,F> lineParser)	Setter for the field lineParser.
protected void	setMIFileParserListener(MIFileParserListener listener)	setMIFileParserListener.
protected void	setMitabFileParserListener(MitabParserListener listener)	setMitabFileParserListener.
protected void	setOriginalFile(File originalFile)	Setter for the field originalFile.
protected void	setOriginalReader(Reader originalReader)	Setter for the field originalReader.
protected void	setOriginalStream(InputStream originalStream)	Setter for the field originalStream.
protected void	setOriginalURL(URL originalURL)	Setter for the field originalURL.
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

AbstractMitabStreamSource

public AbstractMitabStreamSource()

Empty constructor for the factory

AbstractMitabStreamSource

public AbstractMitabStreamSource(File file)
                          throws IOException

Constructor for AbstractMitabStreamSource.

Parameters:

file - a File object.

Throws:

IOException - if any.

AbstractMitabStreamSource

public AbstractMitabStreamSource(InputStream input)

Constructor for AbstractMitabStreamSource.

Parameters:

input - a InputStream object.

AbstractMitabStreamSource

public AbstractMitabStreamSource(Reader reader)

Constructor for AbstractMitabStreamSource.

Parameters:

reader - a Reader object.

AbstractMitabStreamSource

public AbstractMitabStreamSource(URL url)

Constructor for AbstractMitabStreamSource.

Parameters:

url - a URL object.

Method Detail

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.

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.

validateSyntax

public boolean validateSyntax(MIFileParserListener listener)

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

validateSyntax

public boolean validateSyntax()

validateSyntax.

Specified by:

validateSyntax in interface MIFileDataSource

Returns:

a boolean.

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

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.

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

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.

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.

onAliasWithoutDbSource

public void onAliasWithoutDbSource(MitabAlias alias)

onAliasWithoutDbSource.

Specified by:

onAliasWithoutDbSource in interface MitabParserListener

Parameters:

alias - a MitabAlias object.

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

getInteractionsIterator

public Iterator<T> getInteractionsIterator()

getInteractionsIterator.

Specified by:

getInteractionsIterator in interface InteractionStream<T extends Interaction>

Returns:

a Iterator object.

getInteractorFactory

public InteractorFactory getInteractorFactory()

Getter for the field interactorFactory.

Returns:

a InteractorFactory object.

setInteractorFactory

public void setInteractorFactory(InteractorFactory interactorFactory)

Setter for the field interactorFactory.

Parameters:

interactorFactory - a InteractorFactory object.

getLineParser

protected MitabLineParser<T,P,F> getLineParser()

Getter for the field lineParser.

Returns:

a MitabLineParser object.

setLineParser

protected void setLineParser(AbstractInteractionLineParser<T,P,F> lineParser)

Setter for the field lineParser.

Parameters:

lineParser - a AbstractInteractionLineParser object.

initialiseMitabLineParser

protected abstract void initialiseMitabLineParser(Reader reader)

initialiseMitabLineParser.

Parameters:

reader - a Reader object.

initialiseMitabLineParser

protected abstract void initialiseMitabLineParser(File file)

initialiseMitabLineParser.

Parameters:

file - a File object.

initialiseMitabLineParser

protected abstract void initialiseMitabLineParser(InputStream input)

initialiseMitabLineParser.

Parameters:

input - a InputStream object.

initialiseMitabLineParser

protected abstract void initialiseMitabLineParser(URL url)

initialiseMitabLineParser.

Parameters:

url - a URL object.

createMitabIterator

protected abstract Iterator<T> createMitabIterator()

createMitabIterator.

Returns:

a Iterator object.

reInit

protected void reInit()
               throws MIIOException

reInit.

Throws:

MIIOException - if any.

setOriginalFile

protected void setOriginalFile(File originalFile)

Setter for the field originalFile.

Parameters:

originalFile - a File object.

setOriginalStream

protected void setOriginalStream(InputStream originalStream)

Setter for the field originalStream.

Parameters:

originalStream - a InputStream object.

setOriginalReader

protected void setOriginalReader(Reader originalReader)

Setter for the field originalReader.

Parameters:

originalReader - a Reader object.

setOriginalURL

protected void setOriginalURL(URL originalURL)

Setter for the field originalURL.

Parameters:

originalURL - a URL object.

setMitabFileParserListener

protected void setMitabFileParserListener(MitabParserListener listener)

setMitabFileParserListener.

Parameters:

listener - a MitabParserListener object.

setMIFileParserListener

protected void setMIFileParserListener(MIFileParserListener listener)

setMIFileParserListener.

Parameters:

listener - a MIFileParserListener object.