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

Class AbstractCsvSource<T extends InteractionEvidence>

java.lang.Object

psidev.psi.mi.jami.crosslink.extension.datasource.AbstractCsvSource<T>

All Implemented Interfaces:

CsvSource<T>, CsvStreamSource<T>, CsvParserListener, InteractionEvidenceSource<T>, InteractionEvidenceStream<T>, InteractionSource<T>, InteractionStream<T>, MIDataSource, MIFileDataSource, MIFileParserListener

Direct Known Subclasses:

CsvBinaryEvidenceSource, CsvEvidenceSource

public abstract class AbstractCsvSource<T extends InteractionEvidence>
extends Object
implements CsvSource<T>

Abstract class for an InteractionSource coming from a Crosslink CSV 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
AbstractCsvSource()	Empty constructor for the factory
AbstractCsvSource(File file)	Constructor for AbstractCsvSource.
AbstractCsvSource(InputStream input)	Constructor for AbstractCsvSource.
AbstractCsvSource(Reader reader)	Constructor for AbstractCsvSource.
AbstractCsvSource(URL url)	Constructor for AbstractCsvSource.

Method Summary

Modifier and Type	Method	Description
void	close()	close.
protected Iterator<T>	createCsvIterator()	createCsvIterator.
MIFileParserListener	getFileParserListener()	getFileParserListener.
Collection<T>	getInteractions()	Getter for the field interactions.
Iterator<T>	getInteractionsIterator()	getInteractionsIterator.
protected AbstractCsvInteractionEvidenceParser<T>	getLineParser()	Getter for the field lineParser.
long	getNumberOfInteractions()	getNumberOfInteractions.
void	initialiseContext(Map<String,Object> options)	Initialise the context of the MIDataSource given a map of options
protected abstract AbstractCsvInteractionEvidenceParser<T>	instantiateLineParser()	instantiateLineParser.
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	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	onInvalidProteinIdentifierSyntax(String[] identifiers, int lineNumber, int columnNumber)	Event fired when we don't find protein xrefs with db|uniprotId|name
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	onMismatchBetweenPeptideAndLinkedPositions(List<CsvRange> peptidePositions, List<CsvRange> linkedPositions)	Event fired when the number of peptide positions is greater than one and is not the same as the number of linked positions
void	onMismatchBetweenRangePositionsAndProteins(List<CsvRange> rangePositions, List<CsvProtein> proteins)	Event fired when the number of range positions is superior to 1 and the number of proteins is also superior to 1 but does not match the number of ranges
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	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	onMissingProtein1Column(int lineNumber)	Event fired when the column Protein1 is missing or empty
void	onParticipantWithoutInteractor(Participant participant, FileSourceContext context)	Listen to en event fired when a Participant is read and no interactor details has been provided.
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	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.
protected void	setCsvFileParserListener(CsvParserListener listener)	setCsvFileParserListener.
void	setFileParserListener(MIFileParserListener listener)	setFileParserListener
protected void	setLineParser(AbstractCsvInteractionEvidenceParser<T> lineParser)	Setter for the field lineParser.
protected void	setMIFileParserListener(MIFileParserListener listener)	setMIFileParserListener.
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

AbstractCsvSource

public AbstractCsvSource()

Empty constructor for the factory

AbstractCsvSource

public AbstractCsvSource(File file)
                  throws IOException

Constructor for AbstractCsvSource.

Parameters:

file - a File object.

Throws:

IOException - if any.

AbstractCsvSource

public AbstractCsvSource(InputStream input)

Constructor for AbstractCsvSource.

Parameters:

input - a InputStream object.

AbstractCsvSource

public AbstractCsvSource(Reader reader)

Constructor for AbstractCsvSource.

Parameters:

reader - a Reader object.

AbstractCsvSource

public AbstractCsvSource(URL url)

Constructor for AbstractCsvSource.

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

onMismatchBetweenPeptideAndLinkedPositions

public void onMismatchBetweenPeptideAndLinkedPositions(List<CsvRange> peptidePositions,
                                                       List<CsvRange> linkedPositions)

Event fired when the number of peptide positions is greater than one and is not the same as the number of linked positions

Specified by:

onMismatchBetweenPeptideAndLinkedPositions in interface CsvParserListener

Parameters:

peptidePositions - : peptide positions in protein sequence

linkedPositions - : linked feature positions relative to peptide positions

onMismatchBetweenRangePositionsAndProteins

public void onMismatchBetweenRangePositionsAndProteins(List<CsvRange> rangePositions,
                                                       List<CsvProtein> proteins)

Event fired when the number of range positions is superior to 1 and the number of proteins is also superior to 1 but does not match the number of ranges

Specified by:

onMismatchBetweenRangePositionsAndProteins in interface CsvParserListener

Parameters:

rangePositions - : feature ranges

proteins - : proteins

onInvalidProteinIdentifierSyntax

public void onInvalidProteinIdentifierSyntax(String[] identifiers,
                                             int lineNumber,
                                             int columnNumber)

Event fired when we don't find protein xrefs with db|uniprotId|name

Specified by:

onInvalidProteinIdentifierSyntax in interface CsvParserListener

Parameters:

identifiers - : the identifiers

lineNumber - a int.

columnNumber - a int.

onMissingProtein1Column

public void onMissingProtein1Column(int lineNumber)

Event fired when the column Protein1 is missing or empty

Specified by:

onMissingProtein1Column in interface CsvParserListener

Parameters:

lineNumber - : line number

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

getInteractionsIterator

public Iterator<T> getInteractionsIterator()

getInteractionsIterator.

Specified by:

getInteractionsIterator in interface InteractionStream<T extends InteractionEvidence>

Returns:

a Iterator object.

getInteractions

public Collection<T> getInteractions()
                              throws MIIOException

Getter for the field interactions.

Specified by:

getInteractions in interface InteractionSource<T extends InteractionEvidence>

Returns:

a Collection object.

Throws:

MIIOException - if any.

getNumberOfInteractions

public long getNumberOfInteractions()

getNumberOfInteractions.

Specified by:

getNumberOfInteractions in interface InteractionSource<T extends InteractionEvidence>

Returns:

a long.

getLineParser

protected AbstractCsvInteractionEvidenceParser<T> getLineParser()

Getter for the field lineParser.

Returns:

a AbstractCsvInteractionEvidenceParser object.

setLineParser

protected void setLineParser(AbstractCsvInteractionEvidenceParser<T> lineParser)

Setter for the field lineParser.

Parameters:

lineParser - a AbstractCsvInteractionEvidenceParser object.

createCsvIterator

protected Iterator<T> createCsvIterator()

createCsvIterator.

Returns:

a Iterator object.

reInit

protected void reInit()
               throws MIIOException

reInit.

Throws:

MIIOException - if any.

instantiateLineParser

protected abstract AbstractCsvInteractionEvidenceParser<T> instantiateLineParser()

instantiateLineParser.

Returns:

a AbstractCsvInteractionEvidenceParser object.

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.

setCsvFileParserListener

protected void setCsvFileParserListener(CsvParserListener listener)

setCsvFileParserListener.

Parameters:

listener - a CsvParserListener object.

setMIFileParserListener

protected void setMIFileParserListener(MIFileParserListener listener)

setMIFileParserListener.

Parameters:

listener - a MIFileParserListener object.