Package psidev.psi.mi.jami.tab.io.parser

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

java.lang.Object

psidev.psi.mi.jami.tab.io.parser.MitabLineParser<T,P,F>

All Implemented Interfaces:

MitabLineParserConstants

Direct Known Subclasses:

AbstractInteractionLineParser

public abstract class MitabLineParser<T extends Interaction,P extends Participant,F extends Feature>
extends Object
implements MitabLineParserConstants

Field Summary

Fields

Modifier and Type	Field	Description
Token	jj_nt	Next token.
Token	token	Current token.
MitabLineParserTokenManager	token_source	Generated Token Manager.

Fields inherited from interface psidev.psi.mi.jami.tab.io.parser.MitabLineParserConstants

CLOSE_PAREN, COLON, COLUMN_SEPARATOR, COMMENT, DASH, DEFAULT, EOF, FIELD_SEPARATOR, LINE_SEPARATOR, OPEN_PAREN, QUOTED_STRING, RANGE_SEPARATOR, tokenImage, UNRESERVED_STRING

Constructor Summary

Constructors

Constructor	Description
MitabLineParser(InputStream stream)	Constructor with InputStream.
MitabLineParser(InputStream stream, String encoding)	Constructor with InputStream and supplied encoding.
MitabLineParser(Reader stream)	Constructor.
MitabLineParser(MitabLineParserTokenManager tm)	Constructor with generated Token Manager.

Method Summary

Modifier and Type	Method	Description
MitabAlias	alias(int columnNumber)
Collection<MitabAlias>	aliases(int column)
MitabAnnotation	annotation(int columnNumber)
Collection<MitabAnnotation>	annotations(int column)
MitabAuthor	author()
MitabChecksum	checksum(int columnNumber)
Collection<MitabChecksum>	checksums(int column)
Collection<MitabCvTerm>	complexExpansion()
MitabConfidence	confidence()
Collection<MitabConfidence>	confidences()
MitabCvTerm	cvTerm(int column)
Collection<MitabCvTerm>	cvTerms(int columnNumber)
MitabDate	date(int columnNumber)
Collection<MitabDate>	dates(int column)
void	disable_tracing()	Disable tracing.
void	enable_tracing()	Enable tracing.
MitabCvTerm	expansion()
F	feature(int columnNumber)
Collection<F>	features(int column)
Collection<MitabAuthor>	firstAuthors()
ParseException	generateParseException()	Generate ParseException.
Token	getNextToken()	Get the next Token.
abstract MitabParserListener	getParserListener()
Token	getToken(int index)	Get the specific Token.
abstract boolean	hasFinished()
MitabXref	id(CvTerm qualifier, boolean recognizeImexPrimary, int columnNumber)
Collection<MitabXref>	ids(CvTerm qualifier, boolean recognizeImex, int column)
T	MitabLine()
boolean	negative()
MitabOrganism	organism(int columnNumber)
MitabParameter	parameter()
Collection<MitabParameter>	parameters()
MitabRange	range(int columnNumber)
void	ReInit(InputStream stream)	Reinitialise.
void	ReInit(InputStream stream, String encoding)	Reinitialise.
void	ReInit(Reader stream)	Reinitialise.
void	ReInit(MitabLineParserTokenManager tm)	Reinitialise.
String	safeFreeText()
String	safePosition()
String	safeStoichiometry()
String	safeString()
abstract void	setParserListener(MitabParserListener listener)
MitabSource	source()
Collection<MitabSource>	sourceDbs()
MitabStoichiometry	stoichiometry(int columnNumber)
Collection<MitabStoichiometry>	stoichiometryList(int column)
Collection<MitabOrganism>	taxId(int column)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

token_source

public MitabLineParserTokenManager token_source

Generated Token Manager.

token

public Token token

Current token.

jj_nt

public Token jj_nt

Next token.

Constructor Detail

MitabLineParser

public MitabLineParser(InputStream stream)

Constructor with InputStream.

Parameters:

stream - a InputStream object.

MitabLineParser

public MitabLineParser(InputStream stream,
                       String encoding)

Constructor with InputStream and supplied encoding.

Parameters:

stream - a InputStream object.

encoding - a String object.

MitabLineParser

public MitabLineParser(Reader stream)

Constructor.

Parameters:

stream - a InputStream object.

MitabLineParser

public MitabLineParser(MitabLineParserTokenManager tm)

Constructor with generated Token Manager.

Parameters:

tm - a MitabLineParserTokenManager object.

Method Detail

getParserListener

public abstract MitabParserListener getParserListener()

setParserListener

public abstract void setParserListener(MitabParserListener listener)

hasFinished

public abstract boolean hasFinished()

MitabLine

public final T MitabLine()
                  throws ParseException

Throws:

ParseException

ids

public final Collection<MitabXref> ids(CvTerm qualifier,
                                       boolean recognizeImex,
                                       int column)
                                throws ParseException

Throws:

ParseException

aliases

public final Collection<MitabAlias> aliases(int column)
                                     throws ParseException

Throws:

ParseException

cvTerms

public final Collection<MitabCvTerm> cvTerms(int columnNumber)
                                      throws ParseException

Throws:

ParseException

firstAuthors

public final Collection<MitabAuthor> firstAuthors()
                                           throws ParseException

Throws:

ParseException

taxId

public final Collection<MitabOrganism> taxId(int column)
                                      throws ParseException

Throws:

ParseException

sourceDbs

public final Collection<MitabSource> sourceDbs()
                                        throws ParseException

Throws:

ParseException

confidences

public final Collection<MitabConfidence> confidences()
                                              throws ParseException

Throws:

ParseException

complexExpansion

public final Collection<MitabCvTerm> complexExpansion()
                                               throws ParseException

Throws:

ParseException

annotations

public final Collection<MitabAnnotation> annotations(int column)
                                              throws ParseException

Throws:

ParseException

parameters

public final Collection<MitabParameter> parameters()
                                            throws ParseException

Throws:

ParseException

dates

public final Collection<MitabDate> dates(int column)
                                  throws ParseException

Throws:

ParseException

checksums

public final Collection<MitabChecksum> checksums(int column)
                                          throws ParseException

Throws:

ParseException

features

public final Collection<F> features(int column)
                             throws ParseException

Throws:

ParseException

stoichiometryList

public final Collection<MitabStoichiometry> stoichiometryList(int column)
                                                       throws ParseException

Throws:

ParseException

stoichiometry

public final MitabStoichiometry stoichiometry(int columnNumber)
                                       throws ParseException

Throws:

ParseException

feature

public final F feature(int columnNumber)
                throws ParseException

Throws:

ParseException

range

public final MitabRange range(int columnNumber)
                       throws ParseException

Throws:

ParseException

negative

public final boolean negative()
                       throws ParseException

Throws:

ParseException

checksum

public final MitabChecksum checksum(int columnNumber)
                             throws ParseException

Throws:

ParseException

date

public final MitabDate date(int columnNumber)
                     throws ParseException

Throws:

ParseException

parameter

public final MitabParameter parameter()
                               throws ParseException

Throws:

ParseException

annotation

public final MitabAnnotation annotation(int columnNumber)
                                 throws ParseException

Throws:

ParseException

expansion

public final MitabCvTerm expansion()
                            throws ParseException

Throws:

ParseException

confidence

public final MitabConfidence confidence()
                                 throws ParseException

Throws:

ParseException

source

public final MitabSource source()
                         throws ParseException

Throws:

ParseException

organism

public final MitabOrganism organism(int columnNumber)
                             throws ParseException

Throws:

ParseException

author

public final MitabAuthor author()
                         throws ParseException

Throws:

ParseException

cvTerm

public final MitabCvTerm cvTerm(int column)
                         throws ParseException

Throws:

ParseException

alias

public final MitabAlias alias(int columnNumber)
                       throws ParseException

Throws:

ParseException

id

public final MitabXref id(CvTerm qualifier,
                          boolean recognizeImexPrimary,
                          int columnNumber)
                   throws ParseException

Throws:

ParseException

safeString

public final String safeString()
                        throws ParseException

Throws:

ParseException

safeFreeText

public final String safeFreeText()
                          throws ParseException

Throws:

ParseException

safePosition

public final String safePosition()
                          throws ParseException

Throws:

ParseException

safeStoichiometry

public final String safeStoichiometry()
                               throws ParseException

Throws:

ParseException

ReInit

public void ReInit(InputStream stream)

Reinitialise.

Parameters:

stream - a InputStream object.

ReInit

public void ReInit(InputStream stream,
                   String encoding)

Reinitialise.

Parameters:

stream - a InputStream object.

encoding - a String object.

ReInit

public void ReInit(Reader stream)

Reinitialise.

Parameters:

stream - a InputStream object.

ReInit

public void ReInit(MitabLineParserTokenManager tm)

Reinitialise.

Parameters:

tm - a MitabLineParserTokenManager object.

getNextToken

public final Token getNextToken()

Get the next Token.

Returns:

a Token object.

getToken

public final Token getToken(int index)

Get the specific Token.

Parameters:

index - an int value.

Returns:

a Token object.

generateParseException

public ParseException generateParseException()

Generate ParseException.

Returns:

a {link @ParseException} object.

enable_tracing

public final void enable_tracing()

Enable tracing.

disable_tracing

public final void disable_tracing()

Disable tracing.