org.obolibrary.oboformat.parser

Class OBOFormatParser

java.lang.Object

org.obolibrary.oboformat.parser.OBOFormatParser

public class OBOFormatParser
extends Object

implements the OBO Format 1.4 specification.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected static class	OBOFormatParser.MyStream

Field Summary

Fields

Modifier and Type	Field and Description
protected OBOFormatParser.MyStream	stream

Constructor Summary

Constructors

Modifier	Constructor and Description
	OBOFormatParser()
protected	OBOFormatParser(OBOFormatParser.MyStream s)

Method Summary

Modifier and Type	Method and Description
List<String>	checkDanglingReferences(OBODoc doc)
protected void	forceParseNlOrEof()
boolean	getFollowImports()
OBODoc	parse(BufferedReader reader)
OBODoc	parse(File file) Parses a local file to an OBODoc.
OBODoc	parse(String fn) Parses a local file or URL to an OBODoc.
OBODoc	parse(URL url) Parses a remote URL to an OBODoc.
void	parseEntityFrame(OBODoc obodoc)
void	parseEOL(Clause cl)
protected void	parseHeaderClause(Frame h)
protected boolean	parseHeaderClauseNl(Frame h) header-clause ::= format-version-TVP | ...
void	parseHeaderFrame(Frame h)
protected void	parseIdLine(Frame f)
void	parseOBODoc(OBODoc obodoc)
protected void	parseOneOrMoreWs()
void	parseTermFrame(OBODoc obodoc) term-frame ::= nl* '[Term]' nl id-Tag Class-ID EOL { term-frame-clause EOL }.
Clause	parseTermFrameClause()
protected void	parseTermFrameClauseEOL(Frame f)
void	parseTypedefFrame(OBODoc obodoc) Typedef-frame ::= nl* '[Typedef]' nl id-Tag Class-ID EOL { Typedef-frame-clause EOL }.
Clause	parseTypedefFrameClause()
protected void	parseTypedefFrameClauseEOL(Frame f)
protected void	parseUnquotedString(Clause cl)
OBODoc	parseURL(String urlstr) Parses a remote URL to an OBODoc.
protected void	parseWs()
protected void	parseZeroOrMoreWs()
protected void	parseZeroOrMoreWsOptCmtNl()
void	setFollowImports(boolean followImports)
void	setReader(BufferedReader r)

Methods inherited from class java.lang.Object

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

Field Detail

stream

protected OBOFormatParser.MyStream stream

Constructor Detail

OBOFormatParser

public OBOFormatParser()

OBOFormatParser

protected OBOFormatParser(OBOFormatParser.MyStream s)

Method Detail

setReader

public void setReader(BufferedReader r)

Parameters:

r - r

setFollowImports

public void setFollowImports(boolean followImports)

Parameters:

followImports - followImports

getFollowImports

public boolean getFollowImports()

Returns:

follow imports

parse

public OBODoc parse(String fn)
             throws IOException,
                    OBOFormatParserException

Parses a local file or URL to an OBODoc.

Parameters:

fn - fn

Returns:

parsed obo document

Throws:

IOException - io exception

OBOFormatParserException - parser exception

parse

public OBODoc parse(File file)
             throws IOException,
                    OBOFormatParserException

Parses a local file to an OBODoc.

Parameters:

file - file

Returns:

parsed obo document

Throws:

IOException - io exception

OBOFormatParserException - parser exception

parse

public OBODoc parse(URL url)
             throws IOException,
                    OBOFormatParserException

Parses a remote URL to an OBODoc.

Parameters:

url - url

Returns:

parsed obo document

Throws:

IOException - io exception

OBOFormatParserException - parser exception

parseURL

public OBODoc parseURL(String urlstr)
                throws IOException,
                       OBOFormatParserException

Parses a remote URL to an OBODoc.

Parameters:

urlstr - urlstr

Returns:

parsed obo document

Throws:

IOException - io exception

OBOFormatParserException - parser exception

parse

public OBODoc parse(BufferedReader reader)
             throws IOException,
                    OBOFormatParserException

Parameters:

reader - reader

Returns:

parsed obo document

Throws:

IOException - io exception

OBOFormatParserException - parser exception

parseOBODoc

public void parseOBODoc(OBODoc obodoc)
                 throws OBOFormatParserException

Parameters:

obodoc - obodoc

Throws:

OBOFormatParserException - parser exception

checkDanglingReferences

public List<String> checkDanglingReferences(OBODoc doc)
                                     throws OBOFormatDanglingReferenceException

Parameters:

doc - doc

Returns:

list of references

Throws:

OBOFormatDanglingReferenceException - dangling reference error

parseHeaderFrame

public void parseHeaderFrame(Frame h)
                      throws OBOFormatParserException

Parameters:

h - h

Throws:

OBOFormatParserException - parser exception

parseHeaderClauseNl

protected boolean parseHeaderClauseNl(Frame h)
                               throws OBOFormatParserException

header-clause ::= format-version-TVP | ... | ...

Parameters:

h - header frame

Returns:

false if there are no more header clauses, other wise true

Throws:

OBOFormatParserException - parser exception

parseHeaderClause

protected void parseHeaderClause(Frame h)
                          throws OBOFormatParserException

Throws:

OBOFormatParserException

parseEntityFrame

public void parseEntityFrame(OBODoc obodoc)
                      throws OBOFormatParserException

Parameters:

obodoc - obodoc

Throws:

OBOFormatParserException - parser exception

parseTermFrame

public void parseTermFrame(OBODoc obodoc)
                    throws OBOFormatParserException

term-frame ::= nl* '[Term]' nl id-Tag Class-ID EOL { term-frame-clause EOL }.

Parameters:

obodoc - obodoc

Throws:

OBOFormatParserException - parser exception

parseTermFrameClauseEOL

protected void parseTermFrameClauseEOL(Frame f)
                                throws OBOFormatParserException

Parameters:

f - f

Throws:

OBOFormatParserException - parser exception

parseTermFrameClause

public Clause parseTermFrameClause()
                            throws OBOFormatParserException

Returns:

parsed clause

Throws:

OBOFormatParserException - parser exception

parseTypedefFrame

public void parseTypedefFrame(OBODoc obodoc)
                       throws OBOFormatParserException

Typedef-frame ::= nl* '[Typedef]' nl id-Tag Class-ID EOL { Typedef-frame-clause EOL }.

Parameters:

obodoc - obodoc

Throws:

OBOFormatParserException - parser exception

parseTypedefFrameClauseEOL

protected void parseTypedefFrameClauseEOL(Frame f)
                                   throws OBOFormatParserException

Parameters:

f - f

Throws:

OBOFormatParserException - parser exception

parseTypedefFrameClause

public Clause parseTypedefFrameClause()
                               throws OBOFormatParserException

Returns:

parsed clause

Throws:

OBOFormatParserException - parser exception

parseIdLine

protected void parseIdLine(Frame f)
                    throws OBOFormatParserException

Throws:

OBOFormatParserException

parseEOL

public void parseEOL(Clause cl)
              throws OBOFormatParserException

Parameters:

cl - cl

Throws:

OBOFormatParserException - parser exception

parseUnquotedString

protected void parseUnquotedString(Clause cl)
                            throws OBOFormatParserException

Throws:

OBOFormatParserException

forceParseNlOrEof

protected void forceParseNlOrEof()
                          throws OBOFormatParserException

Throws:

OBOFormatParserException

parseZeroOrMoreWsOptCmtNl

protected void parseZeroOrMoreWsOptCmtNl()
                                  throws OBOFormatParserException

Throws:

OBOFormatParserException

parseWs

protected void parseWs()
                throws OBOFormatParserException

Throws:

OBOFormatParserException

parseOneOrMoreWs

protected void parseOneOrMoreWs()
                         throws OBOFormatParserException

Throws:

OBOFormatParserException

parseZeroOrMoreWs

protected void parseZeroOrMoreWs()