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.

Constructor Summary

Constructors

Constructor and Description
OBOFormatParser() Default constructor.
OBOFormatParser(Map<String,OBODoc> importsMap)
OBOFormatParser(OBOFormatParser.MyStream s)

Method Summary

Modifier and Type	Method and Description
boolean	addImport(String key, OBODoc doc)
List<String>	checkDanglingReferences(OBODoc doc)
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)
void	parseHeaderFrame(Frame h)
void	parseOBODoc(OBODoc obodoc)
void	parseTermFrame(OBODoc obodoc) term-frame ::= nl* '[Term]' nl id-Tag Class-ID EOL { term-frame-clause EOL }.
Clause	parseTermFrameClause()
void	parseTypedefFrame(OBODoc obodoc) Typedef-frame ::= nl* '[Typedef]' nl id-Tag Class-ID EOL { Typedef-frame-clause EOL }.
Clause	parseTypedefFrameClause()
OBODoc	parseURL(String urlstr) Parses a remote URL to an OBODoc.
void	setFollowImports(boolean followImports)
void	setReader(BufferedReader r)

Methods inherited from class java.lang.Object

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

Constructor Detail

OBOFormatParser

public OBOFormatParser()

Default constructor.

OBOFormatParser

public OBOFormatParser(OBOFormatParser.MyStream s)

Parameters:

s - stream

OBOFormatParser

public OBOFormatParser(Map<String,OBODoc> importsMap)

Parameters:

importsMap - import map

Method Detail

addImport

public boolean addImport(String key,
                         OBODoc doc)

Parameters:

key - key for the import

doc - document

Returns:

true if the key is new

setReader

public void setReader(BufferedReader r)

Parameters:

r - r

getFollowImports

public boolean getFollowImports()

Returns:

follow imports

setFollowImports

public void setFollowImports(boolean followImports)

Parameters:

followImports - true if imports should be followed

parse

@Nonnull
public OBODoc parse(@Nonnull
                             String fn)
                      throws IOException

Parses a local file or URL to an OBODoc.

Parameters:

fn - file name

Returns:

parsed obo document

Throws:

IOException - io exception

OBOFormatParserException - parser exception

parse

@Nonnull
public OBODoc parse(File file)
                      throws IOException

Parses a local file to an OBODoc.

Parameters:

file - file

Returns:

parsed obo document

Throws:

IOException - io exception

OBOFormatParserException - parser exception

parse

@Nonnull
public OBODoc parse(@Nonnull
                             URL url)
                      throws IOException

Parses a remote URL to an OBODoc.

Parameters:

url - URL to connect to

Returns:

parsed obo document

Throws:

IOException - io exception

OBOFormatParserException - parser exception

parseURL

@Nonnull
public OBODoc parseURL(String urlstr)
                         throws IOException

Parses a remote URL to an OBODoc.

Parameters:

urlstr - URL string

Returns:

parsed obo document

Throws:

IOException - io exception

OBOFormatParserException - parser exception

parse

@Nonnull
public OBODoc parse(BufferedReader reader)
                      throws IOException

Parameters:

reader - reader

Returns:

parsed obo document

Throws:

IOException - io exception

OBOFormatParserException - parser exception

parseOBODoc

public void parseOBODoc(@Nonnull
                        OBODoc obodoc)

Parameters:

obodoc - obodoc

Throws:

OBOFormatParserException - parser exception

checkDanglingReferences

@Nonnull
public List<String> checkDanglingReferences(@Nonnull
                                                     OBODoc doc)

Parameters:

doc - doc

Returns:

list of references

Throws:

OBOFormatDanglingReferenceException - dangling reference error

parseHeaderFrame

public void parseHeaderFrame(@Nonnull
                             Frame h)

Parameters:

h - h

Throws:

OBOFormatParserException - parser exception

parseEntityFrame

public void parseEntityFrame(@Nonnull
                             OBODoc obodoc)

Parameters:

obodoc - obodoc

Throws:

OBOFormatParserException - parser exception

parseTermFrame

public void parseTermFrame(@Nonnull
                           OBODoc obodoc)

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

Parameters:

obodoc - obodoc

Throws:

OBOFormatParserException - parser exception

parseTermFrameClause

@Nonnull
public Clause parseTermFrameClause()

Returns:

parsed clause

Throws:

OBOFormatParserException - parser exception

parseTypedefFrame

public void parseTypedefFrame(@Nonnull
                              OBODoc obodoc)

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

Parameters:

obodoc - obodoc

Throws:

OBOFormatParserException - parser exception

parseTypedefFrameClause

@Nonnull
public Clause parseTypedefFrameClause()

Returns:

parsed clause

Throws:

OBOFormatParserException - parser exception

parseEOL

public void parseEOL(@Nonnull
                     Clause cl)

Parameters:

cl - clause

Throws:

OBOFormatParserException - parser exception