org.obolibrary.oboformat.parser
Class OBOFormatParser

java.lang.Object
  extended by org.obolibrary.oboformat.parser.OBOFormatParser

public class OBOFormatParser
extends Object

implements the OBO Format 1.4 specification


Nested Class Summary
protected  class OBOFormatParser.MyStream
           
 
Field Summary
protected  OBOFormatParser.MyStream s
           
 
Constructor Summary
OBOFormatParser()
           
OBOFormatParser(OBOFormatParser.MyStream s)
           
 
Method Summary
 List<String> checkDanglingReferences(OBODoc doc)
           
protected  boolean 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
 boolean parseEntityFrame(OBODoc obodoc)
           
protected  boolean parseHeaderClause(Frame h)
           
protected  boolean parseHeaderClauseNl(Frame h)
          header-clause ::= format-version-TVP | ...
 boolean parseHeaderFrame(Frame h)
           
protected  boolean parseIdLine(Frame f)
           
protected  boolean parseNlChar()
           
 boolean parseOBODoc(OBODoc obodoc)
           
protected  boolean parseOneOrMoreWs()
           
protected  boolean parseSynonymXrefs(Clause cl, boolean createEmpty)
           
 boolean parseTermFrame(OBODoc obodoc)
          term-frame ::= nl* '[Term]' nl id-Tag Class-ID EOL { term-frame-clause EOL }
 boolean parseTermFrameClause(Clause cl)
           
protected  boolean parseTermFrameClauseEOL(Frame f)
           
 boolean parseTypedefFrame(OBODoc obodoc)
          Typedef-frame ::= nl* '[Typedef]' nl id-Tag Class-ID EOL { Typedef-frame-clause EOL }
 boolean parseTypedefFrameClause(Clause cl)
           
protected  boolean parseTypedefFrameClauseEOL(Frame f)
           
protected  boolean parseUnquotedString(Clause cl)
           
 OBODoc parseURL(String urlstr)
          Parses a remote URL to an OBODoc
protected  boolean parseWs()
           
protected  boolean parseWsOptCmtNl()
           
protected  boolean parseZeroOrMoreWs()
           
protected  boolean 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

s

protected OBOFormatParser.MyStream s
Constructor Detail

OBOFormatParser

public OBOFormatParser()

OBOFormatParser

public OBOFormatParser(OBOFormatParser.MyStream s)
Method Detail

setReader

public void setReader(BufferedReader r)

setFollowImports

public void setFollowImports(boolean followImports)

getFollowImports

public boolean getFollowImports()

parse

public OBODoc parse(String fn)
             throws IOException
Parses a local file or URL to an OBODoc

Parameters:
fn -
Returns:
parsed obo document
Throws:
IOException

parse

public OBODoc parse(File file)
             throws IOException
Parses a local file to an OBODoc

Parameters:
file -
Returns:
parsed obo document
Throws:
IOException

parse

public OBODoc parse(URL url)
             throws IOException
Parses a remote URL to an OBODoc

Parameters:
url -
Returns:
parsed obo document
Throws:
IOException

parseURL

public OBODoc parseURL(String urlstr)
                throws IOException
Parses a remote URL to an OBODoc

Parameters:
urlstr -
Returns:
parsed obo document
Throws:
IOException

parse

public OBODoc parse(BufferedReader reader)
             throws IOException
Parameters:
reader -
Returns:
parsed obo document
Throws:
IOException

parseOBODoc

public boolean parseOBODoc(OBODoc obodoc)

checkDanglingReferences

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

parseHeaderFrame

public boolean parseHeaderFrame(Frame h)

parseHeaderClauseNl

protected boolean parseHeaderClauseNl(Frame h)
header-clause ::= format-version-TVP | ... | ...

Parameters:
h - header frame
Returns:
true if parse was successful

parseHeaderClause

protected boolean parseHeaderClause(Frame h)

parseEntityFrame

public boolean parseEntityFrame(OBODoc obodoc)

parseTermFrame

public boolean parseTermFrame(OBODoc obodoc)
term-frame ::= nl* '[Term]' nl id-Tag Class-ID EOL { term-frame-clause EOL }

Parameters:
obodoc -
Returns:
true if parse was successful

parseTermFrameClauseEOL

protected boolean parseTermFrameClauseEOL(Frame f)
Parameters:
f -
Returns:
true if parse was successful

parseTermFrameClause

public boolean parseTermFrameClause(Clause cl)

parseTypedefFrame

public boolean parseTypedefFrame(OBODoc obodoc)
Typedef-frame ::= nl* '[Typedef]' nl id-Tag Class-ID EOL { Typedef-frame-clause EOL }

Parameters:
obodoc -
Returns:
true if parse was successful

parseTypedefFrameClauseEOL

protected boolean parseTypedefFrameClauseEOL(Frame f)
Parameters:
f -
Returns:
true if parse was successful

parseTypedefFrameClause

public boolean parseTypedefFrameClause(Clause cl)

parseSynonymXrefs

protected boolean parseSynonymXrefs(Clause cl,
                                    boolean createEmpty)

parseIdLine

protected boolean parseIdLine(Frame f)

parseUnquotedString

protected boolean parseUnquotedString(Clause cl)

forceParseNlOrEof

protected boolean forceParseNlOrEof()

parseZeroOrMoreWsOptCmtNl

protected boolean parseZeroOrMoreWsOptCmtNl()

parseWsOptCmtNl

protected boolean parseWsOptCmtNl()

parseWs

protected boolean parseWs()

parseOneOrMoreWs

protected boolean parseOneOrMoreWs()

parseZeroOrMoreWs

protected boolean parseZeroOrMoreWs()

parseNlChar

protected boolean parseNlChar()


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