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  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 }
 void parseTermFrameClause(Clause cl)
           
protected  void parseTermFrameClauseEOL(Frame f)
           
 void parseTypedefFrame(OBODoc obodoc)
          Typedef-frame ::= nl* '[Typedef]' nl id-Tag Class-ID EOL { Typedef-frame-clause EOL }
 void parseTypedefFrameClause(Clause cl)
           
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

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,
                    OBOFormatParserException
Parses a local file or URL to an OBODoc

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

parse

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

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

parse

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

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

parseURL

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

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

parse

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

parseOBODoc

public void parseOBODoc(OBODoc obodoc)
                 throws OBOFormatParserException
Throws:
OBOFormatParserException

checkDanglingReferences

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

parseHeaderFrame

public void parseHeaderFrame(Frame h)
                      throws OBOFormatParserException
Throws:
OBOFormatParserException

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

parseHeaderClause

protected void parseHeaderClause(Frame h)
                          throws OBOFormatParserException
Throws:
OBOFormatParserException

parseEntityFrame

public void parseEntityFrame(OBODoc obodoc)
                      throws OBOFormatParserException
Throws:
OBOFormatParserException

parseTermFrame

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

Parameters:
obodoc -
Throws:
OBOFormatParserException

parseTermFrameClauseEOL

protected void parseTermFrameClauseEOL(Frame f)
                                throws OBOFormatParserException
Parameters:
f -
Throws:
OBOFormatParserException

parseTermFrameClause

public void parseTermFrameClause(Clause cl)
                          throws OBOFormatParserException
Throws:
OBOFormatParserException

parseTypedefFrame

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

Parameters:
obodoc -
Throws:
OBOFormatParserException

parseTypedefFrameClauseEOL

protected void parseTypedefFrameClauseEOL(Frame f)
                                   throws OBOFormatParserException
Parameters:
f -
Throws:
OBOFormatParserException

parseTypedefFrameClause

public void parseTypedefFrameClause(Clause cl)
                             throws OBOFormatParserException
Throws:
OBOFormatParserException

parseIdLine

protected void parseIdLine(Frame f)
                    throws OBOFormatParserException
Throws:
OBOFormatParserException

parseEOL

public void parseEOL(Clause cl)
              throws OBOFormatParserException
Throws:
OBOFormatParserException

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()


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