OBOFormatParser (oboformat parser adapted for direct OWLAPI inclusion 3.5.2 API)

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

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

Fields
Modifier and Type	Field and Description
`protected OBOFormatParser.MyStream`	`stream`

Constructor Summary

Constructors
Modifier Constructor and Description

OBOFormatParser()

protected OBOFormatParser(OBOFormatParser.MyStream s)

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

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`List<String>`	`checkDanglingReferences(OBODoc doc)`
`protected void`	`forceParseNlOrEof()`
`boolean`	`getFollowImports()`
`protected static SimpleDateFormat`	`getISODateFormat()`
`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 final OBOFormatParser.MyStream stream
```
- Constructor Detail
  - OBOFormatParser
```
public OBOFormatParser()
```
  - OBOFormatParser
```
protected OBOFormatParser(OBOFormatParser.MyStream s)
```
- Method Detail
  - getISODateFormat
```
protected static SimpleDateFormat getISODateFormat()
```
  - 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
```
    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
```
    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
```
    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
```
    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
```
    Parameters:
    
    reader - reader
    
    Returns:
    
    parsed obo document
    
    Throws:
    
    IOException - io exception
    
    OBOFormatParserException - parser exception
  - parseOBODoc
```
public void parseOBODoc(OBODoc obodoc)
```
    Parameters:
    
    obodoc - obodoc
    
    Throws:
    
    OBOFormatParserException - parser exception
  - checkDanglingReferences
```
public List<String> checkDanglingReferences(OBODoc doc)
```
    Parameters:
    
    doc - doc
    
    Returns:
    
    list of references
    
    Throws:
    
    OBOFormatDanglingReferenceException - dangling reference error
  - parseHeaderFrame
```
public void parseHeaderFrame(Frame h)
```
    Parameters:
    
    h - h
    
    Throws:
    
    OBOFormatParserException - parser exception
  - parseHeaderClauseNl
```
protected boolean parseHeaderClauseNl(Frame h)
```
    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)
```
  - parseEntityFrame
```
public void parseEntityFrame(OBODoc obodoc)
```
    Parameters:
    
    obodoc - obodoc
    
    Throws:
    
    OBOFormatParserException - parser exception
  - parseTermFrame
```
public void parseTermFrame(OBODoc obodoc)
```
    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)
```
    Parameters:
    
    f - f
    
    Throws:
    
    OBOFormatParserException - parser exception
  - parseTermFrameClause
```
public Clause parseTermFrameClause()
```
    Returns:
    
    parsed clause
    
    Throws:
    
    OBOFormatParserException - parser exception
  - parseTypedefFrame
```
public void parseTypedefFrame(OBODoc obodoc)
```
    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)
```
    Parameters:
    
    f - f
    
    Throws:
    
    OBOFormatParserException - parser exception
  - parseTypedefFrameClause
```
public Clause parseTypedefFrameClause()
```
    Returns:
    
    parsed clause
    
    Throws:
    
    OBOFormatParserException - parser exception
  - parseIdLine
```
protected void parseIdLine(Frame f)
```
  - parseEOL
```
public void parseEOL(Clause cl)
```
    Parameters:
    
    cl - cl
    
    Throws:
    
    OBOFormatParserException - parser exception
  - parseUnquotedString
```
protected void parseUnquotedString(Clause cl)
```
  - forceParseNlOrEof
```
protected void forceParseNlOrEof()
```
  - parseZeroOrMoreWsOptCmtNl
```
protected void parseZeroOrMoreWsOptCmtNl()
```
  - parseWs
```
protected void parseWs()
```
  - parseOneOrMoreWs
```
protected void parseOneOrMoreWs()
```
  - parseZeroOrMoreWs
```
protected void parseZeroOrMoreWs()
```

Class OBOFormatParser

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

stream

Constructor Detail

OBOFormatParser

OBOFormatParser

Method Detail

getISODateFormat

setReader

setFollowImports

getFollowImports

parse

parse

parse

parseURL

parse

parseOBODoc

checkDanglingReferences

parseHeaderFrame

parseHeaderClauseNl

parseHeaderClause

parseEntityFrame

parseTermFrame

parseTermFrameClauseEOL

parseTermFrameClause

parseTypedefFrame

parseTypedefFrameClauseEOL

parseTypedefFrameClause

parseIdLine

parseEOL

parseUnquotedString

forceParseNlOrEof

parseZeroOrMoreWsOptCmtNl

parseWs

parseOneOrMoreWs

parseZeroOrMoreWs