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java.lang.Objectorg.obolibrary.oboformat.parser.OBOFormatParser
public class OBOFormatParser
implements the OBO Format 1.4 specification
Nested Class Summary | |
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protected class |
OBOFormatParser.MyStream
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Field Summary | |
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protected OBOFormatParser.MyStream |
s
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Constructor Summary | |
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OBOFormatParser()
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OBOFormatParser(OBOFormatParser.MyStream s)
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Method Summary | |
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List<String> |
checkDanglingReferences(OBODoc doc)
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protected void |
forceParseNlOrEof()
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boolean |
getFollowImports()
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OBODoc |
parse(BufferedReader reader)
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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)
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void |
parseEOL(Clause cl)
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protected void |
parseHeaderClause(Frame h)
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protected boolean |
parseHeaderClauseNl(Frame h)
header-clause ::= format-version-TVP | ... |
void |
parseHeaderFrame(Frame h)
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protected void |
parseIdLine(Frame f)
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void |
parseOBODoc(OBODoc obodoc)
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protected void |
parseOneOrMoreWs()
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void |
parseTermFrame(OBODoc obodoc)
term-frame ::= nl* '[Term]' nl id-Tag Class-ID EOL { term-frame-clause EOL } |
void |
parseTermFrameClause(Clause cl)
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protected void |
parseTermFrameClauseEOL(Frame f)
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void |
parseTypedefFrame(OBODoc obodoc)
Typedef-frame ::= nl* '[Typedef]' nl id-Tag Class-ID EOL { Typedef-frame-clause EOL } |
void |
parseTypedefFrameClause(Clause cl)
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protected void |
parseTypedefFrameClauseEOL(Frame f)
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protected void |
parseUnquotedString(Clause cl)
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OBODoc |
parseURL(String urlstr)
Parses a remote URL to an OBODoc |
protected void |
parseWs()
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protected void |
parseZeroOrMoreWs()
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protected void |
parseZeroOrMoreWsOptCmtNl()
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void |
setFollowImports(boolean followImports)
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void |
setReader(BufferedReader r)
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Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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protected OBOFormatParser.MyStream s
Constructor Detail |
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public OBOFormatParser()
public OBOFormatParser(OBOFormatParser.MyStream s)
Method Detail |
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public void setReader(BufferedReader r)
public void setFollowImports(boolean followImports)
public boolean getFollowImports()
public OBODoc parse(String fn) throws IOException, OBOFormatParserException
fn
-
IOException
OBOFormatParserException
public OBODoc parse(File file) throws IOException, OBOFormatParserException
file
-
IOException
OBOFormatParserException
public OBODoc parse(URL url) throws IOException, OBOFormatParserException
url
-
IOException
OBOFormatParserException
public OBODoc parseURL(String urlstr) throws IOException, OBOFormatParserException
urlstr
-
IOException
OBOFormatParserException
public OBODoc parse(BufferedReader reader) throws IOException, OBOFormatParserException
reader
-
IOException
OBOFormatParserException
public void parseOBODoc(OBODoc obodoc) throws OBOFormatParserException
OBOFormatParserException
public List<String> checkDanglingReferences(OBODoc doc) throws OBOFormatDanglingReferenceException
OBOFormatDanglingReferenceException
public void parseHeaderFrame(Frame h) throws OBOFormatParserException
OBOFormatParserException
protected boolean parseHeaderClauseNl(Frame h) throws OBOFormatParserException
h
- header frame
OBOFormatParserException
protected void parseHeaderClause(Frame h) throws OBOFormatParserException
OBOFormatParserException
public void parseEntityFrame(OBODoc obodoc) throws OBOFormatParserException
OBOFormatParserException
public void parseTermFrame(OBODoc obodoc) throws OBOFormatParserException
obodoc
-
OBOFormatParserException
protected void parseTermFrameClauseEOL(Frame f) throws OBOFormatParserException
f
-
OBOFormatParserException
public void parseTermFrameClause(Clause cl) throws OBOFormatParserException
OBOFormatParserException
public void parseTypedefFrame(OBODoc obodoc) throws OBOFormatParserException
obodoc
-
OBOFormatParserException
protected void parseTypedefFrameClauseEOL(Frame f) throws OBOFormatParserException
f
-
OBOFormatParserException
public void parseTypedefFrameClause(Clause cl) throws OBOFormatParserException
OBOFormatParserException
protected void parseIdLine(Frame f) throws OBOFormatParserException
OBOFormatParserException
public void parseEOL(Clause cl) throws OBOFormatParserException
OBOFormatParserException
protected void parseUnquotedString(Clause cl) throws OBOFormatParserException
OBOFormatParserException
protected void forceParseNlOrEof() throws OBOFormatParserException
OBOFormatParserException
protected void parseZeroOrMoreWsOptCmtNl() throws OBOFormatParserException
OBOFormatParserException
protected void parseWs() throws OBOFormatParserException
OBOFormatParserException
protected void parseOneOrMoreWs() throws OBOFormatParserException
OBOFormatParserException
protected void parseZeroOrMoreWs()
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