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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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protected static class |
OBOFormatParser.ParseState
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Field Summary | |
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static String |
DEFAULT_CHARACTER_ENCODING
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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 boolean |
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 |
boolean |
parseEntityFrame(OBODoc obodoc)
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protected boolean |
parseHeaderClause(Frame h)
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protected boolean |
parseHeaderClauseNl(Frame h)
header-clause ::= format-version-TVP | ... |
boolean |
parseHeaderFrame(Frame h)
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protected boolean |
parseIdLine(Frame f)
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protected boolean |
parseNlChar()
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boolean |
parseOBODoc(OBODoc obodoc)
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protected boolean |
parseOneOrMoreWs()
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protected boolean |
parseSynonymXrefs(Clause cl,
boolean createEmpty)
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boolean |
parseTermFrame(OBODoc obodoc)
term-frame ::= nl* '[Term]' nl id-Tag Class-ID EOL { term-frame-clause EOL } |
boolean |
parseTermFrameClause(Clause cl)
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protected boolean |
parseTermFrameClauseEOL(Frame f)
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boolean |
parseTypedefFrame(OBODoc obodoc)
Typedef-frame ::= nl* '[Typedef]' nl id-Tag Class-ID EOL { Typedef-frame-clause EOL } |
boolean |
parseTypedefFrameClause(Clause cl)
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protected boolean |
parseTypedefFrameClauseEOL(Frame f)
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protected boolean |
parseUnquotedString(Clause cl)
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OBODoc |
parseURL(String urlstr)
Parses a remote URL to an OBODoc |
protected boolean |
parseWs()
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protected boolean |
parseWsOptCmtNl()
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protected boolean |
parseZeroOrMoreWs()
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protected boolean |
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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public static final String DEFAULT_CHARACTER_ENCODING
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
fn
-
IOException
public OBODoc parse(File file) throws IOException
file
-
IOException
public OBODoc parse(URL url) throws IOException
url
-
IOException
public OBODoc parseURL(String urlstr) throws IOException
urlstr
-
IOException
public OBODoc parse(BufferedReader reader) throws IOException
reader
-
IOException
public boolean parseOBODoc(OBODoc obodoc)
public List<String> checkDanglingReferences(OBODoc doc) throws OBOFormatDanglingReferenceException
OBOFormatDanglingReferenceException
public boolean parseHeaderFrame(Frame h)
protected boolean parseHeaderClauseNl(Frame h)
protected boolean parseHeaderClause(Frame h)
public boolean parseEntityFrame(OBODoc obodoc)
public boolean parseTermFrame(OBODoc obodoc)
protected boolean parseTermFrameClauseEOL(Frame f)
public boolean parseTermFrameClause(Clause cl)
public boolean parseTypedefFrame(OBODoc obodoc)
FrameMergeException
protected boolean parseTypedefFrameClauseEOL(Frame f)
public boolean parseTypedefFrameClause(Clause cl)
protected boolean parseSynonymXrefs(Clause cl, boolean createEmpty)
protected boolean parseIdLine(Frame f)
protected boolean parseUnquotedString(Clause cl)
protected boolean forceParseNlOrEof()
protected boolean parseZeroOrMoreWsOptCmtNl()
protected boolean parseWsOptCmtNl()
protected boolean parseWs()
protected boolean parseOneOrMoreWs()
protected boolean parseZeroOrMoreWs()
protected boolean parseNlChar()
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