org.obolibrary.oboformat.writer

Class OBOFormatWriter

java.lang.Object

org.obolibrary.oboformat.writer.OBOFormatWriter

@ParametersAreNonnullByDefault
public class OBOFormatWriter
extends Object

The Class OBOFormatWriter.

Author:

Shahid Manzoor

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static interface	OBOFormatWriter.NameProvider Provide names for given OBO identifiers.
static class	OBOFormatWriter.OBODocNameProvider Default implementation of a OBOFormatWriter.NameProvider using an underlying.
static class	OBOFormatWriter.OWLOntologyNameProvider Alternative implementation to lookup labels in an OWLOntology.

Constructor Summary

Constructors

Constructor and Description
OBOFormatWriter()

Method Summary

Modifier and Type	Method and Description
boolean	isCheckStructure()
void	setCheckStructure(boolean isCheckStructure)
static void	sortTermClauses(List<Clause> clauses) Sort a list of term frame clauses according to in the OBO format specified tag and value order.
static void	write(Clause clause, Writer writer, OBOFormatWriter.NameProvider nameProvider) Write.
void	write(Frame frame, Writer writer, OBOFormatWriter.NameProvider nameProvider)
void	write(OBODoc doc, File outFile)
void	write(OBODoc doc, String outFilename)
void	write(OBODoc doc, Writer writer)
void	write(OBODoc doc, Writer writer, OBOFormatWriter.NameProvider nameProvider)
void	write(Reader reader, Writer writer)
void	write(String fn, Writer writer)
void	write(URL url, Writer writer) Write.
static void	writeDef(Clause clause, Writer writer) Write def.
void	writeHeader(Frame frame, Writer writer, OBOFormatWriter.NameProvider nameProvider) Write header.
static void	writePropertyValue(Clause clause, Writer writer) Write property value.
static void	writeSynonym(Clause clause, Writer writer) Write synonym.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

OBOFormatWriter

public OBOFormatWriter()

Method Detail

writeDef

public static void writeDef(Clause clause,
                            Writer writer)
                     throws IOException

Write def.

Parameters:

clause - the clause

writer - the writer

Throws:

IOException - Signals that an I/O exception has occurred.

writePropertyValue

public static void writePropertyValue(Clause clause,
                                      Writer writer)
                               throws IOException

Write property value.

Parameters:

clause - the clause

writer - the writer

Throws:

IOException - Signals that an I/O exception has occurred.

writeSynonym

public static void writeSynonym(Clause clause,
                                Writer writer)
                         throws IOException

Write synonym.

Parameters:

clause - the clause

writer - the writer

Throws:

IOException - Signals that an I/O exception has occurred.

write

public static void write(Clause clause,
                         Writer writer,
                         @Nullable
                         OBOFormatWriter.NameProvider nameProvider)
                  throws IOException

Write.

Parameters:

clause - the clause

writer - the writer

nameProvider - the name provider

Throws:

IOException - Signals that an I/O exception has occurred.

sortTermClauses

public static void sortTermClauses(List<Clause> clauses)

Sort a list of term frame clauses according to in the OBO format specified tag and value order.

Parameters:

clauses - the clauses

isCheckStructure

public boolean isCheckStructure()

Returns:

true, if is check structure

setCheckStructure

public void setCheckStructure(boolean isCheckStructure)

Parameters:

isCheckStructure - the new check structure

write

public void write(String fn,
                  Writer writer)
           throws IOException

Parameters:

fn - the file name to read in

writer - the writer

Throws:

IOException - Signals that an I/O exception has occurred.

OBOFormatParserException - the OBO format parser exception

write

public void write(URL url,
                  Writer writer)
           throws IOException

Write.

Parameters:

url - the url

writer - the writer

Throws:

IOException - Signals that an I/O exception has occurred.

OBOFormatParserException - the OBO format parser exception

write

public void write(Reader reader,
                  Writer writer)
           throws IOException

Parameters:

reader - the reader

writer - the writer

Throws:

IOException - Signals that an I/O exception has occurred.

OBOFormatParserException - the OBO format parser exception

write

public void write(OBODoc doc,
                  String outFilename)
           throws IOException

Parameters:

doc - the doc

outFilename - the out file name

Throws:

IOException - Signals that an I/O exception has occurred.

write

public void write(OBODoc doc,
                  File outFile)
           throws IOException

Parameters:

doc - the doc

outFile - the out file

Throws:

IOException - Signals that an I/O exception has occurred.

write

public void write(OBODoc doc,
                  Writer writer)
           throws IOException

Parameters:

doc - the doc

writer - the writer

Throws:

IOException - Signals that an I/O exception has occurred.

write

public void write(OBODoc doc,
                  Writer writer,
                  OBOFormatWriter.NameProvider nameProvider)
           throws IOException

Parameters:

doc - the doc

writer - the writer

nameProvider - the name provider

Throws:

IOException - Signals that an I/O exception has occurred.

writeHeader

public void writeHeader(Frame frame,
                        Writer writer,
                        OBOFormatWriter.NameProvider nameProvider)
                 throws IOException

Write header.

Parameters:

frame - the frame

writer - the writer

nameProvider - the name provider

Throws:

IOException - Signals that an I/O exception has occurred.

write

public void write(Frame frame,
                  Writer writer,
                  @Nullable
                  OBOFormatWriter.NameProvider nameProvider)
           throws IOException

Parameters:

frame - the frame

writer - the writer

nameProvider - the name provider

Throws:

IOException - Signals that an I/O exception has occurred.