org.obolibrary.oboformat.writer

Class OBOFormatWriter

java.lang.Object

org.obolibrary.oboformat.writer.OBOFormatWriter

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. This implementation might be a bit slower as it involves additional id conversion back into OWL.

Constructor Summary

Constructors

Constructor and Description
OBOFormatWriter()

Method Summary

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

isCheckStructure

public boolean isCheckStructure()

Checks if is check structure.

Returns:

true, if is check structure

setCheckStructure

public void setCheckStructure(boolean isCheckStructure)

Sets the check structure.

Parameters:

isCheckStructure - the new check structure

write

public void write(String fn,
                  BufferedWriter writer)
           throws IOException,
                  OBOFormatParserException

Write.

Parameters:

fn - the fn

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,
                  BufferedWriter writer)
           throws IOException,
                  OBOFormatParserException

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(BufferedReader reader,
                  BufferedWriter writer)
           throws IOException,
                  OBOFormatParserException

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 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,
                  BufferedWriter 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,
                  BufferedWriter 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,
                        BufferedWriter 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,
                  BufferedWriter writer,
                  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.

writeDef

public void writeDef(Clause clause,
                     BufferedWriter writer)
              throws IOException

Write def.

Parameters:

clause - the clause

writer - the writer

Throws:

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

writePropertyValue

public void writePropertyValue(Clause clause,
                               BufferedWriter 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 void writeSynonym(Clause clause,
                         BufferedWriter writer)
                  throws IOException

Write synonym.

Parameters:

clause - the clause

writer - the writer

Throws:

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

write

public void write(Clause clause,
                  BufferedWriter writer,
                  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