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.

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.
void	write(BufferedReader reader, BufferedWriter writer)
static 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, File outFile)
void	write(OBODoc doc, String outFilename)
void	write(String fn, BufferedWriter writer)
void	write(URL url, BufferedWriter writer) Write.
static void	writeDef(Clause clause, BufferedWriter writer) Write def.
void	writeHeader(Frame frame, BufferedWriter writer, OBOFormatWriter.NameProvider nameProvider) Write header.
static void	writePropertyValue(Clause clause, BufferedWriter writer) Write property value.
static 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()

Returns:

true, if is check structure

setCheckStructure

public void setCheckStructure(boolean isCheckStructure)

Parameters:

isCheckStructure - the new check structure

write

public void write(@Nonnull
                  String fn,
                  @Nonnull
                  BufferedWriter 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(@Nonnull
                  URL url,
                  @Nonnull
                  BufferedWriter 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(BufferedReader reader,
                  @Nonnull
                  BufferedWriter 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(@Nonnull
                  OBODoc doc,
                  @Nonnull
                  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(@Nonnull
                  OBODoc doc,
                  @Nonnull
                  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(@Nonnull
                  OBODoc doc,
                  @Nonnull
                  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(@Nonnull
                  OBODoc doc,
                  @Nonnull
                  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(@Nonnull
                        Frame frame,
                        @Nonnull
                        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(@Nonnull
                  Frame frame,
                  @Nonnull
                  BufferedWriter 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.

writeDef

public static void writeDef(@Nonnull
                            Clause clause,
                            @Nonnull
                            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 static void writePropertyValue(@Nonnull
                                      Clause clause,
                                      @Nonnull
                                      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 static void writeSynonym(@Nonnull
                                Clause clause,
                                @Nonnull
                                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 static void write(@Nonnull
                         Clause clause,
                         @Nonnull
                         BufferedWriter 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(@Nonnull
                                   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