org.obolibrary.oboformat.writer
Class OBOFormatWriter

java.lang.Object
  extended by org.obolibrary.oboformat.writer.OBOFormatWriter

public class OBOFormatWriter
extends Object

Author:
Shahid Manzoor

Nested Class Summary
static interface OBOFormatWriter.NameProvider
          Provide names for given OBO identifiers.
static class OBOFormatWriter.OBODocNameProvider
          Default implementation of a OBOFormatWriter.NameProvider using an underlying OBODoc.
 
Constructor Summary
OBOFormatWriter()
           
 
Method Summary
 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)
           
 void write(Clause clause, BufferedWriter writer, OBOFormatWriter.NameProvider nameProvider)
           
 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)
           
 void write(URL url, BufferedWriter writer)
           
 void writeDef(Clause clause, BufferedWriter writer)
           
 void writeHeader(Frame frame, BufferedWriter writer, OBOFormatWriter.NameProvider nameProvider)
           
 void writePropertyValue(Clause clause, BufferedWriter writer)
           
 void writeSynonym(Clause clause, BufferedWriter writer)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

OBOFormatWriter

public OBOFormatWriter()
Method Detail

isCheckStructure

public boolean isCheckStructure()

setCheckStructure

public void setCheckStructure(boolean isCheckStructure)

write

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

write

public void write(URL url,
                  BufferedWriter writer)
           throws IOException,
                  OBOFormatParserException
Throws:
IOException
OBOFormatParserException

write

public void write(BufferedReader reader,
                  BufferedWriter writer)
           throws IOException,
                  OBOFormatParserException
Throws:
IOException
OBOFormatParserException

write

public void write(OBODoc doc,
                  String outFile)
           throws IOException
Throws:
IOException

write

public void write(OBODoc doc,
                  BufferedWriter writer)
           throws IOException
Throws:
IOException

write

public void write(OBODoc doc,
                  BufferedWriter writer,
                  OBOFormatWriter.NameProvider nameProvider)
           throws IOException
Throws:
IOException

writeHeader

public void writeHeader(Frame frame,
                        BufferedWriter writer,
                        OBOFormatWriter.NameProvider nameProvider)
                 throws IOException
Throws:
IOException

write

public void write(Frame frame,
                  BufferedWriter writer,
                  OBOFormatWriter.NameProvider nameProvider)
           throws IOException
Throws:
IOException

writeDef

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

writePropertyValue

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

writeSynonym

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

write

public void write(Clause clause,
                  BufferedWriter writer,
                  OBOFormatWriter.NameProvider nameProvider)
           throws IOException
Throws:
IOException

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 -


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