gov.nih.nlm.umls.io
Class OriginalMRFilesConceptOutputStream

java.lang.Object
  gov.nih.nlm.umls.io.OriginalMRFilesConceptOutputStream

All Implemented Interfaces:

ConceptOutputStream, LocalNullValueSupport

Direct Known Subclasses:

OriginalMRMetathesaurusOutputStream

public class OriginalMRFilesConceptOutputStream
extends Object
implements ConceptOutputStream

This ConceptOutputStream generates a subset of standard MR files.

Author:

Deborah Shapiro

Field Summary

protected boolean	add_unicode_bom
protected String	mr_dir
protected Map	mr_targets
protected String	null_value
protected static String[]	target_files
protected boolean	versioned_output
protected List	warnings

Constructor Summary

OriginalMRFilesConceptOutputStream()
Instantiates an empty OriginalMRFilesConceptOutputStream.

Method Summary

protected Map	assignLrl(Atom[] atoms) Assigns the LRL value.
void	close() Closes files opened in open(String).
String	getNullValue() Returns the null value.
String[]	getWarnings() Returns a String[] of warnings accumulated during processing of the output stream.
boolean	isEmptyValue(String token) Indicates whether or not the specified token is null or contains a null value as defined by being either zero length or a value equal to the null value.
protected boolean	isLuiSuppressible(String lui, Atom[] atoms) Returns true if the specified LUI is suppressible.
void	open(String mr_dir) Opens all target files in the specified directory.
protected BufferedWriter	openTargetFile(String name) Opens the specified file in the directory passed to open(String).
protected void	printLine(String line, String file_name) Prints the given line to the file with the given name.
void	setNullValue(String null_value) Sets the null value to use.
void	writeConcept(Concept concept) Writes a Concept to the appropriate MR files.
protected void	writeMRCON(Concept concept) Writes MRCON entries for a Concept
protected void	writeMRCXT(Concept concept) Writes MRCXT entries for a Concept
protected void	writeMRDEF(Concept concept) Writes MRDEF entries for a Concept
protected void	writeMRSAT(Concept concept) Writes MRSAT entries for a Concept
protected void	writeMRSO(Concept concept) Writes MRSO entries for a Concept

Methods inherited from class java.lang.Object

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

Field Detail

mr_targets

protected Map mr_targets

target_files

protected static String[] target_files

mr_dir

protected String mr_dir

versioned_output

protected boolean versioned_output

add_unicode_bom

protected boolean add_unicode_bom

warnings

protected List warnings

null_value

protected String null_value

Constructor Detail

OriginalMRFilesConceptOutputStream

public OriginalMRFilesConceptOutputStream()

Instantiates an empty OriginalMRFilesConceptOutputStream.

Method Detail

setNullValue

public void setNullValue(String null_value)

Sets the null value to use. This is needed if release.dat specifies some non-standard null value char sequence.

Specified by:

setNullValue in interface LocalNullValueSupport

Parameters:

null_value - the new null string value

getNullValue

public String getNullValue()

Returns the null value. This is needed if release.dat specifies some non-standard null value char sequence.

Specified by:

getNullValue in interface LocalNullValueSupport

Returns:

the string value for "null"

isEmptyValue

public boolean isEmptyValue(String token)

Indicates whether or not the specified token is null or contains a null value as defined by being either zero length or a value equal to the null value.

Specified by:

isEmptyValue in interface LocalNullValueSupport

open

public void open(String mr_dir)
          throws IOException

Opens all target files in the specified directory. The set of target files is the standard MR files.

Specified by:

open in interface ConceptOutputStream

Parameters:

mr_dir - the subset directory

Throws:

IOException - if the files cannot be opened

close

public void close()
           throws IOException

Closes files opened in open(String).

Specified by:

close in interface ConceptOutputStream

Throws:

IOException - if the stream cannot be closed

writeConcept

public void writeConcept(Concept concept)
                  throws IOException

Writes a Concept to the appropriate MR files.

Specified by:

writeConcept in interface ConceptOutputStream

Parameters:

concept - the Concept to write

Throws:

IOException - if the files could not be written

writeMRSO

protected void writeMRSO(Concept concept)
                  throws IOException

Writes MRSO entries for a Concept

Parameters:

concept - the Concept to write

Throws:

IOException - if anything goes wrong

writeMRCON

protected void writeMRCON(Concept concept)
                   throws IOException

Writes MRCON entries for a Concept

Parameters:

concept - the Concept to write

Throws:

IOException - if anything goes wrong

isLuiSuppressible

protected boolean isLuiSuppressible(String lui,
                                    Atom[] atoms)

Returns true if the specified LUI is suppressible.

Parameters:

lui - the LUI value to check

atoms - the Atoms

Returns:

true if the LUI is suppressible, false otherwise

assignLrl

protected Map assignLrl(Atom[] atoms)

Assigns the LRL value.

Parameters:

atoms - the Atoms to be assigned

Returns:

Map of cui:sui tuple mapped to lrl

writeMRCXT

protected void writeMRCXT(Concept concept)
                   throws IOException

Writes MRCXT entries for a Concept

Parameters:

concept - the Concept to write

Throws:

IOException - if anything goes wrong

writeMRDEF

protected void writeMRDEF(Concept concept)
                   throws IOException

Writes MRDEF entries for a Concept

Parameters:

concept - the Concept to write

Throws:

IOException - if anything goes wrong

writeMRSAT

protected void writeMRSAT(Concept concept)
                   throws IOException

Writes MRSAT entries for a Concept

Parameters:

concept - the Concept to write

Throws:

IOException - if anything goes wrong

printLine

protected void printLine(String line,
                         String file_name)
                  throws IOException

Prints the given line to the file with the given name.

Parameters:

line - the line to be printed

file_name - filename to print to

Throws:

IOException

openTargetFile

protected BufferedWriter openTargetFile(String name)
                                 throws IOException

Opens the specified file in the directory passed to open(String).

Parameters:

name - the filename

Returns:

a BufferedWriter for the file

Throws:

IOException - if the file could not be opened.

getWarnings

public String[] getWarnings()

Returns a String[] of warnings accumulated during processing of the output stream.

Specified by:

getWarnings in interface ConceptOutputStream

Returns:

String[] of warnings