gov.nih.nlm.umls.io
Class OriginalMRMetathesaurusOutputStream

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

All Implemented Interfaces:

ConceptOutputStream, MetathesaurusOutputStream, LocalNullValueSupport

Direct Known Subclasses:

OriginalMRMetamorphoSysOutputStream

public class OriginalMRMetathesaurusOutputStream
extends OriginalMRFilesConceptOutputStream
implements MetathesaurusOutputStream

This MetathesaurusOutputStream generates standard MR files.

Author:

Deborah Shapiro

Field Summary

protected String[]	ancillary_files
protected String[]	change_files
protected FileStatisticsConfiguration	config
protected Map	lui_to_cui_set
protected Map	sui_to_cui_set

Fields inherited from class gov.nih.nlm.umls.io.OriginalMRFilesConceptOutputStream

add_unicode_bom, mr_dir, mr_targets, null_value, target_files, versioned_output, warnings

Constructor Summary

OriginalMRMetathesaurusOutputStream(FileStatisticsConfiguration config)
Instantiates an empty OriginalMRMetathesaurusOutputStream.

Method Summary

protected void	ambigCheck(Atom atom) Checks the maps to see if the given Atoms sui or lui should be added to the ambiguous maps.
void	close() Closes source files that were opened by this class's openTargets() method.
protected String	getColumnTextFromFileStatistics(FileStatistics file_stats) Returns a MRCOLS line.
protected String	getFileTextFromFileStatistics(FileStatistics file_stats) Returns a MRFILES line.
void	open(String mr_dir) Opens all Original Release Format MR 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	setCandidateAmbiguousStringIdentifiers(List suis) Sets the list of suis that are candidates to be ambiguous.
void	setCandidateAmbiguousStringIdentifiers(String[] suis) Sets the list of suis that are candidates to be ambiguous.
void	setCandidateAmbiguousTermIdentifiers(List luis) Sets the list of luis that are candidates to be ambiguous.
void	setCandidateAmbiguousTermIdentifiers(String[] luis) Sets the list of terms that are candidates to be ambiguous.
void	writeConcept(Concept c) Writes the specified Concept.
protected void	writeFileColumnStats() This method computes the file and columns statistics for the MRFILES and MRCOLS tables themselves.
void	writeIndexEntry(IndexEntry index_entry) Writes an IndexEntry to the appropriate MR index file.
protected void	writeMRCUI(ReleaseMetadata release_metadata) Writes the specified ReleaseMetadata to MRCUI.
protected void	writeMRRANK(ReleaseMetadata release_metadata) Write MRRANK.
protected void	writeMRSAB(ReleaseMetadata release_metadata) Writes MRSAB.
void	writeReleaseMetadata(ReleaseMetadata release_metadata) Writes an ReleaseMetadata to the appropriate MR metadata files.

Methods inherited from class gov.nih.nlm.umls.io.OriginalMRFilesConceptOutputStream

assignLrl, getNullValue, getWarnings, isEmptyValue, isLuiSuppressible, setNullValue, writeMRCON, writeMRCXT, writeMRDEF, writeMRSAT, writeMRSO

Methods inherited from class java.lang.Object

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

Methods inherited from interface gov.nih.nlm.umls.io.ConceptOutputStream

getWarnings

Methods inherited from interface gov.nih.nlm.util.LocalNullValueSupport

getNullValue, isEmptyValue, setNullValue

Field Detail

config

protected FileStatisticsConfiguration config

change_files

protected String[] change_files

ancillary_files

protected String[] ancillary_files

sui_to_cui_set

protected Map sui_to_cui_set

lui_to_cui_set

protected Map lui_to_cui_set

Constructor Detail

OriginalMRMetathesaurusOutputStream

public OriginalMRMetathesaurusOutputStream(FileStatisticsConfiguration config)

Instantiates an empty OriginalMRMetathesaurusOutputStream.

Parameters:

config - FileStatisticsConfiguration

Method Detail

openTargetFile

protected BufferedWriter openTargetFile(String name)
                                 throws IOException

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

Overrides:

openTargetFile in class OriginalMRFilesConceptOutputStream

Parameters:

name - the filename

Returns:

a BufferedWriter for the file

Throws:

IOException - if the file could not be opened.

printLine

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

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

Overrides:

printLine in class OriginalMRFilesConceptOutputStream

Parameters:

line - the line to be printed

file_name - printing destination

Throws:

IOException

open

public void open(String mr_dir)
          throws IOException

Opens all Original Release Format MR files in the specified directory.

Specified by:

open in interface ConceptOutputStream

Overrides:

open in class OriginalMRFilesConceptOutputStream

Parameters:

mr_dir - the subset directory

Throws:

IOException - if the files cannot be opened

close

public void close()
           throws IOException

Closes source files that were opened by this class's openTargets() method.

Specified by:

close in interface ConceptOutputStream

Overrides:

close in class OriginalMRFilesConceptOutputStream

Throws:

IOException

writeConcept

public void writeConcept(Concept c)
                  throws IOException

Writes the specified Concept.

Specified by:

writeConcept in interface ConceptOutputStream

Overrides:

writeConcept in class OriginalMRFilesConceptOutputStream

Parameters:

c - the specified Concept

Throws:

IOException - if anything goes wrong

writeIndexEntry

public void writeIndexEntry(IndexEntry index_entry)
                     throws IOException

Writes an IndexEntry to the appropriate MR index file.

Specified by:

writeIndexEntry in interface MetathesaurusOutputStream

Parameters:

index_entry - the IndexEntry to write

Throws:

IOException - if the file could not be written

writeMRCUI

protected void writeMRCUI(ReleaseMetadata release_metadata)
                   throws IOException

Writes the specified ReleaseMetadata to MRCUI.

Parameters:

release_metadata - the specified ReleaseMetadata

Throws:

IOException - if anything goes wrong

writeMRSAB

protected void writeMRSAB(ReleaseMetadata release_metadata)
                   throws IOException

Writes MRSAB.

Parameters:

release_metadata - the ReleaseMetadata containing MRSAB data

Throws:

IOException - if anything goes wrong

writeMRRANK

protected void writeMRRANK(ReleaseMetadata release_metadata)
                    throws IOException

Write MRRANK.

Parameters:

release_metadata - the ReleaseMetadata containing MRRANK data

Throws:

IOException - if anything goes wrong

writeReleaseMetadata

public void writeReleaseMetadata(ReleaseMetadata release_metadata)
                          throws IOException

Writes an ReleaseMetadata to the appropriate MR metadata files.

Specified by:

writeReleaseMetadata in interface MetathesaurusOutputStream

Parameters:

release_metadata - the ReleaseMetadata to write

Throws:

IOException - if the file could not be written

setCandidateAmbiguousStringIdentifiers

public void setCandidateAmbiguousStringIdentifiers(String[] suis)

Sets the list of suis that are candidates to be ambiguous.

Specified by:

setCandidateAmbiguousStringIdentifiers in interface MetathesaurusOutputStream

Parameters:

suis - the list of suis that are candidates to be ambiguous

setCandidateAmbiguousStringIdentifiers

public void setCandidateAmbiguousStringIdentifiers(List suis)

Sets the list of suis that are candidates to be ambiguous.

Specified by:

setCandidateAmbiguousStringIdentifiers in interface MetathesaurusOutputStream

Parameters:

suis - the list of suis that are candidates to be ambiguous

setCandidateAmbiguousTermIdentifiers

public void setCandidateAmbiguousTermIdentifiers(String[] luis)

Sets the list of terms that are candidates to be ambiguous.

Specified by:

setCandidateAmbiguousTermIdentifiers in interface MetathesaurusOutputStream

Parameters:

luis - candidate terms

setCandidateAmbiguousTermIdentifiers

public void setCandidateAmbiguousTermIdentifiers(List luis)

Sets the list of luis that are candidates to be ambiguous.

Specified by:

setCandidateAmbiguousTermIdentifiers in interface MetathesaurusOutputStream

Parameters:

luis - the list of luis that are candidates to be ambiguous

writeFileColumnStats

protected void writeFileColumnStats()
                             throws IOException

This method computes the file and columns statistics for the MRFILES and MRCOLS tables themselves. Should it be using "\n"?

Throws:

IOException - if problem writing to files

getFileTextFromFileStatistics

protected String getFileTextFromFileStatistics(FileStatistics file_stats)

Returns a MRFILES line.

Parameters:

file_stats - FileStatistics

Returns:

a MRFILES line

getColumnTextFromFileStatistics

protected String getColumnTextFromFileStatistics(FileStatistics file_stats)

Returns a MRCOLS line.

Parameters:

file_stats - FileStatistics

Returns:

a MRCOLS line

ambigCheck

protected void ambigCheck(Atom atom)

Checks the maps to see if the given Atoms sui or lui should be added to the ambiguous maps.

Parameters:

atom - the Atomto check