gov.nih.nlm.umls.io
Class RichMRMetathesaurusOutputStream

java.lang.Object
  gov.nih.nlm.umls.io.RichMRFilesConceptOutputStream
      gov.nih.nlm.umls.io.RichMRMetathesaurusOutputStream

All Implemented Interfaces:

ConceptOutputStream, MetathesaurusOutputStream, LocalNullValueSupport, ProgressReporter

Direct Known Subclasses:

RichMRMetamorphoSysOutputStream

public class RichMRMetathesaurusOutputStream
extends RichMRFilesConceptOutputStream
implements MetathesaurusOutputStream, ProgressReporter

This MetathesaurusOutputStream generates MR files in the "Rich Release Format". It is an extension of RichMRFilesConceptOutputStream with additional code for the ReleaseMetadata content.

Author:

Deborah Shapiro

Field Summary

protected String[]	ancillary_files
protected Atom[]	atoms
protected String[]	change_files
protected FileStatisticsConfiguration	config
protected List	listeners
protected Map	lui_to_cui_set
protected Map	sui_to_cui_set

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

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

Constructor Summary

RichMRMetathesaurusOutputStream(FileStatisticsConfiguration config)
Instantiates an empty RichMRMetathesaurusOutputStream.

Method Summary

void	addProgressListener(ProgressListener l) Adds a ProgressListener.
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 void	fireProgressEvent(int pct, String note) Fires a ProgressEvent.
protected String	getColumnTextFromFileStatistics(FileStatistics file_stats) Returns the MRCOLS.RRF lines for the specified FileStatistics.
protected String	getFileTextFromFileStatistics(FileStatistics file_stats) Returns the MRFILES.RRF line for the specified FileStatistics.
void	open(String mr_dir) Opens all Rich 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	removeProgressListener(ProgressListener l) Removes a ProgressListener.
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 terms that are candidates to be ambiguous.
void	setCandidateAmbiguousTermIdentifiers(String[] luis) Sets the list of terms that are candidates to be ambiguous.
void	writeConcept(Concept concept) Writes a Concept to the appropriate MR files.
protected void	writeFileColumnStats() This method computes the file and columns statistics for the MRFILES.RRF and MRCOLS.RRF files themselves.
void	writeIndexEntry(IndexEntry index_entry) Writes an IndexEntry to the appropriate MR index file.
protected void	writeMRAUI(ReleaseMetadata release_metadata) Writes a line to the MRAUI.RRF file.
protected void	writeMRCUI(ReleaseMetadata release_metadata) Writes a line to the MRCUI.RRF file.
protected void	writeMRDOC(ReleaseMetadata release_metadata) Write a line to the MRDOC.RRF file.
protected void	writeMRRANK(ReleaseMetadata release_metadata) Writes a line to the MRRANK.RRF file.
protected void	writeMRSAB(ReleaseMetadata release_metadata) Write a line to the MRSAB.RRF file.
void	writeReleaseMetadata(ReleaseMetadata release_metadata) Writes an ReleaseMetadata to the appropriate MR metadata files.

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

flush, getFilePosition, getNullValue, getWarnings, isEmptyValue, setNullValue, writeMRCOC, writeMRCONSO, writeMRCXT, writeMRDEF, writeMRHIER, writeMRHIST, writeMRMAP, writeMRREL, writeMRSAT, writeMRSMAP, writeMRSTY

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

listeners

protected List listeners

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

atoms

protected Atom[] atoms

Constructor Detail

RichMRMetathesaurusOutputStream

public RichMRMetathesaurusOutputStream(FileStatisticsConfiguration config)

Instantiates an empty RichMRMetathesaurusOutputStream.

Parameters:

config - FileStatisticsConfiguration

Method Detail

open

public void open(String mr_dir)
          throws IOException

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

Specified by:

open in interface ConceptOutputStream

Overrides:

open in class RichMRFilesConceptOutputStream

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 RichMRFilesConceptOutputStream

Throws:

IOException

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 RichMRFilesConceptOutputStream

Parameters:

line - the line to be printed

file_name - printing destination

Throws:

IOException

writeConcept

public void writeConcept(Concept concept)
                  throws IOException

Writes a Concept to the appropriate MR files.

Specified by:

writeConcept in interface ConceptOutputStream

Overrides:

writeConcept in class RichMRFilesConceptOutputStream

Parameters:

concept - the Concept to write

Throws:

IOException - if the files could not be written

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 a line to the MRCUI.RRF file.

Parameters:

release_metadata - the ReleaseMetadata

Throws:

IOException - if anything goes wrong

writeMRAUI

protected void writeMRAUI(ReleaseMetadata release_metadata)
                   throws IOException

Writes a line to the MRAUI.RRF file.

Parameters:

release_metadata - the ReleaseMetadata

Throws:

IOException - if anything goes wrong

writeMRDOC

protected void writeMRDOC(ReleaseMetadata release_metadata)
                   throws IOException

Write a line to the MRDOC.RRF file.

Parameters:

release_metadata - the ReleaseMetadata

Throws:

IOException - if anything goes wrong

writeMRSAB

protected void writeMRSAB(ReleaseMetadata release_metadata)
                   throws IOException

Write a line to the MRSAB.RRF file.

Parameters:

release_metadata - the ReleaseMetadata

Throws:

IOException - if anything goes wrong

writeMRRANK

protected void writeMRRANK(ReleaseMetadata release_metadata)
                    throws IOException

Writes a line to the MRRANK.RRF file.

Parameters:

release_metadata - the ReleaseMetadata

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 - list of terms that are candidates to be ambiguous

setCandidateAmbiguousTermIdentifiers

public void setCandidateAmbiguousTermIdentifiers(List luis)

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

Specified by:

setCandidateAmbiguousTermIdentifiers in interface MetathesaurusOutputStream

Parameters:

luis - list of terms that are candidates to be ambiguous

openTargetFile

protected BufferedWriter openTargetFile(String name)
                                 throws IOException

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

Overrides:

openTargetFile in class RichMRFilesConceptOutputStream

Parameters:

name - the filename

Returns:

a BufferedWriter for the file

Throws:

IOException - if the file could not be opened.

addProgressListener

public void addProgressListener(ProgressListener l)

Adds a ProgressListener.

Specified by:

addProgressListener in interface ProgressReporter

Parameters:

l - thefProgressListener

removeProgressListener

public void removeProgressListener(ProgressListener l)

Removes a ProgressListener.

Specified by:

removeProgressListener in interface ProgressReporter

Parameters:

l - thefProgressListener

fireProgressEvent

protected void fireProgressEvent(int pct,
                                 String note)

Fires a ProgressEvent.

Parameters:

pct - percent done

note - progress note

writeFileColumnStats

protected void writeFileColumnStats()
                             throws IOException

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

Throws:

IOException - if anything goes wrong

getFileTextFromFileStatistics

protected String getFileTextFromFileStatistics(FileStatistics file_stats)

Returns the MRFILES.RRF line for the specified FileStatistics.

Parameters:

file_stats - the FileStatistics

Returns:

the MRFILES.RRF line for the specified FileStatistics

getColumnTextFromFileStatistics

protected String getColumnTextFromFileStatistics(FileStatistics file_stats)

Returns the MRCOLS.RRF lines for the specified FileStatistics.

Parameters:

file_stats - the FileStatistics

Returns:

the MRCOLS.RRF lines for the specified FileStatistics

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