gov.nih.nlm.mms.cxt
Class MRCXTBuilderOutputStream

java.lang.Object
  gov.nih.nlm.umls.io.RichMRFilesConceptInputStream
      gov.nih.nlm.mms.cxt.MRCXTBuilderOutputStream

All Implemented Interfaces:

ConceptInputStream, LocalNullValueSupport

public class MRCXTBuilderOutputStream
extends RichMRFilesConceptInputStream

Builds MRCXT.RRF from MRHIER.RRF and MRCONSO.RRF with the help of a few indexes. Manages the log.

Author:

Deborah Shapiro

Field Summary

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

add_suffix, atom_hm, file_names, from_rsab, from_vsab, install_paths, mrcoc_source, mrconso_counter, mrconso_lines, mrconso_source, mrcxt_source, mrdef_source, mrdoc_source, mrhier_source, mrhist_source, mrmap_source, mrrel_source, mrsat_source, mrsty_source, null_value, rel_hm, this_concept, to_rsab, to_vsab, tokens, warnings

Constructor Summary

MRCXTBuilderOutputStream(MRCXTBuilder mrcxt_builder)
Instantiates an empty MRCXTBuilderOutputStream.

Method Summary

protected String	getColumnTextFromFileStatistics(FileStatistics file_stats) Returns the MRCOLS.RRF lines for the specified FileStatistics.
protected float	getDecimalProgress() Returns the percentage of the MRHIER.RRF file that has been converted and written to MRCXT.RRF.
protected String	getFileTextFromFileStatistics(FileStatistics file_stats) Returns the MRFILES.RRF line for the specified FileStatistics.
protected int	getProgress() Returns the percentage of the MRHIER.RRF file that has been converted and written to MRCXT.RRF.
boolean	isCancelled() Indicates whether or not the license agreement was cancelled or not accepted.
protected void	openMRFiles() Opens the Rich Release Format MR files.
protected BufferedWriter	openTargetFile(String name) Opens the specified file in the MRCXT Builder source directory.
protected void	writeFileColumnStats() This method computes the file and columns statistics for the MRFILES.RRF and MRCOLS.RRF files themselves.
void	writeMRCXT(ProgressMonitor pm) Writes MRCXT.RRF Should be called from a separate thread.

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

close, getAtoms, getAttributes, getComponentHistories, getConceptProgress, getContexts, getCoocurrences, getDefinitions, getLineCounts, getMappings, getNullValue, getRelationships, getSemanticTypes, getWarnings, isEmptyValue, newInstanceFromMRCOC, newInstanceFromMRCONSO, newInstanceFromMRCXTRel, newInstanceFromMRDEF, newInstanceFromMRHIER, newInstanceFromMRHIST, newInstanceFromMRMAP, newInstanceFromMRREL, newInstanceFromMRSAT, newInstanceFromMRSTY, open, openSourceFile, readConcept, setAdditionalSuffix, setNullValue

Methods inherited from class java.lang.Object

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

Constructor Detail

MRCXTBuilderOutputStream

public MRCXTBuilderOutputStream(MRCXTBuilder mrcxt_builder)

Instantiates an empty MRCXTBuilderOutputStream.

Parameters:

mrcxt_builder - MRCXTBuilder

Method Detail

writeMRCXT

public void writeMRCXT(ProgressMonitor pm)
                throws Exception

Writes MRCXT.RRF Should be called from a separate thread.

Parameters:

pm - the ProgressMonitor

Throws:

Exception - if anything goes wrong

isCancelled

public boolean isCancelled()

Indicates whether or not the license agreement was cancelled or not accepted.

Returns:

true if the GUI was cancelled, false otherwise

getProgress

protected int getProgress()

Returns the percentage of the MRHIER.RRF file that has been converted and written to MRCXT.RRF.

Returns:

int percentage

getDecimalProgress

protected float getDecimalProgress()

Returns the percentage of the MRHIER.RRF file that has been converted and written to MRCXT.RRF.

Returns:

float percentage

openMRFiles

protected void openMRFiles()
                    throws IOException

Opens the Rich Release Format MR files.

Overrides:

openMRFiles in class RichMRFilesConceptInputStream

Throws:

IOException - if any files cannot be opened

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

openTargetFile

protected BufferedWriter openTargetFile(String name)
                                 throws IOException

Opens the specified file in the MRCXT Builder source directory.

Parameters:

name - the filename

Returns:

a BufferedWriter for the file

Throws:

IOException - if the file could not be opened.