gov.nih.nlm.umls.io
Class OriginalMRFilesConceptInputStream

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

All Implemented Interfaces:

ConceptInputStream, LocalNullValueSupport

Direct Known Subclasses:

OriginalMRMetathesaurusInputStream

public class OriginalMRFilesConceptInputStream
extends Object
implements ConceptInputStream

This ConceptInputStream builds Concept objects from a full set of original format MR files.

Author:

Deborah Shapiro

Field Summary

protected String[]	file_names
protected String	mr_dir
protected PushBackReader	mratx_source
protected PushBackReader	mrcoc_source
protected int	mrcon_counter
protected int	mrcon_lines
protected PushBackReader	mrcon_source
protected PushBackReader	mrcxt_source
protected PushBackReader	mrdef_source
protected PushBackReader	mrlo_source
protected PushBackReader	mrrel_source
protected PushBackReader	mrsat_source
protected PushBackReader	mrso_source
protected PushBackReader	mrsty_source
protected String	null_value
protected Concept	this_concept
protected String[]	tokens
protected List	warnings

Constructor Summary

OriginalMRFilesConceptInputStream()
Instantiates an empty OriginalMRFilesConceptInputStream.

Method Summary

void	close() Close files opened during open(String[]).
protected Concept	getAtoms(Concept this_concept, String current_cui) Returns Atoms from the MRCON and MRSO files with the given cui and adds them to the current Concept.
protected void	getAttributes(Concept this_concept, String current_cui) Returns Attributes from the MRSAT files with the given cui and adds them to the current Concept
int	getConceptProgress() Returns the percentage of MRCON lines that have been processed.
protected void	getContexts(Concept this_concept, String current_cui) Returns Contexts from the MRCXT files with the given cui and adds them to the current Concept.
protected void	getCoocurrences(Concept this_concept, String current_cui) Returns a Coocurrences from the MRCOC file with the given cui and adds them to the current Concept.
protected void	getDefinitions(Concept this_concept, String current_cui) Returns Definitions from the MRDEF file with the given cui and adds them to the current Concept.
protected Map	getLineCounts() Reads through MRFILES to determine the size of MRCON.
protected void	getLocators(Concept this_concept, String current_cui) Returns Locators from the MRLO file with the given cui and adds them to the current Concept.
protected void	getMappings(Concept this_concept, String current_cui) Returns Mappings from the MRATX file with the given cui and adds them to the current Concept.
String	getNullValue() Returns the null value.
protected void	getRelationships(Concept this_concept, String current_cui) Returns Relationships from the MRREL file with the given cui and adds them to the current Concept
protected void	getSemanticTypes(Concept this_concept, String current_cui) Returns SemanticTypes from the MRSTY file with the given cui and adds them to the current Concept.
String[]	getWarnings() Returns a String[] of warnings accumulated during processing of the input 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.
void	open(String[] install_paths) Opens all of the MR Files in preparation for subsetting.
protected PushBackReader	openSourceFile(String name) Opens the specified file in the directory passed to open(String[]).
Concept	readConcept() Returns the next Concept from the MR Files.
void	setNullValue(String null_value) Sets the null value to use.

Methods inherited from class java.lang.Object

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

Field Detail

mrso_source

protected PushBackReader mrso_source

mrcon_source

protected PushBackReader mrcon_source

mrsty_source

protected PushBackReader mrsty_source

mrdef_source

protected PushBackReader mrdef_source

mrrel_source

protected PushBackReader mrrel_source

mrcxt_source

protected PushBackReader mrcxt_source

mrcoc_source

protected PushBackReader mrcoc_source

mratx_source

protected PushBackReader mratx_source

mrsat_source

protected PushBackReader mrsat_source

mrlo_source

protected PushBackReader mrlo_source

file_names

protected String[] file_names

mr_dir

protected String mr_dir

this_concept

protected Concept this_concept

mrcon_lines

protected int mrcon_lines

mrcon_counter

protected int mrcon_counter

tokens

protected final String[] tokens

warnings

protected List warnings

null_value

protected String null_value

Constructor Detail

OriginalMRFilesConceptInputStream

public OriginalMRFilesConceptInputStream()

Instantiates an empty OriginalMRFilesConceptInputStream.

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[] install_paths)
          throws IOException

Opens all of the MR Files in preparation for subsetting.

Specified by:

open in interface ConceptInputStream

Parameters:

install_paths - the directory containing the files

Throws:

IOException - if any files can not be opened

close

public void close()
           throws IOException

Close files opened during open(String[]).

Specified by:

close in interface ConceptInputStream

Throws:

IOException - if files can not be closed

getConceptProgress

public int getConceptProgress()

Returns the percentage of MRCON lines that have been processed.

Specified by:

getConceptProgress in interface ConceptInputStream

Returns:

the percentage of MRCON lines that have been processed

readConcept

public Concept readConcept()
                    throws IOException

Returns the next Concept from the MR Files.

Specified by:

readConcept in interface ConceptInputStream

Returns:

the next Conceptfrom the MR Files

Throws:

IOException - if files could not be read

openSourceFile

protected PushBackReader openSourceFile(String name)
                                 throws IOException

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

Parameters:

name - the filename

Returns:

a BufferedReader on the file

Throws:

IOException - if the file could not be opened

getLineCounts

protected Map getLineCounts()
                     throws IOException

Reads through MRFILES to determine the size of MRCON. This is used in the getConceptProgress() method.

Returns:

Map of file names to lines in file

Throws:

IOException - if the file cannot be opened or read

getMappings

protected void getMappings(Concept this_concept,
                           String current_cui)
                    throws IOException

Returns Mappings from the MRATX file with the given cui and adds them to the current Concept.

Parameters:

this_concept - Concept that will contain the Mappings

current_cui - String representation of the cui

Throws:

IOException - if there is a problem with the file

getAtoms

protected Concept getAtoms(Concept this_concept,
                           String current_cui)
                    throws IOException

Returns Atoms from the MRCON and MRSO files with the given cui and adds them to the current Concept.

Parameters:

this_concept - the current Concept

current_cui - the current CUI

Returns:

Concept that will contain the Atoms

Throws:

IOException - if there is a problem with the file

getAttributes

protected void getAttributes(Concept this_concept,
                             String current_cui)
                      throws IOException

Returns Attributes from the MRSAT files with the given cui and adds them to the current Concept

Parameters:

this_concept - the current Concept

current_cui - the current CUI

Throws:

IOException - if there is a problem with the file

getContexts

protected void getContexts(Concept this_concept,
                           String current_cui)
                    throws IOException

Returns Contexts from the MRCXT files with the given cui and adds them to the current Concept.

Parameters:

this_concept - the current Concept

current_cui - the current CUI

Throws:

IOException - if anything wrong with file

getCoocurrences

protected void getCoocurrences(Concept this_concept,
                               String current_cui)
                        throws IOException

Returns a Coocurrences from the MRCOC file with the given cui and adds them to the current Concept.

Parameters:

this_concept - the current Concept

current_cui - the current CUI

Throws:

IOException - if problem reading from file

getDefinitions

protected void getDefinitions(Concept this_concept,
                              String current_cui)
                       throws IOException

Returns Definitions from the MRDEF file with the given cui and adds them to the current Concept.

Parameters:

this_concept - the current Concept

current_cui - the current CUI

Throws:

IOException - if problem reading from the file

getLocators

protected void getLocators(Concept this_concept,
                           String current_cui)
                    throws IOException

Returns Locators from the MRLO file with the given cui and adds them to the current Concept.

Parameters:

this_concept - the current Concept

current_cui - the current CUI

Throws:

IOException - if problem reading from file

getSemanticTypes

protected void getSemanticTypes(Concept this_concept,
                                String current_cui)
                         throws IOException

Returns SemanticTypes from the MRSTY file with the given cui and adds them to the current Concept.

Parameters:

this_concept - the current Concept

current_cui - the current CUI

Throws:

IOException - if problem reading from file

getRelationships

protected void getRelationships(Concept this_concept,
                                String current_cui)
                         throws IOException

Returns Relationships from the MRREL file with the given cui and adds them to the current Concept

Parameters:

this_concept - the current Concept

current_cui - the current CUI

Throws:

IOException - if problem reading from file

getWarnings

public String[] getWarnings()

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

Specified by:

getWarnings in interface ConceptInputStream

Returns:

String[] of warnings