gov.nih.nlm.nls.nlp.textfeatures
Class Variant

java.lang.Object
  gov.nih.nlm.nls.nlp.textfeatures.MmObject
      gov.nih.nlm.nls.nlp.textfeatures.Variant

All Implemented Interfaces:

java.io.Serializable

public class Variant
extends MmObject

Variant Fri Jun 02 17:46:46 EDT 2000, divita Initial Version

Version:

$Id: Variant.java,v 1.13 2005/12/21 20:43:17 divita Exp $

See Also:

Serialized Form

Field Summary

static char	ACRONYM
static int	ACRONYM_COST
static char	ACRONYM_EXPANSION
static int	ACRONYM_EXPANSION_COST
static char	DERIVATION
static int	DERIVATION_COST
static char	INFLECTION
static int	INFLECTION_COST
static char	NO_OPERATION
static int	NO_OPERATION_COST
static char	SPELLING_VARIANT
static int	SPELLING_VARIANT_COST
static char	SYNONYM
static int	SYNONYM_COST

Fields inherited from class gov.nih.nlm.nls.nlp.textfeatures.MmObject

serialVersionUID

Constructor Summary

Variant(java.lang.String pRow)
This is a constructor for Variant used to create the fullVars table from MetaMap's vars, varsan, varsanu, and varsu table.

Variant(java.lang.String pVariant, int pCat, int pDistance, java.lang.String pHistory, Span pSpan, Span pPhraseCharSpan, Span pPhraseWordSpan, int pVariantId)
This is a constructor for Variant

Variant(java.lang.String pVariant, int pCat, int pInfl, java.lang.String pRuleOrFact, java.lang.String pHistory, Span pSpan, int pVariantId)
This is a constructor for Variant

Variant(java.lang.String pOrigTerm, int pOrigCat, java.lang.String pVariant, int pCat, int pInfl, java.lang.String pRuleOrFact, java.lang.String pHistory, int pDistance, int pFoundInFullTable, int pFoundInNounAdjDerivationFilteredTable, int pFoundInNounAdjDerivationAndUniqAcronymFilteredTable, int pFoundInUniqAcronymsFilteredTable)
This is a constructor for Variant used for variant generation.

Method Summary

void	addCategory(int pCategory) Method addCategory
boolean	containsNoAcronymsOrAbbreviations() Method containsNoAcronymsOrAbbreviations returns true if this variant is acronym and abbreviation free.
boolean	containsNoDerivations() Method containsNoDerivations returns true if this variant is derivation free.
java.lang.String	display(gov.nih.nlm.nls.utils.GlobalBehavior settings) Method display returns a string of the variant at the level of detail set by the global behaviors.
boolean	equals(java.lang.Object pVariant) Method equals
int	foundInFullTable() Method foundInFullTable
int	foundInNounAdjDerivationAndUniqAcronymFilteredTable() Method foundInNounAdjDerivationAndUniqAcronymFilteredTable returns 1 if this variant is found in the filtered variants table that filters out all those variants that have derivations that are non noun/adjective pairs and that are unique acronyms or acronym expansions.
int	foundInNounAdjDerivationFilteredTable() Method foundInNounAdjDerivationFilteredTable returns 1 if this variant is found in the filtered variants table that filters out all those variants that have derivations that are non noun/adjective pairs.
int	foundInUniqAcronymsFilteredTable() Method foundInUniqAcronymsFilteredTable returns 1 if this variant is found in the filtered variants table that filters out all those variants that have non-unique acronyms or acronym expansions
static Variant	fromBytes(byte[] pBytes) Method fromBytes ---0----+------1----+---2----+---3---+--4--+-5----+--6--+---7--+--8--+--9--+---10--+---11---+--12-----+ int | int | int | int | int| int | int | int |int | int |n bytes| m bytes| p bytes | term cat|variant cat|distance|FullVar|VarAN|VarANU|VarU | #term|#var |#hist|term | variant| history | --------+-----------+--------+-------+-----+------+-----+------+-----+-----+-------+--------+---------+
static Variant	fromTableRow(java.lang.String pRow) Method fromTableRow creates a variant from a row from the fullVars table.
int	getCategories() Method getCategories returns the category(s) of this variant
int	getDistance() Method getDistance
java.lang.String	getHistory() Method getHistory
int	getInflections() Method getInflections returns the inflection(s) of this variant.
java.lang.String	getNormalizedTerm() Method getNormalizedTerm retrieves the Variant term, lowercased, devoid of punctuation - this is supposed to match the normalization that was done to create the normalized string, string sui table.
int	getOrigCat() Method getOrigCat
java.lang.String	getOrigTerm() Method getOrigTerm
LexicalElement	getParent() Method getParent returns the LexicalElement that this variant came from.
Span	getPhraseCharSpan() Method getPhraseCharSpan
int	getPhrasePosition() getPhrasePosition gets the lexical element position of this variant within the phrase.
int	getPhraseTokenPosition() Method getPhraseTokenPosition
Span	getPhraseWordSpan() Method getPhraseWordSpan
java.lang.String	getTerm() Method getTerm retrieves the Variant term
java.util.Vector	getTokens() Method getTokens computes the tokens (if it has not already done so) of this term, and returns them.
static void	main(java.lang.String[] argv) This is a test main, whose purpose is to test the functionality of each method developed for this class.
void	setDistance(int pDistance) Method setDistance
void	setFoundInFullTable() Method setFoundInFullTable
void	setFoundInNounAdjDerivationAndUniqAcronymFilteredTable() Method setFoundInNounAdjDerivationAndUniqAcronymFilteredTable
void	setFoundInNounAdjDerivationFilteredTable() Method setFoundInNounAdjDerivationFilteredTable
void	setFoundInUniqAcronymsFilteredTable() Method setFoundInUniqAcronymsFilteredTable
void	setHistory(java.lang.String pHistory) Method setHistory
void	setNormalizedTerm(java.lang.String pTerm) Method setNormalizedTerm sets the Variant term, lowercased, devoid of punctuation - this is supposed to match the normalization that was done to create the normalized string, string sui table.
void	setParent(LexicalElement pParent) Method setParent preserves the link from the original LexicalElement to this variant
void	setPhraseCharSpan(Span pSpan) Method setPhraseCharSpan
void	setPhrasePosition(int pPos) setPhrasePosition records the position of this variant (as a lexical Element) within the phrase.
void	setPhraseTokenPosition(int pPos) Method setPhraseTokenPosition.
void	setPhraseWordSpan(Span pSpan) Method setPhraseWordSpan
void	setSpan(Span pSpan) Method setSpan
void	setTokens(java.util.Vector pTokens) Method setTokens adds the set of tokens that make up this variant
byte[]	toBytes() Method toBytes ---0----+------1----+---2----+---3---+--4--+-5----+--6--+---7--+--8--+--9--+---10--+---11---+--12-----+ int | int | int | int | int| int | int | int |int | int |n bytes| m bytes| p bytes | term cat|variant cat|distance|FullVar|VarAN|VarANU|VarU | #term|#var |#hist|term | variant| history | --------+-----------+--------+-------+-----+------+-----+------+-----+-----+-------+--------+---------+
java.lang.String	toFormatedString() Method toFormatedString is the method that prints out a variant in the format used to be absorbed into the db's variant table.
java.lang.String	toMetaMapVarsRow() Method toMetaMapVarsRow is the method that prints out a variant in one of MetaMap's Vars tables.
java.lang.String	toPipedString() Method toPipedString returns a pipe delimited fielded represtentation of some of the attributes of this variant.
java.lang.String	toString() Method toString

Methods inherited from class gov.nih.nlm.nls.nlp.textfeatures.MmObject

appendOriginalString, getCharOffset, getId, getLabel, getOriginalString, getSpan, getStrippedString, getTrimmedString, setId, setLabel, setOriginalString, setSpan, setStrippedString, setTrimmedString

Methods inherited from class java.lang.Object

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

Field Detail

NO_OPERATION_COST

public static final int NO_OPERATION_COST

See Also:

Constant Field Values

SPELLING_VARIANT_COST

public static final int SPELLING_VARIANT_COST

See Also:

Constant Field Values

INFLECTION_COST

public static final int INFLECTION_COST

See Also:

Constant Field Values

SYNONYM_COST

public static final int SYNONYM_COST

See Also:

Constant Field Values

ACRONYM_COST

public static final int ACRONYM_COST

See Also:

Constant Field Values

ACRONYM_EXPANSION_COST

public static final int ACRONYM_EXPANSION_COST

See Also:

Constant Field Values

DERIVATION_COST

public static final int DERIVATION_COST

See Also:

Constant Field Values

NO_OPERATION

public static final char NO_OPERATION

See Also:

Constant Field Values

SPELLING_VARIANT

public static final char SPELLING_VARIANT

See Also:

Constant Field Values

INFLECTION

public static final char INFLECTION

See Also:

Constant Field Values

SYNONYM

public static final char SYNONYM

See Also:

Constant Field Values

ACRONYM

public static final char ACRONYM

See Also:

Constant Field Values

ACRONYM_EXPANSION

public static final char ACRONYM_EXPANSION

See Also:

Constant Field Values

DERIVATION

public static final char DERIVATION

See Also:

Constant Field Values

Constructor Detail

Variant

public Variant(java.lang.String pVariant,
               int pCat,
               int pInfl,
               java.lang.String pRuleOrFact,
               java.lang.String pHistory,
               Span pSpan,
               int pVariantId)

This is a constructor for Variant

Parameters:

pVariant - The variant of the lexicalElement

pCat - The category of this variant.

pInfl - The category of this variant.

pRuleOrFact - String indicating whether this variant came from a rule or fact ie.-> RULE|FACT

pHistory - The history of how this variant came to be from the original term. The history will be composed of the following:

n	None
y	Synonym
d	Derivation
A	Acronym
a	Acronym expansion
s	Spelling variant

pSpan - The span of the original term.

pVariantId - The id of the variant of this lexical element

Variant

public Variant(java.lang.String pVariant,
               int pCat,
               int pDistance,
               java.lang.String pHistory,
               Span pSpan,
               Span pPhraseCharSpan,
               Span pPhraseWordSpan,
               int pVariantId)

This is a constructor for Variant

Parameters:

pVariant - The variant of the lexicalElement

pCat - The category of this variant.

pDistance - Precomputed distance from the history

pHistory - The history of how this variant came to be from the original term. The history will be composed of the following:

n	None
y	Synonym
d	Derivation
A	Acronym
a	Acronym expansion
s	Spelling variant

pSpan - The span of the original term.

pPhraseCharSpan -

pPhraseWordSpan -

pVariantId - The id of the variant of this lexical element

Variant

public Variant(java.lang.String pOrigTerm,
               int pOrigCat,
               java.lang.String pVariant,
               int pCat,
               int pInfl,
               java.lang.String pRuleOrFact,
               java.lang.String pHistory,
               int pDistance,
               int pFoundInFullTable,
               int pFoundInNounAdjDerivationFilteredTable,
               int pFoundInNounAdjDerivationAndUniqAcronymFilteredTable,
               int pFoundInUniqAcronymsFilteredTable)

This is a constructor for Variant used for variant generation. Variants created using this constructor have no span. This variant is a mirror of the information in the vars table.

Parameters:

pOrigTerm - The original term.

pOrigCat - The category of the original term.

pVariant - The variant of the lexicalElement

pCat - The category of this variant.

pInfl - The category of this variant.

pRuleOrFact - String indicating whether this variant came from a rule or fact ie.-> RULE|FACT

pHistory - The history of how this variant came to be from the original term. The history will be composed of the following:

n	None
y	Synonym
d	Derivation
A	Acronym
a	Acronym expansion
s	Spelling variant

pDistance - Precomputed distance from the history

pFoundInFullTable - 1 if in the full Table

pFoundInNounAdjDerivationFilteredTable - 1 if in the table that filters out non noun/adj deriv. variants. 0 otherwise.

pFoundInNounAdjDerivationAndUniqAcronymFilteredTable - 1 if in the table that filters out non noun/adj deriv. and non unique acronym/acronym expansion variants. 0 otherwise.

pFoundInUniqAcronymsFilteredTable - 1 if in the table that filters out non unique acronym/acronym expansion variants. 0 otherwise.

Variant

public Variant(java.lang.String pRow)

This is a constructor for Variant used to create the fullVars table from MetaMap's vars, varsan, varsanu, and varsu table. It takes as a parameter, a line from one of these files. The row is of the form:

Parameters:

pRow - of the format: key|input cat|variant|output cat|history|[]

Method Detail

setTokens

public void setTokens(java.util.Vector pTokens)

Method setTokens adds the set of tokens that make up this variant

Parameters:

pTokens - a Vector of Token

setParent

public void setParent(LexicalElement pParent)

Method setParent preserves the link from the original LexicalElement to this variant

Parameters:

pParent -

addCategory

public void addCategory(int pCategory)

Method addCategory

Parameters:

pCategory -

setHistory

public void setHistory(java.lang.String pHistory)

Method setHistory

Parameters:

pHistory -

getHistory

public java.lang.String getHistory()

Method getHistory

Returns:

String

setDistance

public void setDistance(int pDistance)

Method setDistance

Parameters:

pDistance -

setSpan

public void setSpan(Span pSpan)

Method setSpan

Parameters:

pSpan -

setPhraseCharSpan

public void setPhraseCharSpan(Span pSpan)

Method setPhraseCharSpan

Parameters:

pSpan -

setPhraseWordSpan

public void setPhraseWordSpan(Span pSpan)

Method setPhraseWordSpan

Parameters:

pSpan -

getDistance

public int getDistance()

Method getDistance

Returns:

int

getTerm

public java.lang.String getTerm()

Method getTerm retrieves the Variant term

Returns:

String

getNormalizedTerm

public java.lang.String getNormalizedTerm()

Method getNormalizedTerm retrieves the Variant term, lowercased, devoid of punctuation - this is supposed to match the normalization that was done to create the normalized string, string sui table.

Returns:

String

setNormalizedTerm

public void setNormalizedTerm(java.lang.String pTerm)

Method setNormalizedTerm sets the Variant term, lowercased, devoid of punctuation - this is supposed to match the normalization that was done to create the normalized string, string sui table.

Parameters:

pTerm -

getCategories

public int getCategories()

Method getCategories returns the category(s) of this variant

Returns:

int an int enumerated from the Category class

getInflections

public int getInflections()

Method getInflections returns the inflection(s) of this variant.

Returns:

int an int enumerated from the Inflection class

getTokens

public java.util.Vector getTokens()

Method getTokens computes the tokens (if it has not already done so) of this term, and returns them.

Returns:

Vector of Tokens

display

public java.lang.String display(gov.nih.nlm.nls.utils.GlobalBehavior settings)

Method display returns a string of the variant at the level of detail set by the global behaviors. By default, that is just the trimmed String.

Parameters:

settings -

Returns:

String

toPipedString

public java.lang.String toPipedString()

Method toPipedString returns a pipe delimited fielded represtentation of some of the attributes of this variant. The fielded output is of the following form: Variant|Vid|string|cat|begingChar|endChar|position in phrase|distance|history

Returns:

String

toString

public java.lang.String toString()

Method toString

Overrides:

toString in class MmObject

Returns:

String

setPhrasePosition

public void setPhrasePosition(int pPos)

setPhrasePosition records the position of this variant (as a lexical Element) within the phrase. Note: This is a lexical element counter, not a word counter.

Parameters:

pPos - Position of the lexical Element in the phrase.

getPhrasePosition

public int getPhrasePosition()

getPhrasePosition gets the lexical element position of this variant within the phrase.

Returns:

int Position of the lexical Element in the phrase.

setPhraseTokenPosition

public void setPhraseTokenPosition(int pPos)

Method setPhraseTokenPosition. The phraseTokenPosition is the position of this variant (as if this variant equates to a token) in the phrase.

Parameters:

pPos -

getPhraseTokenPosition

public int getPhraseTokenPosition()

Method getPhraseTokenPosition

Returns:

int of the phraseTokenPosition of this variant.

getPhraseWordSpan

public Span getPhraseWordSpan()

Method getPhraseWordSpan

Returns:

Span

getPhraseCharSpan

public Span getPhraseCharSpan()

Method getPhraseCharSpan

Returns:

Span

foundInFullTable

public int foundInFullTable()

Method foundInFullTable

Returns:

int 1 if this variant is in the full variants table, 0 if it is not (not likely in this case.)

setFoundInFullTable

public void setFoundInFullTable()

Method setFoundInFullTable

foundInNounAdjDerivationFilteredTable

public int foundInNounAdjDerivationFilteredTable()

Method foundInNounAdjDerivationFilteredTable returns 1 if this variant is found in the filtered variants table that filters out all those variants that have derivations that are non noun/adjective pairs.

Returns:

int 1 if this variant is in this filtered variants table, 0 if it is not

setFoundInNounAdjDerivationFilteredTable

public void setFoundInNounAdjDerivationFilteredTable()

Method setFoundInNounAdjDerivationFilteredTable

foundInNounAdjDerivationAndUniqAcronymFilteredTable

public int foundInNounAdjDerivationAndUniqAcronymFilteredTable()

Method foundInNounAdjDerivationAndUniqAcronymFilteredTable returns 1 if this variant is found in the filtered variants table that filters out all those variants that have derivations that are non noun/adjective pairs and that are unique acronyms or acronym expansions.

Returns:

int 1 if this variant is in this filtered variants table, 0 if it is not

setFoundInNounAdjDerivationAndUniqAcronymFilteredTable

public void setFoundInNounAdjDerivationAndUniqAcronymFilteredTable()

Method setFoundInNounAdjDerivationAndUniqAcronymFilteredTable

containsNoDerivations

public boolean containsNoDerivations()

Method containsNoDerivations returns true if this variant is derivation free. That is, this variant is a spelling variant, synonym, acronyn, or expansion, or inflection but not a derivation, or a variant of a derivation

Returns:

boolean

containsNoAcronymsOrAbbreviations

public boolean containsNoAcronymsOrAbbreviations()

Method containsNoAcronymsOrAbbreviations returns true if this variant is acronym and abbreviation free. That is, this variant is a spelling variant, synonym, derivation, or inflection but no acronyms and abbreviations or their expansions or variants based on them.

Returns:

boolean

foundInUniqAcronymsFilteredTable

public int foundInUniqAcronymsFilteredTable()

Method foundInUniqAcronymsFilteredTable returns 1 if this variant is found in the filtered variants table that filters out all those variants that have non-unique acronyms or acronym expansions

Returns:

int 1 if this variant is in this filtered variants table, 0 if it is not

setFoundInUniqAcronymsFilteredTable

public void setFoundInUniqAcronymsFilteredTable()

Method setFoundInUniqAcronymsFilteredTable

getOrigTerm

public java.lang.String getOrigTerm()

Method getOrigTerm

Returns:

String

getParent

public LexicalElement getParent()

Method getParent returns the LexicalElement that this variant came from.

Returns:

LexicalElement

getOrigCat

public int getOrigCat()

Method getOrigCat

Returns:

int

toFormatedString

public java.lang.String toFormatedString()

Method toFormatedString is the method that prints out a variant in the format used to be absorbed into the db's variant table. This method is called by the generateVariants.VariantStore.add method, which is called by the GenerateMMVariants program/class.

Returns:

String

toMetaMapVarsRow

public java.lang.String toMetaMapVarsRow()

Method toMetaMapVarsRow is the method that prints out a variant in one of MetaMap's Vars tables.

Returns:

String

equals

public boolean equals(java.lang.Object pVariant)

Method equals

Overrides:

equals in class java.lang.Object

Parameters:

pVariant -

Returns:

boolean

fromTableRow

public static Variant fromTableRow(java.lang.String pRow)
                            throws java.lang.Exception

Method fromTableRow creates a variant from a row from the fullVars table.

Parameters:

pRow -

Returns:

Variant

Throws:

java.lang.Exception

toBytes

public byte[] toBytes()
               throws java.lang.Exception

Method toBytes ---0----+------1----+---2----+---3---+--4--+-5----+--6--+---7--+--8--+--9--+---10--+---11---+--12-----+ int | int | int | int | int| int | int | int |int | int |n bytes| m bytes| p bytes | term cat|variant cat|distance|FullVar|VarAN|VarANU|VarU | #term|#var |#hist|term | variant| history | --------+-----------+--------+-------+-----+------+-----+------+-----+-----+-------+--------+---------+

Returns:

byte[]

Throws:

java.lang.Exception

fromBytes

public static Variant fromBytes(byte[] pBytes)
                         throws java.lang.Exception

Method fromBytes ---0----+------1----+---2----+---3---+--4--+-5----+--6--+---7--+--8--+--9--+---10--+---11---+--12-----+ int | int | int | int | int| int | int | int |int | int |n bytes| m bytes| p bytes | term cat|variant cat|distance|FullVar|VarAN|VarANU|VarU | #term|#var |#hist|term | variant| history | --------+-----------+--------+-------+-----+------+-----+------+-----+-----+-------+--------+---------+

Parameters:

pBytes -

Returns:

Variant

Throws:

java.lang.Exception

main

public static final void main(java.lang.String[] argv)

This is a test main, whose purpose is to test the functionality of each method developed for this class. This main strives to test the boundary conditions as well as some sample common ways each public method is intended to be used.

Parameters:

argv - The command line input, tokenized