net.maizegenetics.taxa

Class IdentifierSynonymizer

AbstractTableReport

net.maizegenetics.taxa.IdentifierSynonymizer

All Implemented Interfaces:

TableReport

public class IdentifierSynonymizer
extends AbstractTableReport
implements TableReport

User: Ed Date: Mar 30, 2005 Time: 1:39:47 PM

Constructor Detail

IdentifierSynonymizer

public IdentifierSynonymizer(TaxaList preferredTaxa,
                             TaxaList[] alternateTaxaSets)

IdentifierSynonymizer

public IdentifierSynonymizer(TaxaList preferredTaxa,
                             TaxaList[] alternateTaxaSets,
                             int technique)

IdentifierSynonymizer

public IdentifierSynonymizer(TaxaList preferredTaxa,
                             TaxaList[] alternateTaxaSets,
                             int technique,
                             java.lang.String delimiter)

IdentifierSynonymizer

public IdentifierSynonymizer(TaxaList preferredTaxa,
                             TaxaList alternateTaxa)

Method Detail

getTaxaList

public TaxaList getTaxaList()

getTechnique

public int getTechnique()

setGlobalMax

public void setGlobalMax(double max)

findBestMatch

public java.util.ArrayList<java.lang.String> findBestMatch(java.lang.String taxaName,
                                                           TaxaList referenceTaxa)

findOrderedMatches

public java.util.ArrayList<java.lang.String> findOrderedMatches(java.lang.String unmatchedString,
                                                                int levelOfRestriction)

getScore

public static double getScore(java.lang.String s1,
                              java.lang.String s2,
                              boolean ignoreCase,
                              boolean ignoreWhite,
                              boolean ignorePunc,
                              int technique)

getScore

public static double getScore(java.lang.String s1,
                              java.lang.String s2,
                              boolean ignoreCase,
                              boolean ignoreWhite,
                              boolean ignorePunc,
                              int technique,
                              java.lang.String delimiter)

hammingDistSoundex

public static double hammingDistSoundex(java.lang.String s1,
                                        java.lang.String s2,
                                        boolean ignoreCase,
                                        boolean ignoreWhite,
                                        boolean ignorePunc)

diceWithMetaphone

public static double diceWithMetaphone(java.lang.String s1,
                                       java.lang.String s2,
                                       boolean ignoreCase,
                                       boolean ignoreWhite,
                                       boolean ignorePunc)

editWithMetaphone

public static double editWithMetaphone(java.lang.String s1,
                                       java.lang.String s2,
                                       boolean ignoreCase,
                                       boolean ignoreWhite,
                                       boolean ignorePunc)

scoreMatch

public static double scoreMatch(java.lang.String s1,
                                java.lang.String s2,
                                boolean ignoreCase,
                                boolean ignoreWhite,
                                boolean ignorePunc)

Returns:

org.jetbrains.dokka.NodeRenderContent@4417aa8: lexical similarity value in the range [0,1]

editDistanceScoreMatch

public static double editDistanceScoreMatch(java.lang.String s1,
                                            java.lang.String s2,
                                            boolean ignoreCase,
                                            boolean ignoreWhite,
                                            boolean ignorePunc)

metaphone2

public static java.lang.String metaphone2(java.lang.String s1,
                                          boolean ignoreCase,
                                          boolean ignoreWhite,
                                          boolean ignorePunc)

soundex2

public static java.lang.String soundex2(java.lang.String s1,
                                        boolean ignoreCase,
                                        boolean ignoreWhite,
                                        boolean ignorePunc)

changeAlignmentIdentifiers

public void changeAlignmentIdentifiers(TaxaList alternateIdGroups)

toString

public java.lang.String toString()

deleteByThreshold

public void deleteByThreshold(double threshold)

getRealNames

public java.lang.Object[] getRealNames()

report

public void report(java.io.PrintWriter out)

getTableColumnNames

public java.lang.Object[] getTableColumnNames()

getRow

public java.lang.Object[] getRow(long rowLong)

Returns specified row.

Returns:

org.jetbrains.dokka.NodeRenderContent@1fda2856: row

resetTempTaxaList

public void resetTempTaxaList()

saveTempTaxaList

public void saveTempTaxaList()

removeSynonyms

public void removeSynonyms(int rowNumber)

updateSynonym

public void updateSynonym(int rowNumber,
                          java.lang.String newName)

deleteElements

public void deleteElements(java.lang.String name)

checkSynForDups

public boolean checkSynForDups()

swapSynonyms

public java.util.ArrayList<net.maizegenetics.taxa.TaxaList> swapSynonyms()

getTableTitle

public java.lang.String getTableTitle()

getColumnCount

public int getColumnCount()

getRowCount

public long getRowCount()

getElementCount

public long getElementCount()