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1 <html>
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2 <head>
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3 <title>MayaChemTools:Documentation:Fingerprints::FingerprintsBitVector.pm</title>
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4 <meta http-equiv="content-type" content="text/html;charset=utf-8">
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5 <link rel="stylesheet" type="text/css" href="../../css/MayaChemTools.css">
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6 </head>
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7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10">
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8 <br/>
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9 <center>
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10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a>
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11 </center>
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12 <br/>
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13 <div class="DocNav">
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14 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./Fingerprints.html" title="Fingerprints.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./FingerprintsFileUtil.html" title="FingerprintsFileUtil.html">Next</a></td><td width="34%" align="middle"><strong>Fingerprints::FingerprintsBitVector.pm</strong></td><td width="33%" align="right"><a href="././code/FingerprintsBitVector.html" title="View source code">Code</a>&nbsp;|&nbsp;<a href="./../pdf/FingerprintsBitVector.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/FingerprintsBitVector.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/FingerprintsBitVector.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/FingerprintsBitVector.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
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16 </table>
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17 </div>
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18 <p>
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19 </p>
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20 <h2>NAME</h2>
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21 <p>FingerprintsBitVector</p>
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22 <p>
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23 </p>
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24 <h2>SYNOPSIS</h2>
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25 <p>use Fingerprints::FingerprintsBitVector;</p>
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26 <p>use Fingerprints::FingerprintsBitVector qw(:coefficients);</p>
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27 <p>use Fingerprints::FingerprintsBitVector qw(:all);</p>
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28 <p>
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29 </p>
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30 <h2>DESCRIPTION</h2>
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31 <p><strong>FingerprintsBitVector</strong> class provides the following methods:</p>
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32 <p> <a href="#new">new</a>, <a href="#baroniurbanisimilaritycoefficient">BaroniUrbaniSimilarityCoefficient</a>, <a href="#busersimilaritycoefficient">BuserSimilarityCoefficient</a>
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33 , <a href="#cosinesimilaritycoefficient">CosineSimilarityCoefficient</a>, <a href="#dennissimilaritycoefficient">DennisSimilarityCoefficient</a>
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34 , <a href="#dicesimilaritycoefficient">DiceSimilarityCoefficient</a>, <a href="#foldfingerprintsbitvectorbydensity">FoldFingerprintsBitVectorByDensity</a>
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35 , <a href="#foldfingerprintsbitvectorbysize">FoldFingerprintsBitVectorBySize</a>, <a href="#forbessimilaritycoefficient">ForbesSimilarityCoefficient</a>
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36 , <a href="#fossumsimilaritycoefficient">FossumSimilarityCoefficient</a>, <a href="#getbitsasbinarystring">GetBitsAsBinaryString</a>, <a href="#getbitsasdecimalstring">GetBitsAsDecimalString</a>
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37 , <a href="#getbitsashexadecimalstring">GetBitsAsHexadecimalString</a>, <a href="#getbitsasoctalstring">GetBitsAsOctalString</a>, <a href="#getbitsasrawbinarystring">GetBitsAsRawBinaryString</a>
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38 , <a href="#getdescription">GetDescription</a>, <a href="#getfingerprintsbitdensity">GetFingerprintsBitDensity</a>, <a href="#getid">GetID</a>, <a href="#getspecifiedsize">GetSpecifiedSize</a>
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39 , <a href="#getsupportedsimilaritycoefficients">GetSupportedSimilarityCoefficients</a>, <a href="#getvectortype">GetVectorType</a>, <a href="#hamannsimilaritycoefficient">HamannSimilarityCoefficient</a>
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40 , <a href="#isfingerprintsbitvector">IsFingerprintsBitVector</a>, <a href="#issubset">IsSubSet</a>, <a href="#jacardsimilaritycoefficient">JacardSimilarityCoefficient</a>
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41 , <a href="#kulczynski1similaritycoefficient">Kulczynski1SimilarityCoefficient</a>, <a href="#kulczynski2similaritycoefficient">Kulczynski2SimilarityCoefficient</a>
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42 , <a href="#matchingsimilaritycoefficient">MatchingSimilarityCoefficient</a>, <a href="#mcconnaugheysimilaritycoefficient">McConnaugheySimilarityCoefficient</a>
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43 , <a href="#newfrombinarystring">NewFromBinaryString</a>, <a href="#newfromdecimalstring">NewFromDecimalString</a>, <a href="#newfromhexadecimalstring">NewFromHexadecimalString</a>
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44 , <a href="#newfromoctalstring">NewFromOctalString</a>, <a href="#newfromrawbinarystring">NewFromRawBinaryString</a>, <a href="#ochiaisimilaritycoefficient">OchiaiSimilarityCoefficient</a>
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45 , <a href="#pearsonsimilaritycoefficient">PearsonSimilarityCoefficient</a>, <a href="#rogerstanimotosimilaritycoefficient">RogersTanimotoSimilarityCoefficient</a>
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46 , <a href="#russellraosimilaritycoefficient">RussellRaoSimilarityCoefficient</a>, <a href="#setdescription">SetDescription</a>, <a href="#setid">SetID</a>, <a href="#setspecifiedsize">SetSpecifiedSize</a>
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47 , <a href="#setvectortype">SetVectorType</a>, <a href="#simpsonsimilaritycoefficient">SimpsonSimilarityCoefficient</a>, <a href="#skoalsneath1similaritycoefficient">SkoalSneath1SimilarityCoefficient</a>
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48 , <a href="#skoalsneath2similaritycoefficient">SkoalSneath2SimilarityCoefficient</a>, <a href="#skoalsneath3similaritycoefficient">SkoalSneath3SimilarityCoefficient</a>
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49 , <a href="#stringifyfingerprintsbitvector">StringifyFingerprintsBitVector</a>, <a href="#tanimotosimilaritycoefficient">TanimotoSimilarityCoefficient</a>
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50 , <a href="#tverskysimilaritycoefficient">TverskySimilarityCoefficient</a>, <a href="#weightedtanimotosimilaritycoefficient">WeightedTanimotoSimilarityCoefficient</a>
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51 , <a href="#weightedtverskysimilaritycoefficient">WeightedTverskySimilarityCoefficient</a>, <a href="#yulesimilaritycoefficient">YuleSimilarityCoefficient</a>
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52 </p><p>The methods available to create fingerprints bit vector from strings and to calculate similarity
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53 coefficient between two bit vectors can also be invoked as class functions.</p>
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54 <p><strong>FingerprintsBitVector</strong> class is derived from <strong>BitVector</strong> class which provides the functionality
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55 to manipulate bits.</p>
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56 <p>For two fingerprints bit vectors A and B of same size, let:</p>
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57 <div class="OptionsBox">
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58 Na = Number of bits set to &quot;1&quot; in A
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59 <br/> Nb = Number of bits set to &quot;1&quot; in B
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60 <br/> Nc = Number of bits set to &quot;1&quot; in both A and B
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61 <br/> Nd = Number of bits set to &quot;0&quot; in both A and B</div>
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62 <div class="OptionsBox">
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63 Nt = Number of bits set to &quot;1&quot; or &quot;0&quot; in A or B (Size of A or B)
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64 <br/> Nt = Na + Nb - Nc + Nd</div>
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65 <div class="OptionsBox">
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66 Na - Nc = Number of bits set to &quot;1&quot; in A but not in B
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67 <br/> Nb - Nc = Number of bits set to &quot;1&quot; in B but not in A</div>
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68 <p>Then, various similarity coefficients [ Ref. 40 - 42 ] for a pair of bit vectors A and B are
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69 defined as follows:</p>
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70 <p>BaroniUrbani: ( SQRT( Nc * Nd ) + Nc ) / ( SQRT ( Nc * Nd ) + Nc + ( Na - Nc ) + ( Nb - Nc ) ) ( same as Buser )</p>
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71 <p>Buser: ( SQRT ( Nc * Nd ) + Nc ) / ( SQRT ( Nc * Nd ) + Nc + ( Na - Nc ) + ( Nb - Nc ) ) ( same as BaroniUrbani )</p>
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72 <p>Cosine: Nc / SQRT ( Na * Nb ) (same as Ochiai)</p>
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73 <p>Dice: (2 * Nc) / ( Na + Nb )</p>
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74 <p>Dennis: ( Nc * Nd - ( ( Na - Nc ) * ( Nb - Nc ) ) ) / SQRT ( Nt * Na * Nb)</p>
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75 <p>Forbes: ( Nt * Nc ) / ( Na * Nb )</p>
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76 <p>Fossum: ( Nt * ( ( Nc - 1/2 ) ** 2 ) / ( Na * Nb )</p>
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77 <p>Hamann: ( ( Nc + Nd ) - ( Na - Nc ) - ( Nb - Nc ) ) / Nt</p>
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78 <p>Jaccard: Nc / ( ( Na - Nc) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb - Nc ) (same as Tanimoto)</p>
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79 <p>Kulczynski1: Nc / ( ( Na - Nc ) + ( Nb - Nc) ) = Nc / ( Na + Nb - 2Nc )</p>
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80 <p>Kulczynski2: ( ( Nc / 2 ) * ( 2 * Nc + ( Na - Nc ) + ( Nb - Nc) ) ) / ( ( Nc + ( Na - Nc ) ) * ( Nc + ( Nb - Nc ) ) )
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81 = 0.5 * ( Nc / Na + Nc / Nb )</p>
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82 <p>Matching: ( Nc + Nd ) / Nt</p>
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83 <p>McConnaughey: ( Nc ** 2 - ( Na - Nc ) * ( Nb - Nc) ) / ( Na * Nb )</p>
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84 <p>Ochiai: Nc / SQRT ( Na * Nb ) (same as Cosine)</p>
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85 <p>Pearson: ( ( Nc * Nd ) - ( ( Na - Nc ) * ( Nb - Nc ) ) / SQRT ( Na * Nb * ( Na - Nc + Nd ) * ( Nb - Nc + Nd ) )</p>
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86 <p>RogersTanimoto: ( Nc + Nd ) / ( ( Na - Nc) + ( Nb - Nc) + Nt) = ( Nc + Nd ) / ( Na + Nb - 2Nc + Nt)</p>
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87 <p>RussellRao: Nc / Nt</p>
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88 <p>Simpson: Nc / MIN ( Na, Nb)</p>
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89 <p>SkoalSneath1: Nc / ( Nc + 2 * ( Na - Nc) + 2 * ( Nb - Nc) ) = Nc / ( 2 * Na + 2 * Nb - 3 * Nc )</p>
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90 <p>SkoalSneath2: ( 2 * Nc + 2 * Nd ) / ( Nc + Nd + Nt )</p>
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91 <p>SkoalSneath3: ( Nc + Nd ) / ( ( Na - Nc ) + ( Nb - Nc ) ) = ( Nc + Nd ) / ( Na + Nb - 2 * Nc )</p>
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92 <p>Tanimoto: Nc / ( ( Na - Nc) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb - Nc ) (same as Jaccard)</p>
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93 <p>Tversky: Nc / ( alpha * ( Na - Nc ) + ( 1 - alpha) * ( Nb - Nc) + Nc ) = Nc / ( alpha * ( Na - Nb ) + Nb)</p>
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94 <p>Yule: ( ( Nc * Nd ) - ( ( Na - Nc ) * ( Nb - Nc ) ) ) / ( ( Nc * Nd ) + ( ( Na - Nc ) * ( Nb - Nc ) ) )</p>
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95 <p>The values of Tanimoto/Jaccard and Tversky coefficients are dependent on only those bit which
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96 are set to &quot;1&quot; in both A and B. In order to take into account all bit positions, modified versions
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97 of Tanimoto [ Ref. 42 ] and Tversky [ Ref. 43 ] have been developed.</p>
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98 <p>Let:</p>
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99 <div class="OptionsBox">
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100 Na' = Number of bits set to &quot;0&quot; in A
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101 <br/> Nb' = Number of bits set to &quot;0&quot; in B
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102 <br/> Nc' = Number of bits set to &quot;0&quot; in both A and B</div>
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103 <p>Tanimoto': Nc' / ( ( Na' - Nc') + ( Nb' - Nc' ) + Nc' ) = Nc' / ( Na' + Nb' - Nc' )</p>
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104 <p>Tversky': Nc' / ( alpha * ( Na' - Nc' ) + ( 1 - alpha) * ( Nb' - Nc' ) + Nc' ) = Nc' / ( alpha * ( Na' - Nb' ) + Nb')</p>
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105 <p>Then:</p>
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106 <p>WeightedTanimoto = beta * Tanimoto + (1 - beta) * Tanimoto'</p>
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107 <p>WeightedTversky = beta * Tversky + (1 - beta) * Tversky'</p>
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108 <p>
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109 </p>
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110 <h2>METHODS</h2>
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111 <dl>
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112 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt>
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113 <dd>
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114 <div class="OptionsBox">
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115 $NewFPBitVector = new Fingerprints::FingerprintsBitVector($Size);</div>
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116 <p>Creates a new <em>FingerprintsBitVector</em> object of size <em>Size</em> and returns newly created
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117 <strong>FingerprintsBitVector</strong>. Bit numbers range from 0 to 1 less than <em>Size</em>.</p>
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118 </dd>
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119 <dt><strong><a name="baroniurbanisimilaritycoefficient" class="item"><strong>BaroniUrbaniSimilarityCoefficient</strong></a></strong></dt>
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120 <dd>
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121 <div class="OptionsBox">
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122 $Value = $FingerprintsBitVector-&gt;BaroniUrbaniSimilarityCoefficient(
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123 $OtherFingerprintBitVector);
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124 <br/> $Value = Fingerprints::FingerprintsBitVector::
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125 BaroniUrbaniSimilarityCoefficient(
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126 $FingerprintsBitVectorA, $FingerprintBitVectorB);</div>
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127 <p>Returns value of <em>BaroniUrbani</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p>
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128 </dd>
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129 <dt><strong><a name="busersimilaritycoefficient" class="item"><strong>BuserSimilarityCoefficient</strong></a></strong></dt>
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130 <dd>
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131 <div class="OptionsBox">
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132 $Value = $FingerprintsBitVector-&gt;BuserSimilarityCoefficient(
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133 $OtherFingerprintBitVector);
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134 <br/> $Value = Fingerprints::FingerprintsBitVector::BuserSimilarityCoefficient(
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135 $FingerprintsBitVectorA, $FingerprintBitVectorB);</div>
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136 <p>Returns value of <em>Buser</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p>
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137 </dd>
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138 <dt><strong><a name="cosinesimilaritycoefficient" class="item"><strong>CosineSimilarityCoefficient</strong></a></strong></dt>
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139 <dd>
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140 <div class="OptionsBox">
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141 $Value = $FingerprintsBitVector-&gt;CosineSimilarityCoefficient(
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142 $OtherFingerprintBitVector);
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143 <br/> $Value = Fingerprints::FingerprintsBitVector::CosineSimilarityCoefficient(
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144 $FingerprintsBitVectorA, $FingerprintBitVectorB);</div>
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145 <p>Returns value of <em>Cosine</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p>
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146 </dd>
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147 <dt><strong><a name="dennissimilaritycoefficient" class="item"><strong>DennisSimilarityCoefficient</strong></a></strong></dt>
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148 <dd>
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149 <div class="OptionsBox">
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150 $Value = $FingerprintsBitVector-&gt;DennisSimilarityCoefficient(
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151 $OtherFingerprintBitVector);
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152 <br/> $Value = Fingerprints::FingerprintsBitVector::DennisSimilarityCoefficient(
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153 $FingerprintsBitVectorA, $FingerprintBitVectorB);</div>
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154 <p>Returns value of <em>Dennis</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p>
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155 </dd>
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156 <dt><strong><a name="dicesimilaritycoefficient" class="item"><strong>DiceSimilarityCoefficient</strong></a></strong></dt>
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157 <dd>
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158 <div class="OptionsBox">
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159 $Value = $FingerprintsBitVector-&gt;DiceSimilarityCoefficient(
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160 $OtherFingerprintBitVector);
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161 <br/> $Value = Fingerprints::FingerprintsBitVector::DiceSimilarityCoefficient(
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162 $FingerprintsBitVectorA, $FingerprintBitVectorB);</div>
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163 <p>Returns value of <em>Dice</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p>
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164 </dd>
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165 <dt><strong><a name="foldfingerprintsbitvectorbydensity" class="item"><strong>FoldFingerprintsBitVectorByDensity</strong></a></strong></dt>
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166 <dd>
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167 <div class="OptionsBox">
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168 $FingerprintsBitVector-&gt;FoldFingerprintsBitVectorByDensity($Density);</div>
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169 <p>Folds <em>FingerprintsBitVector</em> by recursively reducing its size by half until bit density of set bits is
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170 greater than or equal to specified <em>Density</em> and returns folded <em>FingerprintsBitVector</em>.</p>
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171 </dd>
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172 <dt><strong><a name="foldfingerprintsbitvectorbysize" class="item"><strong>FoldFingerprintsBitVectorBySize</strong></a></strong></dt>
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173 <dd>
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174 <div class="OptionsBox">
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175 $FingerprintsBitVector-&gt;FoldFingerprintsBitVectorBySize($Size);</div>
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176 <p>Folds <em>FingerprintsBitVector</em> by recursively reducing its size by half until size is less than or equal to
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177 specified <em>Size</em> and returns folded <em>FingerprintsBitVector</em>.</p>
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178 </dd>
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179 <dt><strong><a name="forbessimilaritycoefficient" class="item"><strong>ForbesSimilarityCoefficient</strong></a></strong></dt>
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180 <dd>
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181 <div class="OptionsBox">
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182 $Value = $FingerprintsBitVector-&gt;ForbesSimilarityCoefficient(
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183 $OtherFingerprintBitVector);
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184 <br/> $Value = Fingerprints::FingerprintsBitVector::ForbesSimilarityCoefficient(
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185 $FingerprintsBitVectorA, $FingerprintBitVectorB);</div>
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186 <p>Returns value of <em>Forbes</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p>
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187 </dd>
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188 <dt><strong><a name="fossumsimilaritycoefficient" class="item"><strong>FossumSimilarityCoefficient</strong></a></strong></dt>
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189 <dd>
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190 <div class="OptionsBox">
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191 $Value = $FingerprintsBitVector-&gt;FossumSimilarityCoefficient(
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192 $OtherFingerprintBitVector);
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193 <br/> $Value = Fingerprints::FingerprintsBitVector::FossumSimilarityCoefficient(
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194 $FingerprintsBitVectorA, $FingerprintBitVectorB);</div>
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195 <p>Returns value of <em>Fossum</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p>
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196 </dd>
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197 <dt><strong><a name="getbitsasbinarystring" class="item"><strong>GetBitsAsBinaryString</strong></a></strong></dt>
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198 <dd>
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199 <div class="OptionsBox">
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200 $BinaryASCIIString = $FingerprintsBitVector-&gt;GetBitsAsBinaryString();</div>
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201 <p>Returns fingerprints as a binary ASCII string containing 0s and 1s.</p>
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202 </dd>
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203 <dt><strong><a name="getbitsashexadecimalstring" class="item"><strong>GetBitsAsHexadecimalString</strong></a></strong></dt>
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204 <dd>
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205 <div class="OptionsBox">
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206 $HexadecimalString = $FingerprintsBitVector-&gt;GetBitsAsHexadecimalString();</div>
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207 <p>Returns fingerprints as a hexadecimal string.</p>
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208 </dd>
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209 <dt><strong><a name="getbitsasrawbinarystring" class="item"><strong>GetBitsAsRawBinaryString</strong></a></strong></dt>
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210 <dd>
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211 <div class="OptionsBox">
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212 $RawBinaryString = $FingerprintsBitVector-&gt;GetBitsAsRawBinaryString();</div>
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213 <p>Returns fingerprints as a raw binary string containing packed bit values for each byte.</p>
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214 </dd>
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215 <dt><strong><a name="getdescription" class="item"><strong>GetDescription</strong></a></strong></dt>
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216 <dd>
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217 <div class="OptionsBox">
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218 $Description = $FingerprintsBitVector-&gt;GetDescription();</div>
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219 <p>Returns a string containing description of fingerprints bit vector.</p>
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220 </dd>
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221 <dt><strong><a name="getfingerprintsbitdensity" class="item"><strong>GetFingerprintsBitDensity</strong></a></strong></dt>
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222 <dd>
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223 <div class="OptionsBox">
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224 $BitDensity = $FingerprintsBitVector-&gt;GetFingerprintsBitDensity();</div>
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225 <p>Returns <em>BitDensity</em> of <em>FingerprintsBitVector</em> corresponding to bits set to 1s.</p>
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226 </dd>
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227 <dt><strong><a name="getid" class="item"><strong>GetID</strong></a></strong></dt>
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228 <dd>
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229 <div class="OptionsBox">
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230 $ID = $FingerprintsBitVector-&gt;GetID();</div>
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231 <p>Returns <em>ID</em> of <em>FingerprintsBitVector</em>.</p>
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232 </dd>
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233 <dt><strong><a name="getvectortype" class="item"><strong>GetVectorType</strong></a></strong></dt>
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234 <dd>
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235 <div class="OptionsBox">
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236 $VectorType = $FingerprintsBitVector-&gt;GetVectorType();</div>
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237 <p>Returns <em>VectorType</em> of <em>FingerprintsBitVector</em>.</p>
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238 </dd>
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239 <dt><strong><a name="getspecifiedsize" class="item"><strong>GetSpecifiedSize</strong></a></strong></dt>
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240 <dd>
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241 <div class="OptionsBox">
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242 $Size = $FingerprintsBitVector-&gt;GetSpecifiedSize();</div>
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243 <p>Returns value of specified size for bit vector.</p>
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244 </dd>
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245 <dt><strong><a name="getsupportedsimilaritycoefficients" class="item"><strong>GetSupportedSimilarityCoefficients</strong></a></strong></dt>
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246 <dd>
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247 <div class="OptionsBox">
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248 @SimilarityCoefficient =
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249 Fingerprints::FingerprintsBitVector::GetSupportedSimilarityCoefficients();</div>
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250 <p>Returns an array containing names of supported similarity coefficients.</p>
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251 </dd>
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252 <dt><strong><a name="hamannsimilaritycoefficient" class="item"><strong>HamannSimilarityCoefficient</strong></a></strong></dt>
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253 <dd>
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254 <div class="OptionsBox">
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255 $Value = $FingerprintsBitVector-&gt;HamannSimilarityCoefficient(
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256 $OtherFingerprintBitVector);
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257 <br/> $Value = Fingerprints::FingerprintsBitVector::HamannSimilarityCoefficient(
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258 $FingerprintsBitVectorA, $FingerprintBitVectorB);</div>
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259 <p>Returns value of <em>Hamann</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p>
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260 </dd>
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261 <dt><strong><a name="isfingerprintsbitvector" class="item"><strong>IsFingerprintsBitVector</strong></a></strong></dt>
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262 <dd>
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263 <div class="OptionsBox">
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264 $Status = Fingerprints::FingerprintsBitVector::
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265 IsFingerprintsBitVector($Object);</div>
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266 <p>Returns 1 or 0 based on whether <em>Object</em> is a <strong>FingerprintsBitVector</strong> object.</p>
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267 </dd>
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268 <dt><strong><a name="issubset" class="item"><strong>IsSubSet</strong></a></strong></dt>
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269 <dd>
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270 <div class="OptionsBox">
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271 $Status = $FingerprintsBitVector-&gt;IsSubSet($OtherFPBitVector);
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272 <br/> $Status = Fingerprints::FingerprintsBitVector::IsSubSet(
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273 $FPBitVectorA, $FPBitVectorB);</div>
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274 <p>Returns 1 or 0 based on whether first firngerprints bit vector is a subset of second
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275 fingerprints bit vector.</p>
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276 <p>For a bit vector to be a subset of another bit vector, both vectors must be of
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277 the same size and the bit positions set in first vector must also be set in the
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278 second bit vector.</p>
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279 </dd>
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280 <dt><strong><a name="jacardsimilaritycoefficient" class="item"><strong>JacardSimilarityCoefficient</strong></a></strong></dt>
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281 <dd>
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282 <div class="OptionsBox">
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283 $Value = $FingerprintsBitVector-&gt;JacardSimilarityCoefficient(
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284 $OtherFingerprintBitVector);
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285 <br/> $Value = Fingerprints::FingerprintsBitVector::JacardSimilarityCoefficient(
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286 $FingerprintsBitVectorA, $FingerprintBitVectorB);</div>
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287 <p>Returns value of <em>Jacard</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p>
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288 </dd>
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289 <dt><strong><a name="kulczynski1similaritycoefficient" class="item"><strong>Kulczynski1SimilarityCoefficient</strong></a></strong></dt>
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290 <dd>
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291 <div class="OptionsBox">
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292 $Value = $FingerprintsBitVector-&gt;Kulczynski1SimilarityCoefficient(
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293 $OtherFingerprintBitVector);
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294 <br/> $Value = Fingerprints::FingerprintsBitVector::
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295 Kulczynski1SimilarityCoefficient(
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296 $FingerprintsBitVectorA, $FingerprintBitVectorB);</div>
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297 <p>Returns value of <em>Kulczynski1</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p>
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298 </dd>
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299 <dt><strong><a name="kulczynski2similaritycoefficient" class="item"><strong>Kulczynski2SimilarityCoefficient</strong></a></strong></dt>
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300 <dd>
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301 <div class="OptionsBox">
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302 $Value = $FingerprintsBitVector-&gt;Kulczynski2SimilarityCoefficient(
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303 $OtherFingerprintBitVector);
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304 <br/> $Value = Fingerprints::FingerprintsBitVector::
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305 Kulczynski2SimilarityCoefficient(
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306 $FingerprintsBitVectorA, $FingerprintBitVectorB);</div>
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307 <p>Returns value of <em>Kulczynski2</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p>
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308 </dd>
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309 <dt><strong><a name="matchingsimilaritycoefficient" class="item"><strong>MatchingSimilarityCoefficient</strong></a></strong></dt>
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310 <dd>
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311 <div class="OptionsBox">
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312 $Value = $FingerprintsBitVector-&gt;MatchingSimilarityCoefficient(
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313 $OtherFingerprintBitVector);
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314 <br/> $Value = Fingerprints::FingerprintsBitVector::
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315 MatchingSimilarityCoefficient(
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316 $FingerprintsBitVectorA, $FingerprintBitVectorB);</div>
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317 <p>Returns value of <em>Matching</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p>
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318 </dd>
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319 <dt><strong><a name="mcconnaugheysimilaritycoefficient" class="item"><strong>McConnaugheySimilarityCoefficient</strong></a></strong></dt>
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320 <dd>
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321 <div class="OptionsBox">
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deepakjadmin
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diff changeset
322 $Value = $FingerprintsBitVector-&gt;McConnaugheySimilarityCoefficient(
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323 $OtherFingerprintBitVector);
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deepakjadmin
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diff changeset
324 <br/> $Value = Fingerprints::FingerprintsBitVector::
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deepakjadmin
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325 McConnaugheySimilarityCoefficient(
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diff changeset
326 $FingerprintsBitVectorA, $FingerprintBitVectorB);</div>
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deepakjadmin
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327 <p>Returns value of <em>McConnaughey</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p>
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deepakjadmin
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328 </dd>
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329 <dt><strong><a name="newfrombinarystring" class="item"><strong>NewFromBinaryString</strong></a></strong></dt>
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330 <dd>
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331 <div class="OptionsBox">
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deepakjadmin
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332 $NewFPBitVector = $FingerprintsBitVector-&gt;NewFromBinaryString(
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deepakjadmin
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333 $BinaryString);
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deepakjadmin
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334 <br/> $NewFPBitVector = Fingerprints::FingerprintsBitVector::NewFromBinaryString(
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335 $BinaryString);</div>
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336 <p>Creates a new <em>FingerprintsBitVector</em> using <em>BinaryString</em> and returns new
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337 <strong>FingerprintsBitVector</strong> object.</p>
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deepakjadmin
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338 </dd>
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339 <dt><strong><a name="newfromhexadecimalstring" class="item"><strong>NewFromHexadecimalString</strong></a></strong></dt>
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deepakjadmin
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340 <dd>
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deepakjadmin
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341 <div class="OptionsBox">
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deepakjadmin
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342 $NewFPBitVector = $FingerprintsBitVector-&gt;NewFromHexadecimalString(
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deepakjadmin
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343 $HexdecimalString);
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344 <br/> $NewFPBitVector = Fingerprints::FingerprintsBitVector::
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deepakjadmin
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345 NewFromHexadecimalString(
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deepakjadmin
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346 $HexdecimalString);</div>
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deepakjadmin
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347 <p>Creates a new <em>FingerprintsBitVector</em> using <em>HexdecimalString</em> and returns new
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348 <strong>FingerprintsBitVector</strong> object.</p>
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deepakjadmin
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349 </dd>
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deepakjadmin
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350 <dt><strong><a name="newfromrawbinarystring" class="item"><strong>NewFromRawBinaryString</strong></a></strong></dt>
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deepakjadmin
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351 <dd>
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deepakjadmin
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352 <div class="OptionsBox">
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deepakjadmin
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353 $NewFPBitVector = $FingerprintsBitVector-&gt;NewFromRawBinaryString(
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deepakjadmin
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354 $RawBinaryString);
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deepakjadmin
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355 <br/> $NewFPBitVector = Fingerprints::FingerprintsBitVector::
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deepakjadmin
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356 NewFromRawBinaryString(
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deepakjadmin
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357 $RawBinaryString);</div>
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deepakjadmin
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358 <p>Creates a new <em>FingerprintsBitVector</em> using <em>RawBinaryString</em> and returns new
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deepakjadmin
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359 <strong>FingerprintsBitVector</strong> object.</p>
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deepakjadmin
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360 </dd>
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361 <dt><strong><a name="ochiaisimilaritycoefficient" class="item"><strong>OchiaiSimilarityCoefficient</strong></a></strong></dt>
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deepakjadmin
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362 <dd>
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deepakjadmin
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363 <div class="OptionsBox">
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deepakjadmin
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364 $Value = $FingerprintsBitVector-&gt;OchiaiSimilarityCoefficient(
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365 $OtherFingerprintBitVector);
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deepakjadmin
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366 <br/> $Value = Fingerprints::FingerprintsBitVector::OchiaiSimilarityCoefficient(
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367 $FingerprintsBitVectorA, $FingerprintBitVectorB);</div>
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deepakjadmin
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368 <p>Returns value of <em>Ochiai</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p>
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deepakjadmin
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369 </dd>
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370 <dt><strong><a name="pearsonsimilaritycoefficient" class="item"><strong>PearsonSimilarityCoefficient</strong></a></strong></dt>
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deepakjadmin
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371 <dd>
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deepakjadmin
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372 <div class="OptionsBox">
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deepakjadmin
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373 $Value = $FingerprintsBitVector-&gt;PearsonSimilarityCoefficient(
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374 $OtherFingerprintBitVector);
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deepakjadmin
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375 <br/> $Value = Fingerprints::FingerprintsBitVector::PearsonSimilarityCoefficient(
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deepakjadmin
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376 $FingerprintsBitVectorA, $FingerprintBitVectorB);</div>
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deepakjadmin
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377 <p>Returns value of <em>Pearson</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p>
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378 </dd>
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379 <dt><strong><a name="rogerstanimotosimilaritycoefficient" class="item"><strong>RogersTanimotoSimilarityCoefficient</strong></a></strong></dt>
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deepakjadmin
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380 <dd>
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deepakjadmin
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381 <div class="OptionsBox">
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deepakjadmin
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382 $Value = $FingerprintsBitVector-&gt;RogersTanimotoSimilarityCoefficient(
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383 $OtherFingerprintBitVector);
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deepakjadmin
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384 <br/> $Value = Fingerprints::FingerprintsBitVector::
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deepakjadmin
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385 RogersTanimotoSimilarityCoefficient(
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deepakjadmin
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386 $FingerprintsBitVectorA, $FingerprintBitVectorB);</div>
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deepakjadmin
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387 <p>Returns value of <em>RogersTanimoto</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p>
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388 </dd>
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389 <dt><strong><a name="russellraosimilaritycoefficient" class="item"><strong>RussellRaoSimilarityCoefficient</strong></a></strong></dt>
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deepakjadmin
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390 <dd>
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deepakjadmin
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391 <div class="OptionsBox">
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deepakjadmin
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392 $Value = $FingerprintsBitVector-&gt;RussellRaoSimilarityCoefficient(
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393 $OtherFingerprintBitVector);
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deepakjadmin
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394 <br/> $Value = Fingerprints::FingerprintsBitVector::
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deepakjadmin
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395 RussellRaoSimilarityCoefficient(
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deepakjadmin
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diff changeset
396 $FingerprintsBitVectorA, $FingerprintBitVectorB);</div>
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deepakjadmin
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397 <p>Returns value of <em>RussellRao</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p>
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deepakjadmin
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398 </dd>
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deepakjadmin
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399 <dt><strong><a name="setspecifiedsize" class="item"><strong>SetSpecifiedSize</strong></a></strong></dt>
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400 <dd>
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deepakjadmin
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401 <div class="OptionsBox">
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deepakjadmin
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402 $FingerprintsBitVector-&gt;SetSpecifiedSize($Size);</div>
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deepakjadmin
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403 <p>Sets specified size for fingerprints bit vector.</p>
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deepakjadmin
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404 <p>Irrespective of specified size, Perl functions used to handle bit data in <strong>BitVector</strong> class
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405 automatically sets the size to the next nearest power of 2. <em>SpecifiedSize</em> is used by
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deepakjadmin
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406 <strong>FingerprintsBitVector</strong> class to process any aribitray size during similarity coefficient calculations.</p>
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deepakjadmin
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407 </dd>
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deepakjadmin
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408 <dt><strong><a name="setdescription" class="item"><strong>SetDescription</strong></a></strong></dt>
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deepakjadmin
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409 <dd>
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deepakjadmin
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410 <div class="OptionsBox">
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deepakjadmin
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411 $FingerprintsBitVector-&gt;SetDescription($Description);</div>
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deepakjadmin
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412 <p>Sets <em>Description</em> of fingerprints bit vector and returns <em>FingerprintsBitVector</em>.</p>
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413 </dd>
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deepakjadmin
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414 <dt><strong><a name="setid" class="item"><strong>SetID</strong></a></strong></dt>
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deepakjadmin
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415 <dd>
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deepakjadmin
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416 <div class="OptionsBox">
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deepakjadmin
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diff changeset
417 $FingerprintsBitVector-&gt;SetID($ID);</div>
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deepakjadmin
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418 <p>Sets <em>ID</em> of fingerprints bit vector and returns <em>FingerprintsBitVector</em>.</p>
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deepakjadmin
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419 </dd>
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420 <dt><strong><a name="setvectortype" class="item"><strong>SetVectorType</strong></a></strong></dt>
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deepakjadmin
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421 <dd>
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deepakjadmin
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422 <div class="OptionsBox">
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deepakjadmin
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423 $FingerprintsBitVector-&gt;SetVectorType($VectorType);</div>
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deepakjadmin
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424 <p>Sets <em>VectorType</em> of fingerprints bit vector and returns <em>FingerprintsBitVector</em>.</p>
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deepakjadmin
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425 </dd>
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426 <dt><strong><a name="simpsonsimilaritycoefficient" class="item"><strong>SimpsonSimilarityCoefficient</strong></a></strong></dt>
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deepakjadmin
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427 <dd>
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deepakjadmin
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428 <div class="OptionsBox">
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deepakjadmin
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diff changeset
429 $Value = $FingerprintsBitVector-&gt;SimpsonSimilarityCoefficient(
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430 $OtherFingerprintBitVector);
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deepakjadmin
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431 <br/> $Value = Fingerprints::FingerprintsBitVector::SimpsonSimilarityCoefficient(
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deepakjadmin
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432 $FingerprintsBitVectorA, $FingerprintBitVectorB);</div>
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deepakjadmin
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433 <p>Returns value of <em>Simpson</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p>
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diff changeset
434 </dd>
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435 <dt><strong><a name="skoalsneath1similaritycoefficient" class="item"><strong>SkoalSneath1SimilarityCoefficient</strong></a></strong></dt>
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deepakjadmin
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diff changeset
436 <dd>
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deepakjadmin
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diff changeset
437 <div class="OptionsBox">
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deepakjadmin
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diff changeset
438 $Value = $FingerprintsBitVector-&gt;SkoalSneath1SimilarityCoefficient(
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deepakjadmin
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diff changeset
439 $OtherFingerprintBitVector);
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deepakjadmin
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440 <br/> $Value = Fingerprints::FingerprintsBitVector::
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deepakjadmin
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diff changeset
441 SkoalSneath1SimilarityCoefficient(
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deepakjadmin
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diff changeset
442 $FingerprintsBitVectorA, $FingerprintBitVectorB);</div>
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deepakjadmin
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diff changeset
443 <p>Returns value of <em>SkoalSneath1</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p>
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diff changeset
444 </dd>
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445 <dt><strong><a name="skoalsneath2similaritycoefficient" class="item"><strong>SkoalSneath2SimilarityCoefficient</strong></a></strong></dt>
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446 <dd>
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deepakjadmin
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diff changeset
447 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
448 $Value = $FingerprintsBitVector-&gt;SkoalSneath2SimilarityCoefficient(
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deepakjadmin
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449 $OtherFingerprintBitVector);
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deepakjadmin
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diff changeset
450 <br/> $Value = Fingerprints::FingerprintsBitVector::
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deepakjadmin
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diff changeset
451 SkoalSneath2SimilarityCoefficient(
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deepakjadmin
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diff changeset
452 $FingerprintsBitVectorA, $FingerprintBitVectorB);</div>
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deepakjadmin
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diff changeset
453 <p>Returns value of <em>SkoalSneath2</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p>
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deepakjadmin
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diff changeset
454 </dd>
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deepakjadmin
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455 <dt><strong><a name="skoalsneath3similaritycoefficient" class="item"><strong>SkoalSneath3SimilarityCoefficient</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
456 <dd>
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deepakjadmin
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diff changeset
457 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
458 $Value = $FingerprintsBitVector-&gt;SkoalSneath3SimilarityCoefficient(
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deepakjadmin
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diff changeset
459 $OtherFingerprintBitVector);
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deepakjadmin
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diff changeset
460 <br/> $Value = Fingerprints::FingerprintsBitVector::
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deepakjadmin
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diff changeset
461 SkoalSneath3SimilarityCoefficient(
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deepakjadmin
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diff changeset
462 $FingerprintsBitVectorA, $FingerprintBitVectorB);</div>
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deepakjadmin
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diff changeset
463 <p>Returns value of <em>SkoalSneath3</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em></p>
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deepakjadmin
parents:
diff changeset
464 </dd>
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deepakjadmin
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diff changeset
465 <dt><strong><a name="stringifyfingerprintsbitvector" class="item"><strong>StringifyFingerprintsBitVector</strong></a></strong></dt>
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deepakjadmin
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diff changeset
466 <dd>
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deepakjadmin
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diff changeset
467 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
468 $String = $FingerprintsBitVector-&gt;StringifyFingerprintsBitVector();</div>
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deepakjadmin
parents:
diff changeset
469 <p>Returns a string containing information about <em>FingerprintsBitVector</em> object.</p>
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deepakjadmin
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diff changeset
470 </dd>
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deepakjadmin
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diff changeset
471 <dt><strong><a name="tanimotosimilaritycoefficient" class="item"><strong>TanimotoSimilarityCoefficient</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
472 <dd>
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deepakjadmin
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diff changeset
473 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
474 $Value = $FingerprintsBitVector-&gt;TanimotoSimilarityCoefficient(
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deepakjadmin
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diff changeset
475 $OtherFingerprintBitVector);
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deepakjadmin
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diff changeset
476 <br/> $Value = Fingerprints::FingerprintsBitVector::
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deepakjadmin
parents:
diff changeset
477 TanimotoSimilarityCoefficient(
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deepakjadmin
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diff changeset
478 $FingerprintsBitVectorA, $FingerprintBitVectorB);</div>
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deepakjadmin
parents:
diff changeset
479 <p>Returns value of <em>Tanimoto</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p>
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deepakjadmin
parents:
diff changeset
480 </dd>
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deepakjadmin
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diff changeset
481 <dt><strong><a name="tverskysimilaritycoefficient" class="item"><strong>TverskySimilarityCoefficient</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
482 <dd>
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deepakjadmin
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diff changeset
483 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
484 $Value = $FingerprintsBitVector-&gt;TverskySimilarityCoefficient(
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deepakjadmin
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diff changeset
485 $OtherFingerprintBitVector, $Alpha);
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deepakjadmin
parents:
diff changeset
486 <br/> $Value = Fingerprints::FingerprintsBitVector::
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deepakjadmin
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diff changeset
487 TverskySimilarityCoefficient(
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deepakjadmin
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diff changeset
488 $FingerprintsBitVectorA, $FingerprintBitVectorB, $Alpha);</div>
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deepakjadmin
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diff changeset
489 <p>Returns value of <em>Tversky</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p>
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deepakjadmin
parents:
diff changeset
490 </dd>
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deepakjadmin
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491 <dt><strong><a name="weightedtanimotosimilaritycoefficient" class="item"><strong>WeightedTanimotoSimilarityCoefficient</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
492 <dd>
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deepakjadmin
parents:
diff changeset
493 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
494 $Value =
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deepakjadmin
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diff changeset
495 $FingerprintsBitVector-&gt;WeightedTanimotoSimilarityCoefficient(
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deepakjadmin
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diff changeset
496 $OtherFingerprintBitVector, $Beta);
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deepakjadmin
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diff changeset
497 <br/> $Value =
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deepakjadmin
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diff changeset
498 Fingerprints::FingerprintsBitVector::
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499 WeightedTanimotoSimilarityCoefficient(
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500 $FingerprintsBitVectorA, $FingerprintBitVectorB, $Beta);</div>
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501 <p>Returns value of <em>WeightedTanimoto</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p>
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502 </dd>
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503 <dt><strong><a name="weightedtverskysimilaritycoefficient" class="item"><strong>WeightedTverskySimilarityCoefficient</strong></a></strong></dt>
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504 <dd>
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505 <div class="OptionsBox">
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506 $Value =
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507 $FingerprintsBitVector-&gt;WeightedTverskySimilarityCoefficient(
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508 $OtherFingerprintBitVector, $Alpha, $Beta);
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509 <br/> $Value =
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510 Fingerprints::FingerprintsBitVector::
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511 WeightedTverskySimilarityCoefficient(
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512 $FingerprintsBitVectorA, $FingerprintBitVectorB, $Alpha, $Beta);</div>
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513 <p>Returns value of <em>WeightedTversky</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p>
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514 </dd>
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515 <dt><strong><a name="yulesimilaritycoefficient" class="item"><strong>YuleSimilarityCoefficient</strong></a></strong></dt>
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516 <dd>
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517 <div class="OptionsBox">
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518 $Value = $FingerprintsBitVector-&gt;YuleSimilarityCoefficient(
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519 $OtherFingerprintBitVector);
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520 <br/> $Value = Fingerprints::FingerprintsBitVector::YuleSimilarityCoefficient(
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521 $FingerprintsBitVectorA, $FingerprintBitVectorB);</div>
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522 <p>Returns value of <em>Yule</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p>
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523 </dd>
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524 </dl>
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525 <p>
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526 </p>
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527 <h2>AUTHOR</h2>
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528 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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529 <p>
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530 </p>
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531 <h2>SEE ALSO</h2>
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532 <p><a href="./BitVector.html">BitVector.pm</a>,&nbsp<a href="./FingerprintsStringUtil.html">FingerprintsStringUtil.pm</a>,&nbsp<a href="./FingerprintsVector.html">FingerprintsVector.pm</a>,&nbsp<a href="./Vector.html">Vector.pm</a>
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533 </p>
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534 <p>
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535 </p>
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536 <h2>COPYRIGHT</h2>
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537 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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538 <p>This file is part of MayaChemTools.</p>
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539 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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540 the terms of the GNU Lesser General Public License as published by the Free
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541 Software Foundation; either version 3 of the License, or (at your option)
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542 any later version.</p>
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543 <p>&nbsp</p><p>&nbsp</p><div class="DocNav">
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544 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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545 <tr align="left" valign="top"><td width="33%" align="left"><a href="./Fingerprints.html" title="Fingerprints.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./FingerprintsFileUtil.html" title="FingerprintsFileUtil.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>Fingerprints::FingerprintsBitVector.pm</strong></td></tr>
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546 </table>
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547 </div>
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548 <br />
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549 <center>
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550 <img src="../../images/h2o2.png">
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551 </center>
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552 </body>
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553 </html>