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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/modules/html/code/FingerprintsBitVector.html Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,1110 @@ +<html> +<head> +<title>MayaChemTools:Code:Fingerprints::FingerprintsBitVector.pm</title> +<meta http-equiv="content-type" content="text/html;charset=utf-8"> +<link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> +</head> +<body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> +<br/> +<center> +<a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> +</center> +<br/> +<pre> +<a name="package-Fingerprints::FingerprintsBitVector-"></a> 1 <span class="k">package </span><span class="i">Fingerprints::FingerprintsBitVector</span><span class="sc">;</span> + 2 <span class="c">#</span> + 3 <span class="c"># $RCSfile: FingerprintsBitVector.pm,v $</span> + 4 <span class="c"># $Date: 2015/02/28 20:48:54 $</span> + 5 <span class="c"># $Revision: 1.27 $</span> + 6 <span class="c">#</span> + 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> + 8 <span class="c">#</span> + 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> + 10 <span class="c">#</span> + 11 <span class="c"># This file is part of MayaChemTools.</span> + 12 <span class="c">#</span> + 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> + 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> + 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> + 16 <span class="c"># later version.</span> + 17 <span class="c">#</span> + 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> + 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> + 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> + 21 <span class="c"># details.</span> + 22 <span class="c">#</span> + 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> + 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> + 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> + 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> + 27 <span class="c">#</span> + 28 + 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> + 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span> + 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span> + 32 <span class="k">use</span> <span class="w">Scalar::Util</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 33 <span class="k">use</span> <span class="w">BitVector</span><span class="sc">;</span> + 34 <span class="k">use</span> <span class="w">MathUtil</span><span class="sc">;</span> + 35 <span class="k">use</span> <span class="w">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 36 + 37 <span class="k">use</span> <span class="w">vars</span> <span class="q">qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS)</span><span class="sc">;</span> + 38 + 39 <span class="i">@ISA</span> = <span class="q">qw(BitVector Exporter)</span><span class="sc">;</span> + 40 + 41 <span class="c"># Similiarity coefficients...</span> + 42 <span class="k">my</span><span class="s">(</span><span class="i">@SimilarityCoefficients</span><span class="s">)</span> = <span class="q">qw(BaroniUrbaniSimilarityCoefficient BuserSimilarityCoefficient CosineSimilarityCoefficient DiceSimilarityCoefficient DennisSimilarityCoefficient ForbesSimilarityCoefficient FossumSimilarityCoefficient HamannSimilarityCoefficient JacardSimilarityCoefficient Kulczynski1SimilarityCoefficient Kulczynski2SimilarityCoefficient MatchingSimilarityCoefficient McConnaugheySimilarityCoefficient OchiaiSimilarityCoefficient PearsonSimilarityCoefficient RogersTanimotoSimilarityCoefficient RussellRaoSimilarityCoefficient SimpsonSimilarityCoefficient SkoalSneath1SimilarityCoefficient SkoalSneath2SimilarityCoefficient SkoalSneath3SimilarityCoefficient TanimotoSimilarityCoefficient TverskySimilarityCoefficient YuleSimilarityCoefficient WeightedTanimotoSimilarityCoefficient WeightedTverskySimilarityCoefficient)</span><span class="sc">;</span> + 43 + 44 <span class="c"># New from string...</span> + 45 <span class="k">my</span><span class="s">(</span><span class="i">@NewFromString</span><span class="s">)</span> = <span class="q">qw(NewFromBinaryString NewFromHexadecimalString NewFromRawBinaryString)</span><span class="sc">;</span> + 46 + 47 <span class="i">@EXPORT</span> = <span class="q">qw(IsFingerprintsBitVector)</span><span class="sc">;</span> + 48 <span class="i">@EXPORT_OK</span> = <span class="q">qw(GetSupportedSimilarityCoefficients @NewFromString @SimilarityCoefficients)</span><span class="sc">;</span> + 49 + 50 <span class="i">%EXPORT_TAGS</span> = <span class="s">(</span> + 51 <span class="w">new</span> <span class="cm">=></span> <span class="s">[</span><span class="i">@NewFromString</span><span class="s">]</span><span class="cm">,</span> + 52 <span class="w">coefficients</span> <span class="cm">=></span> <span class="s">[</span><span class="i">@SimilarityCoefficients</span><span class="s">]</span><span class="cm">,</span> + 53 <span class="w">all</span> <span class="cm">=></span> <span class="s">[</span><span class="i">@EXPORT</span><span class="cm">,</span> <span class="i">@EXPORT_OK</span><span class="s">]</span> + 54 <span class="s">)</span><span class="sc">;</span> + 55 + 56 <span class="c"># Setup class variables...</span> + 57 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="sc">;</span> + 58 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 59 + 60 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyFingerprintsBitVector'</span><span class="sc">;</span> + 61 + 62 <span class="c"># Class constructor...</span> +<a name="new-"></a> 63 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> + 64 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">$Size</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 65 + 66 <span class="c"># Initialize object...</span> + 67 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="i">$Size</span><span class="s">)</span><span class="sc">;</span> + 68 <span class="k">bless</span> <span class="i">$This</span><span class="cm">,</span> <span class="k">ref</span><span class="s">(</span><span class="i">$Class</span><span class="s">)</span> || <span class="i">$Class</span><span class="sc">;</span> + 69 <span class="i">$This</span><span class="i">->_InitializeFingerprintsBitVector</span><span class="s">(</span><span class="i">$Size</span><span class="s">)</span><span class="sc">;</span> + 70 + 71 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 72 <span class="s">}</span> + 73 + 74 <span class="c"># Initialize object data...</span> + 75 <span class="c">#</span> + 76 <span class="c"># Note:</span> + 77 <span class="c"># . The class, BitVector, used to derive this class provides all the functionality to</span> + 78 <span class="c"># manipulate bits.</span> + 79 <span class="c"># . Irrespective of specified size, Perl functions used to handle bit data in</span> + 80 <span class="c"># BitVector class automatically sets the size to the next nearest power of 2.</span> + 81 <span class="c"># SpecifiedSize is used by this class to process any aribitray size during similarity</span> + 82 <span class="c"># coefficient calculations.</span> + 83 <span class="c">#</span> +<a name="_InitializeFingerprintsBitVector-"></a> 84 <span class="k">sub </span><span class="m">_InitializeFingerprintsBitVector</span> <span class="s">{</span> + 85 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Size</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 86 + 87 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$Size</span><span class="s">)</span> <span class="s">{</span> + 88 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->new: FingerprintsBitVector object instantiated without specifying its size ..."</span><span class="sc">;</span> + 89 <span class="s">}</span> + 90 <span class="k">if</span> <span class="s">(</span><span class="i">$Size</span> <=<span class="n">0</span><span class="s">)</span> <span class="s">{</span> + 91 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->new: Fingerprints bit vector size, $Size, must be a positive integer..."</span><span class="sc">;</span> + 92 <span class="s">}</span> + 93 + 94 <span class="c"># Specified size of fingerprints...</span> + 95 <span class="i">$This</span>->{<span class="w">SpecifiedSize</span>} = <span class="i">$Size</span><span class="sc">;</span> + 96 + 97 <span class="s">}</span> + 98 + 99 <span class="c"># Initialize class ...</span> +<a name="_InitializeClass-"></a> 100 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> + 101 <span class="c">#Class name...</span> + 102 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> + 103 <span class="s">}</span> + 104 + 105 <span class="c"># Set specified size...</span> + 106 <span class="c">#</span> + 107 <span class="c"># Notes:</span> + 108 <span class="c"># Irrespective of specified size, Perl functions used to handle bit data in</span> + 109 <span class="c"># BitVector class automatically sets the size to the next nearest power of 2.</span> + 110 <span class="c"># SpecifiedSize is used by this class to process any aribitray size during similarity</span> + 111 <span class="c"># coefficient calculations.</span> + 112 <span class="c">#</span> +<a name="SetSpecifiedSize-"></a> 113 <span class="k">sub </span><span class="m">SetSpecifiedSize</span> <span class="s">{</span> + 114 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$SpecifiedSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 115 + 116 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$SpecifiedSize</span> > <span class="n">0</span> && <span class="i">$SpecifiedSize</span> <= <span class="i">$This</span>->{<span class="w">Size</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 117 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetSpecifiedSize: Specified size, $SpecifiedSize, is not valid: It must be > 0 && <= "</span><span class="cm">,</span> <span class="i">$This</span><span class="i">->GetSize</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span><span class="q">" ..."</span><span class="sc">;</span> + 118 <span class="s">}</span> + 119 <span class="i">$This</span>->{<span class="w">SpecifiedSize</span>} = <span class="i">$SpecifiedSize</span><span class="sc">;</span> + 120 <span class="s">}</span> + 121 + 122 <span class="c"># Get specified size...</span> +<a name="GetSpecifiedSize-"></a> 123 <span class="k">sub </span><span class="m">GetSpecifiedSize</span> <span class="s">{</span> + 124 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 125 + 126 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">SpecifiedSize</span>}<span class="sc">;</span> + 127 <span class="s">}</span> + 128 + 129 <span class="c"># Set ID...</span> +<a name="SetID-"></a> 130 <span class="k">sub </span><span class="m">SetID</span> <span class="s">{</span> + 131 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 132 + 133 <span class="i">$This</span>->{<span class="w">ID</span>} = <span class="i">$Value</span><span class="sc">;</span> + 134 + 135 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 136 <span class="s">}</span> + 137 + 138 <span class="c"># Get ID...</span> +<a name="GetID-"></a> 139 <span class="k">sub </span><span class="m">GetID</span> <span class="s">{</span> + 140 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 141 + 142 <span class="k">return</span> <span class="k">exists</span> <span class="i">$This</span>->{<span class="w">ID</span>} ? <span class="i">$This</span>->{<span class="w">ID</span>} <span class="co">:</span> <span class="q">'None'</span><span class="sc">;</span> + 143 <span class="s">}</span> + 144 + 145 <span class="c"># Set description...</span> +<a name="SetDescription-"></a> 146 <span class="k">sub </span><span class="m">SetDescription</span> <span class="s">{</span> + 147 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 148 + 149 <span class="i">$This</span>->{<span class="w">Description</span>} = <span class="i">$Value</span><span class="sc">;</span> + 150 + 151 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 152 <span class="s">}</span> + 153 + 154 <span class="c"># Get description...</span> +<a name="GetDescription-"></a> 155 <span class="k">sub </span><span class="m">GetDescription</span> <span class="s">{</span> + 156 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 157 + 158 <span class="k">return</span> <span class="k">exists</span> <span class="i">$This</span>->{<span class="w">Description</span>} ? <span class="i">$This</span>->{<span class="w">Description</span>} <span class="co">:</span> <span class="q">'No description available'</span><span class="sc">;</span> + 159 <span class="s">}</span> + 160 + 161 <span class="c"># Set vector type...</span> +<a name="SetVectorType-"></a> 162 <span class="k">sub </span><span class="m">SetVectorType</span> <span class="s">{</span> + 163 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 164 + 165 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="i">$Value</span><span class="sc">;</span> + 166 + 167 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 168 <span class="s">}</span> + 169 + 170 <span class="c"># Get vector type...</span> +<a name="GetVectorType-"></a> 171 <span class="k">sub </span><span class="m">GetVectorType</span> <span class="s">{</span> + 172 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 173 + 174 <span class="k">return</span> <span class="k">exists</span> <span class="i">$This</span>->{<span class="w">VectorType</span>} ? <span class="i">$This</span>->{<span class="w">VectorType</span>} <span class="co">:</span> <span class="q">'FingerprintsBitVector'</span><span class="sc">;</span> + 175 <span class="s">}</span> + 176 + 177 <span class="c"># Create a new fingerprints bit vector using binary string. This functionality can be</span> + 178 <span class="c"># either invoked as a class function or an object method.</span> + 179 <span class="c">#</span> +<a name="NewFromBinaryString-"></a> 180 <span class="k">sub </span><span class="m">NewFromBinaryString ($;$)</span> <span class="s">{</span> + 181 <span class="k">my</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="cm">,</span> <span class="i">$ThirdParameter</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 182 + 183 <span class="k">if</span> <span class="s">(</span><span class="i">_IsFingerprintsBitVector</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 184 <span class="k">return</span> <span class="i">_NewFingerptinsBitVectorFromString</span><span class="s">(</span><span class="q">'Binary'</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="cm">,</span> <span class="i">$ThirdParameter</span><span class="s">)</span><span class="sc">;</span> + 185 <span class="s">}</span> + 186 <span class="k">else</span> <span class="s">{</span> + 187 <span class="k">return</span> <span class="i">_NewFingerptinsBitVectorFromString</span><span class="s">(</span> <span class="q">'Binary'</span><span class="cm">,</span> <span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span><span class="sc">;</span> + 188 <span class="s">}</span> + 189 <span class="s">}</span> + 190 + 191 <span class="c"># Create a new fingerprints bit vector using hexadecimal string. This functionality can be</span> + 192 <span class="c"># either invoked as a class function or an object method.</span> + 193 <span class="c">#</span> +<a name="NewFromHexadecimalString-"></a> 194 <span class="k">sub </span><span class="m">NewFromHexadecimalString ($;$)</span> <span class="s">{</span> + 195 <span class="k">my</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="cm">,</span> <span class="i">$ThirdParameter</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 196 + 197 <span class="k">if</span> <span class="s">(</span><span class="i">_IsFingerprintsBitVector</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 198 <span class="k">return</span> <span class="i">_NewFingerptinsBitVectorFromString</span><span class="s">(</span><span class="q">'Hexadecimal'</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="cm">,</span> <span class="i">$ThirdParameter</span><span class="s">)</span><span class="sc">;</span> + 199 <span class="s">}</span> + 200 <span class="k">else</span> <span class="s">{</span> + 201 <span class="k">return</span> <span class="i">_NewFingerptinsBitVectorFromString</span><span class="s">(</span> <span class="q">'Hexadecimal'</span><span class="cm">,</span> <span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span><span class="sc">;</span> + 202 <span class="s">}</span> + 203 <span class="s">}</span> + 204 + 205 <span class="c"># Create a new fingerprints bit vector using octal string. This functionality can be</span> + 206 <span class="c"># either invoked as a class function or an object method.</span> + 207 <span class="c">#</span> + 208 <span class="c">#</span> +<a name="NewFromOctalString-"></a> 209 <span class="k">sub </span><span class="m">NewFromOctalString ($)</span> <span class="s">{</span> + 210 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->NewFromOctalString: Creation of fingerprits bit vector from an octal string is not supported ..."</span><span class="sc">;</span> + 211 <span class="s">}</span> + 212 + 213 <span class="c"># Create a new fingerprints bit vector using decimal string. This functionality can be</span> + 214 <span class="c"># either invoked as a class function or an object method.</span> + 215 <span class="c">#</span> +<a name="NewFromDecimalString-"></a> 216 <span class="k">sub </span><span class="m">NewFromDecimalString ($;$)</span> <span class="s">{</span> + 217 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->NewFromDecimalString: Creation of fingerprits bit vector from a decimal string is not supported ..."</span><span class="sc">;</span> + 218 <span class="s">}</span> + 219 + 220 <span class="c"># Create a new fingerprints bit vector using raw binary string. This functionality can be</span> + 221 <span class="c"># either invoked as a class function or an object method.</span> + 222 <span class="c">#</span> +<a name="NewFromRawBinaryString-"></a> 223 <span class="k">sub </span><span class="m">NewFromRawBinaryString ($;$)</span> <span class="s">{</span> + 224 <span class="k">my</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="cm">,</span> <span class="i">$ThirdParameter</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 225 + 226 <span class="k">if</span> <span class="s">(</span><span class="i">_IsFingerprintsBitVector</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 227 <span class="k">return</span> <span class="i">_NewFingerptinsBitVectorFromString</span><span class="s">(</span><span class="q">'RawBinary'</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="cm">,</span> <span class="i">$ThirdParameter</span><span class="s">)</span><span class="sc">;</span> + 228 <span class="s">}</span> + 229 <span class="k">else</span> <span class="s">{</span> + 230 <span class="k">return</span> <span class="i">_NewFingerptinsBitVectorFromString</span><span class="s">(</span> <span class="q">'RawBinary'</span><span class="cm">,</span> <span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span><span class="sc">;</span> + 231 <span class="s">}</span> + 232 <span class="s">}</span> + 233 + 234 <span class="c"># Create a new fingerprints bit vector from a string...</span> + 235 <span class="c">#</span> + 236 <span class="c">#</span> +<a name="_NewFingerptinsBitVectorFromString-"></a> 237 <span class="k">sub </span><span class="m">_NewFingerptinsBitVectorFromString ($$;$)</span> <span class="s">{</span> + 238 <span class="k">my</span><span class="s">(</span><span class="i">$Format</span><span class="cm">,</span> <span class="i">$String</span><span class="cm">,</span> <span class="i">$BitsOrder</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 239 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsBitVector</span><span class="cm">,</span> <span class="i">$Size</span><span class="s">)</span><span class="sc">;</span> + 240 + 241 <span class="i">$Size</span> = <span class="i">BitVector::_CalculateStringSizeInBits</span><span class="s">(</span><span class="i">$Format</span><span class="cm">,</span> <span class="i">$String</span><span class="s">)</span><span class="sc">;</span> + 242 + 243 <span class="i">$FingerprintsBitVector</span> = <span class="i">new</span> <span class="i">Fingerprints::FingerprintsBitVector</span><span class="s">(</span><span class="i">$Size</span><span class="s">)</span><span class="sc">;</span> + 244 <span class="i">$FingerprintsBitVector</span><span class="i">->_SetBitsAsString</span><span class="s">(</span><span class="i">$Format</span><span class="cm">,</span> <span class="i">$String</span><span class="cm">,</span> <span class="i">$BitsOrder</span><span class="s">)</span><span class="sc">;</span> + 245 + 246 <span class="k">return</span> <span class="i">$FingerprintsBitVector</span><span class="sc">;</span> + 247 <span class="s">}</span> + 248 + 249 <span class="c"># Get fingerprint bits as a hexadecimal string...</span> + 250 <span class="c">#</span> +<a name="GetBitsAsHexadecimalString-"></a> 251 <span class="k">sub </span><span class="m">GetBitsAsHexadecimalString</span> <span class="s">{</span> + 252 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$BitsOrder</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 253 + 254 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetFingerprintBitsAsString</span><span class="s">(</span><span class="q">'Hexadecimal'</span><span class="cm">,</span> <span class="i">$BitsOrder</span><span class="s">)</span><span class="sc">;</span> + 255 <span class="s">}</span> + 256 + 257 <span class="c"># Get fingerprint bits as an octal string...</span> + 258 <span class="c">#</span> +<a name="GetBitsAsOctalString-"></a> 259 <span class="k">sub </span><span class="m">GetBitsAsOctalString</span> <span class="s">{</span> + 260 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$BitsOrder</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 261 + 262 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->GetBitsAsOctalString: Retrieval of fingerprits bits as an octal string is not supported ..."</span><span class="sc">;</span> + 263 <span class="s">}</span> + 264 + 265 <span class="c"># Get fingerprint bits as an decimal string...</span> + 266 <span class="c">#</span> +<a name="GetBitsAsDecimalString-"></a> 267 <span class="k">sub </span><span class="m">GetBitsAsDecimalString</span> <span class="s">{</span> + 268 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$BitsOrder</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 269 + 270 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->GetBitsAsOctalString: Retrieval of fingerprits bits as a decimal string is not supported ..."</span><span class="sc">;</span> + 271 <span class="s">}</span> + 272 + 273 <span class="c"># Get fingerprint bits as a binary string conatning 1s and 0s...</span> + 274 <span class="c">#</span> +<a name="GetBitsAsBinaryString-"></a> 275 <span class="k">sub </span><span class="m">GetBitsAsBinaryString</span> <span class="s">{</span> + 276 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$BitsOrder</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 277 + 278 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetFingerprintBitsAsString</span><span class="s">(</span><span class="q">'Binary'</span><span class="cm">,</span> <span class="i">$BitsOrder</span><span class="s">)</span><span class="sc">;</span> + 279 <span class="s">}</span> + 280 + 281 <span class="c"># Get fingerprint bits as a binary string conatning 1s and 0s...</span> + 282 <span class="c">#</span> +<a name="GetBitsAsRawBinaryString-"></a> 283 <span class="k">sub </span><span class="m">GetBitsAsRawBinaryString</span> <span class="s">{</span> + 284 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 285 + 286 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetFingerprintBitsAsString</span><span class="s">(</span><span class="q">'RawBinary'</span><span class="s">)</span><span class="sc">;</span> + 287 <span class="s">}</span> + 288 + 289 <span class="c"># Return fingerprint bits as a string...</span> + 290 <span class="c">#</span> +<a name="_GetFingerprintBitsAsString-"></a> 291 <span class="k">sub </span><span class="m">_GetFingerprintBitsAsString</span> <span class="s">{</span> + 292 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Format</span><span class="cm">,</span> <span class="i">$BitsOrder</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 293 + 294 <span class="i">$BitsOrder</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$BitsOrder</span><span class="s">)</span> && <span class="i">$BitsOrder</span><span class="s">)</span> ? <span class="i">$BitsOrder</span> <span class="co">:</span> <span class="q">'Ascending'</span><span class="sc">;</span> + 295 + 296 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetBitsAsString</span><span class="s">(</span><span class="i">$Format</span><span class="cm">,</span> <span class="i">$BitsOrder</span><span class="s">)</span><span class="sc">;</span> + 297 <span class="s">}</span> + 298 + 299 <span class="c"># Is it a fingerprints bit vector object?</span> +<a name="IsFingerprintsBitVector-"></a> 300 <span class="k">sub </span><span class="m">IsFingerprintsBitVector ($)</span> <span class="s">{</span> + 301 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 302 + 303 <span class="k">return</span> <span class="i">_IsFingerprintsBitVector</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span><span class="sc">;</span> + 304 <span class="s">}</span> + 305 + 306 <span class="c"># Is it a fingerprints bit vector object?</span> +<a name="_IsFingerprintsBitVector-"></a> 307 <span class="k">sub </span><span class="m">_IsFingerprintsBitVector</span> <span class="s">{</span> + 308 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 309 + 310 <span class="k">return</span> <span class="s">(</span><span class="i">Scalar::Util::blessed</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> && <span class="i">$Object</span><span class="i">->isa</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 311 <span class="s">}</span> + 312 + 313 <span class="c"># Return a list of supported similarity coefficients...</span> +<a name="GetSupportedSimilarityCoefficients-"></a> 314 <span class="k">sub </span><span class="m">GetSupportedSimilarityCoefficients ()</span> <span class="s">{</span> + 315 + 316 <span class="k">return</span> <span class="i">@SimilarityCoefficients</span><span class="sc">;</span> + 317 <span class="s">}</span> + 318 + 319 <span class="c"># Get bit density for fingerprints bit vector corresponding to on bits...</span> + 320 <span class="c">#</span> +<a name="GetFingerprintsBitDensity-"></a> 321 <span class="k">sub </span><span class="m">GetFingerprintsBitDensity</span> <span class="s">{</span> + 322 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 323 <span class="k">my</span><span class="s">(</span><span class="i">$BitDensity</span><span class="s">)</span><span class="sc">;</span> + 324 + 325 <span class="i">$BitDensity</span> = <span class="i">$This</span><span class="i">->GetDensityOfSetBits</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 326 + 327 <span class="k">return</span> <span class="i">round</span><span class="s">(</span><span class="i">$BitDensity</span><span class="cm">,</span> <span class="n">2</span><span class="s">)</span><span class="sc">;</span> + 328 <span class="s">}</span> + 329 + 330 <span class="c"># Fold fingerprints bit vector by recursively reducing its size by half untill size is less than or equal to</span> + 331 <span class="c"># specified size...</span> + 332 <span class="c">#</span> +<a name="FoldFingerprintsBitVectorBySize-"></a> 333 <span class="k">sub </span><span class="m">FoldFingerprintsBitVectorBySize</span> <span class="s">{</span> + 334 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Size</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 335 + 336 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$Size</span> > <span class="n">0</span> && <span class="i">$Size</span> <= <span class="i">$This</span><span class="i">->GetSize</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 337 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->FoldFingerprintsBitVectorBySize: Specified size, $Size, is not valid: It must be > 0 && <= "</span><span class="cm">,</span> <span class="i">$This</span><span class="i">->GetSize</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span><span class="q">" ..."</span><span class="sc">;</span> + 338 <span class="s">}</span> + 339 + 340 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetSize</span><span class="s">(</span><span class="s">)</span> <= <span class="i">$Size</span><span class="s">)</span> <span class="s">{</span> + 341 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 342 <span class="s">}</span> + 343 <span class="k">return</span> <span class="i">$This</span><span class="i">->_FoldFingerprintsBitVector</span><span class="s">(</span><span class="q">'BySize'</span><span class="cm">,</span> <span class="i">$Size</span><span class="s">)</span><span class="sc">;</span> + 344 <span class="s">}</span> + 345 + 346 <span class="c"># Fold fingerprints bit vector by recursively reducing its size by half untill bit density of set bits is greater than</span> + 347 <span class="c"># or equal to specified density...</span> + 348 <span class="c">#</span> +<a name="FoldFingerprintsBitVectorByDensity-"></a> 349 <span class="k">sub </span><span class="m">FoldFingerprintsBitVectorByDensity</span> <span class="s">{</span> + 350 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Density</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 351 + 352 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$Density</span> > <span class="n">0</span> && <span class="i">$Density</span> <= <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 353 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->FoldFingerprintsBitVectorByDensity: Specified bit density, $Density, is not valid: It must be > 0 && <= 1 ..."</span><span class="sc">;</span> + 354 <span class="s">}</span> + 355 + 356 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetDensityOfSetBits</span><span class="s">(</span><span class="s">)</span> >= <span class="i">$Density</span><span class="s">)</span> <span class="s">{</span> + 357 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 358 <span class="s">}</span> + 359 <span class="k">return</span> <span class="i">$This</span><span class="i">->_FoldFingerprintsBitVector</span><span class="s">(</span><span class="q">'ByDensity'</span><span class="cm">,</span> <span class="i">$Density</span><span class="s">)</span><span class="sc">;</span> + 360 <span class="s">}</span> + 361 + 362 <span class="c"># Fold fingerprints bit vector using size or density and return folded fingerprint bit vector...</span> + 363 <span class="c">#</span> +<a name="_FoldFingerprintsBitVector-"></a> 364 <span class="k">sub </span><span class="m">_FoldFingerprintsBitVector</span> <span class="s">{</span> + 365 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Mode</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 366 + 367 <span class="c"># Fold upto size of 8 bits...</span> + 368 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetSize</span><span class="s">(</span><span class="s">)</span> <= <span class="n">8</span><span class="s">)</span> <span class="s">{</span> + 369 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 370 <span class="s">}</span> + 371 + 372 <span class="c"># Check size or density....</span> + 373 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^BySize$/i</span><span class="s">)</span> <span class="s">{</span> + 374 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetSize</span><span class="s">(</span><span class="s">)</span> <= <span class="i">$Value</span><span class="s">)</span> <span class="s">{</span> + 375 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 376 <span class="s">}</span> + 377 <span class="s">}</span> + 378 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^ByDensity$/i</span><span class="s">)</span> <span class="s">{</span> + 379 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetDensityOfSetBits</span><span class="s">(</span><span class="s">)</span> >= <span class="i">$Value</span><span class="s">)</span> <span class="s">{</span> + 380 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 381 <span class="s">}</span> + 382 <span class="s">}</span> + 383 <span class="k">else</span> <span class="s">{</span> + 384 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 385 <span class="s">}</span> + 386 + 387 <span class="c"># Recursively reduce its size by half...</span> + 388 <span class="k">my</span><span class="s">(</span><span class="i">$FirstHalfBinaryString</span><span class="cm">,</span> <span class="i">$SecondHalfBinaryString</span><span class="cm">,</span> <span class="i">$FirstHalfFingerprintsBitVector</span><span class="cm">,</span> <span class="i">$SecondHalfFingerprintsBitVector</span><span class="cm">,</span> <span class="i">$FoldedFingerprintsBitVector</span><span class="cm">,</span> <span class="i">$BinaryString</span><span class="cm">,</span> <span class="i">$StringLength</span><span class="s">)</span><span class="sc">;</span> + 389 + 390 <span class="i">$BinaryString</span> = <span class="i">$This</span><span class="i">->GetBitsAsBinaryString</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 391 <span class="i">$StringLength</span> = <span class="k">length</span> <span class="i">$BinaryString</span><span class="sc">;</span> + 392 + 393 <span class="i">$FirstHalfBinaryString</span> = <span class="k">substr</span><span class="s">(</span><span class="i">$BinaryString</span><span class="cm">,</span> <span class="n">0</span><span class="cm">,</span> <span class="i">$StringLength</span>/<span class="n">2</span><span class="s">)</span><span class="sc">;</span> + 394 <span class="i">$SecondHalfBinaryString</span> = <span class="k">substr</span><span class="s">(</span><span class="i">$BinaryString</span><span class="cm">,</span> <span class="i">$StringLength</span>/<span class="n">2</span><span class="s">)</span><span class="sc">;</span> + 395 + 396 <span class="i">$FirstHalfFingerprintsBitVector</span> = <span class="i">NewFromBinaryString</span><span class="s">(</span><span class="i">$FirstHalfBinaryString</span><span class="s">)</span><span class="sc">;</span> + 397 <span class="i">$SecondHalfFingerprintsBitVector</span> = <span class="i">NewFromBinaryString</span><span class="s">(</span><span class="i">$SecondHalfBinaryString</span><span class="s">)</span><span class="sc">;</span> + 398 + 399 <span class="i">$FoldedFingerprintsBitVector</span> = <span class="i">$FirstHalfFingerprintsBitVector</span> | <span class="i">$SecondHalfFingerprintsBitVector</span><span class="sc">;</span> + 400 + 401 <span class="k">return</span> <span class="i">$FoldedFingerprintsBitVector</span><span class="i">->_FoldFingerprintsBitVector</span><span class="s">(</span><span class="i">$Mode</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> + 402 <span class="s">}</span> + 403 + 404 <span class="c"># Is first bit vector subset of second bit vector?</span> + 405 <span class="c">#</span> + 406 <span class="c"># For a bit vector to be a subset of another bit vector, both vectors must be of</span> + 407 <span class="c"># the same size and the bit positions set in first vector must also be set in the</span> + 408 <span class="c"># secons bit vector.</span> + 409 <span class="c">#</span> + 410 <span class="c"># This functionality can be either invoked as a class function or an object method.</span> + 411 <span class="c">#</span> +<a name="IsSubSet-"></a> 412 <span class="k">sub </span><span class="m">IsSubSet ($$)</span> <span class="s">{</span> + 413 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 414 + 415 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="i">->GetSize</span><span class="s">(</span><span class="s">)</span> != <span class="i">$FingerprintsBitVectorB</span><span class="i">->GetSize</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 416 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> + 417 <span class="s">}</span> + 418 <span class="k">my</span><span class="s">(</span><span class="i">$AndFingerprintsBitVector</span><span class="s">)</span><span class="sc">;</span> + 419 + 420 <span class="i">$AndFingerprintsBitVector</span> = <span class="i">$FingerprintsBitVectorA</span> & <span class="i">$FingerprintsBitVectorB</span><span class="sc">;</span> + 421 + 422 <span class="k">return</span> <span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="i">->GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span> == <span class="i">$AndFingerprintsBitVector</span><span class="i">->GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 423 <span class="s">}</span> + 424 + 425 <span class="c"># Return a string containing vector values...</span> +<a name="StringifyFingerprintsBitVector-"></a> 426 <span class="k">sub </span><span class="m">StringifyFingerprintsBitVector</span> <span class="s">{</span> + 427 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 428 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsBitVectorString</span><span class="s">)</span><span class="sc">;</span> + 429 + 430 <span class="c"># BitVector size information...</span> + 431 <span class="c">#</span> + 432 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">SpecifiedSize</span>} != <span class="i">$This</span><span class="i">->GetSize</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 433 <span class="i">$FingerprintsBitVectorString</span> = <span class="q">"SpecifiedSize: "</span> . <span class="i">$This</span>->{<span class="w">SpecifiedSize</span>} . <span class="q">"; BitVectorSize: "</span> . <span class="i">$This</span><span class="i">->GetSize</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 434 <span class="s">}</span> + 435 <span class="k">else</span> <span class="s">{</span> + 436 <span class="i">$FingerprintsBitVectorString</span> = <span class="q">"BitVectorSize: "</span> . <span class="i">$This</span><span class="i">->GetSize</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 437 <span class="s">}</span> + 438 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfSetBits</span><span class="cm">,</span> <span class="i">$BitDensity</span><span class="s">)</span><span class="sc">;</span> + 439 <span class="i">$NumOfSetBits</span> = <span class="i">$This</span><span class="i">->GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 440 <span class="i">$BitDensity</span> = <span class="i">$This</span><span class="i">->GetFingerprintsBitDensity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 441 + 442 <span class="i">$FingerprintsBitVectorString</span> .= <span class="q">"; NumOfOnBits: $NumOfSetBits; BitDensity: $BitDensity"</span><span class="sc">;</span> + 443 + 444 <span class="c"># BitVector values...</span> + 445 <span class="i">$FingerprintsBitVectorString</span> .= <span class="q">"; BitVector: "</span> . <span class="i">$This</span><span class="i">->StringifyBitVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 446 + 447 <span class="k">return</span> <span class="i">$FingerprintsBitVectorString</span><span class="sc">;</span> + 448 <span class="s">}</span> + 449 + 450 <span class="c"># For two fingerprints bit vectors A and B of same size, let:</span> + 451 <span class="c">#</span> + 452 <span class="c"># Na = Number of bits set to "1" in A</span> + 453 <span class="c"># Nb = Number of bits set to "1" in B</span> + 454 <span class="c"># Nc = Number of bits set to "1" in both A and B</span> + 455 <span class="c"># Nd = Number of bits set to "0" in both A and B</span> + 456 <span class="c">#</span> + 457 <span class="c"># Nt = Number of bits set to "1" or "0" in A or B = Size of A or B = Na + Nb - Nc + Nd</span> + 458 <span class="c">#</span> + 459 <span class="c"># Na - Nc = Number of bits set to "1" in A but not in B</span> + 460 <span class="c"># Nb - Nc = Number of bits set to "1" in B but not in A</span> + 461 <span class="c">#</span> + 462 <span class="c"># Various similarity coefficients [ Ref 40 - 42 ] for a pair of bit vectors A and B are</span> + 463 <span class="c"># defined as follows:</span> + 464 <span class="c">#</span> + 465 <span class="c"># . BaroniUrbani: ( SQRT( Nc * Nd ) + Nc ) / ( SQRT ( Nc * Nd ) + Nc + ( Na - Nc ) + ( Nb - Nc ) ) ( same as Buser )</span> + 466 <span class="c">#</span> + 467 <span class="c"># . Buser: ( SQRT ( Nc * Nd ) + Nc ) / ( SQRT ( Nc * Nd ) + Nc + ( Na - Nc ) + ( Nb - Nc ) ) ( same as BaroniUrbani )</span> + 468 <span class="c">#</span> + 469 <span class="c"># . Cosine: Nc / SQRT ( Na * Nb ) (same as Ochiai)</span> + 470 <span class="c">#</span> + 471 <span class="c"># . Dice: (2 * Nc) / ( Na + Nb )</span> + 472 <span class="c">#</span> + 473 <span class="c"># . Dennis: ( Nc * Nd - ( ( Na - Nc ) * ( Nb - Nc ) ) ) / SQRT ( Nt * Na * Nb)</span> + 474 <span class="c">#</span> + 475 <span class="c"># . Forbes: ( Nt * Nc ) / ( Na * Nb )</span> + 476 <span class="c">#</span> + 477 <span class="c"># . Fossum: ( Nt * ( ( Nc - 1/2 ) ** 2 ) / ( Na * Nb )</span> + 478 <span class="c">#</span> + 479 <span class="c"># . Hamann: ( ( Nc + Nd ) - ( Na - Nc ) - ( Nb - Nc ) ) / Nt</span> + 480 <span class="c">#</span> + 481 <span class="c"># . Jaccard: Nc / ( ( Na - Nc) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb - Nc ) (same as Tanimoto)</span> + 482 <span class="c">#</span> + 483 <span class="c"># . Kulczynski1: Nc / ( ( Na - Nc ) + ( Nb - Nc) ) = Nc / ( Na + Nb - 2Nc )</span> + 484 <span class="c">#</span> + 485 <span class="c"># . Kulczynski2: ( ( Nc / 2 ) * ( 2 * Nc + ( Na - Nc ) + ( Nb - Nc) ) ) / ( ( Nc + ( Na - Nc ) ) * ( Nc + ( Nb - Nc ) ) ) = 0.5 * ( Nc / Na + Nc / Nb )</span> + 486 <span class="c">#</span> + 487 <span class="c"># . Matching: ( Nc + Nd ) / Nt</span> + 488 <span class="c">#</span> + 489 <span class="c"># . McConnaughey: ( Nc ** 2 - ( Na - Nc ) * ( Nb - Nc) ) / ( Na * Nb )</span> + 490 <span class="c">#</span> + 491 <span class="c"># . Ochiai: Nc / SQRT ( Na * Nb ) (same as Cosine)</span> + 492 <span class="c">#</span> + 493 <span class="c"># . Pearson: ( ( Nc * Nd ) - ( ( Na - Nc ) * ( Nb - Nc ) ) / SQRT ( Na * Nb * ( Na - Nc + Nd ) * ( Nb - Nc + Nd ) )</span> + 494 <span class="c">#</span> + 495 <span class="c"># . RogersTanimoto: ( Nc + Nd ) / ( ( Na - Nc) + ( Nb - Nc) + Nt) = ( Nc + Nd ) / ( Na + Nb - 2Nc + Nt)</span> + 496 <span class="c">#</span> + 497 <span class="c"># . RussellRao: Nc / Nt</span> + 498 <span class="c">#</span> + 499 <span class="c"># . Simpson: Nc / MIN ( Na, Nb)</span> + 500 <span class="c">#</span> + 501 <span class="c"># . SkoalSneath1: Nc / ( Nc + 2 * ( Na - Nc) + 2 * ( Nb - Nc) ) = Nc / ( 2 * Na + 2 * Nb - 3 * Nc )</span> + 502 <span class="c">#</span> + 503 <span class="c"># . SkoalSneath2: ( 2 * Nc + 2 * Nd ) / ( Nc + Nd + Nt )</span> + 504 <span class="c">#</span> + 505 <span class="c"># . SkoalSneath3: ( Nc + Nd ) / ( ( Na - Nc ) + ( Nb - Nc ) ) = ( Nc + Nd ) / ( Na + Nb - 2 * Nc )</span> + 506 <span class="c">#</span> + 507 <span class="c"># . Tanimoto: Nc / ( ( Na - Nc) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb - Nc ) (same as Jaccard)</span> + 508 <span class="c">#</span> + 509 <span class="c"># . Tversky: Nc / ( alpha * ( Na - Nc ) + ( 1 - alpha) * ( Nb - Nc) + Nc ) = Nc / ( alpha * ( Na - Nb ) + Nb)</span> + 510 <span class="c">#</span> + 511 <span class="c"># . Yule: ( ( Nc * Nd ) - ( ( Na - Nc ) * ( Nb - Nc ) ) ) / ( ( Nc * Nd ) + ( ( Na - Nc ) * ( Nb - Nc ) ) )</span> + 512 <span class="c">#</span> + 513 <span class="c">#</span> + 514 <span class="c"># Values of Tanimoto/Jaccard and Tversky coefficients are dependent on only those bit which</span> + 515 <span class="c"># are set to "1" in both A and B. In order to take into account all bit positions, modified versions</span> + 516 <span class="c"># of Tanimoto [ Ref. 42 ] and Tversky [ Ref. 43 ] have been developed.</span> + 517 <span class="c">#</span> + 518 <span class="c"># Let:</span> + 519 <span class="c">#</span> + 520 <span class="c"># Na' = Number of bits set to "0" in A</span> + 521 <span class="c"># Nb' = Number of bits set to "0" in B</span> + 522 <span class="c"># Nc' = Number of bits set to "0" in both A and B</span> + 523 <span class="c">#</span> + 524 <span class="c"># . Tanimoto': Nc' / ( ( Na' - Nc') + ( Nb' - Nc' ) + Nc' ) = Nc' / ( Na' + Nb' - Nc' )</span> + 525 <span class="c">#</span> + 526 <span class="c"># . Tversky': Nc' / ( alpha * ( Na' - Nc' ) + ( 1 - alpha) * ( Nb' - Nc' ) + Nc' ) = Nc' / ( alpha * ( Na' - Nb' ) + Nb')</span> + 527 <span class="c">#</span> + 528 <span class="c"># Then:</span> + 529 <span class="c">#</span> + 530 <span class="c"># . WeightedTanimoto = beta * Tanimoto + (1 - beta) * Tanimoto'</span> + 531 <span class="c">#</span> + 532 <span class="c"># . WeightedTversky = beta * Tversky + (1 - beta) * Tversky'</span> + 533 <span class="c">#</span> + 534 <span class="c">#</span> + 535 + 536 <span class="c"># Calculate BaroniUrbani similarity coefficient for two same size bit vectors.</span> + 537 <span class="c">#</span> + 538 <span class="c"># This functionality can be either invoked as a class function or an object method.</span> + 539 <span class="c">#</span> +<a name="BaroniUrbaniSimilarityCoefficient-"></a> 540 <span class="k">sub </span><span class="m">BaroniUrbaniSimilarityCoefficient ($$)</span> <span class="s">{</span> + 541 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 542 + 543 <span class="k">return</span> <span class="i">BuserSimilarityCoefficient</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span> + 544 <span class="s">}</span> + 545 + 546 <span class="c"># Calculate Buser similarity coefficient for two same size bit vectors.</span> + 547 <span class="c">#</span> + 548 <span class="c"># This functionality can be either invoked as a class function or an object method.</span> + 549 <span class="c">#</span> +<a name="BuserSimilarityCoefficient-"></a> 550 <span class="k">sub </span><span class="m">BuserSimilarityCoefficient ($$)</span> <span class="s">{</span> + 551 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 552 <span class="k">my</span><span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="cm">,</span> <span class="i">$Nd</span><span class="cm">,</span> <span class="i">$Nt</span><span class="cm">,</span> <span class="i">$Numerator</span><span class="cm">,</span> <span class="i">$Denominator</span><span class="s">)</span><span class="sc">;</span> + 553 + 554 <span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="s">)</span> = <span class="i">_GetNumOfIndividualAndCommonSetBits</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span> + 555 <span class="i">$Nd</span> = <span class="i">_GetNumOfCommonClearBits</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span> + 556 <span class="i">$Nt</span> = <span class="i">$Na</span> + <span class="i">$Nb</span> - <span class="i">$Nc</span> + <span class="i">$Nd</span><span class="sc">;</span> + 557 + 558 <span class="i">$Numerator</span> = <span class="k">sqrt</span><span class="s">(</span><span class="i">$Nc</span>*<span class="i">$Nd</span><span class="s">)</span> + <span class="i">$Nc</span><span class="sc">;</span> + 559 <span class="i">$Denominator</span> = <span class="k">sqrt</span><span class="s">(</span><span class="i">$Nc</span>*<span class="i">$Nd</span><span class="s">)</span> + <span class="s">(</span><span class="i">$Na</span> - <span class="i">$Nc</span><span class="s">)</span> + <span class="s">(</span><span class="i">$Nb</span> - <span class="i">$Nc</span> <span class="s">)</span> + <span class="i">$Nc</span><span class="sc">;</span> + 560 + 561 <span class="k">return</span> <span class="i">$Denominator</span> ? <span class="s">(</span><span class="i">$Numerator</span>/<span class="i">$Denominator</span><span class="s">)</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 562 <span class="s">}</span> + 563 + 564 <span class="c"># Calculate Cosine similarity coefficient for two same size bit vectors.</span> + 565 <span class="c">#</span> + 566 <span class="c"># This functionality can be either invoked as a class function or an object method.</span> + 567 <span class="c">#</span> +<a name="CosineSimilarityCoefficient-"></a> 568 <span class="k">sub </span><span class="m">CosineSimilarityCoefficient ($$)</span> <span class="s">{</span> + 569 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 570 <span class="k">my</span><span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="cm">,</span> <span class="i">$Numerator</span><span class="cm">,</span> <span class="i">$Denominator</span><span class="s">)</span><span class="sc">;</span> + 571 + 572 <span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="s">)</span> = <span class="i">_GetNumOfIndividualAndCommonSetBits</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span> + 573 + 574 <span class="i">$Numerator</span> = <span class="i">$Nc</span><span class="sc">;</span> + 575 <span class="i">$Denominator</span> = <span class="k">sqrt</span><span class="s">(</span><span class="i">$Na</span>*<span class="i">$Nb</span><span class="s">)</span><span class="sc">;</span> + 576 + 577 <span class="k">return</span> <span class="i">$Denominator</span> ? <span class="s">(</span><span class="i">$Numerator</span>/<span class="i">$Denominator</span><span class="s">)</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 578 <span class="s">}</span> + 579 + 580 <span class="c"># Calculate Dice similarity coefficient for two same size bit vectors.</span> + 581 <span class="c">#</span> + 582 <span class="c"># This functionality can be either invoked as a class function or an object method.</span> + 583 <span class="c">#</span> +<a name="DiceSimilarityCoefficient-"></a> 584 <span class="k">sub </span><span class="m">DiceSimilarityCoefficient ($$)</span> <span class="s">{</span> + 585 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 586 <span class="k">my</span><span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="cm">,</span> <span class="i">$Numerator</span><span class="cm">,</span> <span class="i">$Denominator</span><span class="s">)</span><span class="sc">;</span> + 587 + 588 <span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="s">)</span> = <span class="i">_GetNumOfIndividualAndCommonSetBits</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span> + 589 + 590 <span class="i">$Numerator</span> = <span class="n">2</span>*<span class="i">$Nc</span><span class="sc">;</span> + 591 <span class="i">$Denominator</span> = <span class="i">$Na</span> + <span class="i">$Nb</span><span class="sc">;</span> + 592 + 593 <span class="k">return</span> <span class="i">$Denominator</span> ? <span class="s">(</span><span class="i">$Numerator</span>/<span class="i">$Denominator</span><span class="s">)</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 594 <span class="s">}</span> + 595 + 596 <span class="c"># Calculate Dennis similarity coefficient for two same size bit vectors.</span> + 597 <span class="c">#</span> + 598 <span class="c"># This functionality can be either invoked as a class function or an object method.</span> + 599 <span class="c">#</span> +<a name="DennisSimilarityCoefficient-"></a> 600 <span class="k">sub </span><span class="m">DennisSimilarityCoefficient ($$)</span> <span class="s">{</span> + 601 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 602 <span class="k">my</span><span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="cm">,</span> <span class="i">$Nd</span><span class="cm">,</span> <span class="i">$Nt</span><span class="cm">,</span> <span class="i">$Numerator</span><span class="cm">,</span> <span class="i">$Denominator</span><span class="s">)</span><span class="sc">;</span> + 603 + 604 <span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="s">)</span> = <span class="i">_GetNumOfIndividualAndCommonSetBits</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span> + 605 <span class="i">$Nd</span> = <span class="i">_GetNumOfCommonClearBits</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span> + 606 <span class="i">$Nt</span> = <span class="i">$Na</span> + <span class="i">$Nb</span> - <span class="i">$Nc</span> + <span class="i">$Nd</span><span class="sc">;</span> + 607 + 608 <span class="i">$Numerator</span> = <span class="i">$Nc</span>*<span class="i">$Nd</span> - <span class="s">(</span><span class="s">(</span><span class="i">$Na</span> - <span class="i">$Nc</span><span class="s">)</span>*<span class="s">(</span><span class="i">$Nb</span> - <span class="i">$Nc</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> + 609 <span class="i">$Denominator</span> = <span class="k">sqrt</span><span class="s">(</span><span class="i">$Nt</span>*<span class="i">$Na</span>*<span class="i">$Nb</span><span class="s">)</span><span class="sc">;</span> + 610 + 611 <span class="k">return</span> <span class="i">$Denominator</span> ? <span class="s">(</span><span class="i">$Numerator</span>/<span class="i">$Denominator</span><span class="s">)</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 612 <span class="s">}</span> + 613 + 614 <span class="c"># Calculate Forbes similarity coefficient for two same size bit vectors.</span> + 615 <span class="c">#</span> + 616 <span class="c"># This functionality can be either invoked as a class function or an object method.</span> + 617 <span class="c">#</span> +<a name="ForbesSimilarityCoefficient-"></a> 618 <span class="k">sub </span><span class="m">ForbesSimilarityCoefficient ($$)</span> <span class="s">{</span> + 619 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 620 <span class="k">my</span><span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="cm">,</span> <span class="i">$Nd</span><span class="cm">,</span> <span class="i">$Nt</span><span class="cm">,</span> <span class="i">$Numerator</span><span class="cm">,</span> <span class="i">$Denominator</span><span class="s">)</span><span class="sc">;</span> + 621 + 622 <span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="s">)</span> = <span class="i">_GetNumOfIndividualAndCommonSetBits</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span> + 623 <span class="i">$Nd</span> = <span class="i">_GetNumOfCommonClearBits</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span> + 624 <span class="i">$Nt</span> = <span class="i">$Na</span> + <span class="i">$Nb</span> - <span class="i">$Nc</span> + <span class="i">$Nd</span><span class="sc">;</span> + 625 + 626 <span class="i">$Numerator</span> = <span class="i">$Nt</span>*<span class="i">$Nc</span><span class="sc">;</span> + 627 <span class="i">$Denominator</span> = <span class="i">$Na</span>*<span class="i">$Nb</span><span class="sc">;</span> + 628 + 629 <span class="k">return</span> <span class="i">$Denominator</span> ? <span class="s">(</span><span class="i">$Numerator</span>/<span class="i">$Denominator</span><span class="s">)</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 630 <span class="s">}</span> + 631 + 632 <span class="c"># Calculate Fossum similarity coefficient for two same size bit vectors.</span> + 633 <span class="c">#</span> + 634 <span class="c"># This functionality can be either invoked as a class function or an object method.</span> + 635 <span class="c">#</span> +<a name="FossumSimilarityCoefficient-"></a> 636 <span class="k">sub </span><span class="m">FossumSimilarityCoefficient ($$)</span> <span class="s">{</span> + 637 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 638 <span class="k">my</span><span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="cm">,</span> <span class="i">$Nd</span><span class="cm">,</span> <span class="i">$Nt</span><span class="cm">,</span> <span class="i">$Numerator</span><span class="cm">,</span> <span class="i">$Denominator</span><span class="s">)</span><span class="sc">;</span> + 639 + 640 <span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="s">)</span> = <span class="i">_GetNumOfIndividualAndCommonSetBits</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span> + 641 <span class="i">$Nd</span> = <span class="i">_GetNumOfCommonClearBits</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span> + 642 <span class="i">$Nt</span> = <span class="i">$Na</span> + <span class="i">$Nb</span> - <span class="i">$Nc</span> + <span class="i">$Nd</span><span class="sc">;</span> + 643 + 644 <span class="i">$Numerator</span> = <span class="i">$Nt</span>*<span class="s">(</span><span class="s">(</span><span class="i">$Nc</span> - <span class="n">0.5</span><span class="s">)</span>** <span class="n">2</span><span class="s">)</span><span class="sc">;</span> + 645 <span class="i">$Denominator</span> = <span class="i">$Na</span>*<span class="i">$Nb</span> <span class="sc">;</span> + 646 + 647 <span class="k">return</span> <span class="i">$Denominator</span> ? <span class="s">(</span><span class="i">$Numerator</span>/<span class="i">$Denominator</span><span class="s">)</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 648 <span class="s">}</span> + 649 + 650 <span class="c"># Calculate Hamann similarity coefficient for two same size bit vectors.</span> + 651 <span class="c">#</span> + 652 <span class="c"># This functionality can be either invoked as a class function or an object method.</span> + 653 <span class="c">#</span> +<a name="HamannSimilarityCoefficient-"></a> 654 <span class="k">sub </span><span class="m">HamannSimilarityCoefficient ($$)</span> <span class="s">{</span> + 655 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 656 <span class="k">my</span><span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="cm">,</span> <span class="i">$Nd</span><span class="cm">,</span> <span class="i">$Nt</span><span class="cm">,</span> <span class="i">$Numerator</span><span class="cm">,</span> <span class="i">$Denominator</span><span class="s">)</span><span class="sc">;</span> + 657 + 658 <span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="s">)</span> = <span class="i">_GetNumOfIndividualAndCommonSetBits</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span> + 659 <span class="i">$Nd</span> = <span class="i">_GetNumOfCommonClearBits</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span> + 660 <span class="i">$Nt</span> = <span class="i">$Na</span> + <span class="i">$Nb</span> - <span class="i">$Nc</span> + <span class="i">$Nd</span><span class="sc">;</span> + 661 + 662 <span class="i">$Numerator</span> = <span class="s">(</span><span class="i">$Nc</span> + <span class="i">$Nd</span> <span class="s">)</span> - <span class="s">(</span><span class="i">$Na</span> - <span class="i">$Nc</span><span class="s">)</span> - <span class="s">(</span><span class="i">$Nb</span> - <span class="i">$Nc</span><span class="s">)</span> <span class="sc">;</span> + 663 <span class="i">$Denominator</span> = <span class="i">$Nt</span><span class="sc">;</span> + 664 + 665 <span class="k">return</span> <span class="i">$Denominator</span> ? <span class="s">(</span><span class="i">$Numerator</span>/<span class="i">$Denominator</span><span class="s">)</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 666 <span class="s">}</span> + 667 + 668 <span class="c"># Calculate Jacard similarity coefficient for two same size bit vectors.</span> + 669 <span class="c">#</span> + 670 <span class="c"># This functionality can be either invoked as a class function or an object method.</span> + 671 <span class="c">#</span> +<a name="JacardSimilarityCoefficient-"></a> 672 <span class="k">sub </span><span class="m">JacardSimilarityCoefficient ($$)</span> <span class="s">{</span> + 673 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 674 + 675 <span class="k">return</span> <span class="i">TanimotoSimilarityCoefficient</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span> + 676 <span class="s">}</span> + 677 + 678 <span class="c"># Calculate Kulczynski1 similarity coefficient for two same size bit vectors.</span> + 679 <span class="c">#</span> + 680 <span class="c"># This functionality can be either invoked as a class function or an object method.</span> + 681 <span class="c">#</span> +<a name="Kulczynski1SimilarityCoefficient-"></a> 682 <span class="k">sub </span><span class="m">Kulczynski1SimilarityCoefficient ($$)</span> <span class="s">{</span> + 683 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 684 <span class="k">my</span><span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="cm">,</span> <span class="i">$Numerator</span><span class="cm">,</span> <span class="i">$Denominator</span><span class="s">)</span><span class="sc">;</span> + 685 + 686 <span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="s">)</span> = <span class="i">_GetNumOfIndividualAndCommonSetBits</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span> + 687 + 688 <span class="i">$Numerator</span> = <span class="i">$Nc</span><span class="sc">;</span> + 689 <span class="i">$Denominator</span> = <span class="i">$Na</span> + <span class="i">$Nb</span> - <span class="n">2</span>*<span class="i">$Nc</span><span class="sc">;</span> + 690 + 691 <span class="k">return</span> <span class="i">$Denominator</span> ? <span class="s">(</span><span class="i">$Numerator</span>/<span class="i">$Denominator</span><span class="s">)</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 692 <span class="s">}</span> + 693 + 694 <span class="c"># Calculate Kulczynski2 similarity coefficient for two same size bit vectors.</span> + 695 <span class="c">#</span> + 696 <span class="c"># This functionality can be either invoked as a class function or an object method.</span> + 697 <span class="c">#</span> +<a name="Kulczynski2SimilarityCoefficient-"></a> 698 <span class="k">sub </span><span class="m">Kulczynski2SimilarityCoefficient ($$)</span> <span class="s">{</span> + 699 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 700 <span class="k">my</span><span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="cm">,</span> <span class="i">$Numerator</span><span class="cm">,</span> <span class="i">$Denominator</span><span class="s">)</span><span class="sc">;</span> + 701 + 702 <span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="s">)</span> = <span class="i">_GetNumOfIndividualAndCommonSetBits</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span> + 703 + 704 <span class="i">$Numerator</span> = <span class="n">0.5</span>*<span class="s">(</span><span class="i">$Na</span>*<span class="i">$Nc</span> + <span class="i">$Nb</span>*<span class="i">$Nc</span><span class="s">)</span><span class="sc">;</span> + 705 <span class="i">$Denominator</span> = <span class="i">$Na</span>*<span class="i">$Nb</span><span class="sc">;</span> + 706 + 707 <span class="k">return</span> <span class="i">$Denominator</span> ? <span class="s">(</span><span class="i">$Numerator</span>/<span class="i">$Denominator</span><span class="s">)</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 708 <span class="s">}</span> + 709 + 710 <span class="c"># Calculate Matching similarity coefficient for two same size bit vectors.</span> + 711 <span class="c">#</span> + 712 <span class="c"># This functionality can be either invoked as a class function or an object method.</span> + 713 <span class="c">#</span> +<a name="MatchingSimilarityCoefficient-"></a> 714 <span class="k">sub </span><span class="m">MatchingSimilarityCoefficient ($$)</span> <span class="s">{</span> + 715 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 716 <span class="k">my</span><span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="cm">,</span> <span class="i">$Nd</span><span class="cm">,</span> <span class="i">$Nt</span><span class="cm">,</span> <span class="i">$Numerator</span><span class="cm">,</span> <span class="i">$Denominator</span><span class="s">)</span><span class="sc">;</span> + 717 + 718 <span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="s">)</span> = <span class="i">_GetNumOfIndividualAndCommonSetBits</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span> + 719 <span class="i">$Nd</span> = <span class="i">_GetNumOfCommonClearBits</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span> + 720 <span class="i">$Nt</span> = <span class="i">$Na</span> + <span class="i">$Nb</span> - <span class="i">$Nc</span> + <span class="i">$Nd</span><span class="sc">;</span> + 721 + 722 <span class="i">$Numerator</span> = <span class="i">$Nc</span> + <span class="i">$Nd</span><span class="sc">;</span> + 723 <span class="i">$Denominator</span> = <span class="i">$Nt</span><span class="sc">;</span> + 724 + 725 <span class="k">return</span> <span class="i">$Denominator</span> ? <span class="s">(</span><span class="i">$Numerator</span>/<span class="i">$Denominator</span><span class="s">)</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 726 <span class="s">}</span> + 727 + 728 <span class="c"># Calculate McConnaughey similarity coefficient for two same size bit vectors.</span> + 729 <span class="c">#</span> + 730 <span class="c"># This functionality can be either invoked as a class function or an object method.</span> + 731 <span class="c">#</span> +<a name="McConnaugheySimilarityCoefficient-"></a> 732 <span class="k">sub </span><span class="m">McConnaugheySimilarityCoefficient ($$)</span> <span class="s">{</span> + 733 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 734 <span class="k">my</span><span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="cm">,</span> <span class="i">$Numerator</span><span class="cm">,</span> <span class="i">$Denominator</span><span class="s">)</span><span class="sc">;</span> + 735 + 736 <span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="s">)</span> = <span class="i">_GetNumOfIndividualAndCommonSetBits</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span> + 737 + 738 <span class="i">$Numerator</span> = <span class="i">$Nc</span>**<span class="n">2</span> - <span class="s">(</span><span class="s">(</span><span class="i">$Na</span> - <span class="i">$Nc</span><span class="s">)</span>*<span class="s">(</span><span class="i">$Nb</span> - <span class="i">$Nc</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> + 739 <span class="i">$Denominator</span> = <span class="i">$Na</span>*<span class="i">$Nb</span> <span class="sc">;</span> + 740 + 741 <span class="k">return</span> <span class="i">$Denominator</span> ? <span class="s">(</span><span class="i">$Numerator</span>/<span class="i">$Denominator</span><span class="s">)</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 742 <span class="s">}</span> + 743 + 744 <span class="c"># Calculate Ochiai similarity coefficient for two same size bit vectors.</span> + 745 <span class="c">#</span> + 746 <span class="c"># This functionality can be either invoked as a class function or an object method.</span> + 747 <span class="c">#</span> +<a name="OchiaiSimilarityCoefficient-"></a> 748 <span class="k">sub </span><span class="m">OchiaiSimilarityCoefficient ($$)</span> <span class="s">{</span> + 749 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 750 + 751 <span class="k">return</span> <span class="i">CosineSimilarityCoefficient</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span> + 752 <span class="s">}</span> + 753 + 754 <span class="c"># Calculate Pearson similarity coefficient for two same size bit vectors.</span> + 755 <span class="c">#</span> + 756 <span class="c"># This functionality can be either invoked as a class function or an object method.</span> + 757 <span class="c">#</span> +<a name="PearsonSimilarityCoefficient-"></a> 758 <span class="k">sub </span><span class="m">PearsonSimilarityCoefficient ($$)</span> <span class="s">{</span> + 759 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 760 <span class="k">my</span><span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="cm">,</span> <span class="i">$Nd</span><span class="cm">,</span> <span class="i">$Nt</span><span class="cm">,</span> <span class="i">$Numerator</span><span class="cm">,</span> <span class="i">$Denominator</span><span class="s">)</span><span class="sc">;</span> + 761 + 762 <span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="s">)</span> = <span class="i">_GetNumOfIndividualAndCommonSetBits</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span> + 763 <span class="i">$Nd</span> = <span class="i">_GetNumOfCommonClearBits</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span> + 764 <span class="i">$Nt</span> = <span class="i">$Na</span> + <span class="i">$Nb</span> - <span class="i">$Nc</span> + <span class="i">$Nd</span><span class="sc">;</span> + 765 + 766 <span class="i">$Numerator</span> = <span class="s">(</span><span class="i">$Nc</span>*<span class="i">$Nd</span> <span class="s">)</span> - <span class="s">(</span><span class="s">(</span><span class="i">$Na</span> - <span class="i">$Nc</span><span class="s">)</span>*<span class="s">(</span><span class="i">$Nb</span> - <span class="i">$Nc</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> + 767 <span class="i">$Denominator</span> = <span class="k">sqrt</span><span class="s">(</span><span class="i">$Na</span>*<span class="i">$Nb</span>*<span class="s">(</span><span class="i">$Na</span> - <span class="i">$Nc</span> + <span class="i">$Nd</span> <span class="s">)</span>*<span class="s">(</span><span class="i">$Nb</span> - <span class="i">$Nc</span> + <span class="i">$Nd</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> + 768 + 769 <span class="k">return</span> <span class="i">$Denominator</span> ? <span class="s">(</span><span class="i">$Numerator</span>/<span class="i">$Denominator</span><span class="s">)</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 770 <span class="s">}</span> + 771 + 772 <span class="c"># Calculate RogersTanimoto similarity coefficient for two same size bit vectors.</span> + 773 <span class="c">#</span> + 774 <span class="c"># This functionality can be either invoked as a class function or an object method.</span> + 775 <span class="c">#</span> +<a name="RogersTanimotoSimilarityCoefficient-"></a> 776 <span class="k">sub </span><span class="m">RogersTanimotoSimilarityCoefficient ($$)</span> <span class="s">{</span> + 777 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 778 <span class="k">my</span><span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="cm">,</span> <span class="i">$Nd</span><span class="cm">,</span> <span class="i">$Nt</span><span class="cm">,</span> <span class="i">$Numerator</span><span class="cm">,</span> <span class="i">$Denominator</span><span class="s">)</span><span class="sc">;</span> + 779 + 780 <span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="s">)</span> = <span class="i">_GetNumOfIndividualAndCommonSetBits</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span> + 781 <span class="i">$Nd</span> = <span class="i">_GetNumOfCommonClearBits</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span> + 782 <span class="i">$Nt</span> = <span class="i">$Na</span> + <span class="i">$Nb</span> - <span class="i">$Nc</span> + <span class="i">$Nd</span><span class="sc">;</span> + 783 + 784 <span class="i">$Numerator</span> = <span class="i">$Nc</span> + <span class="i">$Nd</span><span class="sc">;</span> + 785 <span class="i">$Denominator</span> = <span class="s">(</span><span class="i">$Na</span> - <span class="i">$Nc</span><span class="s">)</span> + <span class="s">(</span><span class="i">$Nb</span> - <span class="i">$Nc</span><span class="s">)</span> + <span class="i">$Nt</span><span class="sc">;</span> + 786 + 787 <span class="k">return</span> <span class="i">$Denominator</span> ? <span class="s">(</span><span class="i">$Numerator</span>/<span class="i">$Denominator</span><span class="s">)</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 788 <span class="s">}</span> + 789 + 790 <span class="c"># Calculate RussellRao similarity coefficient for two same size bit vectors.</span> + 791 <span class="c">#</span> + 792 <span class="c"># This functionality can be either invoked as a class function or an object method.</span> + 793 <span class="c">#</span> +<a name="RussellRaoSimilarityCoefficient-"></a> 794 <span class="k">sub </span><span class="m">RussellRaoSimilarityCoefficient ($$)</span> <span class="s">{</span> + 795 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 796 <span class="k">my</span><span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="cm">,</span> <span class="i">$Nd</span><span class="cm">,</span> <span class="i">$Nt</span><span class="cm">,</span> <span class="i">$Numerator</span><span class="cm">,</span> <span class="i">$Denominator</span><span class="s">)</span><span class="sc">;</span> + 797 + 798 <span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="s">)</span> = <span class="i">_GetNumOfIndividualAndCommonSetBits</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span> + 799 <span class="i">$Nd</span> = <span class="i">_GetNumOfCommonClearBits</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span> + 800 <span class="i">$Nt</span> = <span class="i">$Na</span> + <span class="i">$Nb</span> - <span class="i">$Nc</span> + <span class="i">$Nd</span><span class="sc">;</span> + 801 + 802 <span class="i">$Numerator</span> = <span class="i">$Nc</span><span class="sc">;</span> + 803 <span class="i">$Denominator</span> = <span class="i">$Nt</span><span class="sc">;</span> + 804 + 805 <span class="k">return</span> <span class="i">$Denominator</span> ? <span class="s">(</span><span class="i">$Numerator</span>/<span class="i">$Denominator</span><span class="s">)</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 806 <span class="s">}</span> + 807 + 808 <span class="c"># Calculate Simpson similarity coefficient for two same size bit vectors.</span> + 809 <span class="c">#</span> + 810 <span class="c"># This functionality can be either invoked as a class function or an object method.</span> + 811 <span class="c">#</span> +<a name="SimpsonSimilarityCoefficient-"></a> 812 <span class="k">sub </span><span class="m">SimpsonSimilarityCoefficient ($$)</span> <span class="s">{</span> + 813 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 814 <span class="k">my</span><span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="cm">,</span> <span class="i">$Numerator</span><span class="cm">,</span> <span class="i">$Denominator</span><span class="s">)</span><span class="sc">;</span> + 815 + 816 <span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="s">)</span> = <span class="i">_GetNumOfIndividualAndCommonSetBits</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span> + 817 + 818 <span class="i">$Numerator</span> = <span class="i">$Nc</span><span class="sc">;</span> + 819 <span class="i">$Denominator</span> = <span class="i">min</span><span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="s">)</span><span class="sc">;</span> + 820 + 821 <span class="k">return</span> <span class="i">$Denominator</span> ? <span class="s">(</span><span class="i">$Numerator</span>/<span class="i">$Denominator</span><span class="s">)</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 822 <span class="s">}</span> + 823 + 824 <span class="c"># Calculate SkoalSneath1 similarity coefficient for two same size bit vectors.</span> + 825 <span class="c">#</span> + 826 <span class="c"># This functionality can be either invoked as a class function or an object method.</span> + 827 <span class="c">#</span> +<a name="SkoalSneath1SimilarityCoefficient-"></a> 828 <span class="k">sub </span><span class="m">SkoalSneath1SimilarityCoefficient ($$)</span> <span class="s">{</span> + 829 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 830 <span class="k">my</span><span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="cm">,</span> <span class="i">$Numerator</span><span class="cm">,</span> <span class="i">$Denominator</span><span class="s">)</span><span class="sc">;</span> + 831 + 832 <span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="s">)</span> = <span class="i">_GetNumOfIndividualAndCommonSetBits</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span> + 833 + 834 <span class="i">$Numerator</span> = <span class="i">$Nc</span><span class="sc">;</span> + 835 <span class="i">$Denominator</span> = <span class="i">$Nc</span> + <span class="n">2</span>*<span class="s">(</span><span class="i">$Na</span> - <span class="i">$Nc</span><span class="s">)</span> + <span class="n">2</span>*<span class="s">(</span><span class="i">$Nb</span> - <span class="i">$Nc</span><span class="s">)</span><span class="sc">;</span> + 836 + 837 <span class="k">return</span> <span class="i">$Denominator</span> ? <span class="s">(</span><span class="i">$Numerator</span>/<span class="i">$Denominator</span><span class="s">)</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 838 <span class="s">}</span> + 839 + 840 <span class="c"># Calculate SkoalSneath2 similarity coefficient for two same size bit vectors.</span> + 841 <span class="c">#</span> + 842 <span class="c"># This functionality can be either invoked as a class function or an object method.</span> + 843 <span class="c">#</span> +<a name="SkoalSneath2SimilarityCoefficient-"></a> 844 <span class="k">sub </span><span class="m">SkoalSneath2SimilarityCoefficient ($$)</span> <span class="s">{</span> + 845 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 846 <span class="k">my</span><span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="cm">,</span> <span class="i">$Nd</span><span class="cm">,</span> <span class="i">$Nt</span><span class="cm">,</span> <span class="i">$Numerator</span><span class="cm">,</span> <span class="i">$Denominator</span><span class="s">)</span><span class="sc">;</span> + 847 + 848 <span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="s">)</span> = <span class="i">_GetNumOfIndividualAndCommonSetBits</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span> + 849 <span class="i">$Nd</span> = <span class="i">_GetNumOfCommonClearBits</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span> + 850 <span class="i">$Nt</span> = <span class="i">$Na</span> + <span class="i">$Nb</span> - <span class="i">$Nc</span> + <span class="i">$Nd</span><span class="sc">;</span> + 851 + 852 <span class="i">$Numerator</span> = <span class="n">2</span>*<span class="i">$Nc</span> + <span class="n">2</span>*<span class="i">$Nd</span> <span class="sc">;</span> + 853 <span class="i">$Denominator</span> = <span class="i">$Nc</span> + <span class="i">$Nd</span> + <span class="i">$Nt</span> <span class="sc">;</span> + 854 + 855 <span class="k">return</span> <span class="i">$Denominator</span> ? <span class="s">(</span><span class="i">$Numerator</span>/<span class="i">$Denominator</span><span class="s">)</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 856 <span class="s">}</span> + 857 + 858 <span class="c"># Calculate SkoalSneath3 similarity coefficient for two same size bit vectors.</span> + 859 <span class="c">#</span> + 860 <span class="c"># This functionality can be either invoked as a class function or an object method.</span> + 861 <span class="c">#</span> +<a name="SkoalSneath3SimilarityCoefficient-"></a> 862 <span class="k">sub </span><span class="m">SkoalSneath3SimilarityCoefficient ($$)</span> <span class="s">{</span> + 863 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 864 <span class="k">my</span><span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="cm">,</span> <span class="i">$Nd</span><span class="cm">,</span> <span class="i">$Nt</span><span class="cm">,</span> <span class="i">$Numerator</span><span class="cm">,</span> <span class="i">$Denominator</span><span class="s">)</span><span class="sc">;</span> + 865 + 866 <span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="s">)</span> = <span class="i">_GetNumOfIndividualAndCommonSetBits</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span> + 867 <span class="i">$Nd</span> = <span class="i">_GetNumOfCommonClearBits</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span> + 868 <span class="i">$Nt</span> = <span class="i">$Na</span> + <span class="i">$Nb</span> - <span class="i">$Nc</span> + <span class="i">$Nd</span><span class="sc">;</span> + 869 + 870 <span class="i">$Numerator</span> = <span class="i">$Nc</span> + <span class="i">$Nd</span><span class="sc">;</span> + 871 <span class="i">$Denominator</span> = <span class="s">(</span><span class="i">$Na</span> - <span class="i">$Nc</span><span class="s">)</span> + <span class="s">(</span><span class="i">$Nb</span> - <span class="i">$Nc</span> <span class="s">)</span> <span class="sc">;</span> + 872 + 873 <span class="k">return</span> <span class="i">$Denominator</span> ? <span class="s">(</span><span class="i">$Numerator</span>/<span class="i">$Denominator</span><span class="s">)</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 874 <span class="s">}</span> + 875 + 876 <span class="c"># Calculate Tanimoto similarity coefficient for two same size bit vectors.</span> + 877 <span class="c">#</span> + 878 <span class="c"># This functionality can be either invoked as a class function or an object method.</span> + 879 <span class="c">#</span> +<a name="TanimotoSimilarityCoefficient-"></a> 880 <span class="k">sub </span><span class="m">TanimotoSimilarityCoefficient ($$)</span> <span class="s">{</span> + 881 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 882 <span class="k">my</span><span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="cm">,</span> <span class="i">$Numerator</span><span class="cm">,</span> <span class="i">$Denominator</span><span class="s">)</span><span class="sc">;</span> + 883 + 884 <span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="s">)</span> = <span class="i">_GetNumOfIndividualAndCommonSetBits</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span> + 885 + 886 <span class="i">$Numerator</span> = <span class="i">$Nc</span><span class="sc">;</span> + 887 <span class="i">$Denominator</span> = <span class="i">$Na</span> + <span class="i">$Nb</span> - <span class="i">$Nc</span><span class="sc">;</span> + 888 + 889 <span class="k">return</span> <span class="i">$Denominator</span> ? <span class="s">(</span><span class="i">$Numerator</span>/<span class="i">$Denominator</span><span class="s">)</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 890 <span class="s">}</span> + 891 + 892 <span class="c"># Calculate Tversky similarity coefficient for two same size bit vectors.</span> + 893 <span class="c">#</span> + 894 <span class="c"># This functionality can be either invoked as a class function or an object method.</span> + 895 <span class="c">#</span> +<a name="TverskySimilarityCoefficient-"></a> 896 <span class="k">sub </span><span class="m">TverskySimilarityCoefficient ($$$)</span> <span class="s">{</span> + 897 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="cm">,</span> <span class="i">$Alpha</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 898 <span class="k">my</span><span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="cm">,</span> <span class="i">$Numerator</span><span class="cm">,</span> <span class="i">$Denominator</span><span class="s">)</span><span class="sc">;</span> + 899 + 900 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Alpha</span><span class="s">)</span> && <span class="s">(</span><span class="i">$Alpha</span> >= <span class="n">0</span> && <span class="i">$Alpha</span> <= <span class="n">1</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 901 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->TverskySimilarityCoefficient: Alpha parameters must be defined and its value must be >=0 and <=1 ..."</span><span class="sc">;</span> + 902 <span class="s">}</span> + 903 + 904 <span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="s">)</span> = <span class="i">_GetNumOfIndividualAndCommonSetBits</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span> + 905 + 906 <span class="i">$Numerator</span> = <span class="i">$Nc</span><span class="sc">;</span> + 907 <span class="i">$Denominator</span> = <span class="i">$Alpha</span>*<span class="s">(</span><span class="i">$Na</span> - <span class="i">$Nb</span> <span class="s">)</span> + <span class="i">$Nb</span><span class="sc">;</span> + 908 + 909 <span class="k">return</span> <span class="i">$Denominator</span> ? <span class="s">(</span><span class="i">$Numerator</span>/<span class="i">$Denominator</span><span class="s">)</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 910 <span class="s">}</span> + 911 + 912 <span class="c"># Calculate Yule similarity coefficient for two same size bit vectors.</span> + 913 <span class="c">#</span> + 914 <span class="c"># This functionality can be either invoked as a class function or an object method.</span> + 915 <span class="c">#</span> +<a name="YuleSimilarityCoefficient-"></a> 916 <span class="k">sub </span><span class="m">YuleSimilarityCoefficient ($$)</span> <span class="s">{</span> + 917 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 918 <span class="k">my</span><span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="cm">,</span> <span class="i">$Nd</span><span class="cm">,</span> <span class="i">$Nt</span><span class="cm">,</span> <span class="i">$Numerator</span><span class="cm">,</span> <span class="i">$Denominator</span><span class="s">)</span><span class="sc">;</span> + 919 + 920 <span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="s">)</span> = <span class="i">_GetNumOfIndividualAndCommonSetBits</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span> + 921 <span class="i">$Nd</span> = <span class="i">_GetNumOfCommonClearBits</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span> + 922 <span class="i">$Nt</span> = <span class="i">$Na</span> + <span class="i">$Nb</span> - <span class="i">$Nc</span> + <span class="i">$Nd</span><span class="sc">;</span> + 923 + 924 <span class="i">$Numerator</span> = <span class="s">(</span><span class="i">$Nc</span>*<span class="i">$Nd</span><span class="s">)</span> - <span class="s">(</span><span class="s">(</span><span class="i">$Na</span> - <span class="i">$Nc</span><span class="s">)</span>*<span class="s">(</span><span class="i">$Nb</span> - <span class="i">$Nc</span><span class="s">)</span><span class="s">)</span> <span class="sc">;</span> + 925 <span class="i">$Denominator</span> = <span class="s">(</span><span class="i">$Nc</span>*<span class="i">$Nd</span><span class="s">)</span> + <span class="s">(</span><span class="s">(</span><span class="i">$Na</span> - <span class="i">$Nc</span><span class="s">)</span>*<span class="s">(</span><span class="i">$Nb</span> - <span class="i">$Nc</span><span class="s">)</span><span class="s">)</span> <span class="sc">;</span> + 926 + 927 <span class="k">return</span> <span class="i">$Denominator</span> ? <span class="s">(</span><span class="i">$Numerator</span>/<span class="i">$Denominator</span><span class="s">)</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 928 <span class="s">}</span> + 929 + 930 <span class="c"># Calculate WeightedTanimoto similarity coefficient for two same size bit vectors.</span> + 931 <span class="c">#</span> + 932 <span class="c"># This functionality can be either invoked as a class function or an object method.</span> + 933 <span class="c">#</span> +<a name="WeightedTanimotoSimilarityCoefficient-"></a> 934 <span class="k">sub </span><span class="m">WeightedTanimotoSimilarityCoefficient ($$$)</span> <span class="s">{</span> + 935 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="cm">,</span> <span class="i">$Beta</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 936 <span class="k">my</span><span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="cm">,</span> <span class="i">$TanimotoForSetBits</span><span class="cm">,</span> <span class="i">$TanimotoForClearBits</span><span class="cm">,</span> <span class="i">$Numerator</span><span class="cm">,</span> <span class="i">$Denominator</span><span class="cm">,</span> <span class="i">$WeightedTanimoto</span><span class="s">)</span><span class="sc">;</span> + 937 + 938 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Beta</span><span class="s">)</span> && <span class="s">(</span><span class="i">$Beta</span> >= <span class="n">0</span> && <span class="i">$Beta</span> <= <span class="n">1</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 939 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->WeightedTanimotoSimilarityCoefficient: Beta parameters must be defined and its value must be >=0 and <=1 ..."</span><span class="sc">;</span> + 940 <span class="s">}</span> + 941 + 942 <span class="c"># Get Tanimoto for set bits...</span> + 943 <span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="s">)</span> = <span class="i">_GetNumOfIndividualAndCommonSetBits</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span> + 944 + 945 <span class="i">$Numerator</span> = <span class="i">$Nc</span><span class="sc">;</span> + 946 <span class="i">$Denominator</span> = <span class="i">$Na</span> + <span class="i">$Nb</span> - <span class="i">$Nc</span><span class="sc">;</span> + 947 <span class="i">$TanimotoForSetBits</span> = <span class="i">$Denominator</span> ? <span class="s">(</span><span class="i">$Numerator</span>/<span class="i">$Denominator</span><span class="s">)</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 948 + 949 <span class="c"># Get Tanimoto for clear bits...</span> + 950 <span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="s">)</span> = <span class="i">_GetNumOfIndividualAndCommonClearBits</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span> + 951 + 952 <span class="i">$Numerator</span> = <span class="i">$Nc</span><span class="sc">;</span> + 953 <span class="i">$Denominator</span> = <span class="i">$Na</span> + <span class="i">$Nb</span> - <span class="i">$Nc</span><span class="sc">;</span> + 954 <span class="i">$TanimotoForClearBits</span> = <span class="i">$Denominator</span> ? <span class="s">(</span><span class="i">$Numerator</span>/<span class="i">$Denominator</span><span class="s">)</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 955 + 956 <span class="i">$WeightedTanimoto</span> = <span class="i">$Beta</span>*<span class="i">$TanimotoForSetBits</span> + <span class="s">(</span><span class="n">1</span> - <span class="i">$Beta</span><span class="s">)</span>*<span class="i">$TanimotoForClearBits</span><span class="sc">;</span> + 957 + 958 <span class="k">return</span> <span class="i">$WeightedTanimoto</span><span class="sc">;</span> + 959 <span class="s">}</span> + 960 + 961 <span class="c"># Calculate WeightedTversky similarity coefficient for two same size bit vectors.</span> + 962 <span class="c">#</span> + 963 <span class="c"># This functionality can be either invoked as a class function or an object method.</span> + 964 <span class="c">#</span> +<a name="WeightedTverskySimilarityCoefficient-"></a> 965 <span class="k">sub </span><span class="m">WeightedTverskySimilarityCoefficient ($$$)</span> <span class="s">{</span> + 966 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="cm">,</span> <span class="i">$Alpha</span><span class="cm">,</span> <span class="i">$Beta</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 967 <span class="k">my</span><span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="cm">,</span> <span class="i">$TverskyForSetBits</span><span class="cm">,</span> <span class="i">$TverskyForClearBits</span><span class="cm">,</span> <span class="i">$Numerator</span><span class="cm">,</span> <span class="i">$Denominator</span><span class="cm">,</span> <span class="i">$WeightedTversky</span><span class="s">)</span><span class="sc">;</span> + 968 + 969 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Alpha</span><span class="s">)</span> && <span class="s">(</span><span class="i">$Alpha</span> >= <span class="n">0</span> && <span class="i">$Alpha</span> <= <span class="n">1</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 970 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->WeightedTverskySimilarityCoefficient: Alpha parameters must be defined and its value must be >=0 and <=1 ..."</span><span class="sc">;</span> + 971 <span class="s">}</span> + 972 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Beta</span><span class="s">)</span> && <span class="s">(</span><span class="i">$Beta</span> >= <span class="n">0</span> && <span class="i">$Beta</span> <= <span class="n">1</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 973 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->WeightedTverskySimilarityCoefficient: Beta parameters must be defined and its value must be >=0 and <=1 ..."</span><span class="sc">;</span> + 974 <span class="s">}</span> + 975 + 976 <span class="c"># Get Tversky for set bits...</span> + 977 <span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="s">)</span> = <span class="i">_GetNumOfIndividualAndCommonSetBits</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span> + 978 + 979 <span class="i">$Numerator</span> = <span class="i">$Nc</span><span class="sc">;</span> + 980 <span class="i">$Denominator</span> = <span class="i">$Alpha</span>*<span class="s">(</span><span class="i">$Na</span> - <span class="i">$Nb</span> <span class="s">)</span> + <span class="i">$Nb</span><span class="sc">;</span> + 981 <span class="i">$TverskyForSetBits</span> = <span class="i">$Denominator</span> ? <span class="s">(</span><span class="i">$Numerator</span>/<span class="i">$Denominator</span><span class="s">)</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 982 + 983 <span class="c"># Get Tversky for clear bits...</span> + 984 <span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="s">)</span> = <span class="i">_GetNumOfIndividualAndCommonClearBits</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span> + 985 + 986 <span class="i">$Numerator</span> = <span class="i">$Nc</span><span class="sc">;</span> + 987 <span class="i">$Denominator</span> = <span class="i">$Alpha</span>*<span class="s">(</span><span class="i">$Na</span> - <span class="i">$Nb</span> <span class="s">)</span> + <span class="i">$Nb</span><span class="sc">;</span> + 988 <span class="i">$TverskyForClearBits</span> = <span class="i">$Denominator</span> ? <span class="s">(</span><span class="i">$Numerator</span>/<span class="i">$Denominator</span><span class="s">)</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 989 + 990 <span class="i">$WeightedTversky</span> = <span class="i">$Beta</span>*<span class="i">$TverskyForSetBits</span> + <span class="s">(</span><span class="n">1</span> - <span class="i">$Beta</span><span class="s">)</span>*<span class="i">$TverskyForClearBits</span><span class="sc">;</span> + 991 + 992 <span class="k">return</span> <span class="i">$WeightedTversky</span><span class="sc">;</span> + 993 <span class="s">}</span> + 994 + 995 <span class="c"># Get number of Na, Nb and Nc bits in bit vector A and B to be used for similarity coefficient calculations...</span> + 996 <span class="c">#</span> +<a name="_GetNumOfIndividualAndCommonSetBits-"></a> 997 <span class="k">sub </span><span class="m">_GetNumOfIndividualAndCommonSetBits ($$)</span> <span class="s">{</span> + 998 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 999 <span class="k">my</span><span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="cm">,</span> <span class="i">$Nd</span><span class="s">)</span><span class="sc">;</span> +1000 +1001 <span class="c"># Number of bits set to "1" in A</span> +1002 <span class="i">$Na</span> = <span class="i">$FingerprintsBitVectorA</span><span class="i">->GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1003 +1004 <span class="c"># Number of bits set to "1" in B</span> +1005 <span class="i">$Nb</span> = <span class="i">$FingerprintsBitVectorB</span><span class="i">->GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1006 +1007 <span class="c"># Number of bits set to "1" in both A and B</span> +1008 <span class="k">my</span><span class="s">(</span><span class="i">$NcBitVector</span><span class="s">)</span><span class="sc">;</span> +1009 <span class="i">$NcBitVector</span> = <span class="i">$FingerprintsBitVectorA</span> & <span class="i">$FingerprintsBitVectorB</span><span class="sc">;</span> +1010 <span class="i">$Nc</span> = <span class="i">$NcBitVector</span><span class="i">->GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1011 +1012 <span class="k">return</span> <span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="s">)</span><span class="sc">;</span> +1013 <span class="s">}</span> +1014 +1015 <span class="c"># Get number of Nd bits in bit vector A and B to be used for similarity coefficient calculations...</span> +1016 <span class="c">#</span> +<a name="_GetNumOfCommonClearBits-"></a>1017 <span class="k">sub </span><span class="m">_GetNumOfCommonClearBits ($$)</span> <span class="s">{</span> +1018 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> +1019 <span class="k">my</span><span class="s">(</span><span class="i">$Nd</span><span class="cm">,</span> <span class="i">$NdBitVector</span><span class="s">)</span><span class="sc">;</span> +1020 +1021 <span class="c"># Number of bits set to "0" in both A and B</span> +1022 <span class="i">$NdBitVector</span> = ~<span class="i">$FingerprintsBitVectorA</span> & ~<span class="i">$FingerprintsBitVectorB</span><span class="sc">;</span> +1023 <span class="i">$Nd</span> = <span class="i">$NdBitVector</span><span class="i">->GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1024 +1025 <span class="c"># Correct for number of clear bits used for padding...</span> +1026 <span class="k">if</span> <span class="s">(</span><span class="i">_IsNumOfClearBitsCorrectionRequired</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1027 <span class="i">$Nd</span> = <span class="i">$Nd</span> - <span class="i">_GetNumOfClearBitsCorrection</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="s">)</span><span class="sc">;</span> +1028 <span class="s">}</span> +1029 <span class="k">elsif</span> <span class="s">(</span><span class="i">_IsNumOfClearBitsCorrectionRequired</span><span class="s">(</span><span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1030 <span class="i">$Nd</span> = <span class="i">$Nd</span> - <span class="i">_GetNumOfClearBitsCorrection</span><span class="s">(</span><span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span> +1031 <span class="s">}</span> +1032 +1033 <span class="k">return</span> <span class="i">$Nd</span><span class="sc">;</span> +1034 <span class="s">}</span> +1035 +1036 <span class="c"># Get number of Na, Nb and Nc bits in bit vector A and B to be used for similarity coefficient calculations...</span> +1037 <span class="c">#</span> +<a name="_GetNumOfIndividualAndCommonClearBits-"></a>1038 <span class="k">sub </span><span class="m">_GetNumOfIndividualAndCommonClearBits ($$)</span> <span class="s">{</span> +1039 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> +1040 <span class="k">my</span><span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="cm">,</span> <span class="i">$Nd</span><span class="s">)</span><span class="sc">;</span> +1041 +1042 <span class="c"># Number of bits set to "0" in A</span> +1043 <span class="i">$Na</span> = <span class="i">$FingerprintsBitVectorA</span><span class="i">->GetNumOfClearBits</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1044 +1045 <span class="c"># Correct for number of clear bits used for padding...</span> +1046 <span class="k">if</span> <span class="s">(</span><span class="i">_IsNumOfClearBitsCorrectionRequired</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1047 <span class="i">$Na</span> = <span class="i">$Na</span> - <span class="i">_GetNumOfClearBitsCorrection</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="s">)</span><span class="sc">;</span> +1048 <span class="s">}</span> +1049 +1050 <span class="c"># Number of bits set to "0" in B</span> +1051 <span class="i">$Nb</span> = <span class="i">$FingerprintsBitVectorB</span><span class="i">->GetNumOfClearBits</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> +1052 +1053 <span class="c"># Correct for number of clear bits used for padding...</span> +1054 <span class="k">if</span> <span class="s">(</span><span class="i">_IsNumOfClearBitsCorrectionRequired</span><span class="s">(</span><span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> +1055 <span class="i">$Nb</span> = <span class="i">$Nb</span> - <span class="i">_GetNumOfClearBitsCorrection</span><span class="s">(</span><span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span> +1056 <span class="s">}</span> +1057 +1058 <span class="c"># Number of bits set to "0" in both A and B</span> +1059 <span class="i">$Nc</span> = <span class="i">_GetNumOfCommonClearBits</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span> +1060 +1061 <span class="k">return</span> <span class="s">(</span><span class="i">$Na</span><span class="cm">,</span> <span class="i">$Nb</span><span class="cm">,</span> <span class="i">$Nc</span><span class="s">)</span><span class="sc">;</span> +1062 <span class="s">}</span> +1063 +1064 <span class="c"># Irrespective of specified size, Perl functions used to handle bit data data in</span> +1065 <span class="c"># BitVector class automatically sets the size to the next nearest power of 2</span> +1066 <span class="c"># and clear the extra bits.</span> +1067 <span class="c">#</span> +1068 <span class="c"># SpecifiedSize is used by this class to process any aribitray size during similarity</span> +1069 <span class="c"># coefficient calculations.</span> +1070 <span class="c">#</span> +1071 <span class="c"># Assuming the FingerprintsBitBector class only manipulates bits upto specified</span> +1072 <span class="c"># size, a correction for the extra bits added by BitVector class needs to be applied</span> +1073 <span class="c"># to number of clear bits.</span> +1074 <span class="c">#</span> +<a name="_GetNumOfClearBitsCorrection-"></a>1075 <span class="k">sub </span><span class="m">_GetNumOfClearBitsCorrection</span> <span class="s">{</span> +1076 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsBitVector</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> +1077 +1078 <span class="k">return</span> <span class="s">(</span><span class="i">$FingerprintsBitVector</span>->{<span class="w">Size</span>} - <span class="i">$FingerprintsBitVector</span>->{<span class="w">SpecifiedSize</span>}<span class="s">)</span><span class="sc">;</span> +1079 <span class="s">}</span> +1080 +1081 <span class="c"># Is number of clear bits correction required?</span> +1082 <span class="c">#</span> +<a name="_IsNumOfClearBitsCorrectionRequired-"></a>1083 <span class="k">sub </span><span class="m">_IsNumOfClearBitsCorrectionRequired</span> <span class="s">{</span> +1084 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsBitVector</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> +1085 +1086 <span class="k">return</span> <span class="s">(</span><span class="i">$FingerprintsBitVector</span>->{<span class="w">Size</span>} > <span class="i">$FingerprintsBitVector</span>->{<span class="w">SpecifiedSize</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> +1087 <span class="s">}</span> +1088 +1089 +<a name="EOF-"></a></pre> +<p> </p> +<br /> +<center> +<img src="../../../images/h2o2.png"> +</center> +</body> +</html>