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14 <a name="package-Fingerprints::FingerprintsBitVector-"></a> 1 <span class="k">package </span><span class="i">Fingerprints::FingerprintsBitVector</span><span class="sc">;</span>
15 2 <span class="c">#</span>
16 3 <span class="c"># $RCSfile: FingerprintsBitVector.pm,v $</span>
17 4 <span class="c"># $Date: 2015/02/28 20:48:54 $</span>
18 5 <span class="c"># $Revision: 1.27 $</span>
19 6 <span class="c">#</span>
20 7 <span class="c"># Author: Manish Sud &lt;msud@san.rr.com&gt;</span>
21 8 <span class="c">#</span>
22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
23 10 <span class="c">#</span>
24 11 <span class="c"># This file is part of MayaChemTools.</span>
25 12 <span class="c">#</span>
26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
29 16 <span class="c"># later version.</span>
30 17 <span class="c">#</span>
31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span>
34 21 <span class="c"># details.</span>
35 22 <span class="c">#</span>
36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
37 24 <span class="c"># along with MayaChemTools; if not, see &lt;http://www.gnu.org/licenses/&gt; or</span>
38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
40 27 <span class="c">#</span>
41 28
42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
43 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span>
44 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span>
45 32 <span class="k">use</span> <span class="w">Scalar::Util</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
46 33 <span class="k">use</span> <span class="w">BitVector</span><span class="sc">;</span>
47 34 <span class="k">use</span> <span class="w">MathUtil</span><span class="sc">;</span>
48 35 <span class="k">use</span> <span class="w">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
49 36
50 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>
51 38
52 39 <span class="i">@ISA</span> = <span class="q">qw(BitVector Exporter)</span><span class="sc">;</span>
53 40
54 41 <span class="c"># Similiarity coefficients...</span>
55 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>
56 43
57 44 <span class="c"># New from string...</span>
58 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>
59 46
60 47 <span class="i">@EXPORT</span> = <span class="q">qw(IsFingerprintsBitVector)</span><span class="sc">;</span>
61 48 <span class="i">@EXPORT_OK</span> = <span class="q">qw(GetSupportedSimilarityCoefficients @NewFromString @SimilarityCoefficients)</span><span class="sc">;</span>
62 49
63 50 <span class="i">%EXPORT_TAGS</span> = <span class="s">(</span>
64 51 <span class="w">new</span> <span class="cm">=&gt;</span> <span class="s">[</span><span class="i">@NewFromString</span><span class="s">]</span><span class="cm">,</span>
65 52 <span class="w">coefficients</span> <span class="cm">=&gt;</span> <span class="s">[</span><span class="i">@SimilarityCoefficients</span><span class="s">]</span><span class="cm">,</span>
66 53 <span class="w">all</span> <span class="cm">=&gt;</span> <span class="s">[</span><span class="i">@EXPORT</span><span class="cm">,</span> <span class="i">@EXPORT_OK</span><span class="s">]</span>
67 54 <span class="s">)</span><span class="sc">;</span>
68 55
69 56 <span class="c"># Setup class variables...</span>
70 57 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="sc">;</span>
71 58 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
72 59
73 60 <span class="k">use</span> <span class="w">overload</span> <span class="q">&#39;&quot;&quot;&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;StringifyFingerprintsBitVector&#39;</span><span class="sc">;</span>
74 61
75 62 <span class="c"># Class constructor...</span>
76 <a name="new-"></a> 63 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span>
77 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>
78 65
79 66 <span class="c"># Initialize object...</span>
80 67 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">-&gt;SUPER::new</span><span class="s">(</span><span class="i">$Size</span><span class="s">)</span><span class="sc">;</span>
81 68 <span class="k">bless</span> <span class="i">$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>
82 69 <span class="i">$This</span><span class="i">-&gt;_InitializeFingerprintsBitVector</span><span class="s">(</span><span class="i">$Size</span><span class="s">)</span><span class="sc">;</span>
83 70
84 71 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
85 72 <span class="s">}</span>
86 73
87 74 <span class="c"># Initialize object data...</span>
88 75 <span class="c">#</span>
89 76 <span class="c"># Note:</span>
90 77 <span class="c"># . The class, BitVector, used to derive this class provides all the functionality to</span>
91 78 <span class="c"># manipulate bits.</span>
92 79 <span class="c"># . Irrespective of specified size, Perl functions used to handle bit data in</span>
93 80 <span class="c"># BitVector class automatically sets the size to the next nearest power of 2.</span>
94 81 <span class="c"># SpecifiedSize is used by this class to process any aribitray size during similarity</span>
95 82 <span class="c"># coefficient calculations.</span>
96 83 <span class="c">#</span>
97 <a name="_InitializeFingerprintsBitVector-"></a> 84 <span class="k">sub </span><span class="m">_InitializeFingerprintsBitVector</span> <span class="s">{</span>
98 85 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Size</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
99 86
100 87 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$Size</span><span class="s">)</span> <span class="s">{</span>
101 88 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;new: FingerprintsBitVector object instantiated without specifying its size ...&quot;</span><span class="sc">;</span>
102 89 <span class="s">}</span>
103 90 <span class="k">if</span> <span class="s">(</span><span class="i">$Size</span> &lt;=<span class="n">0</span><span class="s">)</span> <span class="s">{</span>
104 91 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;new: Fingerprints bit vector size, $Size, must be a positive integer...&quot;</span><span class="sc">;</span>
105 92 <span class="s">}</span>
106 93
107 94 <span class="c"># Specified size of fingerprints...</span>
108 95 <span class="i">$This</span>-&gt;{<span class="w">SpecifiedSize</span>} = <span class="i">$Size</span><span class="sc">;</span>
109 96
110 97 <span class="s">}</span>
111 98
112 99 <span class="c"># Initialize class ...</span>
113 <a name="_InitializeClass-"></a> 100 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span>
114 101 <span class="c">#Class name...</span>
115 102 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span>
116 103 <span class="s">}</span>
117 104
118 105 <span class="c"># Set specified size...</span>
119 106 <span class="c">#</span>
120 107 <span class="c"># Notes:</span>
121 108 <span class="c"># Irrespective of specified size, Perl functions used to handle bit data in</span>
122 109 <span class="c"># BitVector class automatically sets the size to the next nearest power of 2.</span>
123 110 <span class="c"># SpecifiedSize is used by this class to process any aribitray size during similarity</span>
124 111 <span class="c"># coefficient calculations.</span>
125 112 <span class="c">#</span>
126 <a name="SetSpecifiedSize-"></a> 113 <span class="k">sub </span><span class="m">SetSpecifiedSize</span> <span class="s">{</span>
127 114 <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>
128 115
129 116 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$SpecifiedSize</span> &gt; <span class="n">0</span> &amp;&amp; <span class="i">$SpecifiedSize</span> &lt;= <span class="i">$This</span>-&gt;{<span class="w">Size</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
130 117 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetSpecifiedSize: Specified size, $SpecifiedSize, is not valid: It must be &gt; 0 &amp;&amp; &lt;= &quot;</span><span class="cm">,</span> <span class="i">$This</span><span class="i">-&gt;GetSize</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span><span class="q">&quot; ...&quot;</span><span class="sc">;</span>
131 118 <span class="s">}</span>
132 119 <span class="i">$This</span>-&gt;{<span class="w">SpecifiedSize</span>} = <span class="i">$SpecifiedSize</span><span class="sc">;</span>
133 120 <span class="s">}</span>
134 121
135 122 <span class="c"># Get specified size...</span>
136 <a name="GetSpecifiedSize-"></a> 123 <span class="k">sub </span><span class="m">GetSpecifiedSize</span> <span class="s">{</span>
137 124 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
138 125
139 126 <span class="k">return</span> <span class="i">$This</span>-&gt;{<span class="w">SpecifiedSize</span>}<span class="sc">;</span>
140 127 <span class="s">}</span>
141 128
142 129 <span class="c"># Set ID...</span>
143 <a name="SetID-"></a> 130 <span class="k">sub </span><span class="m">SetID</span> <span class="s">{</span>
144 131 <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>
145 132
146 133 <span class="i">$This</span>-&gt;{<span class="w">ID</span>} = <span class="i">$Value</span><span class="sc">;</span>
147 134
148 135 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
149 136 <span class="s">}</span>
150 137
151 138 <span class="c"># Get ID...</span>
152 <a name="GetID-"></a> 139 <span class="k">sub </span><span class="m">GetID</span> <span class="s">{</span>
153 140 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
154 141
155 142 <span class="k">return</span> <span class="k">exists</span> <span class="i">$This</span>-&gt;{<span class="w">ID</span>} ? <span class="i">$This</span>-&gt;{<span class="w">ID</span>} <span class="co">:</span> <span class="q">&#39;None&#39;</span><span class="sc">;</span>
156 143 <span class="s">}</span>
157 144
158 145 <span class="c"># Set description...</span>
159 <a name="SetDescription-"></a> 146 <span class="k">sub </span><span class="m">SetDescription</span> <span class="s">{</span>
160 147 <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>
161 148
162 149 <span class="i">$This</span>-&gt;{<span class="w">Description</span>} = <span class="i">$Value</span><span class="sc">;</span>
163 150
164 151 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
165 152 <span class="s">}</span>
166 153
167 154 <span class="c"># Get description...</span>
168 <a name="GetDescription-"></a> 155 <span class="k">sub </span><span class="m">GetDescription</span> <span class="s">{</span>
169 156 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
170 157
171 158 <span class="k">return</span> <span class="k">exists</span> <span class="i">$This</span>-&gt;{<span class="w">Description</span>} ? <span class="i">$This</span>-&gt;{<span class="w">Description</span>} <span class="co">:</span> <span class="q">&#39;No description available&#39;</span><span class="sc">;</span>
172 159 <span class="s">}</span>
173 160
174 161 <span class="c"># Set vector type...</span>
175 <a name="SetVectorType-"></a> 162 <span class="k">sub </span><span class="m">SetVectorType</span> <span class="s">{</span>
176 163 <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>
177 164
178 165 <span class="i">$This</span>-&gt;{<span class="w">VectorType</span>} = <span class="i">$Value</span><span class="sc">;</span>
179 166
180 167 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
181 168 <span class="s">}</span>
182 169
183 170 <span class="c"># Get vector type...</span>
184 <a name="GetVectorType-"></a> 171 <span class="k">sub </span><span class="m">GetVectorType</span> <span class="s">{</span>
185 172 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
186 173
187 174 <span class="k">return</span> <span class="k">exists</span> <span class="i">$This</span>-&gt;{<span class="w">VectorType</span>} ? <span class="i">$This</span>-&gt;{<span class="w">VectorType</span>} <span class="co">:</span> <span class="q">&#39;FingerprintsBitVector&#39;</span><span class="sc">;</span>
188 175 <span class="s">}</span>
189 176
190 177 <span class="c"># Create a new fingerprints bit vector using binary string. This functionality can be</span>
191 178 <span class="c"># either invoked as a class function or an object method.</span>
192 179 <span class="c">#</span>
193 <a name="NewFromBinaryString-"></a> 180 <span class="k">sub </span><span class="m">NewFromBinaryString ($;$)</span> <span class="s">{</span>
194 181 <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">$ThirdParameter</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
195 182
196 183 <span class="k">if</span> <span class="s">(</span><span class="i">_IsFingerprintsBitVector</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
197 184 <span class="k">return</span> <span class="i">_NewFingerptinsBitVectorFromString</span><span class="s">(</span><span class="q">&#39;Binary&#39;</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>
198 185 <span class="s">}</span>
199 186 <span class="k">else</span> <span class="s">{</span>
200 187 <span class="k">return</span> <span class="i">_NewFingerptinsBitVectorFromString</span><span class="s">(</span> <span class="q">&#39;Binary&#39;</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>
201 188 <span class="s">}</span>
202 189 <span class="s">}</span>
203 190
204 191 <span class="c"># Create a new fingerprints bit vector using hexadecimal string. This functionality can be</span>
205 192 <span class="c"># either invoked as a class function or an object method.</span>
206 193 <span class="c">#</span>
207 <a name="NewFromHexadecimalString-"></a> 194 <span class="k">sub </span><span class="m">NewFromHexadecimalString ($;$)</span> <span class="s">{</span>
208 195 <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">$ThirdParameter</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
209 196
210 197 <span class="k">if</span> <span class="s">(</span><span class="i">_IsFingerprintsBitVector</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
211 198 <span class="k">return</span> <span class="i">_NewFingerptinsBitVectorFromString</span><span class="s">(</span><span class="q">&#39;Hexadecimal&#39;</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>
212 199 <span class="s">}</span>
213 200 <span class="k">else</span> <span class="s">{</span>
214 201 <span class="k">return</span> <span class="i">_NewFingerptinsBitVectorFromString</span><span class="s">(</span> <span class="q">&#39;Hexadecimal&#39;</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>
215 202 <span class="s">}</span>
216 203 <span class="s">}</span>
217 204
218 205 <span class="c"># Create a new fingerprints bit vector using octal string. This functionality can be</span>
219 206 <span class="c"># either invoked as a class function or an object method.</span>
220 207 <span class="c">#</span>
221 208 <span class="c">#</span>
222 <a name="NewFromOctalString-"></a> 209 <span class="k">sub </span><span class="m">NewFromOctalString ($)</span> <span class="s">{</span>
223 210 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;NewFromOctalString: Creation of fingerprits bit vector from an octal string is not supported ...&quot;</span><span class="sc">;</span>
224 211 <span class="s">}</span>
225 212
226 213 <span class="c"># Create a new fingerprints bit vector using decimal string. This functionality can be</span>
227 214 <span class="c"># either invoked as a class function or an object method.</span>
228 215 <span class="c">#</span>
229 <a name="NewFromDecimalString-"></a> 216 <span class="k">sub </span><span class="m">NewFromDecimalString ($;$)</span> <span class="s">{</span>
230 217 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;NewFromDecimalString: Creation of fingerprits bit vector from a decimal string is not supported ...&quot;</span><span class="sc">;</span>
231 218 <span class="s">}</span>
232 219
233 220 <span class="c"># Create a new fingerprints bit vector using raw binary string. This functionality can be</span>
234 221 <span class="c"># either invoked as a class function or an object method.</span>
235 222 <span class="c">#</span>
236 <a name="NewFromRawBinaryString-"></a> 223 <span class="k">sub </span><span class="m">NewFromRawBinaryString ($;$)</span> <span class="s">{</span>
237 224 <span class="k">my</span><span class="s">(</span><span class="i">$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>
238 225
239 226 <span class="k">if</span> <span class="s">(</span><span class="i">_IsFingerprintsBitVector</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
240 227 <span class="k">return</span> <span class="i">_NewFingerptinsBitVectorFromString</span><span class="s">(</span><span class="q">&#39;RawBinary&#39;</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="cm">,</span> <span class="i">$ThirdParameter</span><span class="s">)</span><span class="sc">;</span>
241 228 <span class="s">}</span>
242 229 <span class="k">else</span> <span class="s">{</span>
243 230 <span class="k">return</span> <span class="i">_NewFingerptinsBitVectorFromString</span><span class="s">(</span> <span class="q">&#39;RawBinary&#39;</span><span class="cm">,</span> <span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span><span class="sc">;</span>
244 231 <span class="s">}</span>
245 232 <span class="s">}</span>
246 233
247 234 <span class="c"># Create a new fingerprints bit vector from a string...</span>
248 235 <span class="c">#</span>
249 236 <span class="c">#</span>
250 <a name="_NewFingerptinsBitVectorFromString-"></a> 237 <span class="k">sub </span><span class="m">_NewFingerptinsBitVectorFromString ($$;$)</span> <span class="s">{</span>
251 238 <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>
252 239 <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>
253 240
254 241 <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>
255 242
256 243 <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>
257 244 <span class="i">$FingerprintsBitVector</span><span class="i">-&gt;_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>
258 245
259 246 <span class="k">return</span> <span class="i">$FingerprintsBitVector</span><span class="sc">;</span>
260 247 <span class="s">}</span>
261 248
262 249 <span class="c"># Get fingerprint bits as a hexadecimal string...</span>
263 250 <span class="c">#</span>
264 <a name="GetBitsAsHexadecimalString-"></a> 251 <span class="k">sub </span><span class="m">GetBitsAsHexadecimalString</span> <span class="s">{</span>
265 252 <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>
266 253
267 254 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;_GetFingerprintBitsAsString</span><span class="s">(</span><span class="q">&#39;Hexadecimal&#39;</span><span class="cm">,</span> <span class="i">$BitsOrder</span><span class="s">)</span><span class="sc">;</span>
268 255 <span class="s">}</span>
269 256
270 257 <span class="c"># Get fingerprint bits as an octal string...</span>
271 258 <span class="c">#</span>
272 <a name="GetBitsAsOctalString-"></a> 259 <span class="k">sub </span><span class="m">GetBitsAsOctalString</span> <span class="s">{</span>
273 260 <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>
274 261
275 262 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;GetBitsAsOctalString: Retrieval of fingerprits bits as an octal string is not supported ...&quot;</span><span class="sc">;</span>
276 263 <span class="s">}</span>
277 264
278 265 <span class="c"># Get fingerprint bits as an decimal string...</span>
279 266 <span class="c">#</span>
280 <a name="GetBitsAsDecimalString-"></a> 267 <span class="k">sub </span><span class="m">GetBitsAsDecimalString</span> <span class="s">{</span>
281 268 <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>
282 269
283 270 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;GetBitsAsOctalString: Retrieval of fingerprits bits as a decimal string is not supported ...&quot;</span><span class="sc">;</span>
284 271 <span class="s">}</span>
285 272
286 273 <span class="c"># Get fingerprint bits as a binary string conatning 1s and 0s...</span>
287 274 <span class="c">#</span>
288 <a name="GetBitsAsBinaryString-"></a> 275 <span class="k">sub </span><span class="m">GetBitsAsBinaryString</span> <span class="s">{</span>
289 276 <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>
290 277
291 278 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;_GetFingerprintBitsAsString</span><span class="s">(</span><span class="q">&#39;Binary&#39;</span><span class="cm">,</span> <span class="i">$BitsOrder</span><span class="s">)</span><span class="sc">;</span>
292 279 <span class="s">}</span>
293 280
294 281 <span class="c"># Get fingerprint bits as a binary string conatning 1s and 0s...</span>
295 282 <span class="c">#</span>
296 <a name="GetBitsAsRawBinaryString-"></a> 283 <span class="k">sub </span><span class="m">GetBitsAsRawBinaryString</span> <span class="s">{</span>
297 284 <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>
298 285
299 286 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;_GetFingerprintBitsAsString</span><span class="s">(</span><span class="q">&#39;RawBinary&#39;</span><span class="s">)</span><span class="sc">;</span>
300 287 <span class="s">}</span>
301 288
302 289 <span class="c"># Return fingerprint bits as a string...</span>
303 290 <span class="c">#</span>
304 <a name="_GetFingerprintBitsAsString-"></a> 291 <span class="k">sub </span><span class="m">_GetFingerprintBitsAsString</span> <span class="s">{</span>
305 292 <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>
306 293
307 294 <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> &amp;&amp; <span class="i">$BitsOrder</span><span class="s">)</span> ? <span class="i">$BitsOrder</span> <span class="co">:</span> <span class="q">&#39;Ascending&#39;</span><span class="sc">;</span>
308 295
309 296 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;_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>
310 297 <span class="s">}</span>
311 298
312 299 <span class="c"># Is it a fingerprints bit vector object?</span>
313 <a name="IsFingerprintsBitVector-"></a> 300 <span class="k">sub </span><span class="m">IsFingerprintsBitVector ($)</span> <span class="s">{</span>
314 301 <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>
315 302
316 303 <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>
317 304 <span class="s">}</span>
318 305
319 306 <span class="c"># Is it a fingerprints bit vector object?</span>
320 <a name="_IsFingerprintsBitVector-"></a> 307 <span class="k">sub </span><span class="m">_IsFingerprintsBitVector</span> <span class="s">{</span>
321 308 <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>
322 309
323 310 <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> &amp;&amp; <span class="i">$Object</span><span class="i">-&gt;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>
324 311 <span class="s">}</span>
325 312
326 313 <span class="c"># Return a list of supported similarity coefficients...</span>
327 <a name="GetSupportedSimilarityCoefficients-"></a> 314 <span class="k">sub </span><span class="m">GetSupportedSimilarityCoefficients ()</span> <span class="s">{</span>
328 315
329 316 <span class="k">return</span> <span class="i">@SimilarityCoefficients</span><span class="sc">;</span>
330 317 <span class="s">}</span>
331 318
332 319 <span class="c"># Get bit density for fingerprints bit vector corresponding to on bits...</span>
333 320 <span class="c">#</span>
334 <a name="GetFingerprintsBitDensity-"></a> 321 <span class="k">sub </span><span class="m">GetFingerprintsBitDensity</span> <span class="s">{</span>
335 322 <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>
336 323 <span class="k">my</span><span class="s">(</span><span class="i">$BitDensity</span><span class="s">)</span><span class="sc">;</span>
337 324
338 325 <span class="i">$BitDensity</span> = <span class="i">$This</span><span class="i">-&gt;GetDensityOfSetBits</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
339 326
340 327 <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>
341 328 <span class="s">}</span>
342 329
343 330 <span class="c"># Fold fingerprints bit vector by recursively reducing its size by half untill size is less than or equal to</span>
344 331 <span class="c"># specified size...</span>
345 332 <span class="c">#</span>
346 <a name="FoldFingerprintsBitVectorBySize-"></a> 333 <span class="k">sub </span><span class="m">FoldFingerprintsBitVectorBySize</span> <span class="s">{</span>
347 334 <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>
348 335
349 336 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$Size</span> &gt; <span class="n">0</span> &amp;&amp; <span class="i">$Size</span> &lt;= <span class="i">$This</span><span class="i">-&gt;GetSize</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
350 337 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;FoldFingerprintsBitVectorBySize: Specified size, $Size, is not valid: It must be &gt; 0 &amp;&amp; &lt;= &quot;</span><span class="cm">,</span> <span class="i">$This</span><span class="i">-&gt;GetSize</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span><span class="q">&quot; ...&quot;</span><span class="sc">;</span>
351 338 <span class="s">}</span>
352 339
353 340 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">-&gt;GetSize</span><span class="s">(</span><span class="s">)</span> &lt;= <span class="i">$Size</span><span class="s">)</span> <span class="s">{</span>
354 341 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
355 342 <span class="s">}</span>
356 343 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;_FoldFingerprintsBitVector</span><span class="s">(</span><span class="q">&#39;BySize&#39;</span><span class="cm">,</span> <span class="i">$Size</span><span class="s">)</span><span class="sc">;</span>
357 344 <span class="s">}</span>
358 345
359 346 <span class="c"># Fold fingerprints bit vector by recursively reducing its size by half untill bit density of set bits is greater than</span>
360 347 <span class="c"># or equal to specified density...</span>
361 348 <span class="c">#</span>
362 <a name="FoldFingerprintsBitVectorByDensity-"></a> 349 <span class="k">sub </span><span class="m">FoldFingerprintsBitVectorByDensity</span> <span class="s">{</span>
363 350 <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>
364 351
365 352 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$Density</span> &gt; <span class="n">0</span> &amp;&amp; <span class="i">$Density</span> &lt;= <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
366 353 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;FoldFingerprintsBitVectorByDensity: Specified bit density, $Density, is not valid: It must be &gt; 0 &amp;&amp; &lt;= 1 ...&quot;</span><span class="sc">;</span>
367 354 <span class="s">}</span>
368 355
369 356 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">-&gt;GetDensityOfSetBits</span><span class="s">(</span><span class="s">)</span> &gt;= <span class="i">$Density</span><span class="s">)</span> <span class="s">{</span>
370 357 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
371 358 <span class="s">}</span>
372 359 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;_FoldFingerprintsBitVector</span><span class="s">(</span><span class="q">&#39;ByDensity&#39;</span><span class="cm">,</span> <span class="i">$Density</span><span class="s">)</span><span class="sc">;</span>
373 360 <span class="s">}</span>
374 361
375 362 <span class="c"># Fold fingerprints bit vector using size or density and return folded fingerprint bit vector...</span>
376 363 <span class="c">#</span>
377 <a name="_FoldFingerprintsBitVector-"></a> 364 <span class="k">sub </span><span class="m">_FoldFingerprintsBitVector</span> <span class="s">{</span>
378 365 <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>
379 366
380 367 <span class="c"># Fold upto size of 8 bits...</span>
381 368 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">-&gt;GetSize</span><span class="s">(</span><span class="s">)</span> &lt;= <span class="n">8</span><span class="s">)</span> <span class="s">{</span>
382 369 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
383 370 <span class="s">}</span>
384 371
385 372 <span class="c"># Check size or density....</span>
386 373 <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>
387 374 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">-&gt;GetSize</span><span class="s">(</span><span class="s">)</span> &lt;= <span class="i">$Value</span><span class="s">)</span> <span class="s">{</span>
388 375 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
389 376 <span class="s">}</span>
390 377 <span class="s">}</span>
391 378 <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>
392 379 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">-&gt;GetDensityOfSetBits</span><span class="s">(</span><span class="s">)</span> &gt;= <span class="i">$Value</span><span class="s">)</span> <span class="s">{</span>
393 380 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
394 381 <span class="s">}</span>
395 382 <span class="s">}</span>
396 383 <span class="k">else</span> <span class="s">{</span>
397 384 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
398 385 <span class="s">}</span>
399 386
400 387 <span class="c"># Recursively reduce its size by half...</span>
401 388 <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>
402 389
403 390 <span class="i">$BinaryString</span> = <span class="i">$This</span><span class="i">-&gt;GetBitsAsBinaryString</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
404 391 <span class="i">$StringLength</span> = <span class="k">length</span> <span class="i">$BinaryString</span><span class="sc">;</span>
405 392
406 393 <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>
407 394 <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>
408 395
409 396 <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>
410 397 <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>
411 398
412 399 <span class="i">$FoldedFingerprintsBitVector</span> = <span class="i">$FirstHalfFingerprintsBitVector</span> | <span class="i">$SecondHalfFingerprintsBitVector</span><span class="sc">;</span>
413 400
414 401 <span class="k">return</span> <span class="i">$FoldedFingerprintsBitVector</span><span class="i">-&gt;_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>
415 402 <span class="s">}</span>
416 403
417 404 <span class="c"># Is first bit vector subset of second bit vector?</span>
418 405 <span class="c">#</span>
419 406 <span class="c"># For a bit vector to be a subset of another bit vector, both vectors must be of</span>
420 407 <span class="c"># the same size and the bit positions set in first vector must also be set in the</span>
421 408 <span class="c"># secons bit vector.</span>
422 409 <span class="c">#</span>
423 410 <span class="c"># This functionality can be either invoked as a class function or an object method.</span>
424 411 <span class="c">#</span>
425 <a name="IsSubSet-"></a> 412 <span class="k">sub </span><span class="m">IsSubSet ($$)</span> <span class="s">{</span>
426 413 <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>
427 414
428 415 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="i">-&gt;GetSize</span><span class="s">(</span><span class="s">)</span> != <span class="i">$FingerprintsBitVectorB</span><span class="i">-&gt;GetSize</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
429 416 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
430 417 <span class="s">}</span>
431 418 <span class="k">my</span><span class="s">(</span><span class="i">$AndFingerprintsBitVector</span><span class="s">)</span><span class="sc">;</span>
432 419
433 420 <span class="i">$AndFingerprintsBitVector</span> = <span class="i">$FingerprintsBitVectorA</span> &amp; <span class="i">$FingerprintsBitVectorB</span><span class="sc">;</span>
434 421
435 422 <span class="k">return</span> <span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="i">-&gt;GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span> == <span class="i">$AndFingerprintsBitVector</span><span class="i">-&gt;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>
436 423 <span class="s">}</span>
437 424
438 425 <span class="c"># Return a string containing vector values...</span>
439 <a name="StringifyFingerprintsBitVector-"></a> 426 <span class="k">sub </span><span class="m">StringifyFingerprintsBitVector</span> <span class="s">{</span>
440 427 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
441 428 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsBitVectorString</span><span class="s">)</span><span class="sc">;</span>
442 429
443 430 <span class="c"># BitVector size information...</span>
444 431 <span class="c">#</span>
445 432 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">SpecifiedSize</span>} != <span class="i">$This</span><span class="i">-&gt;GetSize</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
446 433 <span class="i">$FingerprintsBitVectorString</span> = <span class="q">&quot;SpecifiedSize: &quot;</span> . <span class="i">$This</span>-&gt;{<span class="w">SpecifiedSize</span>} . <span class="q">&quot;; BitVectorSize: &quot;</span> . <span class="i">$This</span><span class="i">-&gt;GetSize</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
447 434 <span class="s">}</span>
448 435 <span class="k">else</span> <span class="s">{</span>
449 436 <span class="i">$FingerprintsBitVectorString</span> = <span class="q">&quot;BitVectorSize: &quot;</span> . <span class="i">$This</span><span class="i">-&gt;GetSize</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
450 437 <span class="s">}</span>
451 438 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfSetBits</span><span class="cm">,</span> <span class="i">$BitDensity</span><span class="s">)</span><span class="sc">;</span>
452 439 <span class="i">$NumOfSetBits</span> = <span class="i">$This</span><span class="i">-&gt;GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
453 440 <span class="i">$BitDensity</span> = <span class="i">$This</span><span class="i">-&gt;GetFingerprintsBitDensity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
454 441
455 442 <span class="i">$FingerprintsBitVectorString</span> .= <span class="q">&quot;; NumOfOnBits: $NumOfSetBits; BitDensity: $BitDensity&quot;</span><span class="sc">;</span>
456 443
457 444 <span class="c"># BitVector values...</span>
458 445 <span class="i">$FingerprintsBitVectorString</span> .= <span class="q">&quot;; BitVector: &quot;</span> . <span class="i">$This</span><span class="i">-&gt;StringifyBitVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
459 446
460 447 <span class="k">return</span> <span class="i">$FingerprintsBitVectorString</span><span class="sc">;</span>
461 448 <span class="s">}</span>
462 449
463 450 <span class="c"># For two fingerprints bit vectors A and B of same size, let:</span>
464 451 <span class="c">#</span>
465 452 <span class="c"># Na = Number of bits set to &quot;1&quot; in A</span>
466 453 <span class="c"># Nb = Number of bits set to &quot;1&quot; in B</span>
467 454 <span class="c"># Nc = Number of bits set to &quot;1&quot; in both A and B</span>
468 455 <span class="c"># Nd = Number of bits set to &quot;0&quot; in both A and B</span>
469 456 <span class="c">#</span>
470 457 <span class="c"># Nt = Number of bits set to &quot;1&quot; or &quot;0&quot; in A or B = Size of A or B = Na + Nb - Nc + Nd</span>
471 458 <span class="c">#</span>
472 459 <span class="c"># Na - Nc = Number of bits set to &quot;1&quot; in A but not in B</span>
473 460 <span class="c"># Nb - Nc = Number of bits set to &quot;1&quot; in B but not in A</span>
474 461 <span class="c">#</span>
475 462 <span class="c"># Various similarity coefficients [ Ref 40 - 42 ] for a pair of bit vectors A and B are</span>
476 463 <span class="c"># defined as follows:</span>
477 464 <span class="c">#</span>
478 465 <span class="c"># . BaroniUrbani: ( SQRT( Nc * Nd ) + Nc ) / ( SQRT ( Nc * Nd ) + Nc + ( Na - Nc ) + ( Nb - Nc ) ) ( same as Buser )</span>
479 466 <span class="c">#</span>
480 467 <span class="c"># . Buser: ( SQRT ( Nc * Nd ) + Nc ) / ( SQRT ( Nc * Nd ) + Nc + ( Na - Nc ) + ( Nb - Nc ) ) ( same as BaroniUrbani )</span>
481 468 <span class="c">#</span>
482 469 <span class="c"># . Cosine: Nc / SQRT ( Na * Nb ) (same as Ochiai)</span>
483 470 <span class="c">#</span>
484 471 <span class="c"># . Dice: (2 * Nc) / ( Na + Nb )</span>
485 472 <span class="c">#</span>
486 473 <span class="c"># . Dennis: ( Nc * Nd - ( ( Na - Nc ) * ( Nb - Nc ) ) ) / SQRT ( Nt * Na * Nb)</span>
487 474 <span class="c">#</span>
488 475 <span class="c"># . Forbes: ( Nt * Nc ) / ( Na * Nb )</span>
489 476 <span class="c">#</span>
490 477 <span class="c"># . Fossum: ( Nt * ( ( Nc - 1/2 ) ** 2 ) / ( Na * Nb )</span>
491 478 <span class="c">#</span>
492 479 <span class="c"># . Hamann: ( ( Nc + Nd ) - ( Na - Nc ) - ( Nb - Nc ) ) / Nt</span>
493 480 <span class="c">#</span>
494 481 <span class="c"># . Jaccard: Nc / ( ( Na - Nc) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb - Nc ) (same as Tanimoto)</span>
495 482 <span class="c">#</span>
496 483 <span class="c"># . Kulczynski1: Nc / ( ( Na - Nc ) + ( Nb - Nc) ) = Nc / ( Na + Nb - 2Nc )</span>
497 484 <span class="c">#</span>
498 485 <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>
499 486 <span class="c">#</span>
500 487 <span class="c"># . Matching: ( Nc + Nd ) / Nt</span>
501 488 <span class="c">#</span>
502 489 <span class="c"># . McConnaughey: ( Nc ** 2 - ( Na - Nc ) * ( Nb - Nc) ) / ( Na * Nb )</span>
503 490 <span class="c">#</span>
504 491 <span class="c"># . Ochiai: Nc / SQRT ( Na * Nb ) (same as Cosine)</span>
505 492 <span class="c">#</span>
506 493 <span class="c"># . Pearson: ( ( Nc * Nd ) - ( ( Na - Nc ) * ( Nb - Nc ) ) / SQRT ( Na * Nb * ( Na - Nc + Nd ) * ( Nb - Nc + Nd ) )</span>
507 494 <span class="c">#</span>
508 495 <span class="c"># . RogersTanimoto: ( Nc + Nd ) / ( ( Na - Nc) + ( Nb - Nc) + Nt) = ( Nc + Nd ) / ( Na + Nb - 2Nc + Nt)</span>
509 496 <span class="c">#</span>
510 497 <span class="c"># . RussellRao: Nc / Nt</span>
511 498 <span class="c">#</span>
512 499 <span class="c"># . Simpson: Nc / MIN ( Na, Nb)</span>
513 500 <span class="c">#</span>
514 501 <span class="c"># . SkoalSneath1: Nc / ( Nc + 2 * ( Na - Nc) + 2 * ( Nb - Nc) ) = Nc / ( 2 * Na + 2 * Nb - 3 * Nc )</span>
515 502 <span class="c">#</span>
516 503 <span class="c"># . SkoalSneath2: ( 2 * Nc + 2 * Nd ) / ( Nc + Nd + Nt )</span>
517 504 <span class="c">#</span>
518 505 <span class="c"># . SkoalSneath3: ( Nc + Nd ) / ( ( Na - Nc ) + ( Nb - Nc ) ) = ( Nc + Nd ) / ( Na + Nb - 2 * Nc )</span>
519 506 <span class="c">#</span>
520 507 <span class="c"># . Tanimoto: Nc / ( ( Na - Nc) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb - Nc ) (same as Jaccard)</span>
521 508 <span class="c">#</span>
522 509 <span class="c"># . Tversky: Nc / ( alpha * ( Na - Nc ) + ( 1 - alpha) * ( Nb - Nc) + Nc ) = Nc / ( alpha * ( Na - Nb ) + Nb)</span>
523 510 <span class="c">#</span>
524 511 <span class="c"># . Yule: ( ( Nc * Nd ) - ( ( Na - Nc ) * ( Nb - Nc ) ) ) / ( ( Nc * Nd ) + ( ( Na - Nc ) * ( Nb - Nc ) ) )</span>
525 512 <span class="c">#</span>
526 513 <span class="c">#</span>
527 514 <span class="c"># Values of Tanimoto/Jaccard and Tversky coefficients are dependent on only those bit which</span>
528 515 <span class="c"># are set to &quot;1&quot; in both A and B. In order to take into account all bit positions, modified versions</span>
529 516 <span class="c"># of Tanimoto [ Ref. 42 ] and Tversky [ Ref. 43 ] have been developed.</span>
530 517 <span class="c">#</span>
531 518 <span class="c"># Let:</span>
532 519 <span class="c">#</span>
533 520 <span class="c"># Na&#39; = Number of bits set to &quot;0&quot; in A</span>
534 521 <span class="c"># Nb&#39; = Number of bits set to &quot;0&quot; in B</span>
535 522 <span class="c"># Nc&#39; = Number of bits set to &quot;0&quot; in both A and B</span>
536 523 <span class="c">#</span>
537 524 <span class="c"># . Tanimoto&#39;: Nc&#39; / ( ( Na&#39; - Nc&#39;) + ( Nb&#39; - Nc&#39; ) + Nc&#39; ) = Nc&#39; / ( Na&#39; + Nb&#39; - Nc&#39; )</span>
538 525 <span class="c">#</span>
539 526 <span class="c"># . Tversky&#39;: Nc&#39; / ( alpha * ( Na&#39; - Nc&#39; ) + ( 1 - alpha) * ( Nb&#39; - Nc&#39; ) + Nc&#39; ) = Nc&#39; / ( alpha * ( Na&#39; - Nb&#39; ) + Nb&#39;)</span>
540 527 <span class="c">#</span>
541 528 <span class="c"># Then:</span>
542 529 <span class="c">#</span>
543 530 <span class="c"># . WeightedTanimoto = beta * Tanimoto + (1 - beta) * Tanimoto&#39;</span>
544 531 <span class="c">#</span>
545 532 <span class="c"># . WeightedTversky = beta * Tversky + (1 - beta) * Tversky&#39;</span>
546 533 <span class="c">#</span>
547 534 <span class="c">#</span>
548 535
549 536 <span class="c"># Calculate BaroniUrbani similarity coefficient for two same size bit vectors.</span>
550 537 <span class="c">#</span>
551 538 <span class="c"># This functionality can be either invoked as a class function or an object method.</span>
552 539 <span class="c">#</span>
553 <a name="BaroniUrbaniSimilarityCoefficient-"></a> 540 <span class="k">sub </span><span class="m">BaroniUrbaniSimilarityCoefficient ($$)</span> <span class="s">{</span>
554 541 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
555 542
556 543 <span class="k">return</span> <span class="i">BuserSimilarityCoefficient</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span>
557 544 <span class="s">}</span>
558 545
559 546 <span class="c"># Calculate Buser similarity coefficient for two same size bit vectors.</span>
560 547 <span class="c">#</span>
561 548 <span class="c"># This functionality can be either invoked as a class function or an object method.</span>
562 549 <span class="c">#</span>
563 <a name="BuserSimilarityCoefficient-"></a> 550 <span class="k">sub </span><span class="m">BuserSimilarityCoefficient ($$)</span> <span class="s">{</span>
564 551 <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>
565 552 <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">$Denominator</span><span class="s">)</span><span class="sc">;</span>
566 553
567 554 <span class="s">(</span><span class="i">$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>
568 555 <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">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span>
569 556 <span class="i">$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>
570 557
571 558 <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>
572 559 <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>
573 560
574 561 <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>
575 562 <span class="s">}</span>
576 563
577 564 <span class="c"># Calculate Cosine similarity coefficient for two same size bit vectors.</span>
578 565 <span class="c">#</span>
579 566 <span class="c"># This functionality can be either invoked as a class function or an object method.</span>
580 567 <span class="c">#</span>
581 <a name="CosineSimilarityCoefficient-"></a> 568 <span class="k">sub </span><span class="m">CosineSimilarityCoefficient ($$)</span> <span class="s">{</span>
582 569 <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>
583 570 <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>
584 571
585 572 <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>
586 573
587 574 <span class="i">$Numerator</span> = <span class="i">$Nc</span><span class="sc">;</span>
588 575 <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>
589 576
590 577 <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>
591 578 <span class="s">}</span>
592 579
593 580 <span class="c"># Calculate Dice similarity coefficient for two same size bit vectors.</span>
594 581 <span class="c">#</span>
595 582 <span class="c"># This functionality can be either invoked as a class function or an object method.</span>
596 583 <span class="c">#</span>
597 <a name="DiceSimilarityCoefficient-"></a> 584 <span class="k">sub </span><span class="m">DiceSimilarityCoefficient ($$)</span> <span class="s">{</span>
598 585 <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>
599 586 <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">$Denominator</span><span class="s">)</span><span class="sc">;</span>
600 587
601 588 <span class="s">(</span><span class="i">$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>
602 589
603 590 <span class="i">$Numerator</span> = <span class="n">2</span>*<span class="i">$Nc</span><span class="sc">;</span>
604 591 <span class="i">$Denominator</span> = <span class="i">$Na</span> + <span class="i">$Nb</span><span class="sc">;</span>
605 592
606 593 <span class="k">return</span> <span class="i">$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>
607 594 <span class="s">}</span>
608 595
609 596 <span class="c"># Calculate Dennis similarity coefficient for two same size bit vectors.</span>
610 597 <span class="c">#</span>
611 598 <span class="c"># This functionality can be either invoked as a class function or an object method.</span>
612 599 <span class="c">#</span>
613 <a name="DennisSimilarityCoefficient-"></a> 600 <span class="k">sub </span><span class="m">DennisSimilarityCoefficient ($$)</span> <span class="s">{</span>
614 601 <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>
615 602 <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>
616 603
617 604 <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>
618 605 <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>
619 606 <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>
620 607
621 608 <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>
622 609 <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>
623 610
624 611 <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>
625 612 <span class="s">}</span>
626 613
627 614 <span class="c"># Calculate Forbes similarity coefficient for two same size bit vectors.</span>
628 615 <span class="c">#</span>
629 616 <span class="c"># This functionality can be either invoked as a class function or an object method.</span>
630 617 <span class="c">#</span>
631 <a name="ForbesSimilarityCoefficient-"></a> 618 <span class="k">sub </span><span class="m">ForbesSimilarityCoefficient ($$)</span> <span class="s">{</span>
632 619 <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>
633 620 <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">$Denominator</span><span class="s">)</span><span class="sc">;</span>
634 621
635 622 <span class="s">(</span><span class="i">$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>
636 623 <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">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span>
637 624 <span class="i">$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>
638 625
639 626 <span class="i">$Numerator</span> = <span class="i">$Nt</span>*<span class="i">$Nc</span><span class="sc">;</span>
640 627 <span class="i">$Denominator</span> = <span class="i">$Na</span>*<span class="i">$Nb</span><span class="sc">;</span>
641 628
642 629 <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>
643 630 <span class="s">}</span>
644 631
645 632 <span class="c"># Calculate Fossum similarity coefficient for two same size bit vectors.</span>
646 633 <span class="c">#</span>
647 634 <span class="c"># This functionality can be either invoked as a class function or an object method.</span>
648 635 <span class="c">#</span>
649 <a name="FossumSimilarityCoefficient-"></a> 636 <span class="k">sub </span><span class="m">FossumSimilarityCoefficient ($$)</span> <span class="s">{</span>
650 637 <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>
651 638 <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>
652 639
653 640 <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>
654 641 <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>
655 642 <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>
656 643
657 644 <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>
658 645 <span class="i">$Denominator</span> = <span class="i">$Na</span>*<span class="i">$Nb</span> <span class="sc">;</span>
659 646
660 647 <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>
661 648 <span class="s">}</span>
662 649
663 650 <span class="c"># Calculate Hamann similarity coefficient for two same size bit vectors.</span>
664 651 <span class="c">#</span>
665 652 <span class="c"># This functionality can be either invoked as a class function or an object method.</span>
666 653 <span class="c">#</span>
667 <a name="HamannSimilarityCoefficient-"></a> 654 <span class="k">sub </span><span class="m">HamannSimilarityCoefficient ($$)</span> <span class="s">{</span>
668 655 <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>
669 656 <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">$Denominator</span><span class="s">)</span><span class="sc">;</span>
670 657
671 658 <span class="s">(</span><span class="i">$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>
672 659 <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">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span>
673 660 <span class="i">$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>
674 661
675 662 <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">$Nc</span><span class="s">)</span> <span class="sc">;</span>
676 663 <span class="i">$Denominator</span> = <span class="i">$Nt</span><span class="sc">;</span>
677 664
678 665 <span class="k">return</span> <span class="i">$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>
679 666 <span class="s">}</span>
680 667
681 668 <span class="c"># Calculate Jacard similarity coefficient for two same size bit vectors.</span>
682 669 <span class="c">#</span>
683 670 <span class="c"># This functionality can be either invoked as a class function or an object method.</span>
684 671 <span class="c">#</span>
685 <a name="JacardSimilarityCoefficient-"></a> 672 <span class="k">sub </span><span class="m">JacardSimilarityCoefficient ($$)</span> <span class="s">{</span>
686 673 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
687 674
688 675 <span class="k">return</span> <span class="i">TanimotoSimilarityCoefficient</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span>
689 676 <span class="s">}</span>
690 677
691 678 <span class="c"># Calculate Kulczynski1 similarity coefficient for two same size bit vectors.</span>
692 679 <span class="c">#</span>
693 680 <span class="c"># This functionality can be either invoked as a class function or an object method.</span>
694 681 <span class="c">#</span>
695 <a name="Kulczynski1SimilarityCoefficient-"></a> 682 <span class="k">sub </span><span class="m">Kulczynski1SimilarityCoefficient ($$)</span> <span class="s">{</span>
696 683 <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>
697 684 <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">$Denominator</span><span class="s">)</span><span class="sc">;</span>
698 685
699 686 <span class="s">(</span><span class="i">$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>
700 687
701 688 <span class="i">$Numerator</span> = <span class="i">$Nc</span><span class="sc">;</span>
702 689 <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>
703 690
704 691 <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>
705 692 <span class="s">}</span>
706 693
707 694 <span class="c"># Calculate Kulczynski2 similarity coefficient for two same size bit vectors.</span>
708 695 <span class="c">#</span>
709 696 <span class="c"># This functionality can be either invoked as a class function or an object method.</span>
710 697 <span class="c">#</span>
711 <a name="Kulczynski2SimilarityCoefficient-"></a> 698 <span class="k">sub </span><span class="m">Kulczynski2SimilarityCoefficient ($$)</span> <span class="s">{</span>
712 699 <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>
713 700 <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>
714 701
715 702 <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>
716 703
717 704 <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>
718 705 <span class="i">$Denominator</span> = <span class="i">$Na</span>*<span class="i">$Nb</span><span class="sc">;</span>
719 706
720 707 <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>
721 708 <span class="s">}</span>
722 709
723 710 <span class="c"># Calculate Matching similarity coefficient for two same size bit vectors.</span>
724 711 <span class="c">#</span>
725 712 <span class="c"># This functionality can be either invoked as a class function or an object method.</span>
726 713 <span class="c">#</span>
727 <a name="MatchingSimilarityCoefficient-"></a> 714 <span class="k">sub </span><span class="m">MatchingSimilarityCoefficient ($$)</span> <span class="s">{</span>
728 715 <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>
729 716 <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">$Denominator</span><span class="s">)</span><span class="sc">;</span>
730 717
731 718 <span class="s">(</span><span class="i">$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>
732 719 <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">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span>
733 720 <span class="i">$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>
734 721
735 722 <span class="i">$Numerator</span> = <span class="i">$Nc</span> + <span class="i">$Nd</span><span class="sc">;</span>
736 723 <span class="i">$Denominator</span> = <span class="i">$Nt</span><span class="sc">;</span>
737 724
738 725 <span class="k">return</span> <span class="i">$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>
739 726 <span class="s">}</span>
740 727
741 728 <span class="c"># Calculate McConnaughey similarity coefficient for two same size bit vectors.</span>
742 729 <span class="c">#</span>
743 730 <span class="c"># This functionality can be either invoked as a class function or an object method.</span>
744 731 <span class="c">#</span>
745 <a name="McConnaugheySimilarityCoefficient-"></a> 732 <span class="k">sub </span><span class="m">McConnaugheySimilarityCoefficient ($$)</span> <span class="s">{</span>
746 733 <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>
747 734 <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>
748 735
749 736 <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>
750 737
751 738 <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>
752 739 <span class="i">$Denominator</span> = <span class="i">$Na</span>*<span class="i">$Nb</span> <span class="sc">;</span>
753 740
754 741 <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>
755 742 <span class="s">}</span>
756 743
757 744 <span class="c"># Calculate Ochiai similarity coefficient for two same size bit vectors.</span>
758 745 <span class="c">#</span>
759 746 <span class="c"># This functionality can be either invoked as a class function or an object method.</span>
760 747 <span class="c">#</span>
761 <a name="OchiaiSimilarityCoefficient-"></a> 748 <span class="k">sub </span><span class="m">OchiaiSimilarityCoefficient ($$)</span> <span class="s">{</span>
762 749 <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>
763 750
764 751 <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>
765 752 <span class="s">}</span>
766 753
767 754 <span class="c"># Calculate Pearson similarity coefficient for two same size bit vectors.</span>
768 755 <span class="c">#</span>
769 756 <span class="c"># This functionality can be either invoked as a class function or an object method.</span>
770 757 <span class="c">#</span>
771 <a name="PearsonSimilarityCoefficient-"></a> 758 <span class="k">sub </span><span class="m">PearsonSimilarityCoefficient ($$)</span> <span class="s">{</span>
772 759 <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>
773 760 <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>
774 761
775 762 <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>
776 763 <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>
777 764 <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>
778 765
779 766 <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>
780 767 <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>
781 768
782 769 <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>
783 770 <span class="s">}</span>
784 771
785 772 <span class="c"># Calculate RogersTanimoto similarity coefficient for two same size bit vectors.</span>
786 773 <span class="c">#</span>
787 774 <span class="c"># This functionality can be either invoked as a class function or an object method.</span>
788 775 <span class="c">#</span>
789 <a name="RogersTanimotoSimilarityCoefficient-"></a> 776 <span class="k">sub </span><span class="m">RogersTanimotoSimilarityCoefficient ($$)</span> <span class="s">{</span>
790 777 <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>
791 778 <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">$Denominator</span><span class="s">)</span><span class="sc">;</span>
792 779
793 780 <span class="s">(</span><span class="i">$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>
794 781 <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">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span>
795 782 <span class="i">$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>
796 783
797 784 <span class="i">$Numerator</span> = <span class="i">$Nc</span> + <span class="i">$Nd</span><span class="sc">;</span>
798 785 <span class="i">$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">$Nt</span><span class="sc">;</span>
799 786
800 787 <span class="k">return</span> <span class="i">$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>
801 788 <span class="s">}</span>
802 789
803 790 <span class="c"># Calculate RussellRao similarity coefficient for two same size bit vectors.</span>
804 791 <span class="c">#</span>
805 792 <span class="c"># This functionality can be either invoked as a class function or an object method.</span>
806 793 <span class="c">#</span>
807 <a name="RussellRaoSimilarityCoefficient-"></a> 794 <span class="k">sub </span><span class="m">RussellRaoSimilarityCoefficient ($$)</span> <span class="s">{</span>
808 795 <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>
809 796 <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>
810 797
811 798 <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>
812 799 <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>
813 800 <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>
814 801
815 802 <span class="i">$Numerator</span> = <span class="i">$Nc</span><span class="sc">;</span>
816 803 <span class="i">$Denominator</span> = <span class="i">$Nt</span><span class="sc">;</span>
817 804
818 805 <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>
819 806 <span class="s">}</span>
820 807
821 808 <span class="c"># Calculate Simpson similarity coefficient for two same size bit vectors.</span>
822 809 <span class="c">#</span>
823 810 <span class="c"># This functionality can be either invoked as a class function or an object method.</span>
824 811 <span class="c">#</span>
825 <a name="SimpsonSimilarityCoefficient-"></a> 812 <span class="k">sub </span><span class="m">SimpsonSimilarityCoefficient ($$)</span> <span class="s">{</span>
826 813 <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>
827 814 <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">$Denominator</span><span class="s">)</span><span class="sc">;</span>
828 815
829 816 <span class="s">(</span><span class="i">$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>
830 817
831 818 <span class="i">$Numerator</span> = <span class="i">$Nc</span><span class="sc">;</span>
832 819 <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">$Nb</span><span class="s">)</span><span class="sc">;</span>
833 820
834 821 <span class="k">return</span> <span class="i">$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>
835 822 <span class="s">}</span>
836 823
837 824 <span class="c"># Calculate SkoalSneath1 similarity coefficient for two same size bit vectors.</span>
838 825 <span class="c">#</span>
839 826 <span class="c"># This functionality can be either invoked as a class function or an object method.</span>
840 827 <span class="c">#</span>
841 <a name="SkoalSneath1SimilarityCoefficient-"></a> 828 <span class="k">sub </span><span class="m">SkoalSneath1SimilarityCoefficient ($$)</span> <span class="s">{</span>
842 829 <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>
843 830 <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>
844 831
845 832 <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>
846 833
847 834 <span class="i">$Numerator</span> = <span class="i">$Nc</span><span class="sc">;</span>
848 835 <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>
849 836
850 837 <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>
851 838 <span class="s">}</span>
852 839
853 840 <span class="c"># Calculate SkoalSneath2 similarity coefficient for two same size bit vectors.</span>
854 841 <span class="c">#</span>
855 842 <span class="c"># This functionality can be either invoked as a class function or an object method.</span>
856 843 <span class="c">#</span>
857 <a name="SkoalSneath2SimilarityCoefficient-"></a> 844 <span class="k">sub </span><span class="m">SkoalSneath2SimilarityCoefficient ($$)</span> <span class="s">{</span>
858 845 <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>
859 846 <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">$Denominator</span><span class="s">)</span><span class="sc">;</span>
860 847
861 848 <span class="s">(</span><span class="i">$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>
862 849 <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">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span>
863 850 <span class="i">$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>
864 851
865 852 <span class="i">$Numerator</span> = <span class="n">2</span>*<span class="i">$Nc</span> + <span class="n">2</span>*<span class="i">$Nd</span> <span class="sc">;</span>
866 853 <span class="i">$Denominator</span> = <span class="i">$Nc</span> + <span class="i">$Nd</span> + <span class="i">$Nt</span> <span class="sc">;</span>
867 854
868 855 <span class="k">return</span> <span class="i">$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>
869 856 <span class="s">}</span>
870 857
871 858 <span class="c"># Calculate SkoalSneath3 similarity coefficient for two same size bit vectors.</span>
872 859 <span class="c">#</span>
873 860 <span class="c"># This functionality can be either invoked as a class function or an object method.</span>
874 861 <span class="c">#</span>
875 <a name="SkoalSneath3SimilarityCoefficient-"></a> 862 <span class="k">sub </span><span class="m">SkoalSneath3SimilarityCoefficient ($$)</span> <span class="s">{</span>
876 863 <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>
877 864 <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>
878 865
879 866 <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>
880 867 <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>
881 868 <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>
882 869
883 870 <span class="i">$Numerator</span> = <span class="i">$Nc</span> + <span class="i">$Nd</span><span class="sc">;</span>
884 871 <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>
885 872
886 873 <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>
887 874 <span class="s">}</span>
888 875
889 876 <span class="c"># Calculate Tanimoto similarity coefficient for two same size bit vectors.</span>
890 877 <span class="c">#</span>
891 878 <span class="c"># This functionality can be either invoked as a class function or an object method.</span>
892 879 <span class="c">#</span>
893 <a name="TanimotoSimilarityCoefficient-"></a> 880 <span class="k">sub </span><span class="m">TanimotoSimilarityCoefficient ($$)</span> <span class="s">{</span>
894 881 <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>
895 882 <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">$Denominator</span><span class="s">)</span><span class="sc">;</span>
896 883
897 884 <span class="s">(</span><span class="i">$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>
898 885
899 886 <span class="i">$Numerator</span> = <span class="i">$Nc</span><span class="sc">;</span>
900 887 <span class="i">$Denominator</span> = <span class="i">$Na</span> + <span class="i">$Nb</span> - <span class="i">$Nc</span><span class="sc">;</span>
901 888
902 889 <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>
903 890 <span class="s">}</span>
904 891
905 892 <span class="c"># Calculate Tversky similarity coefficient for two same size bit vectors.</span>
906 893 <span class="c">#</span>
907 894 <span class="c"># This functionality can be either invoked as a class function or an object method.</span>
908 895 <span class="c">#</span>
909 <a name="TverskySimilarityCoefficient-"></a> 896 <span class="k">sub </span><span class="m">TverskySimilarityCoefficient ($$$)</span> <span class="s">{</span>
910 897 <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>
911 898 <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>
912 899
913 900 <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> &amp;&amp; <span class="s">(</span><span class="i">$Alpha</span> &gt;= <span class="n">0</span> &amp;&amp; <span class="i">$Alpha</span> &lt;= <span class="n">1</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
914 901 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;TverskySimilarityCoefficient: Alpha parameters must be defined and its value must be &gt;=0 and &lt;=1 ...&quot;</span><span class="sc">;</span>
915 902 <span class="s">}</span>
916 903
917 904 <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>
918 905
919 906 <span class="i">$Numerator</span> = <span class="i">$Nc</span><span class="sc">;</span>
920 907 <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>
921 908
922 909 <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>
923 910 <span class="s">}</span>
924 911
925 912 <span class="c"># Calculate Yule similarity coefficient for two same size bit vectors.</span>
926 913 <span class="c">#</span>
927 914 <span class="c"># This functionality can be either invoked as a class function or an object method.</span>
928 915 <span class="c">#</span>
929 <a name="YuleSimilarityCoefficient-"></a> 916 <span class="k">sub </span><span class="m">YuleSimilarityCoefficient ($$)</span> <span class="s">{</span>
930 917 <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>
931 918 <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">$Denominator</span><span class="s">)</span><span class="sc">;</span>
932 919
933 920 <span class="s">(</span><span class="i">$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>
934 921 <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">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span>
935 922 <span class="i">$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>
936 923
937 924 <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">$Nc</span><span class="s">)</span><span class="s">)</span> <span class="sc">;</span>
938 925 <span class="i">$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>
939 926
940 927 <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>
941 928 <span class="s">}</span>
942 929
943 930 <span class="c"># Calculate WeightedTanimoto similarity coefficient for two same size bit vectors.</span>
944 931 <span class="c">#</span>
945 932 <span class="c"># This functionality can be either invoked as a class function or an object method.</span>
946 933 <span class="c">#</span>
947 <a name="WeightedTanimotoSimilarityCoefficient-"></a> 934 <span class="k">sub </span><span class="m">WeightedTanimotoSimilarityCoefficient ($$$)</span> <span class="s">{</span>
948 935 <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>
949 936 <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>
950 937
951 938 <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> &amp;&amp; <span class="s">(</span><span class="i">$Beta</span> &gt;= <span class="n">0</span> &amp;&amp; <span class="i">$Beta</span> &lt;= <span class="n">1</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
952 939 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;WeightedTanimotoSimilarityCoefficient: Beta parameters must be defined and its value must be &gt;=0 and &lt;=1 ...&quot;</span><span class="sc">;</span>
953 940 <span class="s">}</span>
954 941
955 942 <span class="c"># Get Tanimoto for set bits...</span>
956 943 <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>
957 944
958 945 <span class="i">$Numerator</span> = <span class="i">$Nc</span><span class="sc">;</span>
959 946 <span class="i">$Denominator</span> = <span class="i">$Na</span> + <span class="i">$Nb</span> - <span class="i">$Nc</span><span class="sc">;</span>
960 947 <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>
961 948
962 949 <span class="c"># Get Tanimoto for clear bits...</span>
963 950 <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>
964 951
965 952 <span class="i">$Numerator</span> = <span class="i">$Nc</span><span class="sc">;</span>
966 953 <span class="i">$Denominator</span> = <span class="i">$Na</span> + <span class="i">$Nb</span> - <span class="i">$Nc</span><span class="sc">;</span>
967 954 <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>
968 955
969 956 <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>
970 957
971 958 <span class="k">return</span> <span class="i">$WeightedTanimoto</span><span class="sc">;</span>
972 959 <span class="s">}</span>
973 960
974 961 <span class="c"># Calculate WeightedTversky similarity coefficient for two same size bit vectors.</span>
975 962 <span class="c">#</span>
976 963 <span class="c"># This functionality can be either invoked as a class function or an object method.</span>
977 964 <span class="c">#</span>
978 <a name="WeightedTverskySimilarityCoefficient-"></a> 965 <span class="k">sub </span><span class="m">WeightedTverskySimilarityCoefficient ($$$)</span> <span class="s">{</span>
979 966 <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>
980 967 <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>
981 968
982 969 <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">$Alpha</span><span class="s">)</span> &amp;&amp; <span class="s">(</span><span class="i">$Alpha</span> &gt;= <span class="n">0</span> &amp;&amp; <span class="i">$Alpha</span> &lt;= <span class="n">1</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
983 970 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;WeightedTverskySimilarityCoefficient: Alpha parameters must be defined and its value must be &gt;=0 and &lt;=1 ...&quot;</span><span class="sc">;</span>
984 971 <span class="s">}</span>
985 972 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Beta</span><span class="s">)</span> &amp;&amp; <span class="s">(</span><span class="i">$Beta</span> &gt;= <span class="n">0</span> &amp;&amp; <span class="i">$Beta</span> &lt;= <span class="n">1</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
986 973 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;WeightedTverskySimilarityCoefficient: Beta parameters must be defined and its value must be &gt;=0 and &lt;=1 ...&quot;</span><span class="sc">;</span>
987 974 <span class="s">}</span>
988 975
989 976 <span class="c"># Get Tversky for set bits...</span>
990 977 <span class="s">(</span><span class="i">$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>
991 978
992 979 <span class="i">$Numerator</span> = <span class="i">$Nc</span><span class="sc">;</span>
993 980 <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">$Nb</span><span class="sc">;</span>
994 981 <span class="i">$TverskyForSetBits</span> = <span class="i">$Denominator</span> ? <span class="s">(</span><span class="i">$Numerator</span>/<span class="i">$Denominator</span><span class="s">)</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
995 982
996 983 <span class="c"># Get Tversky for clear bits...</span>
997 984 <span class="s">(</span><span class="i">$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>
998 985
999 986 <span class="i">$Numerator</span> = <span class="i">$Nc</span><span class="sc">;</span>
1000 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">$Nb</span><span class="sc">;</span>
1001 988 <span class="i">$TverskyForClearBits</span> = <span class="i">$Denominator</span> ? <span class="s">(</span><span class="i">$Numerator</span>/<span class="i">$Denominator</span><span class="s">)</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
1002 989
1003 990 <span class="i">$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>
1004 991
1005 992 <span class="k">return</span> <span class="i">$WeightedTversky</span><span class="sc">;</span>
1006 993 <span class="s">}</span>
1007 994
1008 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>
1009 996 <span class="c">#</span>
1010 <a name="_GetNumOfIndividualAndCommonSetBits-"></a> 997 <span class="k">sub </span><span class="m">_GetNumOfIndividualAndCommonSetBits ($$)</span> <span class="s">{</span>
1011 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>
1012 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>
1013 1000
1014 1001 <span class="c"># Number of bits set to &quot;1&quot; in A</span>
1015 1002 <span class="i">$Na</span> = <span class="i">$FingerprintsBitVectorA</span><span class="i">-&gt;GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1016 1003
1017 1004 <span class="c"># Number of bits set to &quot;1&quot; in B</span>
1018 1005 <span class="i">$Nb</span> = <span class="i">$FingerprintsBitVectorB</span><span class="i">-&gt;GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1019 1006
1020 1007 <span class="c"># Number of bits set to &quot;1&quot; in both A and B</span>
1021 1008 <span class="k">my</span><span class="s">(</span><span class="i">$NcBitVector</span><span class="s">)</span><span class="sc">;</span>
1022 1009 <span class="i">$NcBitVector</span> = <span class="i">$FingerprintsBitVectorA</span> &amp; <span class="i">$FingerprintsBitVectorB</span><span class="sc">;</span>
1023 1010 <span class="i">$Nc</span> = <span class="i">$NcBitVector</span><span class="i">-&gt;GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1024 1011
1025 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>
1026 1013 <span class="s">}</span>
1027 1014
1028 1015 <span class="c"># Get number of Nd bits in bit vector A and B to be used for similarity coefficient calculations...</span>
1029 1016 <span class="c">#</span>
1030 <a name="_GetNumOfCommonClearBits-"></a>1017 <span class="k">sub </span><span class="m">_GetNumOfCommonClearBits ($$)</span> <span class="s">{</span>
1031 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>
1032 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>
1033 1020
1034 1021 <span class="c"># Number of bits set to &quot;0&quot; in both A and B</span>
1035 1022 <span class="i">$NdBitVector</span> = ~<span class="i">$FingerprintsBitVectorA</span> &amp; ~<span class="i">$FingerprintsBitVectorB</span><span class="sc">;</span>
1036 1023 <span class="i">$Nd</span> = <span class="i">$NdBitVector</span><span class="i">-&gt;GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1037 1024
1038 1025 <span class="c"># Correct for number of clear bits used for padding...</span>
1039 1026 <span class="k">if</span> <span class="s">(</span><span class="i">_IsNumOfClearBitsCorrectionRequired</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
1040 1027 <span class="i">$Nd</span> = <span class="i">$Nd</span> - <span class="i">_GetNumOfClearBitsCorrection</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="s">)</span><span class="sc">;</span>
1041 1028 <span class="s">}</span>
1042 1029 <span class="k">elsif</span> <span class="s">(</span><span class="i">_IsNumOfClearBitsCorrectionRequired</span><span class="s">(</span><span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
1043 1030 <span class="i">$Nd</span> = <span class="i">$Nd</span> - <span class="i">_GetNumOfClearBitsCorrection</span><span class="s">(</span><span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span>
1044 1031 <span class="s">}</span>
1045 1032
1046 1033 <span class="k">return</span> <span class="i">$Nd</span><span class="sc">;</span>
1047 1034 <span class="s">}</span>
1048 1035
1049 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>
1050 1037 <span class="c">#</span>
1051 <a name="_GetNumOfIndividualAndCommonClearBits-"></a>1038 <span class="k">sub </span><span class="m">_GetNumOfIndividualAndCommonClearBits ($$)</span> <span class="s">{</span>
1052 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>
1053 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>
1054 1041
1055 1042 <span class="c"># Number of bits set to &quot;0&quot; in A</span>
1056 1043 <span class="i">$Na</span> = <span class="i">$FingerprintsBitVectorA</span><span class="i">-&gt;GetNumOfClearBits</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1057 1044
1058 1045 <span class="c"># Correct for number of clear bits used for padding...</span>
1059 1046 <span class="k">if</span> <span class="s">(</span><span class="i">_IsNumOfClearBitsCorrectionRequired</span><span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
1060 1047 <span class="i">$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>
1061 1048 <span class="s">}</span>
1062 1049
1063 1050 <span class="c"># Number of bits set to &quot;0&quot; in B</span>
1064 1051 <span class="i">$Nb</span> = <span class="i">$FingerprintsBitVectorB</span><span class="i">-&gt;GetNumOfClearBits</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
1065 1052
1066 1053 <span class="c"># Correct for number of clear bits used for padding...</span>
1067 1054 <span class="k">if</span> <span class="s">(</span><span class="i">_IsNumOfClearBitsCorrectionRequired</span><span class="s">(</span><span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
1068 1055 <span class="i">$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>
1069 1056 <span class="s">}</span>
1070 1057
1071 1058 <span class="c"># Number of bits set to &quot;0&quot; in both A and B</span>
1072 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">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span>
1073 1060
1074 1061 <span class="k">return</span> <span class="s">(</span><span class="i">$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>
1075 1062 <span class="s">}</span>
1076 1063
1077 1064 <span class="c"># Irrespective of specified size, Perl functions used to handle bit data data in</span>
1078 1065 <span class="c"># BitVector class automatically sets the size to the next nearest power of 2</span>
1079 1066 <span class="c"># and clear the extra bits.</span>
1080 1067 <span class="c">#</span>
1081 1068 <span class="c"># SpecifiedSize is used by this class to process any aribitray size during similarity</span>
1082 1069 <span class="c"># coefficient calculations.</span>
1083 1070 <span class="c">#</span>
1084 1071 <span class="c"># Assuming the FingerprintsBitBector class only manipulates bits upto specified</span>
1085 1072 <span class="c"># size, a correction for the extra bits added by BitVector class needs to be applied</span>
1086 1073 <span class="c"># to number of clear bits.</span>
1087 1074 <span class="c">#</span>
1088 <a name="_GetNumOfClearBitsCorrection-"></a>1075 <span class="k">sub </span><span class="m">_GetNumOfClearBitsCorrection</span> <span class="s">{</span>
1089 1076 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsBitVector</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
1090 1077
1091 1078 <span class="k">return</span> <span class="s">(</span><span class="i">$FingerprintsBitVector</span>-&gt;{<span class="w">Size</span>} - <span class="i">$FingerprintsBitVector</span>-&gt;{<span class="w">SpecifiedSize</span>}<span class="s">)</span><span class="sc">;</span>
1092 1079 <span class="s">}</span>
1093 1080
1094 1081 <span class="c"># Is number of clear bits correction required?</span>
1095 1082 <span class="c">#</span>
1096 <a name="_IsNumOfClearBitsCorrectionRequired-"></a>1083 <span class="k">sub </span><span class="m">_IsNumOfClearBitsCorrectionRequired</span> <span class="s">{</span>
1097 1084 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsBitVector</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
1098 1085
1099 1086 <span class="k">return</span> <span class="s">(</span><span class="i">$FingerprintsBitVector</span>-&gt;{<span class="w">Size</span>} &gt; <span class="i">$FingerprintsBitVector</span>-&gt;{<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>
1100 1087 <span class="s">}</span>
1101 1088
1102 1089
1103 <a name="EOF-"></a></pre>
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