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1 <html> | |
2 <head> | |
3 <title>MayaChemTools:Code:Fingerprints::FingerprintsBitVector.pm</title> | |
4 <meta http-equiv="content-type" content="text/html;charset=utf-8"> | |
5 <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> | |
6 </head> | |
7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> | |
8 <br/> | |
9 <center> | |
10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> | |
11 </center> | |
12 <br/> | |
13 <pre> | |
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 <msud@san.rr.com></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 <http://www.gnu.org/licenses/> 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">=></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">=></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">=></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">'""'</span> <span class="cm">=></span> <span class="q">'StringifyFingerprintsBitVector'</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">->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">$This</span><span class="i">->_InitializeFingerprintsBitVector</span><span class="s">(</span><span class="i">$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">"Error: ${ClassName}->new: FingerprintsBitVector object instantiated without specifying its size ..."</span><span class="sc">;</span> | |
102 89 <span class="s">}</span> | |
103 90 <span class="k">if</span> <span class="s">(</span><span class="i">$Size</span> <=<span class="n">0</span><span class="s">)</span> <span class="s">{</span> | |
104 91 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->new: Fingerprints bit vector size, $Size, must be a positive integer..."</span><span class="sc">;</span> | |
105 92 <span class="s">}</span> | |
106 93 | |
107 94 <span class="c"># Specified size of fingerprints...</span> | |
108 95 <span class="i">$This</span>->{<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">$SpecifiedSize</span> > <span class="n">0</span> && <span class="i">$SpecifiedSize</span> <= <span class="i">$This</span>->{<span class="w">Size</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
130 117 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetSpecifiedSize: Specified size, $SpecifiedSize, is not valid: It must be > 0 && <= "</span><span class="cm">,</span> <span class="i">$This</span><span class="i">->GetSize</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span><span class="q">" ..."</span><span class="sc">;</span> | |
131 118 <span class="s">}</span> | |
132 119 <span class="i">$This</span>->{<span class="w">SpecifiedSize</span>} = <span class="i">$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>->{<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">$This</span>->{<span class="w">ID</span>} = <span class="i">$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">$This</span>->{<span class="w">ID</span>} ? <span class="i">$This</span>->{<span class="w">ID</span>} <span class="co">:</span> <span class="q">'None'</span><span class="sc">;</span> | |
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">$This</span>->{<span class="w">Description</span>} = <span class="i">$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">$This</span>->{<span class="w">Description</span>} ? <span class="i">$This</span>->{<span class="w">Description</span>} <span class="co">:</span> <span class="q">'No description available'</span><span class="sc">;</span> | |
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">$This</span>->{<span class="w">VectorType</span>} = <span class="i">$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">$This</span>->{<span class="w">VectorType</span>} ? <span class="i">$This</span>->{<span class="w">VectorType</span>} <span class="co">:</span> <span class="q">'FingerprintsBitVector'</span><span class="sc">;</span> | |
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">'Binary'</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="cm">,</span> <span class="i">$ThirdParameter</span><span class="s">)</span><span class="sc">;</span> | |
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">'Binary'</span><span class="cm">,</span> <span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span><span class="sc">;</span> | |
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">'Hexadecimal'</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="cm">,</span> <span class="i">$ThirdParameter</span><span class="s">)</span><span class="sc">;</span> | |
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">'Hexadecimal'</span><span class="cm">,</span> <span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span><span class="sc">;</span> | |
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">"Error: ${ClassName}->NewFromOctalString: Creation of fingerprits bit vector from an octal string is not supported ..."</span><span class="sc">;</span> | |
224 211 <span class="s">}</span> | |
225 212 | |
226 213 <span class="c"># Create a new fingerprints bit vector using decimal string. This functionality can be</span> | |
227 214 <span class="c"># either invoked as a class function or an object method.</span> | |
228 215 <span class="c">#</span> | |
229 <a name="NewFromDecimalString-"></a> 216 <span class="k">sub </span><span class="m">NewFromDecimalString ($;$)</span> <span class="s">{</span> | |
230 217 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->NewFromDecimalString: Creation of fingerprits bit vector from a decimal string is not supported ..."</span><span class="sc">;</span> | |
231 218 <span class="s">}</span> | |
232 219 | |
233 220 <span class="c"># Create a new fingerprints bit vector using raw binary string. This functionality can be</span> | |
234 221 <span class="c"># either invoked as a class function or an object method.</span> | |
235 222 <span class="c">#</span> | |
236 <a name="NewFromRawBinaryString-"></a> 223 <span class="k">sub </span><span class="m">NewFromRawBinaryString ($;$)</span> <span class="s">{</span> | |
237 224 <span class="k">my</span><span class="s">(</span><span class="i">$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">$FirstParameter</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
240 227 <span class="k">return</span> <span class="i">_NewFingerptinsBitVectorFromString</span><span class="s">(</span><span class="q">'RawBinary'</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="cm">,</span> <span class="i">$ThirdParameter</span><span class="s">)</span><span class="sc">;</span> | |
241 228 <span class="s">}</span> | |
242 229 <span class="k">else</span> <span class="s">{</span> | |
243 230 <span class="k">return</span> <span class="i">_NewFingerptinsBitVectorFromString</span><span class="s">(</span> <span class="q">'RawBinary'</span><span class="cm">,</span> <span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span><span class="sc">;</span> | |
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">->_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">->_GetFingerprintBitsAsString</span><span class="s">(</span><span class="q">'Hexadecimal'</span><span class="cm">,</span> <span class="i">$BitsOrder</span><span class="s">)</span><span class="sc">;</span> | |
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">"Error: ${ClassName}->GetBitsAsOctalString: Retrieval of fingerprits bits as an octal string is not supported ..."</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">"Error: ${ClassName}->GetBitsAsOctalString: Retrieval of fingerprits bits as a decimal string is not supported ..."</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">->_GetFingerprintBitsAsString</span><span class="s">(</span><span class="q">'Binary'</span><span class="cm">,</span> <span class="i">$BitsOrder</span><span class="s">)</span><span class="sc">;</span> | |
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">->_GetFingerprintBitsAsString</span><span class="s">(</span><span class="q">'RawBinary'</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> && <span class="i">$BitsOrder</span><span class="s">)</span> ? <span class="i">$BitsOrder</span> <span class="co">:</span> <span class="q">'Ascending'</span><span class="sc">;</span> | |
308 295 | |
309 296 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetBitsAsString</span><span class="s">(</span><span class="i">$Format</span><span class="cm">,</span> <span class="i">$BitsOrder</span><span class="s">)</span><span class="sc">;</span> | |
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> && <span class="i">$Object</span><span class="i">->isa</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
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">->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> > <span class="n">0</span> && <span class="i">$Size</span> <= <span class="i">$This</span><span class="i">->GetSize</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
350 337 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->FoldFingerprintsBitVectorBySize: Specified size, $Size, is not valid: It must be > 0 && <= "</span><span class="cm">,</span> <span class="i">$This</span><span class="i">->GetSize</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span><span class="q">" ..."</span><span class="sc">;</span> | |
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">->GetSize</span><span class="s">(</span><span class="s">)</span> <= <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">->_FoldFingerprintsBitVector</span><span class="s">(</span><span class="q">'BySize'</span><span class="cm">,</span> <span class="i">$Size</span><span class="s">)</span><span class="sc">;</span> | |
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> > <span class="n">0</span> && <span class="i">$Density</span> <= <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
366 353 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->FoldFingerprintsBitVectorByDensity: Specified bit density, $Density, is not valid: It must be > 0 && <= 1 ..."</span><span class="sc">;</span> | |
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">->GetDensityOfSetBits</span><span class="s">(</span><span class="s">)</span> >= <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">->_FoldFingerprintsBitVector</span><span class="s">(</span><span class="q">'ByDensity'</span><span class="cm">,</span> <span class="i">$Density</span><span class="s">)</span><span class="sc">;</span> | |
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">->GetSize</span><span class="s">(</span><span class="s">)</span> <= <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">->GetSize</span><span class="s">(</span><span class="s">)</span> <= <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">->GetDensityOfSetBits</span><span class="s">(</span><span class="s">)</span> >= <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">->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">->_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">$FingerprintsBitVectorA</span><span class="i">->GetSize</span><span class="s">(</span><span class="s">)</span> != <span class="i">$FingerprintsBitVectorB</span><span class="i">->GetSize</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
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">$FingerprintsBitVectorA</span> & <span class="i">$FingerprintsBitVectorB</span><span class="sc">;</span> | |
434 421 | |
435 422 <span class="k">return</span> <span class="s">(</span><span class="i">$FingerprintsBitVectorA</span><span class="i">->GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span> == <span class="i">$AndFingerprintsBitVector</span><span class="i">->GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
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">$This</span>->{<span class="w">SpecifiedSize</span>} != <span class="i">$This</span><span class="i">->GetSize</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
446 433 <span class="i">$FingerprintsBitVectorString</span> = <span class="q">"SpecifiedSize: "</span> . <span class="i">$This</span>->{<span class="w">SpecifiedSize</span>} . <span class="q">"; BitVectorSize: "</span> . <span class="i">$This</span><span class="i">->GetSize</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
447 434 <span class="s">}</span> | |
448 435 <span class="k">else</span> <span class="s">{</span> | |
449 436 <span class="i">$FingerprintsBitVectorString</span> = <span class="q">"BitVectorSize: "</span> . <span class="i">$This</span><span class="i">->GetSize</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
450 437 <span class="s">}</span> | |
451 438 <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span><span class="i">->GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
453 440 <span class="i">$BitDensity</span> = <span class="i">$This</span><span class="i">->GetFingerprintsBitDensity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
454 441 | |
455 442 <span class="i">$FingerprintsBitVectorString</span> .= <span class="q">"; NumOfOnBits: $NumOfSetBits; BitDensity: $BitDensity"</span><span class="sc">;</span> | |
456 443 | |
457 444 <span class="c"># BitVector values...</span> | |
458 445 <span class="i">$FingerprintsBitVectorString</span> .= <span class="q">"; BitVector: "</span> . <span class="i">$This</span><span class="i">->StringifyBitVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
459 446 | |
460 447 <span class="k">return</span> <span class="i">$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 "1" in A</span> | |
466 453 <span class="c"># Nb = Number of bits set to "1" in B</span> | |
467 454 <span class="c"># Nc = Number of bits set to "1" in both A and B</span> | |
468 455 <span class="c"># Nd = Number of bits set to "0" in both A and B</span> | |
469 456 <span class="c">#</span> | |
470 457 <span class="c"># Nt = Number of bits set to "1" or "0" in A or B = Size of A or B = Na + Nb - Nc + Nd</span> | |
471 458 <span class="c">#</span> | |
472 459 <span class="c"># Na - Nc = Number of bits set to "1" in A but not in B</span> | |
473 460 <span class="c"># Nb - Nc = Number of bits set to "1" 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 "1" 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' = Number of bits set to "0" in A</span> | |
534 521 <span class="c"># Nb' = Number of bits set to "0" in B</span> | |
535 522 <span class="c"># Nc' = Number of bits set to "0" in both A and B</span> | |
536 523 <span class="c">#</span> | |
537 524 <span class="c"># . Tanimoto': Nc' / ( ( Na' - Nc') + ( Nb' - Nc' ) + Nc' ) = Nc' / ( Na' + Nb' - Nc' )</span> | |
538 525 <span class="c">#</span> | |
539 526 <span class="c"># . Tversky': Nc' / ( alpha * ( Na' - Nc' ) + ( 1 - alpha) * ( Nb' - Nc' ) + Nc' ) = Nc' / ( alpha * ( Na' - Nb' ) + Nb')</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'</span> | |
544 531 <span class="c">#</span> | |
545 532 <span class="c"># . WeightedTversky = beta * Tversky + (1 - beta) * Tversky'</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> && <span class="s">(</span><span class="i">$Alpha</span> >= <span class="n">0</span> && <span class="i">$Alpha</span> <= <span class="n">1</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
914 901 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->TverskySimilarityCoefficient: Alpha parameters must be defined and its value must be >=0 and <=1 ..."</span><span class="sc">;</span> | |
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> && <span class="s">(</span><span class="i">$Beta</span> >= <span class="n">0</span> && <span class="i">$Beta</span> <= <span class="n">1</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
952 939 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->WeightedTanimotoSimilarityCoefficient: Beta parameters must be defined and its value must be >=0 and <=1 ..."</span><span class="sc">;</span> | |
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">$Alpha</span><span class="s">)</span> && <span class="s">(</span><span class="i">$Alpha</span> >= <span class="n">0</span> && <span class="i">$Alpha</span> <= <span class="n">1</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
983 970 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->WeightedTverskySimilarityCoefficient: Alpha parameters must be defined and its value must be >=0 and <=1 ..."</span><span class="sc">;</span> | |
984 971 <span class="s">}</span> | |
985 972 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Beta</span><span class="s">)</span> && <span class="s">(</span><span class="i">$Beta</span> >= <span class="n">0</span> && <span class="i">$Beta</span> <= <span class="n">1</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
986 973 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->WeightedTverskySimilarityCoefficient: Beta parameters must be defined and its value must be >=0 and <=1 ..."</span><span class="sc">;</span> | |
987 974 <span class="s">}</span> | |
988 975 | |
989 976 <span class="c"># Get Tversky for set bits...</span> | |
990 977 <span class="s">(</span><span class="i">$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 "1" in A</span> | |
1015 1002 <span class="i">$Na</span> = <span class="i">$FingerprintsBitVectorA</span><span class="i">->GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
1016 1003 | |
1017 1004 <span class="c"># Number of bits set to "1" in B</span> | |
1018 1005 <span class="i">$Nb</span> = <span class="i">$FingerprintsBitVectorB</span><span class="i">->GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
1019 1006 | |
1020 1007 <span class="c"># Number of bits set to "1" 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> & <span class="i">$FingerprintsBitVectorB</span><span class="sc">;</span> | |
1023 1010 <span class="i">$Nc</span> = <span class="i">$NcBitVector</span><span class="i">->GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
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 "0" in both A and B</span> | |
1035 1022 <span class="i">$NdBitVector</span> = ~<span class="i">$FingerprintsBitVectorA</span> & ~<span class="i">$FingerprintsBitVectorB</span><span class="sc">;</span> | |
1036 1023 <span class="i">$Nd</span> = <span class="i">$NdBitVector</span><span class="i">->GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
1037 1024 | |
1038 1025 <span class="c"># Correct for number of clear bits used for padding...</span> | |
1039 1026 <span class="k">if</span> <span class="s">(</span><span class="i">_IsNumOfClearBitsCorrectionRequired</span><span class="s">(</span><span class="i">$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 "0" in A</span> | |
1056 1043 <span class="i">$Na</span> = <span class="i">$FingerprintsBitVectorA</span><span class="i">->GetNumOfClearBits</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
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 "0" in B</span> | |
1064 1051 <span class="i">$Nb</span> = <span class="i">$FingerprintsBitVectorB</span><span class="i">->GetNumOfClearBits</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
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 "0" 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>->{<span class="w">Size</span>} - <span class="i">$FingerprintsBitVector</span>->{<span class="w">SpecifiedSize</span>}<span class="s">)</span><span class="sc">;</span> | |
1092 1079 <span class="s">}</span> | |
1093 1080 | |
1094 1081 <span class="c"># Is number of clear bits correction required?</span> | |
1095 1082 <span class="c">#</span> | |
1096 <a name="_IsNumOfClearBitsCorrectionRequired-"></a>1083 <span class="k">sub </span><span class="m">_IsNumOfClearBitsCorrectionRequired</span> <span class="s">{</span> | |
1097 1084 <span class="k">my</span><span class="s">(</span><span class="i">$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">$FingerprintsBitVector</span>->{<span class="w">Size</span>} > <span class="i">$FingerprintsBitVector</span>->{<span class="w">SpecifiedSize</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
1100 1087 <span class="s">}</span> | |
1101 1088 | |
1102 1089 | |
1103 <a name="EOF-"></a></pre> | |
1104 <p> </p> | |
1105 <br /> | |
1106 <center> | |
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