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3 <title>MayaChemTools:Code:Fingerprints::FingerprintsVector.pm</title>
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14 <a name="package-Fingerprints::FingerprintsVector-"></a> 1 <span class="k">package </span><span class="i">Fingerprints::FingerprintsVector</span><span class="sc">;</span>
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15 2 <span class="c">#</span>
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16 3 <span class="c"># $RCSfile: FingerprintsVector.pm,v $</span>
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17 4 <span class="c"># $Date: 2015/02/28 20:48:54 $</span>
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18 5 <span class="c"># $Revision: 1.31 $</span>
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19 6 <span class="c">#</span>
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20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span>
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21 8 <span class="c">#</span>
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22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
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23 10 <span class="c">#</span>
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24 11 <span class="c"># This file is part of MayaChemTools.</span>
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25 12 <span class="c">#</span>
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26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
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27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
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28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
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29 16 <span class="c"># later version.</span>
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30 17 <span class="c">#</span>
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31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
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32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
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33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span>
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34 21 <span class="c"># details.</span>
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35 22 <span class="c">#</span>
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36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
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37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span>
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38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
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39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
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40 27 <span class="c">#</span>
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41 28
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42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
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43 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span>
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44 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span>
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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>
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46 33 <span class="k">use</span> <span class="w">MathUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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47 34 <span class="k">use</span> <span class="w">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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48 35 <span class="k">use</span> <span class="w">StatisticsUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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49 36 <span class="k">use</span> <span class="w">BitVector</span><span class="sc">;</span>
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50 37 <span class="k">use</span> <span class="w">Vector</span><span class="sc">;</span>
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51 38
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52 39 <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>
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53 40
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54 41 <span class="i">@ISA</span> = <span class="q">qw(Exporter)</span><span class="sc">;</span>
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55 42
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56 43 <span class="c"># Distance coefficients</span>
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57 44 <span class="k">my</span><span class="s">(</span><span class="i">@DistanceCoefficients</span><span class="s">)</span> = <span class="q">qw(CityBlockDistanceCoefficient EuclideanDistanceCoefficient HammingDistanceCoefficient ManhattanDistanceCoefficient SoergelDistanceCoefficient)</span><span class="sc">;</span>
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58 45
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59 46 <span class="c"># Similarity coefficients...</span>
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60 47 <span class="k">my</span><span class="s">(</span><span class="i">@SimilarityCoefficients</span><span class="s">)</span> = <span class="q">qw(CosineSimilarityCoefficient CzekanowskiSimilarityCoefficient DiceSimilarityCoefficient OchiaiSimilarityCoefficient JaccardSimilarityCoefficient SorensonSimilarityCoefficient TanimotoSimilarityCoefficient)</span><span class="sc">;</span>
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61 48
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62 49 <span class="c"># New from string...</span>
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63 50 <span class="k">my</span><span class="s">(</span><span class="i">@NewFromString</span><span class="s">)</span> = <span class="q">qw(NewFromValuesString NewFromValuesAndIDsString NewFromIDsAndValuesString NewFromValuesAndIDsPairsString NewFromIDsAndValuesPairsString)</span><span class="sc">;</span>
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64 51
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65 52 <span class="i">@EXPORT</span> = <span class="q">qw(IsFingerprintsVector)</span><span class="sc">;</span>
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66 53 <span class="i">@EXPORT_OK</span> = <span class="q">qw(GetSupportedDistanceCoefficients GetSupportedSimilarityCoefficients GetSupportedDistanceAndSimilarityCoefficients @DistanceCoefficients @SimilarityCoefficients)</span><span class="sc">;</span>
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67 54
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68 55 <span class="i">%EXPORT_TAGS</span> = <span class="s">(</span>
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69 56 <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>
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70 57 <span class="w">distancecoefficients</span> <span class="cm">=></span> <span class="s">[</span><span class="i">@DistanceCoefficients</span><span class="s">]</span><span class="cm">,</span>
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71 58 <span class="w">similaritycoefficients</span> <span class="cm">=></span> <span class="s">[</span><span class="i">@SimilarityCoefficients</span><span class="s">]</span><span class="cm">,</span>
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72 59 <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>
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73 60 <span class="s">)</span><span class="sc">;</span>
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74 61
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75 62 <span class="c"># Setup class variables...</span>
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76 63 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="sc">;</span>
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77 64 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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78 65
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79 66 <span class="c"># Overload Perl functions...</span>
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80 67 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyFingerprintsVector'</span><span class="sc">;</span>
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81 68
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82 69 <span class="c"># Class constructor...</span>
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83 <a name="new-"></a> 70 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span>
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84 71 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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85 72
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86 73 <span class="c"># Initialize object...</span>
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87 74 <span class="k">my</span> <span class="i">$This</span> = <span class="s">{</span><span class="s">}</span><span class="sc">;</span>
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88 75 <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">$Class</span><span class="sc">;</span>
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89 76
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90 77 <span class="i">$This</span><span class="i">->_InitializeFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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91 78
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92 79 <span class="i">$This</span><span class="i">->_InitializeFingerprintsVectorProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span>
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93 80
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94 81 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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95 82 <span class="s">}</span>
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96 83
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97 84 <span class="c"># Initialize object data...</span>
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98 85 <span class="c">#</span>
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99 <a name="_InitializeFingerprintsVector-"></a> 86 <span class="k">sub </span><span class="m">_InitializeFingerprintsVector</span> <span class="s">{</span>
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100 87 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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101 88
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102 89 <span class="c"># Type of fingerprint vector...</span>
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103 90 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">''</span><span class="sc">;</span>
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104 91
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105 92 <span class="c"># Fingerprint vector values...</span>
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106 93 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Values</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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107 94
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108 95 <span class="c"># Fingerprint vector value IDs...</span>
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109 96 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">ValueIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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110 97
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111 98 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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112 99 <span class="s">}</span>
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113 100
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114 101 <span class="c"># Initialize class ...</span>
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115 <a name="_InitializeClass-"></a> 102 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span>
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116 103 <span class="c">#Class name...</span>
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117 104 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span>
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118 105 <span class="s">}</span>
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119 106
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120 107 <span class="c"># Initialize object properties....</span>
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121 <a name="_InitializeFingerprintsVectorProperties-"></a> 108 <span class="k">sub </span><span class="m">_InitializeFingerprintsVectorProperties</span> <span class="s">{</span>
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122 109 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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123 110
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124 111 <span class="k">my</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">$MethodName</span><span class="s">)</span><span class="sc">;</span>
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125 112 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span>
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126 113 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span>
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127 114 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
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128 115 <span class="s">}</span>
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129 116
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130 117 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">Type</span>}<span class="s">)</span> <span class="s">{</span>
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131 118 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying type..."</span><span class="sc">;</span>
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132 119 <span class="s">}</span>
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133 120 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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134 121 <span class="s">}</span>
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135 122
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136 123 <span class="c"># Create a new fingerprints vector using space delimited values string. This functionality can be</span>
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137 124 <span class="c"># either invoked as a class function or an object method.</span>
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138 125 <span class="c">#</span>
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139 <a name="NewFromValuesString-"></a> 126 <span class="k">sub </span><span class="m">NewFromValuesString ($$;$)</span> <span class="s">{</span>
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140 127 <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">$ThirdParamater</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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141 128 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="cm">,</span> <span class="i">$ValuesString</span><span class="s">)</span><span class="sc">;</span>
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142 129
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143 130 <span class="k">if</span> <span class="s">(</span><span class="i">@_</span> == <span class="n">3</span><span class="s">)</span> <span class="s">{</span>
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144 131 <span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="cm">,</span> <span class="i">$ValuesString</span><span class="s">)</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">$ThirdParamater</span><span class="s">)</span><span class="sc">;</span>
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145 132 <span class="s">}</span>
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146 133 <span class="k">else</span> <span class="s">{</span>
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147 134 <span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="cm">,</span> <span class="i">$ValuesString</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</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>
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148 135 <span class="s">}</span>
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149 136 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVector</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span><span class="sc">;</span>
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150 137
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151 138 <span class="i">@Values</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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152 139 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$ValuesString</span><span class="s">)</span> && <span class="k">length</span><span class="s">(</span><span class="i">$ValuesString</span><span class="s">)</span> && <span class="i">$ValuesString</span> !~ <span class="q">/^None$/i</span><span class="s">)</span> <span class="s">{</span>
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153 140 <span class="i">@Values</span> = <span class="k">split</span><span class="s">(</span><span class="q">' '</span><span class="cm">,</span> <span class="i">$ValuesString</span><span class="s">)</span><span class="sc">;</span>
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154 141 <span class="s">}</span>
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155 142
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156 143 <span class="i">$FingerprintsVector</span> = <span class="i">new</span> <span class="i">Fingerprints::FingerprintsVector</span><span class="s">(</span><span class="q">'Type'</span> <span class="cm">=></span> <span class="i">$Type</span><span class="cm">,</span> <span class="q">'Values'</span> <span class="cm">=></span> \<span class="i">@Values</span><span class="s">)</span><span class="sc">;</span>
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157 144
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158 145 <span class="k">return</span> <span class="i">$FingerprintsVector</span><span class="sc">;</span>
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159 146 <span class="s">}</span>
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160 147
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161 148 <span class="c"># Create a new fingerprints vector using values and IDs string containing semicolon</span>
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162 149 <span class="c"># delimited value string and value IDs strings. The values within value and value IDs</span>
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163 150 <span class="c"># string are delimited by spaces.</span>
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164 151 <span class="c">#</span>
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165 152 <span class="c"># This functionality can be either invoked as a class function or an object method.</span>
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166 153 <span class="c">#</span>
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167 <a name="NewFromValuesAndIDsString-"></a> 154 <span class="k">sub </span><span class="m">NewFromValuesAndIDsString ($$;$)</span> <span class="s">{</span>
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168 155 <span class="k">my</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="cm">,</span> <span class="i">$ThirdParamater</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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169 156 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="cm">,</span> <span class="i">$ValuesAndIDsString</span><span class="s">)</span><span class="sc">;</span>
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170 157
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171 158 <span class="k">if</span> <span class="s">(</span><span class="i">@_</span> == <span class="n">3</span><span class="s">)</span> <span class="s">{</span>
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172 159 <span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="cm">,</span> <span class="i">$ValuesAndIDsString</span><span class="s">)</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">$ThirdParamater</span><span class="s">)</span><span class="sc">;</span>
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173 160 <span class="s">}</span>
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174 161 <span class="k">else</span> <span class="s">{</span>
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175 162 <span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="cm">,</span> <span class="i">$ValuesAndIDsString</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</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>
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176 163 <span class="s">}</span>
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177 164 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVector</span><span class="cm">,</span> <span class="i">$ValuesString</span><span class="cm">,</span> <span class="i">$ValueIDsString</span><span class="cm">,</span> <span class="i">@Values</span><span class="cm">,</span> <span class="i">@ValueIDs</span><span class="s">)</span><span class="sc">;</span>
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178 165
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179 166 <span class="s">(</span><span class="i">$ValuesString</span><span class="cm">,</span> <span class="i">$ValueIDsString</span><span class="s">)</span> = <span class="k">split</span><span class="s">(</span><span class="q">';'</span><span class="cm">,</span> <span class="i">$ValuesAndIDsString</span><span class="s">)</span><span class="sc">;</span>
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180 167
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181 168 <span class="i">@Values</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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182 169 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$ValuesString</span><span class="s">)</span> && <span class="k">length</span><span class="s">(</span><span class="i">$ValuesString</span><span class="s">)</span> && <span class="i">$ValuesString</span> !~ <span class="q">/^None$/i</span><span class="s">)</span> <span class="s">{</span>
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183 170 <span class="i">@Values</span> = <span class="k">split</span><span class="s">(</span><span class="q">' '</span><span class="cm">,</span> <span class="i">$ValuesString</span><span class="s">)</span><span class="sc">;</span>
|
|
|
184 171 <span class="s">}</span>
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|
185 172 <span class="i">@ValueIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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|
186 173 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$ValueIDsString</span><span class="s">)</span> && <span class="k">length</span><span class="s">(</span><span class="i">$ValueIDsString</span><span class="s">)</span> && <span class="i">$ValueIDsString</span> !~ <span class="q">/^None$/i</span><span class="s">)</span> <span class="s">{</span>
|
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|
187 174 <span class="i">@ValueIDs</span> = <span class="k">split</span><span class="s">(</span><span class="q">' '</span><span class="cm">,</span> <span class="i">$ValueIDsString</span><span class="s">)</span><span class="sc">;</span>
|
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188 175 <span class="s">}</span>
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189 176
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190 177 <span class="k">if</span> <span class="s">(</span><span class="i">@Values</span> != <span class="i">@ValueIDs</span> <span class="s">)</span> <span class="s">{</span>
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|
|
191 178 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->NewFromValuesAndIDsString: Object can't be instantiated: Number specified values, "</span> . <span class="k">scalar</span> <span class="i">@Values</span> . <span class="q">", must be equal to number of specified value IDs, "</span> . <span class="k">scalar</span> <span class="i">@ValueIDs</span> . <span class="q">"..."</span><span class="sc">;</span>
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192 179 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
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193 180 <span class="s">}</span>
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194 181
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195 182 <span class="i">$FingerprintsVector</span> = <span class="i">new</span> <span class="i">Fingerprints::FingerprintsVector</span><span class="s">(</span><span class="q">'Type'</span> <span class="cm">=></span> <span class="i">$Type</span><span class="cm">,</span> <span class="q">'Values'</span> <span class="cm">=></span> \<span class="i">@Values</span><span class="cm">,</span> <span class="q">'ValueIDs'</span> <span class="cm">=></span> \<span class="i">@ValueIDs</span><span class="s">)</span><span class="sc">;</span>
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196 183
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|
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197 184 <span class="k">return</span> <span class="i">$FingerprintsVector</span><span class="sc">;</span>
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198 185 <span class="s">}</span>
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199 186
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200 187 <span class="c"># Create a new fingerprints vector using IDs and values string containing semicolon</span>
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201 188 <span class="c"># delimited value IDs string and values strings. The values within value and value IDs</span>
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202 189 <span class="c"># string are delimited by spaces.</span>
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203 190 <span class="c">#</span>
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204 191 <span class="c"># This functionality can be either invoked as a class function or an object method.</span>
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205 192 <span class="c">#</span>
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206 <a name="NewFromIDsAndValuesString-"></a> 193 <span class="k">sub </span><span class="m">NewFromIDsAndValuesString ($$;$)</span> <span class="s">{</span>
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207 194 <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">$ThirdParamater</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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|
208 195 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="cm">,</span> <span class="i">$IDsAndValuesString</span><span class="s">)</span><span class="sc">;</span>
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209 196
|
|
|
210 197 <span class="k">if</span> <span class="s">(</span><span class="i">@_</span> == <span class="n">3</span><span class="s">)</span> <span class="s">{</span>
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|
|
211 198 <span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="cm">,</span> <span class="i">$IDsAndValuesString</span><span class="s">)</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">$ThirdParamater</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="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="cm">,</span> <span class="i">$IDsAndValuesString</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</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="k">my</span><span class="s">(</span><span class="i">$FingerprintsVector</span><span class="cm">,</span> <span class="i">$ValuesString</span><span class="cm">,</span> <span class="i">$ValueIDsString</span><span class="cm">,</span> <span class="i">@Values</span><span class="cm">,</span> <span class="i">@ValueIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
217 204
|
|
|
218 205 <span class="s">(</span><span class="i">$ValueIDsString</span><span class="cm">,</span> <span class="i">$ValuesString</span><span class="s">)</span> = <span class="k">split</span><span class="s">(</span><span class="q">';'</span><span class="cm">,</span> <span class="i">$IDsAndValuesString</span><span class="s">)</span><span class="sc">;</span>
|
|
|
219 206
|
|
|
220 207 <span class="i">@Values</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
221 208 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$ValuesString</span><span class="s">)</span> && <span class="k">length</span><span class="s">(</span><span class="i">$ValuesString</span><span class="s">)</span> && <span class="i">$ValuesString</span> !~ <span class="q">/^None$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
222 209 <span class="i">@Values</span> = <span class="k">split</span><span class="s">(</span><span class="q">' '</span><span class="cm">,</span> <span class="i">$ValuesString</span><span class="s">)</span><span class="sc">;</span>
|
|
|
223 210 <span class="s">}</span>
|
|
|
224 211 <span class="i">@ValueIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
225 212 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$ValueIDsString</span><span class="s">)</span> && <span class="k">length</span><span class="s">(</span><span class="i">$ValueIDsString</span><span class="s">)</span> && <span class="i">$ValueIDsString</span> !~ <span class="q">/^None$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
226 213 <span class="i">@ValueIDs</span> = <span class="k">split</span><span class="s">(</span><span class="q">' '</span><span class="cm">,</span> <span class="i">$ValueIDsString</span><span class="s">)</span><span class="sc">;</span>
|
|
|
227 214 <span class="s">}</span>
|
|
|
228 215
|
|
|
229 216 <span class="k">if</span> <span class="s">(</span><span class="i">@Values</span> != <span class="i">@ValueIDs</span> <span class="s">)</span> <span class="s">{</span>
|
|
|
230 217 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->NewFromIDsAndValuesString: Object can't be instantiated: Number specified values, "</span> . <span class="k">scalar</span> <span class="i">@Values</span> . <span class="q">", must be equal to number of specified value IDs, "</span> . <span class="k">scalar</span> <span class="i">@ValueIDs</span> . <span class="q">"..."</span><span class="sc">;</span>
|
|
|
231 218 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
232 219 <span class="s">}</span>
|
|
|
233 220
|
|
|
234 221 <span class="i">$FingerprintsVector</span> = <span class="i">new</span> <span class="i">Fingerprints::FingerprintsVector</span><span class="s">(</span><span class="q">'Type'</span> <span class="cm">=></span> <span class="i">$Type</span><span class="cm">,</span> <span class="q">'Values'</span> <span class="cm">=></span> \<span class="i">@Values</span><span class="cm">,</span> <span class="q">'ValueIDs'</span> <span class="cm">=></span> \<span class="i">@ValueIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
235 222
|
|
|
236 223 <span class="k">return</span> <span class="i">$FingerprintsVector</span><span class="sc">;</span>
|
|
|
237 224 <span class="s">}</span>
|
|
|
238 225
|
|
|
239 226 <span class="c"># Create a new fingerprints vector using values and IDs pairs string containing space</span>
|
|
|
240 227 <span class="c"># value and value IDs pairs.</span>
|
|
|
241 228 <span class="c">#</span>
|
|
|
242 229 <span class="c"># This functionality can be either invoked as a class function or an object method.</span>
|
|
|
243 230 <span class="c">#</span>
|
|
|
244 <a name="NewFromValuesAndIDsPairsString-"></a> 231 <span class="k">sub </span><span class="m">NewFromValuesAndIDsPairsString ($$;$)</span> <span class="s">{</span>
|
|
|
245 232 <span class="k">my</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="cm">,</span> <span class="i">$ThirdParamater</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
246 233 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="cm">,</span> <span class="i">$ValuesAndIDsPairsString</span><span class="s">)</span><span class="sc">;</span>
|
|
|
247 234
|
|
|
248 235 <span class="k">if</span> <span class="s">(</span><span class="i">@_</span> == <span class="n">3</span><span class="s">)</span> <span class="s">{</span>
|
|
|
249 236 <span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="cm">,</span> <span class="i">$ValuesAndIDsPairsString</span><span class="s">)</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">$ThirdParamater</span><span class="s">)</span><span class="sc">;</span>
|
|
|
250 237 <span class="s">}</span>
|
|
|
251 238 <span class="k">else</span> <span class="s">{</span>
|
|
|
252 239 <span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="cm">,</span> <span class="i">$ValuesAndIDsPairsString</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</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>
|
|
|
253 240 <span class="s">}</span>
|
|
|
254 241 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVector</span><span class="cm">,</span> <span class="i">$Index</span><span class="cm">,</span> <span class="i">@Values</span><span class="cm">,</span> <span class="i">@ValueIDs</span><span class="cm">,</span> <span class="i">@ValuesAndIDsPairs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
255 242
|
|
|
256 243 <span class="i">@ValuesAndIDsPairs</span> = <span class="k">split</span><span class="s">(</span><span class="q">' '</span><span class="cm">,</span> <span class="i">$ValuesAndIDsPairsString</span><span class="s">)</span><span class="sc">;</span>
|
|
|
257 244 <span class="k">if</span> <span class="s">(</span><span class="i">@ValuesAndIDsPairs</span> % <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
|
|
|
258 245 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->NewFromValuesAndIDsPairsString: No fingerprint vector created: Invalid values and IDs pairs data: Input list must contain even number of values and IDs pairs..."</span><span class="sc">;</span>
|
|
|
259 246 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
260 247 <span class="s">}</span>
|
|
|
261 248
|
|
|
262 249 <span class="i">@Values</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@ValueIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
263 250 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">@ValuesAndIDsPairs</span> == <span class="n">2</span> && <span class="i">$ValuesAndIDsPairs</span>[<span class="n">0</span>] =~ <span class="q">/^None$/i</span> && <span class="i">$ValuesAndIDsPairs</span>[<span class="n">1</span>] =~ <span class="q">/^None$/i</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
264 251 <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$Index</span> < <span class="i">$#ValuesAndIDsPairs</span><span class="sc">;</span> <span class="i">$Index</span> += <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
|
|
|
265 252 <span class="k">push</span> <span class="i">@Values</span><span class="cm">,</span> <span class="i">$ValuesAndIDsPairs</span>[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
266 253 <span class="k">push</span> <span class="i">@ValueIDs</span><span class="cm">,</span> <span class="i">$ValuesAndIDsPairs</span>[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span>
|
|
|
267 254 <span class="s">}</span>
|
|
|
268 255 <span class="s">}</span>
|
|
|
269 256 <span class="i">$FingerprintsVector</span> = <span class="i">new</span> <span class="i">Fingerprints::FingerprintsVector</span><span class="s">(</span><span class="q">'Type'</span> <span class="cm">=></span> <span class="i">$Type</span><span class="cm">,</span> <span class="q">'Values'</span> <span class="cm">=></span> \<span class="i">@Values</span><span class="cm">,</span> <span class="q">'ValueIDs'</span> <span class="cm">=></span> \<span class="i">@ValueIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
270 257
|
|
|
271 258 <span class="k">return</span> <span class="i">$FingerprintsVector</span><span class="sc">;</span>
|
|
|
272 259 <span class="s">}</span>
|
|
|
273 260
|
|
|
274 261 <span class="c"># Create a new fingerprints vector using IDs and values pairs string containing space</span>
|
|
|
275 262 <span class="c"># value IDs and valus pairs.</span>
|
|
|
276 263 <span class="c">#</span>
|
|
|
277 264 <span class="c"># This functionality can be either invoked as a class function or an object method.</span>
|
|
|
278 265 <span class="c">#</span>
|
|
|
279 <a name="NewFromIDsAndValuesPairsString-"></a> 266 <span class="k">sub </span><span class="m">NewFromIDsAndValuesPairsString ($$;$)</span> <span class="s">{</span>
|
|
|
280 267 <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">$ThirdParamater</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
281 268 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="cm">,</span> <span class="i">$IDsAndValuesPairsString</span><span class="s">)</span><span class="sc">;</span>
|
|
|
282 269
|
|
|
283 270 <span class="k">if</span> <span class="s">(</span><span class="i">@_</span> == <span class="n">3</span><span class="s">)</span> <span class="s">{</span>
|
|
|
284 271 <span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="cm">,</span> <span class="i">$IDsAndValuesPairsString</span><span class="s">)</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">$ThirdParamater</span><span class="s">)</span><span class="sc">;</span>
|
|
|
285 272 <span class="s">}</span>
|
|
|
286 273 <span class="k">else</span> <span class="s">{</span>
|
|
|
287 274 <span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="cm">,</span> <span class="i">$IDsAndValuesPairsString</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</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>
|
|
|
288 275 <span class="s">}</span>
|
|
|
289 276 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVector</span><span class="cm">,</span> <span class="i">$Index</span><span class="cm">,</span> <span class="i">@Values</span><span class="cm">,</span> <span class="i">@ValueIDs</span><span class="cm">,</span> <span class="i">@IDsAndValuesPairs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
290 277
|
|
|
291 278 <span class="i">@IDsAndValuesPairs</span> = <span class="k">split</span><span class="s">(</span><span class="q">' '</span><span class="cm">,</span> <span class="i">$IDsAndValuesPairsString</span><span class="s">)</span><span class="sc">;</span>
|
|
|
292 279 <span class="k">if</span> <span class="s">(</span><span class="i">@IDsAndValuesPairs</span> % <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
|
|
|
293 280 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->NewFromIDsAndValuesPairsString: No fingerprint vector created: Invalid values and IDs pairs data: Input list must contain even number of values and IDs pairs..."</span><span class="sc">;</span>
|
|
|
294 281 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
295 282 <span class="s">}</span>
|
|
|
296 283
|
|
|
297 284 <span class="i">@Values</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@ValueIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
298 285 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">@IDsAndValuesPairs</span> == <span class="n">2</span> && <span class="i">$IDsAndValuesPairs</span>[<span class="n">0</span>] =~ <span class="q">/^None$/i</span> && <span class="i">$IDsAndValuesPairs</span>[<span class="n">1</span>] =~ <span class="q">/^None$/i</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
299 286 <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$Index</span> < <span class="i">$#IDsAndValuesPairs</span><span class="sc">;</span> <span class="i">$Index</span> += <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
|
|
|
300 287 <span class="k">push</span> <span class="i">@ValueIDs</span><span class="cm">,</span> <span class="i">$IDsAndValuesPairs</span>[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
301 288 <span class="k">push</span> <span class="i">@Values</span><span class="cm">,</span> <span class="i">$IDsAndValuesPairs</span>[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span>
|
|
|
302 289 <span class="s">}</span>
|
|
|
303 290 <span class="s">}</span>
|
|
|
304 291 <span class="i">$FingerprintsVector</span> = <span class="i">new</span> <span class="i">Fingerprints::FingerprintsVector</span><span class="s">(</span><span class="q">'Type'</span> <span class="cm">=></span> <span class="i">$Type</span><span class="cm">,</span> <span class="q">'Values'</span> <span class="cm">=></span> \<span class="i">@Values</span><span class="cm">,</span> <span class="q">'ValueIDs'</span> <span class="cm">=></span> \<span class="i">@ValueIDs</span><span class="s">)</span><span class="sc">;</span>
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|
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305 292
|
|
|
306 293 <span class="k">return</span> <span class="i">$FingerprintsVector</span><span class="sc">;</span>
|
|
|
307 294 <span class="s">}</span>
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308 295
|
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309 296 <span class="c"># Set type of fingerprint vector. Supported types are: OrderedNumericalValues, NumericalValues, and</span>
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310 297 <span class="c"># AlphaNumericalValues</span>
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311 298 <span class="c">#</span>
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312 299 <span class="c"># . For OrderedNumericalValues type, both vectors must be of the same size and contain similar</span>
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|
313 300 <span class="c"># types of numerical values in the same order.</span>
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314 301 <span class="c">#</span>
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315 302 <span class="c"># . For NumericalValues type, vector value IDs for both vectors must be specified; however, their</span>
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316 303 <span class="c"># size and order of IDs and numerical values may be different. For each vector, value IDs must</span>
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317 304 <span class="c"># correspond to vector values.</span>
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318 305 <span class="c">#</span>
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319 306 <span class="c"># . For AlphaNumericalValues type, vectors may contain both numerical and alphanumerical values</span>
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|
320 307 <span class="c"># and their sizes may be different.</span>
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321 308 <span class="c">#</span>
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322 <a name="SetType-"></a> 309 <span class="k">sub </span><span class="m">SetType</span> <span class="s">{</span>
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323 310 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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324 311
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325 312 <span class="k">if</span> <span class="s">(</span><span class="i">$Type</span> !~ <span class="q">/^(OrderedNumericalValues|NumericalValues|AlphaNumericalValues)$/i</span><span class="s">)</span> <span class="s">{</span>
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|
326 313 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetType: Specified value, $Type, for Type is not vaild. Supported types in current release of MayaChemTools: OrderedNumericalValues, NumericalValues or AlphaNumericalValues"</span><span class="sc">;</span>
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327 314 <span class="s">}</span>
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328 315
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|
329 316 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>}<span class="s">)</span> <span class="s">{</span>
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330 317 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetType: Can't change intial fingerprints vector type: It's already set..."</span><span class="sc">;</span>
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|
331 318 <span class="s">}</span>
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|
332 319 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="i">$Type</span><span class="sc">;</span>
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333 320
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334 321 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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|
335 322 <span class="s">}</span>
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336 323
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337 324 <span class="c"># Get fingerpints vector type...</span>
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|
338 325 <span class="c">#</span>
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339 <a name="GetType-"></a> 326 <span class="k">sub </span><span class="m">GetType</span> <span class="s">{</span>
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340 327 <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>
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341 328
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342 329 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">Type</span>}<span class="sc">;</span>
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343 330 <span class="s">}</span>
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344 331
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345 332 <span class="c"># Set ID...</span>
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346 <a name="SetID-"></a> 333 <span class="k">sub </span><span class="m">SetID</span> <span class="s">{</span>
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|
347 334 <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>
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|
348 335
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|
|
349 336 <span class="i">$This</span>->{<span class="w">ID</span>} = <span class="i">$Value</span><span class="sc">;</span>
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|
350 337
|
|
|
351 338 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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|
|
352 339 <span class="s">}</span>
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353 340
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|
354 341 <span class="c"># Get ID...</span>
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|
355 <a name="GetID-"></a> 342 <span class="k">sub </span><span class="m">GetID</span> <span class="s">{</span>
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|
356 343 <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>
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|
|
357 344
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|
|
358 345 <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>
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|
|
359 346 <span class="s">}</span>
|
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|
360 347
|
|
|
361 348 <span class="c"># Set description...</span>
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|
|
362 <a name="SetDescription-"></a> 349 <span class="k">sub </span><span class="m">SetDescription</span> <span class="s">{</span>
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|
363 350 <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>
|
|
|
364 351
|
|
|
365 352 <span class="i">$This</span>->{<span class="w">Description</span>} = <span class="i">$Value</span><span class="sc">;</span>
|
|
|
366 353
|
|
|
367 354 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
368 355 <span class="s">}</span>
|
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|
369 356
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|
370 357 <span class="c"># Get description...</span>
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|
371 <a name="GetDescription-"></a> 358 <span class="k">sub </span><span class="m">GetDescription</span> <span class="s">{</span>
|
|
|
372 359 <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>
|
|
|
373 360
|
|
|
374 361 <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>
|
|
|
375 362 <span class="s">}</span>
|
|
|
376 363
|
|
|
377 364 <span class="c"># Set vector type...</span>
|
|
|
378 <a name="SetVectorType-"></a> 365 <span class="k">sub </span><span class="m">SetVectorType</span> <span class="s">{</span>
|
|
|
379 366 <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>
|
|
|
380 367
|
|
|
381 368 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="i">$Value</span><span class="sc">;</span>
|
|
|
382 369
|
|
|
383 370 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
384 371 <span class="s">}</span>
|
|
|
385 372
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|
|
386 373 <span class="c"># Get vector type...</span>
|
|
|
387 <a name="GetVectorType-"></a> 374 <span class="k">sub </span><span class="m">GetVectorType</span> <span class="s">{</span>
|
|
|
388 375 <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>
|
|
|
389 376
|
|
|
390 377 <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">'FingerprintsVector'</span><span class="sc">;</span>
|
|
|
391 378 <span class="s">}</span>
|
|
|
392 379
|
|
|
393 380 <span class="c"># Set values of a fingerprint vector using a vector, reference to an array or an array...</span>
|
|
|
394 381 <span class="c">#</span>
|
|
|
395 <a name="SetValues-"></a> 382 <span class="k">sub </span><span class="m">SetValues</span> <span class="s">{</span>
|
|
|
396 383 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
397 384
|
|
|
398 385 <span class="i">$This</span><span class="i">->_SetOrAddValuesOrValueIDs</span><span class="s">(</span><span class="q">"SetValues"</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span><span class="sc">;</span>
|
|
|
399 386
|
|
|
400 387 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
401 388 <span class="s">}</span>
|
|
|
402 389
|
|
|
403 390 <span class="c"># Set value IDs of a fingerprint vector using a vector, reference to an array or an array...</span>
|
|
|
404 391 <span class="c">#</span>
|
|
|
405 <a name="SetValueIDs-"></a> 392 <span class="k">sub </span><span class="m">SetValueIDs</span> <span class="s">{</span>
|
|
|
406 393 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
407 394
|
|
|
408 395 <span class="i">$This</span><span class="i">->_SetOrAddValuesOrValueIDs</span><span class="s">(</span><span class="q">"SetValueIDs"</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span><span class="sc">;</span>
|
|
|
409 396
|
|
|
410 397 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
411 398 <span class="s">}</span>
|
|
|
412 399
|
|
|
413 400 <span class="c"># Add values to a fingerprint vector using a vector, reference to an array or an array...</span>
|
|
|
414 401 <span class="c">#</span>
|
|
|
415 <a name="AddValues-"></a> 402 <span class="k">sub </span><span class="m">AddValues</span> <span class="s">{</span>
|
|
|
416 403 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
417 404
|
|
|
418 405 <span class="i">$This</span><span class="i">->_SetOrAddValuesOrValueIDs</span><span class="s">(</span><span class="q">"AddValues"</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span><span class="sc">;</span>
|
|
|
419 406
|
|
|
420 407 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
421 408 <span class="s">}</span>
|
|
|
422 409
|
|
|
423 410 <span class="c"># Add value IDs to a fingerprint vector using a vector, reference to an array or an array...</span>
|
|
|
424 411 <span class="c">#</span>
|
|
|
425 <a name="AddValueIDs-"></a> 412 <span class="k">sub </span><span class="m">AddValueIDs</span> <span class="s">{</span>
|
|
|
426 413 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
427 414
|
|
|
428 415 <span class="i">$This</span><span class="i">->_SetOrAddValuesOrValueIDs</span><span class="s">(</span><span class="q">"AddValueIDs"</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span><span class="sc">;</span>
|
|
|
429 416
|
|
|
430 417 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
431 418 <span class="s">}</span>
|
|
|
432 419
|
|
|
433 420 <span class="c"># Set or add values or value IDs using:</span>
|
|
|
434 421 <span class="c">#</span>
|
|
|
435 422 <span class="c"># o List of values or ValueIDs</span>
|
|
|
436 423 <span class="c"># o Reference to an list of values or ValuesIDs</span>
|
|
|
437 424 <span class="c"># o A vector containing values or ValueIDs</span>
|
|
|
438 425 <span class="c">#</span>
|
|
|
439 <a name="_SetOrAddValuesOrValueIDs-"></a> 426 <span class="k">sub </span><span class="m">_SetOrAddValuesOrValueIDs</span> <span class="s">{</span>
|
|
|
440 427 <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">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
441 428
|
|
|
442 429 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span>
|
|
|
443 430 <span class="k">return</span><span class="sc">;</span>
|
|
|
444 431 <span class="s">}</span>
|
|
|
445 432
|
|
|
446 433 <span class="c"># Collect specified values or valueIDs...</span>
|
|
|
447 434 <span class="k">my</span><span class="s">(</span><span class="i">$FirstValue</span><span class="cm">,</span> <span class="i">$TypeOfFirstValue</span><span class="cm">,</span> <span class="i">$ValuesRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
448 435
|
|
|
449 436 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span>
|
|
|
450 437 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span>
|
|
|
451 438 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^(SCALAR|HASH|CODE|REF|GLOB)/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
452 439 <span class="w">croak</span> <span class="q">"Error: ${ClassName}-> _SetOrAddValuesOrValueIDs: Trying to add values to vector object with a reference to unsupported value format..."</span><span class="sc">;</span>
|
|
|
453 440 <span class="s">}</span>
|
|
|
454 441
|
|
|
455 442 <span class="k">if</span> <span class="s">(</span><span class="i">Vector::IsVector</span><span class="s">(</span><span class="i">$FirstValue</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
456 443 <span class="c"># It's a vector...</span>
|
|
|
457 444 <span class="i">$ValuesRef</span> = <span class="i">$FirstValue</span><span class="i">->GetValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
458 445 <span class="s">}</span>
|
|
|
459 446 <span class="k">elsif</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
460 447 <span class="c"># It's an array refernce...</span>
|
|
|
461 448 <span class="i">$ValuesRef</span> = <span class="i">$FirstValue</span><span class="sc">;</span>
|
|
|
462 449 <span class="s">}</span>
|
|
|
463 450 <span class="k">else</span> <span class="s">{</span>
|
|
|
464 451 <span class="c"># It's a list of values...</span>
|
|
|
465 452 <span class="i">$ValuesRef</span> = \<span class="i">@Values</span><span class="sc">;</span>
|
|
|
466 453 <span class="s">}</span>
|
|
|
467 454
|
|
|
468 455 <span class="c"># Set or add values or value IDs...</span>
|
|
|
469 456 <span class="j">MODE:</span> <span class="s">{</span>
|
|
|
470 457 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^SetValues$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Values</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Values</span>}}<span class="cm">,</span> <span class="i">@</span>{<span class="i">$ValuesRef</span>}<span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
471 458 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^SetValueIDs$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">ValueIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">ValueIDs</span>}}<span class="cm">,</span> <span class="i">@</span>{<span class="i">$ValuesRef</span>}<span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
472 459 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^AddValues$/i</span><span class="s">)</span> <span class="s">{</span> <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Values</span>}}<span class="cm">,</span> <span class="i">@</span>{<span class="i">$ValuesRef</span>}<span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
473 460 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^AddValueIDs$/i</span><span class="s">)</span> <span class="s">{</span> <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">ValueIDs</span>}}<span class="cm">,</span> <span class="i">@</span>{<span class="i">$ValuesRef</span>}<span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
474 461 <span class="w">croak</span> <span class="q">"Error: ${ClassName}-> _SetOrAddValuesOrValueIDs: Unknown mode $Mode..."</span><span class="sc">;</span>
|
|
|
475 462 <span class="s">}</span>
|
|
|
476 463 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
477 464 <span class="s">}</span>
|
|
|
478 465
|
|
|
479 466 <span class="c"># Set a specific value in fingerprint vector with indicies starting from 0..</span>
|
|
|
480 467 <span class="c">#</span>
|
|
|
481 <a name="SetValue-"></a> 468 <span class="k">sub </span><span class="m">SetValue</span> <span class="s">{</span>
|
|
|
482 469 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Index</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">$SkipCheck</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
483 470
|
|
|
484 471 <span class="c"># Just set it...</span>
|
|
|
485 472 <span class="k">if</span> <span class="s">(</span><span class="i">$SkipCheck</span><span class="s">)</span> <span class="s">{</span>
|
|
|
486 473 <span class="k">return</span> <span class="i">$This</span><span class="i">->_SetValue</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
|
|
|
487 474 <span class="s">}</span>
|
|
|
488 475
|
|
|
489 476 <span class="c"># Check and set...</span>
|
|
|
490 477 <span class="k">if</span> <span class="s">(</span><span class="i">$Index</span> < <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
|
|
|
491 478 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetValue: Index value must be a positive number..."</span><span class="sc">;</span>
|
|
|
492 479 <span class="s">}</span>
|
|
|
493 480 <span class="k">if</span> <span class="s">(</span><span class="i">$Index</span> >= <span class="i">$This</span><span class="i">->GetNumOfValues</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
494 481 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetValue: Index vaue must be less than number of values..."</span><span class="sc">;</span>
|
|
|
495 482 <span class="s">}</span>
|
|
|
496 483
|
|
|
497 484 <span class="k">return</span> <span class="i">$This</span><span class="i">->_SetValue</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
|
|
|
498 485 <span class="s">}</span>
|
|
|
499 486
|
|
|
500 487 <span class="c"># Set a fingerprint vector value...</span>
|
|
|
501 488 <span class="c">#</span>
|
|
|
502 <a name="_SetValue-"></a> 489 <span class="k">sub </span><span class="m">_SetValue</span> <span class="s">{</span>
|
|
|
503 490 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Index</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
504 491
|
|
|
505 492 <span class="i">$This</span>->{<span class="w">Values</span>}[<span class="i">$Index</span>] = <span class="i">$Value</span><span class="sc">;</span>
|
|
|
506 493
|
|
|
507 494 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
508 495 <span class="s">}</span>
|
|
|
509 496
|
|
|
510 497 <span class="c"># Get a specific value from fingerprint vector with indicies starting from 0...</span>
|
|
|
511 498 <span class="c">#</span>
|
|
|
512 <a name="GetValue-"></a> 499 <span class="k">sub </span><span class="m">GetValue</span> <span class="s">{</span>
|
|
|
513 500 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Index</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
514 501
|
|
|
515 502 <span class="k">if</span> <span class="s">(</span><span class="i">$Index</span> < <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
|
|
|
516 503 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->GetValue: Index value must be a positive number..."</span><span class="sc">;</span>
|
|
|
517 504 <span class="s">}</span>
|
|
|
518 505 <span class="k">if</span> <span class="s">(</span><span class="i">$Index</span> >= <span class="i">$This</span><span class="i">->GetNumOfValues</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
519 506 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->GetValue: Index value must be less than number of values..."</span><span class="sc">;</span>
|
|
|
520 507 <span class="s">}</span>
|
|
|
521 508 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetValue</span><span class="s">(</span><span class="i">$Index</span><span class="s">)</span><span class="sc">;</span>
|
|
|
522 509 <span class="s">}</span>
|
|
|
523 510
|
|
|
524 511 <span class="c"># Get a fingerprint vector value...</span>
|
|
|
525 <a name="_GetValue-"></a> 512 <span class="k">sub </span><span class="m">_GetValue</span> <span class="s">{</span>
|
|
|
526 513 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Index</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
527 514
|
|
|
528 515 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">Values</span>}[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
529 516 <span class="s">}</span>
|
|
|
530 517
|
|
|
531 518 <span class="c"># Return vector values as an array or reference to an array...</span>
|
|
|
532 519 <span class="c">#</span>
|
|
|
533 <a name="GetValues-"></a> 520 <span class="k">sub </span><span class="m">GetValues</span> <span class="s">{</span>
|
|
|
534 521 <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>
|
|
|
535 522
|
|
|
536 523 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Values</span>}} <span class="co">:</span> \<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Values</span>}}<span class="sc">;</span>
|
|
|
537 524 <span class="s">}</span>
|
|
|
538 525
|
|
|
539 526 <span class="c"># Set a specific value ID in fingerprint vector with indicies starting from 0..</span>
|
|
|
540 527 <span class="c">#</span>
|
|
|
541 <a name="SetValueID-"></a> 528 <span class="k">sub </span><span class="m">SetValueID</span> <span class="s">{</span>
|
|
|
542 529 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Index</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">$SkipCheck</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
543 530
|
|
|
544 531 <span class="c"># Just set it...</span>
|
|
|
545 532 <span class="k">if</span> <span class="s">(</span><span class="i">$SkipCheck</span><span class="s">)</span> <span class="s">{</span>
|
|
|
546 533 <span class="k">return</span> <span class="i">$This</span><span class="i">->_SetValueID</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
|
|
|
547 534 <span class="s">}</span>
|
|
|
548 535
|
|
|
549 536 <span class="c"># Check and set...</span>
|
|
|
550 537 <span class="k">if</span> <span class="s">(</span><span class="i">$Index</span> < <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
|
|
|
551 538 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetValueID: Index value must be a positive number..."</span><span class="sc">;</span>
|
|
|
552 539 <span class="s">}</span>
|
|
|
553 540 <span class="k">if</span> <span class="s">(</span><span class="i">$Index</span> >= <span class="i">$This</span><span class="i">->GetNumOfValueIDs</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
554 541 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetValueID: Index vaue must be less than number of value IDs..."</span><span class="sc">;</span>
|
|
|
555 542 <span class="s">}</span>
|
|
|
556 543
|
|
|
557 544 <span class="k">return</span> <span class="i">$This</span><span class="i">->_SetValueID</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
|
|
|
558 545 <span class="s">}</span>
|
|
|
559 546
|
|
|
560 547 <span class="c"># Set a fingerprint vector value ID...</span>
|
|
|
561 548 <span class="c">#</span>
|
|
|
562 <a name="_SetValueID-"></a> 549 <span class="k">sub </span><span class="m">_SetValueID</span> <span class="s">{</span>
|
|
|
563 550 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Index</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
564 551
|
|
|
565 552 <span class="i">$This</span>->{<span class="w">ValueIDs</span>}[<span class="i">$Index</span>] = <span class="i">$Value</span><span class="sc">;</span>
|
|
|
566 553
|
|
|
567 554 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
568 555 <span class="s">}</span>
|
|
|
569 556
|
|
|
570 557 <span class="c"># Get a specific value ID from fingerprint vector with indicies starting from 0...</span>
|
|
|
571 558 <span class="c">#</span>
|
|
|
572 <a name="GetValueID-"></a> 559 <span class="k">sub </span><span class="m">GetValueID</span> <span class="s">{</span>
|
|
|
573 560 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Index</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
574 561
|
|
|
575 562 <span class="k">if</span> <span class="s">(</span><span class="i">$Index</span> < <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
|
|
|
576 563 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->GetValueID: Index value must be a positive number..."</span><span class="sc">;</span>
|
|
|
577 564 <span class="s">}</span>
|
|
|
578 565 <span class="k">if</span> <span class="s">(</span><span class="i">$Index</span> >= <span class="i">$This</span><span class="i">->GetNumOfValueIDs</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
579 566 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->GetValueID: Index value must be less than number of value IDs..."</span><span class="sc">;</span>
|
|
|
580 567 <span class="s">}</span>
|
|
|
581 568 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetValueID</span><span class="s">(</span><span class="i">$Index</span><span class="s">)</span><span class="sc">;</span>
|
|
|
582 569 <span class="s">}</span>
|
|
|
583 570
|
|
|
584 571 <span class="c"># Get a fingerprint vector value ID...</span>
|
|
|
585 572 <span class="c">#</span>
|
|
|
586 <a name="_GetValueID-"></a> 573 <span class="k">sub </span><span class="m">_GetValueID</span> <span class="s">{</span>
|
|
|
587 574 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Index</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
588 575
|
|
|
589 576 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">ValueIDs</span>}[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
590 577 <span class="s">}</span>
|
|
|
591 578
|
|
|
592 579 <span class="c"># Return vector value IDs as an array or reference to an array...</span>
|
|
|
593 580 <span class="c">#</span>
|
|
|
594 <a name="GetValueIDs-"></a> 581 <span class="k">sub </span><span class="m">GetValueIDs</span> <span class="s">{</span>
|
|
|
595 582 <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>
|
|
|
596 583
|
|
|
597 584 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">ValueIDs</span>}} <span class="co">:</span> \<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">ValueIDs</span>}}<span class="sc">;</span>
|
|
|
598 585 <span class="s">}</span>
|
|
|
599 586
|
|
|
600 587 <span class="c"># Get fingerprints vector string containing values and/or IDs string in a specifed format...</span>
|
|
|
601 588 <span class="c">#</span>
|
|
|
602 <a name="GetFingerprintsVectorString-"></a> 589 <span class="k">sub </span><span class="m">GetFingerprintsVectorString</span> <span class="s">{</span>
|
|
|
603 590 <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="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
604 591
|
|
|
605 592 <span class="j">FORMAT :</span> <span class="s">{</span>
|
|
|
606 593 <span class="k">if</span> <span class="s">(</span><span class="i">$Format</span> =~ <span class="q">/^(IDsAndValuesString|IDsAndValues)$/i</span><span class="s">)</span> <span class="s">{</span> <span class="k">return</span> <span class="i">$This</span><span class="i">->GetIDsAndValuesString</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">FORMAT</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
607 594 <span class="k">if</span> <span class="s">(</span><span class="i">$Format</span> =~ <span class="q">/^(IDsAndValuesPairsString|IDsAndValuesPairs)$/i</span><span class="s">)</span> <span class="s">{</span> <span class="k">return</span> <span class="i">$This</span><span class="i">->GetIDsAndValuesPairsString</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">FORMAT</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
608 595 <span class="k">if</span> <span class="s">(</span><span class="i">$Format</span> =~ <span class="q">/^(ValuesAndIDsString|ValuesAndIDs)$/i</span><span class="s">)</span> <span class="s">{</span> <span class="k">return</span> <span class="i">$This</span><span class="i">->GetValuesAndIDsString</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">FORMAT</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
609 596 <span class="k">if</span> <span class="s">(</span><span class="i">$Format</span> =~ <span class="q">/^(ValuesAndIDsPairsString|ValuesAndIDsPairs)$/i</span><span class="s">)</span> <span class="s">{</span> <span class="k">return</span> <span class="i">$This</span><span class="i">->GetValuesAndIDsPairsString</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">FORMAT</span><span class="sc">;</span><span class="s">}</span>
|
|
|
610 597 <span class="k">if</span> <span class="s">(</span><span class="i">$Format</span> =~ <span class="q">/^(ValueIDsString|ValueIDs)$/i</span><span class="s">)</span> <span class="s">{</span> <span class="k">return</span> <span class="i">$This</span><span class="i">->GetValueIDsString</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">FORMAT</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
611 598 <span class="k">if</span> <span class="s">(</span><span class="i">$Format</span> =~ <span class="q">/^(ValuesString|Values)$/i</span><span class="s">)</span> <span class="s">{</span> <span class="k">return</span> <span class="i">$This</span><span class="i">->GetValuesString</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">FORMAT</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
612 599 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->GetFingerprintsVectorString: Specified vector string format, $Format, is not supported. Value values: IDsAndValuesString, IDsAndValues, IDsAndValuesPairsString, IDsAndValuesPairs, ValuesAndIDsString, ValuesAndIDs, ValuesAndIDsPairsString, ValuesAndIDsPairs, ValueIDsString, ValueIDs, ValuesString, Values..."</span><span class="sc">;</span>
|
|
|
613 600 <span class="s">}</span>
|
|
|
614 601 <span class="k">return</span> <span class="q">''</span><span class="sc">;</span>
|
|
|
615 602 <span class="s">}</span>
|
|
|
616 603 <span class="c"># Get vector value IDs and values string as space delimited ASCII string separated</span>
|
|
|
617 604 <span class="c"># by semicolon...</span>
|
|
|
618 605 <span class="c">#</span>
|
|
|
619 <a name="GetIDsAndValuesString-"></a> 606 <span class="k">sub </span><span class="m">GetIDsAndValuesString</span> <span class="s">{</span>
|
|
|
620 607 <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>
|
|
|
621 608
|
|
|
622 609 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">ValueIDs</span>}} && <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Values</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
623 610 <span class="c"># Both IDs and values are available...</span>
|
|
|
624 611 <span class="k">return</span> <span class="k">join</span><span class="s">(</span><span class="q">' '</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">ValueIDs</span>}}<span class="s">)</span> . <span class="q">";"</span> . <span class="k">join</span><span class="s">(</span><span class="q">' '</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Values</span>}}<span class="s">)</span><span class="sc">;</span>
|
|
|
625 612 <span class="s">}</span>
|
|
|
626 613 <span class="k">elsif</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Values</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
627 614 <span class="c"># Only values are available...</span>
|
|
|
628 615 <span class="k">return</span> <span class="q">"None;"</span> . <span class="k">join</span><span class="s">(</span><span class="q">' '</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Values</span>}}<span class="s">)</span><span class="sc">;</span>
|
|
|
629 616 <span class="s">}</span>
|
|
|
630 617 <span class="k">else</span> <span class="s">{</span>
|
|
|
631 618 <span class="c"># Values are not available...</span>
|
|
|
632 619 <span class="k">return</span> <span class="q">"None;None"</span><span class="sc">;</span>
|
|
|
633 620 <span class="s">}</span>
|
|
|
634 621 <span class="s">}</span>
|
|
|
635 622
|
|
|
636 623 <span class="c"># Get vector value IDs and value pairs string as space delimited ASCII string...</span>
|
|
|
637 624 <span class="c">#</span>
|
|
|
638 <a name="GetIDsAndValuesPairsString-"></a> 625 <span class="k">sub </span><span class="m">GetIDsAndValuesPairsString</span> <span class="s">{</span>
|
|
|
639 626 <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>
|
|
|
640 627 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$ValueIDsPresent</span><span class="cm">,</span> <span class="i">@IDsAndValuesPairs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
641 628
|
|
|
642 629 <span class="k">if</span> <span class="s">(</span>!<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Values</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
643 630 <span class="c"># Values are unavailable...</span>
|
|
|
644 631 <span class="k">return</span> <span class="q">"None None"</span><span class="sc">;</span>
|
|
|
645 632 <span class="s">}</span>
|
|
|
646 633
|
|
|
647 634 <span class="i">$ValueIDsPresent</span> = <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">ValueIDs</span>}} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
648 635
|
|
|
649 636 <span class="i">@IDsAndValuesPairs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
650 637 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$This</span>->{<span class="w">Values</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
651 638 <span class="k">if</span> <span class="s">(</span><span class="i">$ValueIDsPresent</span><span class="s">)</span> <span class="s">{</span>
|
|
|
652 639 <span class="k">push</span> <span class="i">@IDsAndValuesPairs</span><span class="cm">,</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">ValueIDs</span>}->[<span class="i">$Index</span>]<span class="cm">,</span> <span class="i">$This</span>->{<span class="w">Values</span>}->[<span class="i">$Index</span>]<span class="s">)</span><span class="sc">;</span>
|
|
|
653 640 <span class="s">}</span>
|
|
|
654 641 <span class="k">else</span> <span class="s">{</span>
|
|
|
655 642 <span class="k">push</span> <span class="i">@IDsAndValuesPairs</span><span class="cm">,</span> <span class="s">(</span><span class="q">'None'</span><span class="cm">,</span> <span class="i">$This</span>->{<span class="w">Values</span>}->[<span class="i">$Index</span>]<span class="s">)</span><span class="sc">;</span>
|
|
|
656 643 <span class="s">}</span>
|
|
|
657 644 <span class="s">}</span>
|
|
|
658 645 <span class="k">return</span> <span class="k">join</span><span class="s">(</span><span class="q">' '</span><span class="cm">,</span> <span class="i">@IDsAndValuesPairs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
659 646 <span class="s">}</span>
|
|
|
660 647
|
|
|
661 648 <span class="c"># Get vector value and value IDs string as space delimited ASCII string separated</span>
|
|
|
662 649 <span class="c"># by semicolon...</span>
|
|
|
663 650 <span class="c">#</span>
|
|
|
664 <a name="GetValuesAndIDsString-"></a> 651 <span class="k">sub </span><span class="m">GetValuesAndIDsString</span> <span class="s">{</span>
|
|
|
665 652 <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>
|
|
|
666 653
|
|
|
667 654 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">ValueIDs</span>}} && <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Values</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
668 655 <span class="c"># Both IDs and values are available...</span>
|
|
|
669 656 <span class="k">return</span> <span class="k">join</span><span class="s">(</span><span class="q">' '</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Values</span>}}<span class="s">)</span> . <span class="q">";"</span> . <span class="k">join</span><span class="s">(</span><span class="q">' '</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">ValueIDs</span>}}<span class="s">)</span><span class="sc">;</span>
|
|
|
670 657 <span class="s">}</span>
|
|
|
671 658 <span class="k">elsif</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Values</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
672 659 <span class="c"># Only values are available...</span>
|
|
|
673 660 <span class="k">return</span> <span class="k">join</span><span class="s">(</span><span class="q">' '</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Values</span>}}<span class="s">)</span> . <span class="q">";None"</span><span class="sc">;</span>
|
|
|
674 661 <span class="s">}</span>
|
|
|
675 662 <span class="k">else</span> <span class="s">{</span>
|
|
|
676 663 <span class="c"># Values are not available...</span>
|
|
|
677 664 <span class="k">return</span> <span class="q">"None;None"</span><span class="sc">;</span>
|
|
|
678 665 <span class="s">}</span>
|
|
|
679 666 <span class="s">}</span>
|
|
|
680 667
|
|
|
681 668 <span class="c"># Get vector value and value ID pairs string as space delimited ASCII string...</span>
|
|
|
682 669 <span class="c">#</span>
|
|
|
683 <a name="GetValuesAndIDsPairsString-"></a> 670 <span class="k">sub </span><span class="m">GetValuesAndIDsPairsString</span> <span class="s">{</span>
|
|
|
684 671 <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>
|
|
|
685 672 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$ValueIDsPresent</span><span class="cm">,</span> <span class="i">@ValuesAndIDsPairs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
686 673
|
|
|
687 674 <span class="k">if</span> <span class="s">(</span>!<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Values</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
688 675 <span class="c"># Values are unavailable...</span>
|
|
|
689 676 <span class="k">return</span> <span class="q">"None None"</span><span class="sc">;</span>
|
|
|
690 677 <span class="s">}</span>
|
|
|
691 678
|
|
|
692 679 <span class="i">$ValueIDsPresent</span> = <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">ValueIDs</span>}} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
693 680
|
|
|
694 681 <span class="i">@ValuesAndIDsPairs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
695 682 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$This</span>->{<span class="w">Values</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
696 683 <span class="k">if</span> <span class="s">(</span><span class="i">$ValueIDsPresent</span><span class="s">)</span> <span class="s">{</span>
|
|
|
697 684 <span class="k">push</span> <span class="i">@ValuesAndIDsPairs</span><span class="cm">,</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Values</span>}->[<span class="i">$Index</span>]<span class="cm">,</span> <span class="i">$This</span>->{<span class="w">ValueIDs</span>}->[<span class="i">$Index</span>]<span class="s">)</span><span class="sc">;</span>
|
|
|
698 685 <span class="s">}</span>
|
|
|
699 686 <span class="k">else</span> <span class="s">{</span>
|
|
|
700 687 <span class="k">push</span> <span class="i">@ValuesAndIDsPairs</span><span class="cm">,</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Values</span>}->[<span class="i">$Index</span>]<span class="cm">,</span> <span class="q">'None'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
701 688 <span class="s">}</span>
|
|
|
702 689 <span class="s">}</span>
|
|
|
703 690 <span class="k">return</span> <span class="k">join</span><span class="s">(</span><span class="q">' '</span><span class="cm">,</span> <span class="i">@ValuesAndIDsPairs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
704 691 <span class="s">}</span>
|
|
|
705 692
|
|
|
706 693 <span class="c"># Get vector value IDs string as space delimited ASCII string...</span>
|
|
|
707 694 <span class="c">#</span>
|
|
|
708 <a name="GetValueIDsString-"></a> 695 <span class="k">sub </span><span class="m">GetValueIDsString</span> <span class="s">{</span>
|
|
|
709 696 <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>
|
|
|
710 697
|
|
|
711 698 <span class="k">return</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">ValueIDs</span>}} ? <span class="k">join</span><span class="s">(</span><span class="q">' '</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">ValueIDs</span>}}<span class="s">)</span> <span class="co">:</span> <span class="q">'None'</span><span class="sc">;</span>
|
|
|
712 699 <span class="s">}</span>
|
|
|
713 700
|
|
|
714 701 <span class="c"># Get vector value string as space delimited ASCII string...</span>
|
|
|
715 702 <span class="c">#</span>
|
|
|
716 <a name="GetValuesString-"></a> 703 <span class="k">sub </span><span class="m">GetValuesString</span> <span class="s">{</span>
|
|
|
717 704 <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>
|
|
|
718 705
|
|
|
719 706 <span class="k">return</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Values</span>}} ? <span class="k">join</span><span class="s">(</span><span class="q">' '</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Values</span>}}<span class="s">)</span> <span class="co">:</span> <span class="q">'None'</span><span class="sc">;</span>
|
|
|
720 707 <span class="s">}</span>
|
|
|
721 708
|
|
|
722 709 <span class="c"># Get number of values...</span>
|
|
|
723 <a name="GetNumOfValues-"></a> 710 <span class="k">sub </span><span class="m">GetNumOfValues</span> <span class="s">{</span>
|
|
|
724 711 <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>
|
|
|
725 712
|
|
|
726 713 <span class="k">return</span> <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Values</span>}}<span class="sc">;</span>
|
|
|
727 714 <span class="s">}</span>
|
|
|
728 715
|
|
|
729 716 <span class="c"># Get number of non-zero values...</span>
|
|
|
730 <a name="GetNumOfNonZeroValues-"></a> 717 <span class="k">sub </span><span class="m">GetNumOfNonZeroValues</span> <span class="s">{</span>
|
|
|
731 718 <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>
|
|
|
732 719 <span class="k">my</span><span class="s">(</span><span class="i">$Count</span><span class="cm">,</span> <span class="i">$Index</span><span class="cm">,</span> <span class="i">$Size</span><span class="s">)</span><span class="sc">;</span>
|
|
|
733 720
|
|
|
734 721 <span class="i">$Count</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
735 722 <span class="i">$Size</span> = <span class="i">$This</span><span class="i">->GetNumOfValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
736 723
|
|
|
737 724 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$Size</span> -<span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
738 725 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Values</span>}[<span class="i">$Index</span>] != <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
|
|
|
739 726 <span class="i">$Count</span>++<span class="sc">;</span>
|
|
|
740 727 <span class="s">}</span>
|
|
|
741 728 <span class="s">}</span>
|
|
|
742 729 <span class="k">return</span> <span class="i">$Count</span><span class="sc">;</span>
|
|
|
743 730 <span class="s">}</span>
|
|
|
744 731
|
|
|
745 732 <span class="c"># Get number of value IDs...</span>
|
|
|
746 <a name="GetNumOfValueIDs-"></a> 733 <span class="k">sub </span><span class="m">GetNumOfValueIDs</span> <span class="s">{</span>
|
|
|
747 734 <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>
|
|
|
748 735
|
|
|
749 736 <span class="k">return</span> <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">ValueIDs</span>}}<span class="sc">;</span>
|
|
|
750 737 <span class="s">}</span>
|
|
|
751 738
|
|
|
752 739 <span class="c"># FinegerprintsVectors class provides methods to calculate similarity between vectors</span>
|
|
|
753 740 <span class="c"># containing three different types of values:</span>
|
|
|
754 741 <span class="c">#</span>
|
|
|
755 742 <span class="c"># Type I: OrderedNumericalValues</span>
|
|
|
756 743 <span class="c">#</span>
|
|
|
757 744 <span class="c"># . Size of two vectors are same</span>
|
|
|
758 745 <span class="c"># . Vectors contain real values in a specific order. For example: MACCS keys count, Topological</span>
|
|
|
759 746 <span class="c"># pharnacophore atom pairs and so on.</span>
|
|
|
760 747 <span class="c"># . Option to calculate similarity value using continious values or binary values</span>
|
|
|
761 748 <span class="c">#</span>
|
|
|
762 749 <span class="c"># Type II: UnorderedNumericalValues</span>
|
|
|
763 750 <span class="c">#</span>
|
|
|
764 751 <span class="c"># . Size of two vectors might not be same</span>
|
|
|
765 752 <span class="c"># . Vectors contain unordered real value identified by value IDs. For example: Toplogical atom pairs,</span>
|
|
|
766 753 <span class="c"># Topological atom torsions and so on</span>
|
|
|
767 754 <span class="c"># . Option to calculate similarity value using continous values or binary values</span>
|
|
|
768 755 <span class="c">#</span>
|
|
|
769 756 <span class="c"># Type III: AlphaNumericalValues</span>
|
|
|
770 757 <span class="c">#</span>
|
|
|
771 758 <span class="c"># . Size of two vectors might not be same</span>
|
|
|
772 759 <span class="c"># . Vectors contain unordered alphanumerical values. For example: Extended connectivity fingerprints,</span>
|
|
|
773 760 <span class="c"># atom neighbothood fingerpritns.</span>
|
|
|
774 761 <span class="c"># . The vector values are treated as keys or bit indices and similarity value is calculated accordingly.</span>
|
|
|
775 762 <span class="c">#</span>
|
|
|
776 763 <span class="c"># Before performing similarity or distance calculations between vectors containing UnorderedNumericalValues</span>
|
|
|
777 764 <span class="c"># or AlphaNumericalValues, the vectors are tranformed into vectors containing unique OrderedNumericalValues</span>
|
|
|
778 765 <span class="c"># using value IDs for UnorderedNumericalValues and values itself for AlphaNumericalValues.</span>
|
|
|
779 766 <span class="c">#</span>
|
|
|
780 767 <span class="c"># Three forms similarity or distance calculation between two vectors: AlgebraicForm, BinaryForm or</span>
|
|
|
781 768 <span class="c"># SetTheoreticForm.</span>
|
|
|
782 769 <span class="c">#</span>
|
|
|
783 770 <span class="c"># The value of an extra paramter, CalculationMode, passed to each similarity or distance function</span>
|
|
|
784 771 <span class="c"># controls the calculation. Supported values for CalculationMode: AlgebraicForm, BinaryForm and</span>
|
|
|
785 772 <span class="c"># SetTheoreticForm. Default: AlgebraicForm.</span>
|
|
|
786 773 <span class="c">#</span>
|
|
|
787 774 <span class="c"># For BinaryForm CalculationMode, the ordered list of processed final vector values containing the value or</span>
|
|
|
788 775 <span class="c"># count of each unique value type is simply converted into a binary vector containing 1s and 0s</span>
|
|
|
789 776 <span class="c"># corresponding to presence or absence of values before calculating similarity or distance between</span>
|
|
|
790 777 <span class="c"># two vectors.</span>
|
|
|
791 778 <span class="c">#</span>
|
|
|
792 779 <span class="c"># For two fingerprint vectors A and B of same size containing OrderedNumericalValues, let:</span>
|
|
|
793 780 <span class="c">#</span>
|
|
|
794 781 <span class="c"># N = Number values in A or B</span>
|
|
|
795 782 <span class="c">#</span>
|
|
|
796 783 <span class="c"># Xa = Values of vector A</span>
|
|
|
797 784 <span class="c"># Xb = Values of vector B</span>
|
|
|
798 785 <span class="c">#</span>
|
|
|
799 786 <span class="c"># Xai = Value of ith element in A</span>
|
|
|
800 787 <span class="c"># Xbi = Value of ith element in B</span>
|
|
|
801 788 <span class="c">#</span>
|
|
|
802 789 <span class="c"># SUM = Sum of i over N values</span>
|
|
|
803 790 <span class="c">#</span>
|
|
|
804 791 <span class="c"># For SetTheoreticForm of calculation between two vectors, let:</span>
|
|
|
805 792 <span class="c">#</span>
|
|
|
806 793 <span class="c"># SetIntersectionXaXb = SUM ( MIN ( Xai, Xbi ) )</span>
|
|
|
807 794 <span class="c"># SetDifferenceXaXb = SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN ( Xai, Xbi ) )</span>
|
|
|
808 795 <span class="c">#</span>
|
|
|
809 796 <span class="c"># For BinaryForm of calculation between two vectors, let:</span>
|
|
|
810 797 <span class="c">#</span>
|
|
|
811 798 <span class="c"># Na = Number of bits set to "1" in A = SUM ( Xai )</span>
|
|
|
812 799 <span class="c"># Nb = Number of bits set to "1" in B = SUM ( Xbi )</span>
|
|
|
813 800 <span class="c"># Nc = Number of bits set to "1" in both A and B = SUM ( Xai * Xbi )</span>
|
|
|
814 801 <span class="c"># Nd = Number of bits set to "0" in both A and B = SUM ( 1 - Xai - Xbi + Xai * Xbi)</span>
|
|
|
815 802 <span class="c">#</span>
|
|
|
816 803 <span class="c"># N = Number of bits set to "1" or "0" in A or B = Size of A or B = Na + Nb - Nc + Nd</span>
|
|
|
817 804 <span class="c">#</span>
|
|
|
818 805 <span class="c"># Additionally, for BinaryForm various values also correspond to:</span>
|
|
|
819 806 <span class="c">#</span>
|
|
|
820 807 <span class="c"># Na = | Xa |</span>
|
|
|
821 808 <span class="c"># Nb = | Xb |</span>
|
|
|
822 809 <span class="c"># Nc = | SetIntersectionXaXb |</span>
|
|
|
823 810 <span class="c"># Nd = N - | SetDifferenceXaXb |</span>
|
|
|
824 811 <span class="c">#</span>
|
|
|
825 812 <span class="c"># | SetDifferenceXaXb | = N - Nd = Na + Nb - Nc + Nd - Nd = Na + Nb - Nc</span>
|
|
|
826 813 <span class="c"># = | Xa | + | Xb | - | SetIntersectionXaXb |</span>
|
|
|
827 814 <span class="c">#</span>
|
|
|
828 815 <span class="c"># Various distance coefficients and similarity coefficients [ Ref 40, Ref 62, Ref 64 ] for a pair vectors A and B</span>
|
|
|
829 816 <span class="c"># in AlgebraicForm and BinaryForm are defined as follows:</span>
|
|
|
830 817 <span class="c">#</span>
|
|
|
831 818 <span class="c"># . CityBlockDistanceCoefficient: ( same as HammingDistanceCoefficient and ManhattanDistanceCoefficient)</span>
|
|
|
832 819 <span class="c">#</span>
|
|
|
833 820 <span class="c"># . AlgebraicForm: SUM ( ABS ( Xai - Xbi ) )</span>
|
|
|
834 821 <span class="c">#</span>
|
|
|
835 822 <span class="c"># . BinaryForm: ( Na - Nc ) + ( Nb - Nc ) = Na + Nb - 2 * Nc</span>
|
|
|
836 823 <span class="c">#</span>
|
|
|
837 824 <span class="c"># . SetTheoreticForm: | SetDifferenceXaXb | - | SetIntersectionXaXb |</span>
|
|
|
838 825 <span class="c"># = SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) )</span>
|
|
|
839 826 <span class="c">#</span>
|
|
|
840 827 <span class="c"># . CosineSimilarityCoefficient: ( same as OchiaiSimilarityCoefficient)</span>
|
|
|
841 828 <span class="c">#</span>
|
|
|
842 829 <span class="c"># . AlgebraicForm: SUM ( Xai * Xbi ) / SQRT ( SUM ( Xai ** 2) * SUM ( Xbi ** 2) )</span>
|
|
|
843 830 <span class="c">#</span>
|
|
|
844 831 <span class="c"># . BinaryForm: Nc / SQRT ( Na * Nb)</span>
|
|
|
845 832 <span class="c">#</span>
|
|
|
846 833 <span class="c"># . SetTheoreticForm: | SetIntersectionXaXb | / SQRT ( |Xa| * |Xb| )</span>
|
|
|
847 834 <span class="c"># = SUM ( MIN ( Xai, Xbi ) ) / SQRT ( SUM ( Xai ) * SUM ( Xbi ) )</span>
|
|
|
848 835 <span class="c">#</span>
|
|
|
849 836 <span class="c"># . CzekanowskiSimilarityCoefficient: ( same as DiceSimilarityCoefficient and SorensonSimilarityCoefficient)</span>
|
|
|
850 837 <span class="c">#</span>
|
|
|
851 838 <span class="c"># . AlgebraicForm: ( 2 * ( SUM ( Xai * Xbi ) ) ) / ( SUM ( Xai ** 2) + SUM ( Xbi **2 ) )</span>
|
|
|
852 839 <span class="c">#</span>
|
|
|
853 840 <span class="c"># . BinaryForm: 2 * Nc / ( Na + Nb )</span>
|
|
|
854 841 <span class="c">#</span>
|
|
|
855 842 <span class="c"># . SetTheoreticForm: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| )</span>
|
|
|
856 843 <span class="c"># = 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) )</span>
|
|
|
857 844 <span class="c">#</span>
|
|
|
858 845 <span class="c"># . DiceSimilarityCoefficient: ( same as CzekanowskiSimilarityCoefficient and SorensonSimilarityCoefficient)</span>
|
|
|
859 846 <span class="c">#</span>
|
|
|
860 847 <span class="c"># . AlgebraicForm: ( 2 * ( SUM ( Xai * Xbi ) ) ) / ( SUM ( Xai ** 2) + SUM ( Xbi **2 ) )</span>
|
|
|
861 848 <span class="c">#</span>
|
|
|
862 849 <span class="c"># . BinaryForm: 2 * Nc / ( Na + Nb )</span>
|
|
|
863 850 <span class="c">#</span>
|
|
|
864 851 <span class="c"># . SetTheoreticForm: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| )</span>
|
|
|
865 852 <span class="c"># = 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) )</span>
|
|
|
866 853 <span class="c">#</span>
|
|
|
867 854 <span class="c"># . EuclideanDistanceCoefficient:</span>
|
|
|
868 855 <span class="c">#</span>
|
|
|
869 856 <span class="c"># . AlgebraicForm: SQRT ( SUM ( ( ( Xai - Xbi ) ** 2 ) ) )</span>
|
|
|
870 857 <span class="c">#</span>
|
|
|
871 858 <span class="c"># . BinaryForm: SQRT ( ( Na - Nc ) + ( Nb - Nc ) ) = SQRT ( Na + Nb - 2 * Nc )</span>
|
|
|
872 859 <span class="c">#</span>
|
|
|
873 860 <span class="c"># . SetTheoreticForm: SQRT ( | SetDifferenceXaXb | - | SetIntersectionXaXb | )</span>
|
|
|
874 861 <span class="c"># = SQRT ( SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) )</span>
|
|
|
875 862 <span class="c">#</span>
|
|
|
876 863 <span class="c"># . HammingDistanceCoefficient: ( same as CityBlockDistanceCoefficient and ManhattanDistanceCoefficient)</span>
|
|
|
877 864 <span class="c">#</span>
|
|
|
878 865 <span class="c"># . AlgebraicForm: SUM ( ABS ( Xai - Xbi ) )</span>
|
|
|
879 866 <span class="c">#</span>
|
|
|
880 867 <span class="c"># . BinaryForm: ( Na - Nc ) + ( Nb - Nc ) = Na + Nb - 2 * Nc</span>
|
|
|
881 868 <span class="c">#</span>
|
|
|
882 869 <span class="c"># . SetTheoreticForm: | SetDifferenceXaXb | - | SetIntersectionXaXb |</span>
|
|
|
883 870 <span class="c"># = SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) )</span>
|
|
|
884 871 <span class="c">#</span>
|
|
|
885 872 <span class="c"># . JaccardSimilarityCoefficient: ( same as TanimotoSimilarityCoefficient)</span>
|
|
|
886 873 <span class="c">#</span>
|
|
|
887 874 <span class="c"># . AlgebraicForm: SUM ( Xai * Xbi ) / ( SUM ( Xai ** 2 ) + SUM ( Xbi ** 2 ) - SUM ( Xai * Xbi ) )</span>
|
|
|
888 875 <span class="c">#</span>
|
|
|
889 876 <span class="c"># . BinaryForm: Nc / ( ( Na - Nc ) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb - Nc )</span>
|
|
|
890 877 <span class="c">#</span>
|
|
|
891 878 <span class="c"># . SetTheoreticForm: | SetIntersectionXaXb | / | SetDifferenceXaXb |</span>
|
|
|
892 879 <span class="c"># = SUM ( MIN ( Xai, Xbi ) ) / ( SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN ( Xai, Xbi ) ) )</span>
|
|
|
893 880 <span class="c">#</span>
|
|
|
894 881 <span class="c"># . ManhattanDistanceCoefficient: ( same as CityBlockDistanceCoefficient and HammingDistanceCoefficient)</span>
|
|
|
895 882 <span class="c">#</span>
|
|
|
896 883 <span class="c"># . AlgebraicForm: SUM ( ABS ( Xai - Xbi ) )</span>
|
|
|
897 884 <span class="c">#</span>
|
|
|
898 885 <span class="c"># . BinaryForm: ( Na - Nc ) + ( Nb - Nc ) = Na + Nb - 2 * Nc</span>
|
|
|
899 886 <span class="c">#</span>
|
|
|
900 887 <span class="c"># . SetTheoreticForm: | SetDifferenceXaXb | - | SetIntersectionXaXb |</span>
|
|
|
901 888 <span class="c"># = SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) )</span>
|
|
|
902 889 <span class="c">#</span>
|
|
|
903 890 <span class="c"># . OchiaiSimilarityCoefficient: ( same as CosineSimilarityCoefficient)</span>
|
|
|
904 891 <span class="c">#</span>
|
|
|
905 892 <span class="c"># . AlgebraicForm: SUM ( Xai * Xbi ) / SQRT ( SUM ( Xai ** 2) * SUM ( Xbi ** 2) )</span>
|
|
|
906 893 <span class="c">#</span>
|
|
|
907 894 <span class="c"># . BinaryForm: Nc / SQRT ( Na * Nb)</span>
|
|
|
908 895 <span class="c">#</span>
|
|
|
909 896 <span class="c"># . SetTheoreticForm: | SetIntersectionXaXb | / SQRT ( |Xa| * |Xb| )</span>
|
|
|
910 897 <span class="c"># = SUM ( MIN ( Xai, Xbi ) ) / SQRT ( SUM ( Xai ) * SUM ( Xbi ) )</span>
|
|
|
911 898 <span class="c">#</span>
|
|
|
912 899 <span class="c"># . SorensonSimilarityCoefficient: ( same as CzekanowskiSimilarityCoefficient and DiceSimilarityCoefficient)</span>
|
|
|
913 900 <span class="c">#</span>
|
|
|
914 901 <span class="c"># . AlgebraicForm: ( 2 * ( SUM ( Xai * Xbi ) ) ) / ( SUM ( Xai ** 2) + SUM ( Xbi **2 ) )</span>
|
|
|
915 902 <span class="c">#</span>
|
|
|
916 903 <span class="c"># . BinaryForm: 2 * Nc / ( Na + Nb )</span>
|
|
|
917 904 <span class="c">#</span>
|
|
|
918 905 <span class="c"># . SetTheoreticForm: 2 * | SetIntersectionXaXb | / ( |Xa| + |Xb| )</span>
|
|
|
919 906 <span class="c"># = 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) )</span>
|
|
|
920 907 <span class="c">#</span>
|
|
|
921 908 <span class="c"># . SoergelDistanceCoefficient:</span>
|
|
|
922 909 <span class="c">#</span>
|
|
|
923 910 <span class="c"># . AlgebraicForm: SUM ( ABS ( Xai - Xbi ) ) / SUM ( MAX ( Xai, Xbi ) )</span>
|
|
|
924 911 <span class="c">#</span>
|
|
|
925 912 <span class="c"># . BinaryForm: 1 - Nc / ( Na + Nb - Nc ) = ( Na + Nb - 2 * Nc ) / ( Na + Nb - Nc )</span>
|
|
|
926 913 <span class="c">#</span>
|
|
|
927 914 <span class="c"># . SetTheoreticForm: ( | SetDifferenceXaXb | - | SetIntersectionXaXb | ) / | SetDifferenceXaXb |</span>
|
|
|
928 915 <span class="c"># = ( SUM ( Xai ) + SUM ( Xbi ) - 2 * ( SUM ( MIN ( Xai, Xbi ) ) ) ) / ( SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN ( Xai, Xbi ) ) )</span>
|
|
|
929 916 <span class="c">#</span>
|
|
|
930 917 <span class="c"># . TanimotoSimilarityCoefficient: ( same as JaccardSimilarityCoefficient)</span>
|
|
|
931 918 <span class="c">#</span>
|
|
|
932 919 <span class="c"># . AlgebraicForm: SUM ( Xai * Xbi ) / ( SUM ( Xai ** 2 ) + SUM ( Xbi ** 2 ) - SUM ( Xai * Xbi ) )</span>
|
|
|
933 920 <span class="c">#</span>
|
|
|
934 921 <span class="c"># . BinaryForm: Nc / ( ( Na - Nc ) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb - Nc )</span>
|
|
|
935 922 <span class="c">#</span>
|
|
|
936 923 <span class="c"># . SetTheoreticForm: | SetIntersectionXaXb | / | SetDifferenceXaXb |</span>
|
|
|
937 924 <span class="c"># = SUM ( MIN ( Xai, Xbi ) ) / ( SUM ( Xai ) + SUM ( Xbi ) - SUM ( MIN ( Xai, Xbi ) ) )</span>
|
|
|
938 925 <span class="c">#</span>
|
|
|
939 926 <span class="c">#</span>
|
|
|
940 927
|
|
|
941 928 <span class="c"># Calculate Hamming distance coefficient between two fingerprint vectors.</span>
|
|
|
942 929 <span class="c">#</span>
|
|
|
943 930 <span class="c"># This functionality can be either invoked as a class function or an object method.</span>
|
|
|
944 931 <span class="c">#</span>
|
|
|
945 <a name="HammingDistanceCoefficient-"></a> 932 <span class="k">sub </span><span class="m">HammingDistanceCoefficient ($$;$$)</span> <span class="s">{</span>
|
|
|
946 933 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="cm">,</span> <span class="i">$CalculationMode</span><span class="cm">,</span> <span class="i">$SkipValuesCheck</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
947 934
|
|
|
948 935 <span class="k">return</span> <span class="i">CityBlockDistanceCoefficient</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="cm">,</span> <span class="i">$CalculationMode</span><span class="cm">,</span> <span class="i">$SkipValuesCheck</span><span class="s">)</span><span class="sc">;</span>
|
|
|
949 936 <span class="s">}</span>
|
|
|
950 937
|
|
|
951 938 <span class="c"># Calculate Hamming distance coefficient between two fingerprint vectors.</span>
|
|
|
952 939 <span class="c">#</span>
|
|
|
953 940 <span class="c"># This functionality can be either invoked as a class function or an object method.</span>
|
|
|
954 941 <span class="c">#</span>
|
|
|
955 <a name="ManhattanDistanceCoefficient-"></a> 942 <span class="k">sub </span><span class="m">ManhattanDistanceCoefficient ($$;$$)</span> <span class="s">{</span>
|
|
|
956 943 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="cm">,</span> <span class="i">$CalculationMode</span><span class="cm">,</span> <span class="i">$SkipValuesCheck</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
957 944
|
|
|
958 945 <span class="k">return</span> <span class="i">CityBlockDistanceCoefficient</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="cm">,</span> <span class="i">$CalculationMode</span><span class="cm">,</span> <span class="i">$SkipValuesCheck</span><span class="s">)</span><span class="sc">;</span>
|
|
|
959 946 <span class="s">}</span>
|
|
|
960 947
|
|
|
961 948 <span class="c"># Calculate CityBlock distance coefficient between two fingerprint vectors.</span>
|
|
|
962 949 <span class="c">#</span>
|
|
|
963 950 <span class="c"># This functionality can be either invoked as a class function or an object method.</span>
|
|
|
964 951 <span class="c">#</span>
|
|
|
965 <a name="CityBlockDistanceCoefficient-"></a> 952 <span class="k">sub </span><span class="m">CityBlockDistanceCoefficient ($$;$$)</span> <span class="s">{</span>
|
|
|
966 953 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="cm">,</span> <span class="i">$CalculationMode</span><span class="cm">,</span> <span class="i">$SkipValuesCheck</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
967 954
|
|
|
968 955 <span class="i">$CalculationMode</span> = <span class="k">defined</span> <span class="i">$CalculationMode</span> ? <span class="i">$CalculationMode</span> <span class="co">:</span> <span class="q">'AlgebraicForm'</span><span class="sc">;</span>
|
|
|
969 956 <span class="i">$SkipValuesCheck</span> = <span class="k">defined</span> <span class="i">$SkipValuesCheck</span> ? <span class="i">$SkipValuesCheck</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
970 957
|
|
|
971 958 <span class="c"># Validate and process fingerprints vectors for similarity calculations...</span>
|
|
|
972 959 <span class="c">#</span>
|
|
|
973 960 <span class="i">_ValidateAndProcessFingerprintsVectorsForSimilarityCalculation</span><span class="s">(</span><span class="q">"CityBlockDistanceCoefficient: Calculation failed"</span><span class="cm">,</span> <span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="cm">,</span> <span class="i">$CalculationMode</span><span class="cm">,</span> <span class="i">$SkipValuesCheck</span><span class="s">)</span><span class="sc">;</span>
|
|
|
974 961
|
|
|
975 962 <span class="c"># Perform the calculation...</span>
|
|
|
976 963 <span class="k">if</span> <span class="s">(</span><span class="i">$CalculationMode</span> =~ <span class="q">/^AlgebraicForm$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
977 964 <span class="k">return</span> <span class="i">_CityBlockDistanceCoefficientUsingAlgebraicForm</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
978 965 <span class="s">}</span>
|
|
|
979 966 <span class="k">elsif</span> <span class="s">(</span><span class="i">$CalculationMode</span> =~ <span class="q">/^BinaryForm$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
980 967 <span class="k">return</span> <span class="i">_CityBlockDistanceCoefficientUsingBinaryForm</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
981 968 <span class="s">}</span>
|
|
|
982 969 <span class="k">elsif</span> <span class="s">(</span><span class="i">$CalculationMode</span> =~ <span class="q">/^SetTheoreticForm$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
983 970 <span class="k">return</span> <span class="i">_CityBlockDistanceCoefficientUsingSetTheoreticForm</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
984 971 <span class="s">}</span>
|
|
|
985 972 <span class="k">else</span> <span class="s">{</span>
|
|
|
986 973 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
987 974 <span class="s">}</span>
|
|
|
988 975 <span class="s">}</span>
|
|
|
989 976
|
|
|
990 977 <span class="c"># Calculate CityBlock distance coefficient using algebraic form...</span>
|
|
|
991 978 <span class="c">#</span>
|
|
|
992 <a name="_CityBlockDistanceCoefficientUsingAlgebraicForm-"></a> 979 <span class="k">sub </span><span class="m">_CityBlockDistanceCoefficientUsingAlgebraicForm</span> <span class="s">{</span>
|
|
|
993 980 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
994 981 <span class="k">my</span><span class="s">(</span><span class="i">$SumAbsSubtractionXaiXbi</span><span class="s">)</span><span class="sc">;</span>
|
|
|
995 982
|
|
|
996 983 <span class="i">$SumAbsSubtractionXaiXbi</span> = <span class="i">_GetSumOfAbsoluteValueOfSubtractionOfFingerprintsOrderedValues</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
997 984
|
|
|
998 985 <span class="k">return</span> <span class="i">$SumAbsSubtractionXaiXbi</span><span class="sc">;</span>
|
|
|
999 986 <span class="s">}</span>
|
|
|
1000 987
|
|
|
1001 988 <span class="c"># Calculate CityBlock distance coefficient using binary form...</span>
|
|
|
1002 989 <span class="c">#</span>
|
|
|
1003 <a name="_CityBlockDistanceCoefficientUsingBinaryForm-"></a> 990 <span class="k">sub </span><span class="m">_CityBlockDistanceCoefficientUsingBinaryForm</span> <span class="s">{</span>
|
|
|
1004 991 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1005 992 <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="s">)</span><span class="sc">;</span>
|
|
|
1006 993
|
|
|
1007 994 <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">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1008 995
|
|
|
1009 996 <span class="k">return</span> <span class="s">(</span><span class="i">$Na</span> + <span class="i">$Nb</span> - <span class="n">2</span> * <span class="i">$Nc</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1010 997 <span class="s">}</span>
|
|
|
1011 998
|
|
|
1012 999 <span class="c"># Calculate CityBlock distance coefficient using set theoretic form...</span>
|
|
|
1013 1000 <span class="c">#</span>
|
|
|
1014 <a name="_CityBlockDistanceCoefficientUsingSetTheoreticForm-"></a>1001 <span class="k">sub </span><span class="m">_CityBlockDistanceCoefficientUsingSetTheoreticForm</span> <span class="s">{</span>
|
|
|
1015 1002 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1016 1003 <span class="k">my</span><span class="s">(</span><span class="i">$SumMinXaiXbi</span><span class="cm">,</span> <span class="i">$SumXai</span><span class="cm">,</span> <span class="i">$SumXbi</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1017 1004
|
|
|
1018 1005 <span class="i">$SumXai</span> = <span class="i">_GetSumOfFingerprintsOrderedValues</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1019 1006 <span class="i">$SumXbi</span> = <span class="i">_GetSumOfFingerprintsOrderedValues</span><span class="s">(</span><span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1020 1007 <span class="i">$SumMinXaiXbi</span> = <span class="i">_GetSumOfMinimumOfFingerprintsOrderdedValues</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1021 1008
|
|
|
1022 1009 <span class="k">return</span> <span class="s">(</span><span class="i">$SumXai</span> + <span class="i">$SumXbi</span> - <span class="n">2</span> * <span class="i">$SumMinXaiXbi</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1023 1010 <span class="s">}</span>
|
|
|
1024 1011
|
|
|
1025 1012 <span class="c"># Calculate Ochiai similarity cofficient between two fingerprint vectors.</span>
|
|
|
1026 1013 <span class="c">#</span>
|
|
|
1027 1014 <span class="c"># This functionality can be either invoked as a class function or an object method.</span>
|
|
|
1028 1015 <span class="c">#</span>
|
|
|
1029 <a name="OchiaiSimilarityCoefficient-"></a>1016 <span class="k">sub </span><span class="m">OchiaiSimilarityCoefficient ($$;$$)</span> <span class="s">{</span>
|
|
|
1030 1017 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="cm">,</span> <span class="i">$CalculationMode</span><span class="cm">,</span> <span class="i">$SkipValuesCheck</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1031 1018
|
|
|
1032 1019 <span class="k">return</span> <span class="i">CosineSimilarityCoefficient</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="cm">,</span> <span class="i">$CalculationMode</span><span class="cm">,</span> <span class="i">$SkipValuesCheck</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1033 1020 <span class="s">}</span>
|
|
|
1034 1021
|
|
|
1035 1022 <span class="c"># Calculate Cosine similarity cofficient between two fingerprint vectors.</span>
|
|
|
1036 1023 <span class="c">#</span>
|
|
|
1037 1024 <span class="c"># This functionality can be either invoked as a class function or an object method.</span>
|
|
|
1038 1025 <span class="c">#</span>
|
|
|
1039 <a name="CosineSimilarityCoefficient-"></a>1026 <span class="k">sub </span><span class="m">CosineSimilarityCoefficient ($$;$$)</span> <span class="s">{</span>
|
|
|
1040 1027 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="cm">,</span> <span class="i">$CalculationMode</span><span class="cm">,</span> <span class="i">$SkipValuesCheck</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1041 1028
|
|
|
1042 1029 <span class="i">$CalculationMode</span> = <span class="k">defined</span> <span class="i">$CalculationMode</span> ? <span class="i">$CalculationMode</span> <span class="co">:</span> <span class="q">'AlgebraicForm'</span><span class="sc">;</span>
|
|
|
1043 1030 <span class="i">$SkipValuesCheck</span> = <span class="k">defined</span> <span class="i">$SkipValuesCheck</span> ? <span class="i">$SkipValuesCheck</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1044 1031
|
|
|
1045 1032 <span class="c"># Validate and process fingerprints vectors for similarity calculations...</span>
|
|
|
1046 1033 <span class="c">#</span>
|
|
|
1047 1034 <span class="i">_ValidateAndProcessFingerprintsVectorsForSimilarityCalculation</span><span class="s">(</span><span class="q">"CosineSimilarityCoefficient: Calculation failed"</span><span class="cm">,</span> <span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="cm">,</span> <span class="i">$CalculationMode</span><span class="cm">,</span> <span class="i">$SkipValuesCheck</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1048 1035
|
|
|
1049 1036 <span class="c"># Perform the calculation...</span>
|
|
|
1050 1037 <span class="k">if</span> <span class="s">(</span><span class="i">$CalculationMode</span> =~ <span class="q">/^AlgebraicForm$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1051 1038 <span class="k">return</span> <span class="i">_CosineSimilarityCoefficientUsingAlgebraicForm</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1052 1039 <span class="s">}</span>
|
|
|
1053 1040 <span class="k">elsif</span> <span class="s">(</span><span class="i">$CalculationMode</span> =~ <span class="q">/^BinaryForm$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1054 1041 <span class="k">return</span> <span class="i">_CosineSimilarityCoefficientUsingBinaryForm</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1055 1042 <span class="s">}</span>
|
|
|
1056 1043 <span class="k">elsif</span> <span class="s">(</span><span class="i">$CalculationMode</span> =~ <span class="q">/^SetTheoreticForm$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1057 1044 <span class="k">return</span> <span class="i">_CosineSimilarityCoefficientUsingSetTheoreticForm</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1058 1045 <span class="s">}</span>
|
|
|
1059 1046 <span class="k">else</span> <span class="s">{</span>
|
|
|
1060 1047 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
1061 1048 <span class="s">}</span>
|
|
|
1062 1049 <span class="s">}</span>
|
|
|
1063 1050
|
|
|
1064 1051 <span class="c"># Calculate Cosine similarity coefficient using algebraic form...</span>
|
|
|
1065 1052 <span class="c">#</span>
|
|
|
1066 <a name="_CosineSimilarityCoefficientUsingAlgebraicForm-"></a>1053 <span class="k">sub </span><span class="m">_CosineSimilarityCoefficientUsingAlgebraicForm</span> <span class="s">{</span>
|
|
|
1067 1054 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1068 1055 <span class="k">my</span><span class="s">(</span><span class="i">$SumProductXaiXbi</span><span class="cm">,</span> <span class="i">$SumXai2</span><span class="cm">,</span> <span class="i">$SumXbi2</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>
|
|
|
1069 1056
|
|
|
1070 1057 <span class="i">$SumXai2</span> = <span class="i">_GetSumOfSquaresOfFingerprintsOrderedValues</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1071 1058 <span class="i">$SumXbi2</span> = <span class="i">_GetSumOfSquaresOfFingerprintsOrderedValues</span><span class="s">(</span><span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1072 1059 <span class="i">$SumProductXaiXbi</span> = <span class="i">_GetSumOfProductOfFingerprintsOrderedValues</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1073 1060
|
|
|
1074 1061 <span class="i">$Numerator</span> = <span class="i">$SumProductXaiXbi</span><span class="sc">;</span>
|
|
|
1075 1062 <span class="i">$Denominator</span> = <span class="k">sqrt</span><span class="s">(</span><span class="i">$SumXai2</span> * <span class="i">$SumXbi2</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1076 1063
|
|
|
1077 1064 <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>
|
|
|
1078 1065 <span class="s">}</span>
|
|
|
1079 1066
|
|
|
1080 1067 <span class="c"># CalculateCosine similarity coefficient using binary form...</span>
|
|
|
1081 1068 <span class="c">#</span>
|
|
|
1082 <a name="_CosineSimilarityCoefficientUsingBinaryForm-"></a>1069 <span class="k">sub </span><span class="m">_CosineSimilarityCoefficientUsingBinaryForm</span> <span class="s">{</span>
|
|
|
1083 1070 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1084 1071 <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>
|
|
|
1085 1072
|
|
|
1086 1073 <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">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1087 1074
|
|
|
1088 1075 <span class="i">$Numerator</span> = <span class="i">$Nc</span><span class="sc">;</span>
|
|
|
1089 1076 <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>
|
|
|
1090 1077
|
|
|
1091 1078 <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>
|
|
|
1092 1079 <span class="s">}</span>
|
|
|
1093 1080
|
|
|
1094 1081 <span class="c"># Calculate Cosine similarity coefficient using set theoretic form...</span>
|
|
|
1095 1082 <span class="c">#</span>
|
|
|
1096 <a name="_CosineSimilarityCoefficientUsingSetTheoreticForm-"></a>1083 <span class="k">sub </span><span class="m">_CosineSimilarityCoefficientUsingSetTheoreticForm</span> <span class="s">{</span>
|
|
|
1097 1084 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1098 1085 <span class="k">my</span><span class="s">(</span><span class="i">$SumMinXaiXbi</span><span class="cm">,</span> <span class="i">$SumXai</span><span class="cm">,</span> <span class="i">$SumXbi</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>
|
|
|
1099 1086
|
|
|
1100 1087 <span class="i">$SumXai</span> = <span class="i">_GetSumOfFingerprintsOrderedValues</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1101 1088 <span class="i">$SumXbi</span> = <span class="i">_GetSumOfFingerprintsOrderedValues</span><span class="s">(</span><span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1102 1089 <span class="i">$SumMinXaiXbi</span> = <span class="i">_GetSumOfMinimumOfFingerprintsOrderdedValues</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1103 1090
|
|
|
1104 1091 <span class="i">$Numerator</span> = <span class="i">$SumMinXaiXbi</span><span class="sc">;</span>
|
|
|
1105 1092 <span class="i">$Denominator</span> = <span class="k">sqrt</span><span class="s">(</span><span class="i">$SumXai</span> * <span class="i">$SumXbi</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1106 1093
|
|
|
1107 1094 <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>
|
|
|
1108 1095 <span class="s">}</span>
|
|
|
1109 1096
|
|
|
1110 1097 <span class="c"># Calculate Czekanowski similarity cofficient between two fingerprint vectors.</span>
|
|
|
1111 1098 <span class="c">#</span>
|
|
|
1112 1099 <span class="c"># This functionality can be either invoked as a class function or an object method.</span>
|
|
|
1113 1100 <span class="c">#</span>
|
|
|
1114 <a name="CzekanowskiSimilarityCoefficient-"></a>1101 <span class="k">sub </span><span class="m">CzekanowskiSimilarityCoefficient ($$;$$)</span> <span class="s">{</span>
|
|
|
1115 1102 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="cm">,</span> <span class="i">$CalculationMode</span><span class="cm">,</span> <span class="i">$SkipValuesCheck</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1116 1103
|
|
|
1117 1104 <span class="k">return</span> <span class="i">DiceSimilarityCoefficient</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="cm">,</span> <span class="i">$CalculationMode</span><span class="cm">,</span> <span class="i">$SkipValuesCheck</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1118 1105 <span class="s">}</span>
|
|
|
1119 1106
|
|
|
1120 1107 <span class="c"># Calculate Sorenson similarity cofficient between two fingerprint vectors.</span>
|
|
|
1121 1108 <span class="c">#</span>
|
|
|
1122 1109 <span class="c"># This functionality can be either invoked as a class function or an object method.</span>
|
|
|
1123 1110 <span class="c">#</span>
|
|
|
1124 <a name="SorensonSimilarityCoefficient-"></a>1111 <span class="k">sub </span><span class="m">SorensonSimilarityCoefficient ($$;$$)</span> <span class="s">{</span>
|
|
|
1125 1112 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="cm">,</span> <span class="i">$CalculationMode</span><span class="cm">,</span> <span class="i">$SkipValuesCheck</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1126 1113
|
|
|
1127 1114 <span class="k">return</span> <span class="i">DiceSimilarityCoefficient</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="cm">,</span> <span class="i">$CalculationMode</span><span class="cm">,</span> <span class="i">$SkipValuesCheck</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1128 1115 <span class="s">}</span>
|
|
|
1129 1116
|
|
|
1130 1117 <span class="c"># Calculate Dice similarity cofficient between two fingerprint vectors.</span>
|
|
|
1131 1118 <span class="c">#</span>
|
|
|
1132 1119 <span class="c"># This functionality can be either invoked as a class function or an object method.</span>
|
|
|
1133 1120 <span class="c">#</span>
|
|
|
1134 <a name="DiceSimilarityCoefficient-"></a>1121 <span class="k">sub </span><span class="m">DiceSimilarityCoefficient ($$;$$)</span> <span class="s">{</span>
|
|
|
1135 1122 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="cm">,</span> <span class="i">$CalculationMode</span><span class="cm">,</span> <span class="i">$SkipValuesCheck</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1136 1123
|
|
|
1137 1124 <span class="i">$CalculationMode</span> = <span class="k">defined</span> <span class="i">$CalculationMode</span> ? <span class="i">$CalculationMode</span> <span class="co">:</span> <span class="q">'AlgebraicForm'</span><span class="sc">;</span>
|
|
|
1138 1125 <span class="i">$SkipValuesCheck</span> = <span class="k">defined</span> <span class="i">$SkipValuesCheck</span> ? <span class="i">$SkipValuesCheck</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1139 1126
|
|
|
1140 1127 <span class="c"># Validate and process fingerprints vectors for similarity calculations...</span>
|
|
|
1141 1128 <span class="c">#</span>
|
|
|
1142 1129 <span class="i">_ValidateAndProcessFingerprintsVectorsForSimilarityCalculation</span><span class="s">(</span><span class="q">"DiceSimilarityCoefficient: Calculation failed"</span><span class="cm">,</span> <span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="cm">,</span> <span class="i">$CalculationMode</span><span class="cm">,</span> <span class="i">$SkipValuesCheck</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1143 1130
|
|
|
1144 1131 <span class="c"># Perform the calculation...</span>
|
|
|
1145 1132 <span class="k">if</span> <span class="s">(</span><span class="i">$CalculationMode</span> =~ <span class="q">/^AlgebraicForm$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1146 1133 <span class="k">return</span> <span class="i">_DiceSimilarityCoefficientUsingAlgebraicForm</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1147 1134 <span class="s">}</span>
|
|
|
1148 1135 <span class="k">elsif</span> <span class="s">(</span><span class="i">$CalculationMode</span> =~ <span class="q">/^BinaryForm$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1149 1136 <span class="k">return</span> <span class="i">_DiceSimilarityCoefficientUsingBinaryForm</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1150 1137 <span class="s">}</span>
|
|
|
1151 1138 <span class="k">elsif</span> <span class="s">(</span><span class="i">$CalculationMode</span> =~ <span class="q">/^SetTheoreticForm$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1152 1139 <span class="k">return</span> <span class="i">_DiceSimilarityCoefficientUsingSetTheoreticForm</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1153 1140 <span class="s">}</span>
|
|
|
1154 1141 <span class="k">else</span> <span class="s">{</span>
|
|
|
1155 1142 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
1156 1143 <span class="s">}</span>
|
|
|
1157 1144 <span class="s">}</span>
|
|
|
1158 1145
|
|
|
1159 1146 <span class="c"># Calculate Dice similarity coefficient using algebraic form...</span>
|
|
|
1160 1147 <span class="c">#</span>
|
|
|
1161 <a name="_DiceSimilarityCoefficientUsingAlgebraicForm-"></a>1148 <span class="k">sub </span><span class="m">_DiceSimilarityCoefficientUsingAlgebraicForm</span> <span class="s">{</span>
|
|
|
1162 1149 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1163 1150 <span class="k">my</span><span class="s">(</span><span class="i">$SumProductXaiXbi</span><span class="cm">,</span> <span class="i">$SumXai2</span><span class="cm">,</span> <span class="i">$SumXbi2</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>
|
|
|
1164 1151
|
|
|
1165 1152 <span class="i">$SumXai2</span> = <span class="i">_GetSumOfSquaresOfFingerprintsOrderedValues</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1166 1153 <span class="i">$SumXbi2</span> = <span class="i">_GetSumOfSquaresOfFingerprintsOrderedValues</span><span class="s">(</span><span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1167 1154 <span class="i">$SumProductXaiXbi</span> = <span class="i">_GetSumOfProductOfFingerprintsOrderedValues</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1168 1155
|
|
|
1169 1156 <span class="i">$Numerator</span> = <span class="n">2</span> * <span class="i">$SumProductXaiXbi</span><span class="sc">;</span>
|
|
|
1170 1157 <span class="i">$Denominator</span> = <span class="i">$SumXai2</span> + <span class="i">$SumXbi2</span><span class="sc">;</span>
|
|
|
1171 1158
|
|
|
1172 1159 <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>
|
|
|
1173 1160 <span class="s">}</span>
|
|
|
1174 1161
|
|
|
1175 1162 <span class="c"># Calculate Dice similarity coefficient using binary form...</span>
|
|
|
1176 1163 <span class="c">#</span>
|
|
|
1177 <a name="_DiceSimilarityCoefficientUsingBinaryForm-"></a>1164 <span class="k">sub </span><span class="m">_DiceSimilarityCoefficientUsingBinaryForm</span> <span class="s">{</span>
|
|
|
1178 1165 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1179 1166 <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>
|
|
|
1180 1167
|
|
|
1181 1168 <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">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1182 1169
|
|
|
1183 1170 <span class="i">$Numerator</span> = <span class="n">2</span> * <span class="i">$Nc</span><span class="sc">;</span>
|
|
|
1184 1171 <span class="i">$Denominator</span> = <span class="i">$Na</span> + <span class="i">$Nb</span><span class="sc">;</span>
|
|
|
1185 1172
|
|
|
1186 1173 <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>
|
|
|
1187 1174 <span class="s">}</span>
|
|
|
1188 1175
|
|
|
1189 1176 <span class="c"># Calculate Dice similarity coefficient using set theoretic form...</span>
|
|
|
1190 1177 <span class="c">#</span>
|
|
|
1191 <a name="_DiceSimilarityCoefficientUsingSetTheoreticForm-"></a>1178 <span class="k">sub </span><span class="m">_DiceSimilarityCoefficientUsingSetTheoreticForm</span> <span class="s">{</span>
|
|
|
1192 1179 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1193 1180 <span class="k">my</span><span class="s">(</span><span class="i">$SumMinXaiXbi</span><span class="cm">,</span> <span class="i">$SumXai</span><span class="cm">,</span> <span class="i">$SumXbi</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>
|
|
|
1194 1181
|
|
|
1195 1182 <span class="i">$SumXai</span> = <span class="i">_GetSumOfFingerprintsOrderedValues</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1196 1183 <span class="i">$SumXbi</span> = <span class="i">_GetSumOfFingerprintsOrderedValues</span><span class="s">(</span><span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1197 1184 <span class="i">$SumMinXaiXbi</span> = <span class="i">_GetSumOfMinimumOfFingerprintsOrderdedValues</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1198 1185
|
|
|
1199 1186 <span class="i">$Numerator</span> = <span class="n">2</span> * <span class="i">$SumMinXaiXbi</span><span class="sc">;</span>
|
|
|
1200 1187 <span class="i">$Denominator</span> = <span class="i">$SumXai</span> + <span class="i">$SumXbi</span><span class="sc">;</span>
|
|
|
1201 1188
|
|
|
1202 1189 <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>
|
|
|
1203 1190 <span class="s">}</span>
|
|
|
1204 1191
|
|
|
1205 1192
|
|
|
1206 1193 <span class="c"># Calculate Euclidean distance coefficient between two fingerprint vectors.</span>
|
|
|
1207 1194 <span class="c">#</span>
|
|
|
1208 1195 <span class="c"># This functionality can be either invoked as a class function or an object method.</span>
|
|
|
1209 1196 <span class="c">#</span>
|
|
|
1210 <a name="EuclideanDistanceCoefficient-"></a>1197 <span class="k">sub </span><span class="m">EuclideanDistanceCoefficient ($$;$$)</span> <span class="s">{</span>
|
|
|
1211 1198 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="cm">,</span> <span class="i">$CalculationMode</span><span class="cm">,</span> <span class="i">$SkipValuesCheck</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1212 1199
|
|
|
1213 1200 <span class="i">$CalculationMode</span> = <span class="k">defined</span> <span class="i">$CalculationMode</span> ? <span class="i">$CalculationMode</span> <span class="co">:</span> <span class="q">'AlgebraicForm'</span><span class="sc">;</span>
|
|
|
1214 1201 <span class="i">$SkipValuesCheck</span> = <span class="k">defined</span> <span class="i">$SkipValuesCheck</span> ? <span class="i">$SkipValuesCheck</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1215 1202
|
|
|
1216 1203 <span class="c"># Validate and process fingerprints vectors for similarity calculations...</span>
|
|
|
1217 1204 <span class="c">#</span>
|
|
|
1218 1205 <span class="i">_ValidateAndProcessFingerprintsVectorsForSimilarityCalculation</span><span class="s">(</span><span class="q">"EuclideanDistanceCoefficient: Calculation failed"</span><span class="cm">,</span> <span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="cm">,</span> <span class="i">$CalculationMode</span><span class="cm">,</span> <span class="i">$SkipValuesCheck</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1219 1206
|
|
|
1220 1207 <span class="c"># Perform the calculation...</span>
|
|
|
1221 1208 <span class="k">if</span> <span class="s">(</span><span class="i">$CalculationMode</span> =~ <span class="q">/^AlgebraicForm$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1222 1209 <span class="k">return</span> <span class="i">_EuclideanDistanceCoefficientUsingAlgebraicForm</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1223 1210 <span class="s">}</span>
|
|
|
1224 1211 <span class="k">elsif</span> <span class="s">(</span><span class="i">$CalculationMode</span> =~ <span class="q">/^BinaryForm$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1225 1212 <span class="k">return</span> <span class="i">_EuclideanDistanceCoefficientUsingBinaryForm</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1226 1213 <span class="s">}</span>
|
|
|
1227 1214 <span class="k">elsif</span> <span class="s">(</span><span class="i">$CalculationMode</span> =~ <span class="q">/^SetTheoreticForm$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1228 1215 <span class="k">return</span> <span class="i">_EuclideanDistanceCoefficientUsingSetTheoreticForm</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1229 1216 <span class="s">}</span>
|
|
|
1230 1217 <span class="k">else</span> <span class="s">{</span>
|
|
|
1231 1218 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
1232 1219 <span class="s">}</span>
|
|
|
1233 1220 <span class="s">}</span>
|
|
|
1234 1221
|
|
|
1235 1222 <span class="c"># Calculate Euclidean distance coefficient using algebraic form...</span>
|
|
|
1236 1223 <span class="c">#</span>
|
|
|
1237 <a name="_EuclideanDistanceCoefficientUsingAlgebraicForm-"></a>1224 <span class="k">sub </span><span class="m">_EuclideanDistanceCoefficientUsingAlgebraicForm</span> <span class="s">{</span>
|
|
|
1238 1225 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1239 1226 <span class="k">my</span><span class="s">(</span><span class="i">$SumSquaresSubtractionXaiXbi</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1240 1227
|
|
|
1241 1228 <span class="i">$SumSquaresSubtractionXaiXbi</span> = <span class="i">_GetSumOfSquaresOfSubtractionOfFingerprintsOrderedValues</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1242 1229
|
|
|
1243 1230 <span class="k">return</span> <span class="k">sqrt</span><span class="s">(</span><span class="i">$SumSquaresSubtractionXaiXbi</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1244 1231 <span class="s">}</span>
|
|
|
1245 1232
|
|
|
1246 1233 <span class="c"># Calculate Euclidean distance coefficient using binary form...</span>
|
|
|
1247 1234 <span class="c">#</span>
|
|
|
1248 <a name="_EuclideanDistanceCoefficientUsingBinaryForm-"></a>1235 <span class="k">sub </span><span class="m">_EuclideanDistanceCoefficientUsingBinaryForm</span> <span class="s">{</span>
|
|
|
1249 1236 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1250 1237 <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="s">)</span><span class="sc">;</span>
|
|
|
1251 1238
|
|
|
1252 1239 <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">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1253 1240
|
|
|
1254 1241 <span class="k">return</span> <span class="s">(</span><span class="k">sqrt</span><span class="s">(</span><span class="i">$Na</span> + <span class="i">$Nb</span> - <span class="n">2</span> * <span class="i">$Nc</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1255 1242 <span class="s">}</span>
|
|
|
1256 1243
|
|
|
1257 1244 <span class="c"># Calculate Euclidean distance coefficient using set theoretic form...</span>
|
|
|
1258 1245 <span class="c">#</span>
|
|
|
1259 <a name="_EuclideanDistanceCoefficientUsingSetTheoreticForm-"></a>1246 <span class="k">sub </span><span class="m">_EuclideanDistanceCoefficientUsingSetTheoreticForm</span> <span class="s">{</span>
|
|
|
1260 1247 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1261 1248 <span class="k">my</span><span class="s">(</span><span class="i">$SumMinXaiXbi</span><span class="cm">,</span> <span class="i">$SumXai</span><span class="cm">,</span> <span class="i">$SumXbi</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1262 1249
|
|
|
1263 1250 <span class="i">$SumXai</span> = <span class="i">_GetSumOfFingerprintsOrderedValues</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1264 1251 <span class="i">$SumXbi</span> = <span class="i">_GetSumOfFingerprintsOrderedValues</span><span class="s">(</span><span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1265 1252 <span class="i">$SumMinXaiXbi</span> = <span class="i">_GetSumOfMinimumOfFingerprintsOrderdedValues</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1266 1253
|
|
|
1267 1254 <span class="k">return</span> <span class="s">(</span><span class="k">sqrt</span><span class="s">(</span><span class="i">$SumXai</span> + <span class="i">$SumXbi</span> - <span class="n">2</span> * <span class="i">$SumMinXaiXbi</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1268 1255 <span class="s">}</span>
|
|
|
1269 1256
|
|
|
1270 1257 <span class="c"># Calculate Jaccard similarity cofficient between two fingerprint vectors.</span>
|
|
|
1271 1258 <span class="c">#</span>
|
|
|
1272 1259 <span class="c"># This functionality can be either invoked as a class function or an object method.</span>
|
|
|
1273 1260 <span class="c">#</span>
|
|
|
1274 <a name="JaccardSimilarityCoefficient-"></a>1261 <span class="k">sub </span><span class="m">JaccardSimilarityCoefficient ($$;$$)</span> <span class="s">{</span>
|
|
|
1275 1262 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="cm">,</span> <span class="i">$CalculationMode</span><span class="cm">,</span> <span class="i">$SkipValuesCheck</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1276 1263
|
|
|
1277 1264 <span class="k">return</span> <span class="i">TanimotoSimilarityCoefficient</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="cm">,</span> <span class="i">$CalculationMode</span><span class="cm">,</span> <span class="i">$SkipValuesCheck</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1278 1265 <span class="s">}</span>
|
|
|
1279 1266
|
|
|
1280 1267 <span class="c"># Calculate Tanimoto similarity cofficient between two fingerprint vectors.</span>
|
|
|
1281 1268 <span class="c">#</span>
|
|
|
1282 1269 <span class="c"># This functionality can be either invoked as a class function or an object method.</span>
|
|
|
1283 1270 <span class="c">#</span>
|
|
|
1284 <a name="TanimotoSimilarityCoefficient-"></a>1271 <span class="k">sub </span><span class="m">TanimotoSimilarityCoefficient ($$;$$)</span> <span class="s">{</span>
|
|
|
1285 1272 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="cm">,</span> <span class="i">$CalculationMode</span><span class="cm">,</span> <span class="i">$SkipValuesCheck</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1286 1273
|
|
|
1287 1274 <span class="i">$CalculationMode</span> = <span class="k">defined</span> <span class="i">$CalculationMode</span> ? <span class="i">$CalculationMode</span> <span class="co">:</span> <span class="q">'AlgebraicForm'</span><span class="sc">;</span>
|
|
|
1288 1275 <span class="i">$SkipValuesCheck</span> = <span class="k">defined</span> <span class="i">$SkipValuesCheck</span> ? <span class="i">$SkipValuesCheck</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1289 1276
|
|
|
1290 1277 <span class="c"># Validate and process fingerprints vectors for similarity calculations...</span>
|
|
|
1291 1278 <span class="c">#</span>
|
|
|
1292 1279 <span class="i">_ValidateAndProcessFingerprintsVectorsForSimilarityCalculation</span><span class="s">(</span><span class="q">"TanimotoSimilarityCoefficient: Calculation failed"</span><span class="cm">,</span> <span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="cm">,</span> <span class="i">$CalculationMode</span><span class="cm">,</span> <span class="i">$SkipValuesCheck</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1293 1280
|
|
|
1294 1281 <span class="c"># Perform the calculation...</span>
|
|
|
1295 1282 <span class="k">if</span> <span class="s">(</span><span class="i">$CalculationMode</span> =~ <span class="q">/^AlgebraicForm$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1296 1283 <span class="k">return</span> <span class="i">_TanimotoSimilarityCoefficientUsingAlgebraicForm</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1297 1284 <span class="s">}</span>
|
|
|
1298 1285 <span class="k">elsif</span> <span class="s">(</span><span class="i">$CalculationMode</span> =~ <span class="q">/^BinaryForm$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1299 1286 <span class="k">return</span> <span class="i">_TanimotoSimilarityCoefficientUsingBinaryForm</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1300 1287 <span class="s">}</span>
|
|
|
1301 1288 <span class="k">elsif</span> <span class="s">(</span><span class="i">$CalculationMode</span> =~ <span class="q">/^SetTheoreticForm$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1302 1289 <span class="k">return</span> <span class="i">_TanimotoSimilarityCoefficientUsingSetTheoreticForm</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1303 1290 <span class="s">}</span>
|
|
|
1304 1291 <span class="k">else</span> <span class="s">{</span>
|
|
|
1305 1292 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
1306 1293 <span class="s">}</span>
|
|
|
1307 1294 <span class="s">}</span>
|
|
|
1308 1295
|
|
|
1309 1296 <span class="c"># Calculate Tanimoto similarity coefficient using algebraic form...</span>
|
|
|
1310 1297 <span class="c">#</span>
|
|
|
1311 <a name="_TanimotoSimilarityCoefficientUsingAlgebraicForm-"></a>1298 <span class="k">sub </span><span class="m">_TanimotoSimilarityCoefficientUsingAlgebraicForm</span> <span class="s">{</span>
|
|
|
1312 1299 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1313 1300 <span class="k">my</span><span class="s">(</span><span class="i">$SumProductXaiXbi</span><span class="cm">,</span> <span class="i">$SumXai2</span><span class="cm">,</span> <span class="i">$SumXbi2</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>
|
|
|
1314 1301
|
|
|
1315 1302 <span class="i">$SumXai2</span> = <span class="i">_GetSumOfSquaresOfFingerprintsOrderedValues</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1316 1303 <span class="i">$SumXbi2</span> = <span class="i">_GetSumOfSquaresOfFingerprintsOrderedValues</span><span class="s">(</span><span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1317 1304 <span class="i">$SumProductXaiXbi</span> = <span class="i">_GetSumOfProductOfFingerprintsOrderedValues</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1318 1305
|
|
|
1319 1306 <span class="i">$Numerator</span> = <span class="i">$SumProductXaiXbi</span><span class="sc">;</span>
|
|
|
1320 1307 <span class="i">$Denominator</span> = <span class="i">$SumXai2</span> + <span class="i">$SumXbi2</span> - <span class="i">$SumProductXaiXbi</span><span class="sc">;</span>
|
|
|
1321 1308
|
|
|
1322 1309 <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>
|
|
|
1323 1310 <span class="s">}</span>
|
|
|
1324 1311
|
|
|
1325 1312 <span class="c"># Calculate Tanimoto similarity coefficient using binary form...</span>
|
|
|
1326 1313 <span class="c">#</span>
|
|
|
1327 <a name="_TanimotoSimilarityCoefficientUsingBinaryForm-"></a>1314 <span class="k">sub </span><span class="m">_TanimotoSimilarityCoefficientUsingBinaryForm</span> <span class="s">{</span>
|
|
|
1328 1315 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1329 1316 <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>
|
|
|
1330 1317
|
|
|
1331 1318 <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">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1332 1319
|
|
|
1333 1320 <span class="i">$Numerator</span> = <span class="i">$Nc</span><span class="sc">;</span>
|
|
|
1334 1321 <span class="i">$Denominator</span> = <span class="i">$Na</span> + <span class="i">$Nb</span> - <span class="i">$Nc</span><span class="sc">;</span>
|
|
|
1335 1322
|
|
|
1336 1323 <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>
|
|
|
1337 1324 <span class="s">}</span>
|
|
|
1338 1325
|
|
|
1339 1326 <span class="c"># Calculate Tanimoto similarity coefficient using set theoretic form...</span>
|
|
|
1340 1327 <span class="c">#</span>
|
|
|
1341 <a name="_TanimotoSimilarityCoefficientUsingSetTheoreticForm-"></a>1328 <span class="k">sub </span><span class="m">_TanimotoSimilarityCoefficientUsingSetTheoreticForm</span> <span class="s">{</span>
|
|
|
1342 1329 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1343 1330 <span class="k">my</span><span class="s">(</span><span class="i">$SumMinXaiXbi</span><span class="cm">,</span> <span class="i">$SumXai</span><span class="cm">,</span> <span class="i">$SumXbi</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>
|
|
|
1344 1331
|
|
|
1345 1332 <span class="i">$SumXai</span> = <span class="i">_GetSumOfFingerprintsOrderedValues</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1346 1333 <span class="i">$SumXbi</span> = <span class="i">_GetSumOfFingerprintsOrderedValues</span><span class="s">(</span><span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1347 1334 <span class="i">$SumMinXaiXbi</span> = <span class="i">_GetSumOfMinimumOfFingerprintsOrderdedValues</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1348 1335
|
|
|
1349 1336 <span class="i">$Numerator</span> = <span class="i">$SumMinXaiXbi</span><span class="sc">;</span>
|
|
|
1350 1337 <span class="i">$Denominator</span> = <span class="i">$SumXai</span> + <span class="i">$SumXbi</span> - <span class="i">$SumMinXaiXbi</span><span class="sc">;</span>
|
|
|
1351 1338
|
|
|
1352 1339 <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>
|
|
|
1353 1340 <span class="s">}</span>
|
|
|
1354 1341
|
|
|
1355 1342
|
|
|
1356 1343 <span class="c"># Calculate Soergel distance coefficient between two fingerprint vectors.</span>
|
|
|
1357 1344 <span class="c">#</span>
|
|
|
1358 1345 <span class="c"># This functionality can be either invoked as a class function or an object method.</span>
|
|
|
1359 1346 <span class="c">#</span>
|
|
|
1360 <a name="SoergelDistanceCoefficient-"></a>1347 <span class="k">sub </span><span class="m">SoergelDistanceCoefficient ($$;$$)</span> <span class="s">{</span>
|
|
|
1361 1348 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="cm">,</span> <span class="i">$CalculationMode</span><span class="cm">,</span> <span class="i">$SkipValuesCheck</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1362 1349
|
|
|
1363 1350 <span class="i">$CalculationMode</span> = <span class="k">defined</span> <span class="i">$CalculationMode</span> ? <span class="i">$CalculationMode</span> <span class="co">:</span> <span class="q">'AlgebraicForm'</span><span class="sc">;</span>
|
|
|
1364 1351 <span class="i">$SkipValuesCheck</span> = <span class="k">defined</span> <span class="i">$SkipValuesCheck</span> ? <span class="i">$SkipValuesCheck</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1365 1352
|
|
|
1366 1353 <span class="c"># Validate and process fingerprints vectors for similarity calculations...</span>
|
|
|
1367 1354 <span class="c">#</span>
|
|
|
1368 1355 <span class="i">_ValidateAndProcessFingerprintsVectorsForSimilarityCalculation</span><span class="s">(</span><span class="q">"SoergelDistanceCoefficient: Calculation failed"</span><span class="cm">,</span> <span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="cm">,</span> <span class="i">$CalculationMode</span><span class="cm">,</span> <span class="i">$SkipValuesCheck</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1369 1356
|
|
|
1370 1357 <span class="c"># Perform the calculation...</span>
|
|
|
1371 1358 <span class="k">if</span> <span class="s">(</span><span class="i">$CalculationMode</span> =~ <span class="q">/^AlgebraicForm$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1372 1359 <span class="k">return</span> <span class="i">_SoergelDistanceCoefficientUsingAlgebraicForm</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1373 1360 <span class="s">}</span>
|
|
|
1374 1361 <span class="k">elsif</span> <span class="s">(</span><span class="i">$CalculationMode</span> =~ <span class="q">/^BinaryForm$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1375 1362 <span class="k">return</span> <span class="i">_SoergelDistanceCoefficientUsingBinaryForm</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1376 1363 <span class="s">}</span>
|
|
|
1377 1364 <span class="k">elsif</span> <span class="s">(</span><span class="i">$CalculationMode</span> =~ <span class="q">/^SetTheoreticForm$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1378 1365 <span class="k">return</span> <span class="i">_SoergelDistanceCoefficientUsingSetTheoreticForm</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1379 1366 <span class="s">}</span>
|
|
|
1380 1367 <span class="k">else</span> <span class="s">{</span>
|
|
|
1381 1368 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
1382 1369 <span class="s">}</span>
|
|
|
1383 1370 <span class="s">}</span>
|
|
|
1384 1371
|
|
|
1385 1372 <span class="c"># Calculate Soergel distance coefficientusing algebraic form...</span>
|
|
|
1386 1373 <span class="c">#</span>
|
|
|
1387 <a name="_SoergelDistanceCoefficientUsingAlgebraicForm-"></a>1374 <span class="k">sub </span><span class="m">_SoergelDistanceCoefficientUsingAlgebraicForm</span> <span class="s">{</span>
|
|
|
1388 1375 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1389 1376 <span class="k">my</span><span class="s">(</span><span class="i">$SumAbsSubtractionXaiXbi</span><span class="cm">,</span> <span class="i">$SumMaxXaiXbi</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>
|
|
|
1390 1377
|
|
|
1391 1378 <span class="i">$SumAbsSubtractionXaiXbi</span> = <span class="i">_GetSumOfAbsoluteValueOfSubtractionOfFingerprintsOrderedValues</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1392 1379 <span class="i">$SumMaxXaiXbi</span> = <span class="i">_GetSumOfMaximumOfFingerprintsOrderdedValues</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1393 1380
|
|
|
1394 1381 <span class="i">$Numerator</span> = <span class="i">$SumAbsSubtractionXaiXbi</span><span class="sc">;</span>
|
|
|
1395 1382 <span class="i">$Denominator</span> = <span class="i">$SumMaxXaiXbi</span><span class="sc">;</span>
|
|
|
1396 1383
|
|
|
1397 1384 <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>
|
|
|
1398 1385 <span class="s">}</span>
|
|
|
1399 1386
|
|
|
1400 1387 <span class="c"># Calculate Soergel distance coefficient using binary form...</span>
|
|
|
1401 1388 <span class="c">#</span>
|
|
|
1402 <a name="_SoergelDistanceCoefficientUsingBinaryForm-"></a>1389 <span class="k">sub </span><span class="m">_SoergelDistanceCoefficientUsingBinaryForm</span> <span class="s">{</span>
|
|
|
1403 1390 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1404 1391 <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>
|
|
|
1405 1392
|
|
|
1406 1393 <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">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1407 1394
|
|
|
1408 1395 <span class="i">$Numerator</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>
|
|
|
1409 1396 <span class="i">$Denominator</span> = <span class="i">$Na</span> + <span class="i">$Nb</span> - <span class="i">$Nc</span><span class="sc">;</span>
|
|
|
1410 1397
|
|
|
1411 1398 <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>
|
|
|
1412 1399 <span class="s">}</span>
|
|
|
1413 1400
|
|
|
1414 1401 <span class="c"># Calculate SoergelDistanceCoefficient using set theoretic form...</span>
|
|
|
1415 1402 <span class="c">#</span>
|
|
|
1416 <a name="_SoergelDistanceCoefficientUsingSetTheoreticForm-"></a>1403 <span class="k">sub </span><span class="m">_SoergelDistanceCoefficientUsingSetTheoreticForm</span> <span class="s">{</span>
|
|
|
1417 1404 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1418 1405 <span class="k">my</span><span class="s">(</span><span class="i">$SumMinXaiXbi</span><span class="cm">,</span> <span class="i">$SumXai</span><span class="cm">,</span> <span class="i">$SumXbi</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>
|
|
|
1419 1406
|
|
|
1420 1407 <span class="i">$SumXai</span> = <span class="i">_GetSumOfFingerprintsOrderedValues</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1421 1408 <span class="i">$SumXbi</span> = <span class="i">_GetSumOfFingerprintsOrderedValues</span><span class="s">(</span><span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1422 1409 <span class="i">$SumMinXaiXbi</span> = <span class="i">_GetSumOfMinimumOfFingerprintsOrderdedValues</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1423 1410
|
|
|
1424 1411 <span class="i">$Numerator</span> = <span class="i">$SumXai</span> + <span class="i">$SumXbi</span> - <span class="n">2</span> * <span class="i">$SumMinXaiXbi</span><span class="sc">;</span>
|
|
|
1425 1412 <span class="i">$Denominator</span> = <span class="i">$SumXai</span> + <span class="i">$SumXbi</span> - <span class="i">$SumMinXaiXbi</span><span class="sc">;</span>
|
|
|
1426 1413
|
|
|
1427 1414 <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>
|
|
|
1428 1415 <span class="s">}</span>
|
|
|
1429 1416
|
|
|
1430 1417 <span class="c"># Validate and process fingerprints vectors for similarity calculations...</span>
|
|
|
1431 1418 <span class="c">#</span>
|
|
|
1432 <a name="_ValidateAndProcessFingerprintsVectorsForSimilarityCalculation-"></a>1419 <span class="k">sub </span><span class="m">_ValidateAndProcessFingerprintsVectorsForSimilarityCalculation</span> <span class="s">{</span>
|
|
|
1433 1420 <span class="k">my</span><span class="s">(</span><span class="i">$ErrorMsg</span><span class="cm">,</span> <span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="cm">,</span> <span class="i">$CalculationMode</span><span class="cm">,</span> <span class="i">$SkipValuesCheck</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1434 1421
|
|
|
1435 1422 <span class="i">$CalculationMode</span> = <span class="k">defined</span> <span class="i">$CalculationMode</span> ? <span class="i">$CalculationMode</span> <span class="co">:</span> <span class="q">'AlgebraicForm'</span><span class="sc">;</span>
|
|
|
1436 1423 <span class="i">$SkipValuesCheck</span> = <span class="k">defined</span> <span class="i">$SkipValuesCheck</span> ? <span class="i">$SkipValuesCheck</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1437 1424
|
|
|
1438 1425 <span class="k">if</span> <span class="s">(</span>!<span class="i">$SkipValuesCheck</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1439 1426 <span class="i">_ValidateFingerprintsVectorsForSimilarityCalculation</span><span class="s">(</span><span class="i">$ErrorMsg</span><span class="cm">,</span> <span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="cm">,</span> <span class="i">$CalculationMode</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1440 1427 <span class="s">}</span>
|
|
|
1441 1428 <span class="i">_ProcessFingerprintsVectorsForSimilarityCalculation</span><span class="s">(</span><span class="i">$ErrorMsg</span><span class="cm">,</span> <span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="cm">,</span> <span class="i">$CalculationMode</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1442 1429 <span class="s">}</span>
|
|
|
1443 1430
|
|
|
1444 1431 <span class="c"># Make sure fingerprint vectors are good for performing similarity/distance calculation...</span>
|
|
|
1445 1432 <span class="c">#</span>
|
|
|
1446 <a name="_ValidateFingerprintsVectorsForSimilarityCalculation-"></a>1433 <span class="k">sub </span><span class="m">_ValidateFingerprintsVectorsForSimilarityCalculation</span> <span class="s">{</span>
|
|
|
1447 1434 <span class="k">my</span><span class="s">(</span><span class="i">$ErrorMsg</span><span class="cm">,</span> <span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="cm">,</span> <span class="i">$CalculationMode</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1448 1435
|
|
|
1449 1436 <span class="c"># Make sure both are fingerprint vectors..</span>
|
|
|
1450 1437 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">IsFingerprintsVector</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="s">)</span> && <span class="i">IsFingerprintsVector</span><span class="s">(</span><span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1451 1438 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->${ErrorMsg}: Both objects must be fingerprint vectors..."</span><span class="sc">;</span>
|
|
|
1452 1439 <span class="s">}</span>
|
|
|
1453 1440
|
|
|
1454 1441 <span class="c"># Check types...</span>
|
|
|
1455 1442 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsVectorA</span>->{<span class="w">Type</span>} <span class="k">ne</span> <span class="i">$FingerprintsVectorB</span>->{<span class="w">Type</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1456 1443 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->${ErrorMsg}: Type of first fingerprint vector, $FingerprintsVectorA->{Type}, must be same as type of second fingerprint vector, $FingerprintsVectorB->{Type}..."</span><span class="sc">;</span>
|
|
|
1457 1444 <span class="s">}</span>
|
|
|
1458 1445
|
|
|
1459 1446 <span class="c"># Check calculation mode...</span>
|
|
|
1460 1447 <span class="k">if</span> <span class="s">(</span><span class="i">$CalculationMode</span> !~ <span class="q">/^(AlgebraicForm|BinaryForm|SetTheoreticForm)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1461 1448 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->${ErrorMsg}: Specified similarity calculation mode, $CalculationMode, is not valid. Supported values: AlgebraicForm, BinaryForm, and SetTheoreticForm..."</span><span class="sc">;</span>
|
|
|
1462 1449 <span class="s">}</span>
|
|
|
1463 1450
|
|
|
1464 1451 <span class="c"># Check values and value IDs...</span>
|
|
|
1465 1452 <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">$NIDa</span><span class="cm">,</span> <span class="i">$NIDb</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1466 1453 <span class="i">$Na</span> = <span class="i">$FingerprintsVectorA</span><span class="i">->GetNumOfValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">$Nb</span> = <span class="i">$FingerprintsVectorB</span><span class="i">->GetNumOfValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1467 1454 <span class="i">$NIDa</span> = <span class="i">$FingerprintsVectorA</span><span class="i">->GetNumOfValueIDs</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">$NIDb</span> = <span class="i">$FingerprintsVectorB</span><span class="i">->GetNumOfValueIDs</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1468 1455
|
|
|
1469 1456 <span class="k">if</span> <span class="s">(</span><span class="i">$Na</span> == <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1470 1457 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->${ErrorMsg}: Number of values in first fingerprint vector, $Na, must be > 0 for fingerprint vector type $FingerprintsVectorA->{Type} ..."</span><span class="sc">;</span>
|
|
|
1471 1458 <span class="s">}</span>
|
|
|
1472 1459 <span class="k">if</span> <span class="s">(</span><span class="i">$Nb</span> == <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1473 1460 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->${ErrorMsg}: Number of values in second fingerprint vector, $Nb, must be > 0 for fingerprint vector type $FingerprintsVectorB->{Type} ..."</span><span class="sc">;</span>
|
|
|
1474 1461 <span class="s">}</span>
|
|
|
1475 1462
|
|
|
1476 1463 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsVectorA</span>->{<span class="w">Type</span>} =~ <span class="q">/^OrderedNumericalValues$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1477 1464 <span class="k">if</span> <span class="s">(</span><span class="i">$Na</span> != <span class="i">$Nb</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1478 1465 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->${ErrorMsg}: Number of values in first fingerprint vector, $Na, must be equal to number of values, $Nb, in second fingerprint vector for fingerprint vector types $FingerprintsVectorA->{Type} ..."</span><span class="sc">;</span>
|
|
|
1479 1466 <span class="s">}</span>
|
|
|
1480 1467 <span class="s">}</span>
|
|
|
1481 1468 <span class="k">elsif</span> <span class="s">(</span><span class="i">$FingerprintsVectorA</span>->{<span class="w">Type</span>} =~ <span class="q">/^NumericalValues$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1482 1469 <span class="k">if</span> <span class="s">(</span><span class="i">$NIDa</span> == <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1483 1470 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->${ErrorMsg}: Number of value IDs in first fingerprint vector, $NIDa, must be > 0 for fingerprint vector type $FingerprintsVectorA->{Type} ..."</span><span class="sc">;</span>
|
|
|
1484 1471 <span class="s">}</span>
|
|
|
1485 1472 <span class="k">if</span> <span class="s">(</span><span class="i">$NIDb</span> == <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1486 1473 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->${ErrorMsg}: Number of value IDs in first fingerprint vector, $NIDb, must be > 0 for fingerprint vector type $FingerprintsVectorB->{Type} ..."</span><span class="sc">;</span>
|
|
|
1487 1474 <span class="s">}</span>
|
|
|
1488 1475
|
|
|
1489 1476 <span class="k">if</span> <span class="s">(</span><span class="i">$NIDa</span> != <span class="i">$Na</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1490 1477 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->${ErrorMsg}: Number of value IDs in first fingerprint vector, $NIDa, must be equal to its number of values, $Na, for fingerprint vector type $FingerprintsVectorA->{Type} ..."</span><span class="sc">;</span>
|
|
|
1491 1478 <span class="s">}</span>
|
|
|
1492 1479 <span class="k">if</span> <span class="s">(</span><span class="i">$NIDb</span> != <span class="i">$Nb</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1493 1480 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->${ErrorMsg}: Number of value IDs in second fingerprint vector, $NIDb, must be equal to its number of values, $Nb, for fingerprint vector type $FingerprintsVectorA->{Type} ..."</span><span class="sc">;</span>
|
|
|
1494 1481 <span class="s">}</span>
|
|
|
1495 1482 <span class="s">}</span>
|
|
|
1496 1483 <span class="k">elsif</span> <span class="s">(</span><span class="i">$FingerprintsVectorA</span>->{<span class="w">Type</span>} =~ <span class="q">/^AlphaNumericalValues$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1497 1484 <span class="k">if</span> <span class="s">(</span><span class="i">$NIDa</span> || <span class="i">$NIDb</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1498 1485 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->${ErrorMsg}: ValueIDs cann't be specified for fingerprint vector types $FingerprintsVectorA->{Type} ..."</span><span class="sc">;</span>
|
|
|
1499 1486 <span class="s">}</span>
|
|
|
1500 1487 <span class="s">}</span>
|
|
|
1501 1488 <span class="k">else</span> <span class="s">{</span>
|
|
|
1502 1489 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->${ErrorMsg}: Fingerprint vector types $FingerprintsVectorA->{Type} is not valid..."</span><span class="sc">;</span>
|
|
|
1503 1490 <span class="s">}</span>
|
|
|
1504 1491 <span class="s">}</span>
|
|
|
1505 1492
|
|
|
1506 1493 <span class="c"># Process fingerprints vectors for similarity calculation by generating vectors</span>
|
|
|
1507 1494 <span class="c"># containing ordered list of values...</span>
|
|
|
1508 1495 <span class="c">#</span>
|
|
|
1509 <a name="_ProcessFingerprintsVectorsForSimilarityCalculation-"></a>1496 <span class="k">sub </span><span class="m">_ProcessFingerprintsVectorsForSimilarityCalculation</span> <span class="s">{</span>
|
|
|
1510 1497 <span class="k">my</span><span class="s">(</span><span class="i">$ErrorMsg</span><span class="cm">,</span> <span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="cm">,</span> <span class="i">$CalculationMode</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1511 1498
|
|
|
1512 1499 <span class="i">$FingerprintsVectorA</span>->{<span class="w">OrderedValuesRef</span>} = <span class="k">undef</span><span class="sc">;</span> <span class="i">$FingerprintsVectorB</span>->{<span class="w">OrderedValuesRef</span>} = <span class="k">undef</span><span class="sc">;</span>
|
|
|
1513 1500 <span class="i">$FingerprintsVectorA</span>->{<span class="w">BitVector</span>} = <span class="k">undef</span><span class="sc">;</span> <span class="i">$FingerprintsVectorB</span>->{<span class="w">BitVector</span>} = <span class="k">undef</span><span class="sc">;</span>
|
|
|
1514 1501
|
|
|
1515 1502 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsVectorA</span>->{<span class="w">Type</span>} =~ <span class="q">/^OrderedNumericalValues$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1516 1503 <span class="i">_ProcessOrderedNumericalValuesFingerprintsVectorsForSimilarityCalculation</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1517 1504 <span class="s">}</span>
|
|
|
1518 1505 <span class="k">elsif</span> <span class="s">(</span><span class="i">$FingerprintsVectorA</span>->{<span class="w">Type</span>} =~ <span class="q">/^NumericalValues$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1519 1506 <span class="i">_ProcessNumericalValuesFingerprintsVectorsForSimilarityCalculation</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1520 1507 <span class="s">}</span>
|
|
|
1521 1508 <span class="k">elsif</span> <span class="s">(</span><span class="i">$FingerprintsVectorA</span>->{<span class="w">Type</span>} =~ <span class="q">/^AlphaNumericalValues$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1522 1509 <span class="i">_ProcessAlphaNumericalValuesFingerprintsVectorsForSimilarityCalculation</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1523 1510 <span class="s">}</span>
|
|
|
1524 1511 <span class="k">else</span> <span class="s">{</span>
|
|
|
1525 1512 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->${ErrorMsg}: Fingerprint vector types $FingerprintsVectorA->{Type} is not valid..."</span><span class="sc">;</span>
|
|
|
1526 1513 <span class="s">}</span>
|
|
|
1527 1514 <span class="k">if</span> <span class="s">(</span><span class="i">$CalculationMode</span> =~ <span class="q">/^BinaryForm$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1528 1515 <span class="i">_TransformFinalOrderedValuesIntoBitVectorsForSimilarityCalculation</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1529 1516 <span class="s">}</span>
|
|
|
1530 1517 <span class="s">}</span>
|
|
|
1531 1518
|
|
|
1532 1519 <span class="c"># Process fingerprints vectors with ordered numerical values for similarity calculations...</span>
|
|
|
1533 1520 <span class="c">#</span>
|
|
|
1534 <a name="_ProcessOrderedNumericalValuesFingerprintsVectorsForSimilarityCalculation-"></a>1521 <span class="k">sub </span><span class="m">_ProcessOrderedNumericalValuesFingerprintsVectorsForSimilarityCalculation</span> <span class="s">{</span>
|
|
|
1535 1522 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1536 1523
|
|
|
1537 1524 <span class="i">$FingerprintsVectorA</span>->{<span class="w">OrderedValuesRef</span>} = \<span class="i">@</span>{<span class="i">$FingerprintsVectorA</span>->{<span class="w">Values</span>}}<span class="sc">;</span>
|
|
|
1538 1525 <span class="i">$FingerprintsVectorB</span>->{<span class="w">OrderedValuesRef</span>} = \<span class="i">@</span>{<span class="i">$FingerprintsVectorB</span>->{<span class="w">Values</span>}}<span class="sc">;</span>
|
|
|
1539 1526 <span class="s">}</span>
|
|
|
1540 1527
|
|
|
1541 1528 <span class="c"># Process fingerprints vectors with numerical values for similarity calculations...</span>
|
|
|
1542 1529 <span class="c">#</span>
|
|
|
1543 <a name="_ProcessNumericalValuesFingerprintsVectorsForSimilarityCalculation-"></a>1530 <span class="k">sub </span><span class="m">_ProcessNumericalValuesFingerprintsVectorsForSimilarityCalculation</span> <span class="s">{</span>
|
|
|
1544 1531 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1545 1532
|
|
|
1546 1533 <span class="c"># Set up unique IDs and values map for each fingerprint vector...</span>
|
|
|
1547 1534 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">$ValueID</span><span class="cm">,</span> <span class="i">%UniqueFingerprintsVectorAValueIDValues</span><span class="cm">,</span> <span class="i">%UniqueFingerprintsVectorBValueIDValues</span><span class="cm">,</span> <span class="i">%UniqueFingerprintsVectorsValueIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1548 1535
|
|
|
1549 1536 <span class="i">%UniqueFingerprintsVectorAValueIDValues</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1550 1537 <span class="i">%UniqueFingerprintsVectorBValueIDValues</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1551 1538 <span class="i">%UniqueFingerprintsVectorsValueIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1552 1539
|
|
|
1553 1540 <span class="c"># Go over first vector...</span>
|
|
|
1554 1541 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$FingerprintsVectorA</span>->{<span class="w">ValueIDs</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
1555 1542 <span class="i">$ValueID</span> = <span class="i">$FingerprintsVectorA</span>->{<span class="w">ValueIDs</span>}[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
1556 1543 <span class="i">$Value</span> = <span class="i">$FingerprintsVectorA</span>->{<span class="w">Values</span>}[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
1557 1544 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$UniqueFingerprintsVectorAValueIDValues</span>{<span class="i">$ValueID</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1558 1545 <span class="i">$UniqueFingerprintsVectorAValueIDValues</span>{<span class="i">$ValueID</span>} += <span class="i">$Value</span><span class="sc">;</span>
|
|
|
1559 1546 <span class="s">}</span>
|
|
|
1560 1547 <span class="k">else</span> <span class="s">{</span>
|
|
|
1561 1548 <span class="i">$UniqueFingerprintsVectorAValueIDValues</span>{<span class="i">$ValueID</span>} = <span class="i">$Value</span><span class="sc">;</span>
|
|
|
1562 1549 <span class="s">}</span>
|
|
|
1563 1550 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$UniqueFingerprintsVectorsValueIDs</span>{<span class="i">$ValueID</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1564 1551 <span class="i">$UniqueFingerprintsVectorsValueIDs</span>{<span class="i">$ValueID</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
1565 1552 <span class="s">}</span>
|
|
|
1566 1553 <span class="s">}</span>
|
|
|
1567 1554
|
|
|
1568 1555 <span class="c"># Go over second vector...</span>
|
|
|
1569 1556 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$FingerprintsVectorB</span>->{<span class="w">ValueIDs</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
1570 1557 <span class="i">$ValueID</span> = <span class="i">$FingerprintsVectorB</span>->{<span class="w">ValueIDs</span>}[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
1571 1558 <span class="i">$Value</span> = <span class="i">$FingerprintsVectorB</span>->{<span class="w">Values</span>}[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
1572 1559 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$UniqueFingerprintsVectorBValueIDValues</span>{<span class="i">$ValueID</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1573 1560 <span class="i">$UniqueFingerprintsVectorBValueIDValues</span>{<span class="i">$ValueID</span>} += <span class="i">$Value</span><span class="sc">;</span>
|
|
|
1574 1561 <span class="s">}</span>
|
|
|
1575 1562 <span class="k">else</span> <span class="s">{</span>
|
|
|
1576 1563 <span class="i">$UniqueFingerprintsVectorBValueIDValues</span>{<span class="i">$ValueID</span>} = <span class="i">$Value</span><span class="sc">;</span>
|
|
|
1577 1564 <span class="s">}</span>
|
|
|
1578 1565 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$UniqueFingerprintsVectorsValueIDs</span>{<span class="i">$ValueID</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1579 1566 <span class="i">$UniqueFingerprintsVectorsValueIDs</span>{<span class="i">$ValueID</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
1580 1567 <span class="s">}</span>
|
|
|
1581 1568 <span class="s">}</span>
|
|
|
1582 1569
|
|
|
1583 1570 <span class="c"># Setup ordered values...</span>
|
|
|
1584 1571 <span class="k">my</span><span class="s">(</span><span class="i">@UniqueOrderedValueIDs</span><span class="cm">,</span> <span class="i">@OrderedValuesA</span><span class="cm">,</span> <span class="i">@OrderedValuesB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1585 1572
|
|
|
1586 1573 <span class="i">@UniqueOrderedValueIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1587 1574 <span class="i">@UniqueOrderedValueIDs</span> = <span class="k">sort</span> <span class="k">keys</span> <span class="i">%UniqueFingerprintsVectorsValueIDs</span><span class="sc">;</span>
|
|
|
1588 1575
|
|
|
1589 1576 <span class="i">@OrderedValuesA</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1590 1577 <span class="i">@OrderedValuesA</span> = <span class="k">map</span> <span class="s">{</span> <span class="k">exists</span> <span class="i">$UniqueFingerprintsVectorAValueIDValues</span>{<span class="i">$_</span>} ? <span class="i">$UniqueFingerprintsVectorAValueIDValues</span>{<span class="i">$_</span>} <span class="co">:</span> <span class="n">0</span> <span class="s">}</span> <span class="i">@UniqueOrderedValueIDs</span><span class="sc">;</span>
|
|
|
1591 1578
|
|
|
1592 1579 <span class="i">@OrderedValuesB</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1593 1580 <span class="i">@OrderedValuesB</span> = <span class="k">map</span> <span class="s">{</span> <span class="k">exists</span> <span class="i">$UniqueFingerprintsVectorBValueIDValues</span>{<span class="i">$_</span>} ? <span class="i">$UniqueFingerprintsVectorBValueIDValues</span>{<span class="i">$_</span>} <span class="co">:</span> <span class="n">0</span> <span class="s">}</span> <span class="i">@UniqueOrderedValueIDs</span><span class="sc">;</span>
|
|
|
1594 1581
|
|
|
1595 1582 <span class="i">$FingerprintsVectorA</span>->{<span class="w">OrderedValuesRef</span>} = \<span class="i">@OrderedValuesA</span><span class="sc">;</span>
|
|
|
1596 1583 <span class="i">$FingerprintsVectorB</span>->{<span class="w">OrderedValuesRef</span>} = \<span class="i">@OrderedValuesB</span><span class="sc">;</span>
|
|
|
1597 1584 <span class="s">}</span>
|
|
|
1598 1585
|
|
|
1599 1586 <span class="c"># Process fingerprints vectors with allpha numerical values for similarity calculations...</span>
|
|
|
1600 1587 <span class="c">#</span>
|
|
|
1601 <a name="_ProcessAlphaNumericalValuesFingerprintsVectorsForSimilarityCalculation-"></a>1588 <span class="k">sub </span><span class="m">_ProcessAlphaNumericalValuesFingerprintsVectorsForSimilarityCalculation</span> <span class="s">{</span>
|
|
|
1602 1589 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1603 1590
|
|
|
1604 1591 <span class="c"># Set up unique IDs and values map for each vector...</span>
|
|
|
1605 1592 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">$ValueID</span><span class="cm">,</span> <span class="i">%UniqueFingerprintsVectorAValuesCount</span><span class="cm">,</span> <span class="i">%UniqueFingerprintsVectorBValuesCount</span><span class="cm">,</span> <span class="i">%UniqueFingerprintsVectorsValues</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1606 1593
|
|
|
1607 1594 <span class="i">%UniqueFingerprintsVectorAValuesCount</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1608 1595 <span class="i">%UniqueFingerprintsVectorBValuesCount</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1609 1596 <span class="i">%UniqueFingerprintsVectorsValues</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1610 1597
|
|
|
1611 1598 <span class="c"># Go over first vector...</span>
|
|
|
1612 1599 <span class="k">for</span> <span class="i">$Value</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$FingerprintsVectorA</span>->{<span class="w">Values</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
1613 1600 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$UniqueFingerprintsVectorAValuesCount</span>{<span class="i">$Value</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1614 1601 <span class="i">$UniqueFingerprintsVectorAValuesCount</span>{<span class="i">$Value</span>} += <span class="n">1</span><span class="sc">;</span>
|
|
|
1615 1602 <span class="s">}</span>
|
|
|
1616 1603 <span class="k">else</span> <span class="s">{</span>
|
|
|
1617 1604 <span class="i">$UniqueFingerprintsVectorAValuesCount</span>{<span class="i">$Value</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
1618 1605 <span class="s">}</span>
|
|
|
1619 1606 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$UniqueFingerprintsVectorsValues</span>{<span class="i">$Value</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1620 1607 <span class="i">$UniqueFingerprintsVectorsValues</span>{<span class="i">$Value</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
1621 1608 <span class="s">}</span>
|
|
|
1622 1609 <span class="s">}</span>
|
|
|
1623 1610
|
|
|
1624 1611 <span class="c"># Go over second vector...</span>
|
|
|
1625 1612 <span class="k">for</span> <span class="i">$Value</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$FingerprintsVectorB</span>->{<span class="w">Values</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
1626 1613 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$UniqueFingerprintsVectorBValuesCount</span>{<span class="i">$Value</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1627 1614 <span class="i">$UniqueFingerprintsVectorBValuesCount</span>{<span class="i">$Value</span>} += <span class="n">1</span><span class="sc">;</span>
|
|
|
1628 1615 <span class="s">}</span>
|
|
|
1629 1616 <span class="k">else</span> <span class="s">{</span>
|
|
|
1630 1617 <span class="i">$UniqueFingerprintsVectorBValuesCount</span>{<span class="i">$Value</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
1631 1618 <span class="s">}</span>
|
|
|
1632 1619 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$UniqueFingerprintsVectorsValues</span>{<span class="i">$Value</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1633 1620 <span class="i">$UniqueFingerprintsVectorsValues</span>{<span class="i">$Value</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
1634 1621 <span class="s">}</span>
|
|
|
1635 1622 <span class="s">}</span>
|
|
|
1636 1623
|
|
|
1637 1624 <span class="c"># Setup ordered values...</span>
|
|
|
1638 1625 <span class="k">my</span><span class="s">(</span><span class="i">@UniqueOrderedValueIDs</span><span class="cm">,</span> <span class="i">@OrderedValuesA</span><span class="cm">,</span> <span class="i">@OrderedValuesB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1639 1626
|
|
|
1640 1627 <span class="i">@UniqueOrderedValueIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1641 1628 <span class="i">@UniqueOrderedValueIDs</span> = <span class="k">sort</span> <span class="k">keys</span> <span class="i">%UniqueFingerprintsVectorsValues</span><span class="sc">;</span>
|
|
|
1642 1629
|
|
|
1643 1630 <span class="i">@OrderedValuesA</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1644 1631 <span class="i">@OrderedValuesA</span> = <span class="k">map</span> <span class="s">{</span> <span class="k">exists</span> <span class="i">$UniqueFingerprintsVectorAValuesCount</span>{<span class="i">$_</span>} ? <span class="i">$UniqueFingerprintsVectorAValuesCount</span>{<span class="i">$_</span>} <span class="co">:</span> <span class="n">0</span> <span class="s">}</span> <span class="i">@UniqueOrderedValueIDs</span><span class="sc">;</span>
|
|
|
1645 1632
|
|
|
1646 1633 <span class="i">@OrderedValuesB</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1647 1634 <span class="i">@OrderedValuesB</span> = <span class="k">map</span> <span class="s">{</span> <span class="k">exists</span> <span class="i">$UniqueFingerprintsVectorBValuesCount</span>{<span class="i">$_</span>} ? <span class="i">$UniqueFingerprintsVectorBValuesCount</span>{<span class="i">$_</span>} <span class="co">:</span> <span class="n">0</span> <span class="s">}</span> <span class="i">@UniqueOrderedValueIDs</span><span class="sc">;</span>
|
|
|
1648 1635
|
|
|
1649 1636 <span class="i">$FingerprintsVectorA</span>->{<span class="w">OrderedValuesRef</span>} = \<span class="i">@OrderedValuesA</span><span class="sc">;</span>
|
|
|
1650 1637 <span class="i">$FingerprintsVectorB</span>->{<span class="w">OrderedValuesRef</span>} = \<span class="i">@OrderedValuesB</span><span class="sc">;</span>
|
|
|
1651 1638
|
|
|
1652 1639 <span class="s">}</span>
|
|
|
1653 1640
|
|
|
1654 1641 <span class="c"># Transform final ordered values array into a BitVector for similarity calculation...</span>
|
|
|
1655 1642 <span class="c">#</span>
|
|
|
1656 <a name="_TransformFinalOrderedValuesIntoBitVectorsForSimilarityCalculation-"></a>1643 <span class="k">sub </span><span class="m">_TransformFinalOrderedValuesIntoBitVectorsForSimilarityCalculation</span> <span class="s">{</span>
|
|
|
1657 1644 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1658 1645 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$Size</span><span class="cm">,</span> <span class="i">$BitVectorA</span><span class="cm">,</span> <span class="i">$BitVectorB</span><span class="cm">,</span> <span class="i">$SkipCheck</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1659 1646
|
|
|
1660 1647 <span class="c"># Create bit vectors...</span>
|
|
|
1661 1648 <span class="i">$Size</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$FingerprintsVectorA</span>->{<span class="w">OrderedValuesRef</span>}}<span class="sc">;</span>
|
|
|
1662 1649
|
|
|
1663 1650 <span class="i">$FingerprintsVectorA</span>->{<span class="w">BitVector</span>} = <span class="i">new</span> <span class="i">BitVector</span><span class="s">(</span><span class="i">$Size</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1664 1651 <span class="i">$FingerprintsVectorB</span>->{<span class="w">BitVector</span>} = <span class="i">new</span> <span class="i">BitVector</span><span class="s">(</span><span class="i">$Size</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1665 1652
|
|
|
1666 1653 <span class="c"># Set bits...</span>
|
|
|
1667 1654 <span class="i">$SkipCheck</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
1668 1655 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$Size</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1669 1656 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsVectorA</span>->{<span class="w">OrderedValuesRef</span>}[<span class="i">$Index</span>]<span class="s">)</span> <span class="s">{</span>
|
|
|
1670 1657 <span class="i">$FingerprintsVectorA</span>->{<span class="w">BitVector</span>}<span class="i">->SetBit</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$SkipCheck</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1671 1658 <span class="s">}</span>
|
|
|
1672 1659 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsVectorB</span>->{<span class="w">OrderedValuesRef</span>}[<span class="i">$Index</span>]<span class="s">)</span> <span class="s">{</span>
|
|
|
1673 1660 <span class="i">$FingerprintsVectorB</span>->{<span class="w">BitVector</span>}<span class="i">->SetBit</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$SkipCheck</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1674 1661 <span class="s">}</span>
|
|
|
1675 1662 <span class="s">}</span>
|
|
|
1676 1663 <span class="s">}</span>
|
|
|
1677 1664
|
|
|
1678 1665 <span class="c"># Return sum of ordered vector values...</span>
|
|
|
1679 1666 <span class="c">#</span>
|
|
|
1680 <a name="_GetSumOfFingerprintsOrderedValues-"></a>1667 <span class="k">sub </span><span class="m">_GetSumOfFingerprintsOrderedValues</span> <span class="s">{</span>
|
|
|
1681 1668 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintVector</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1682 1669
|
|
|
1683 1670 <span class="k">return</span> <span class="i">StatisticsUtil::Sum</span><span class="s">(</span><span class="i">$FingerprintVector</span>->{<span class="w">OrderedValuesRef</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
1684 1671 <span class="s">}</span>
|
|
|
1685 1672
|
|
|
1686 1673 <span class="c"># Return sum of squared ordered vector values...</span>
|
|
|
1687 1674 <span class="c">#</span>
|
|
|
1688 <a name="_GetSumOfSquaresOfFingerprintsOrderedValues-"></a>1675 <span class="k">sub </span><span class="m">_GetSumOfSquaresOfFingerprintsOrderedValues</span> <span class="s">{</span>
|
|
|
1689 1676 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintVector</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1690 1677
|
|
|
1691 1678 <span class="k">return</span> <span class="i">StatisticsUtil::SumOfSquares</span><span class="s">(</span><span class="i">$FingerprintVector</span>->{<span class="w">OrderedValuesRef</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
1692 1679 <span class="s">}</span>
|
|
|
1693 1680
|
|
|
1694 1681 <span class="c"># Return sum of product of correponding ordered vector values...</span>
|
|
|
1695 1682 <span class="c">#</span>
|
|
|
1696 <a name="_GetSumOfProductOfFingerprintsOrderedValues-"></a>1683 <span class="k">sub </span><span class="m">_GetSumOfProductOfFingerprintsOrderedValues</span> <span class="s">{</span>
|
|
|
1697 1684 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1698 1685 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$SumProductXaiXbi</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1699 1686
|
|
|
1700 1687 <span class="i">$SumProductXaiXbi</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
1701 1688 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$FingerprintsVectorA</span>->{<span class="w">OrderedValuesRef</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
1702 1689 <span class="i">$SumProductXaiXbi</span> += <span class="i">$FingerprintsVectorA</span>->{<span class="w">OrderedValuesRef</span>}[<span class="i">$Index</span>] * <span class="i">$FingerprintsVectorB</span>->{<span class="w">OrderedValuesRef</span>}[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
1703 1690 <span class="s">}</span>
|
|
|
1704 1691 <span class="k">return</span> <span class="i">$SumProductXaiXbi</span><span class="sc">;</span>
|
|
|
1705 1692 <span class="s">}</span>
|
|
|
1706 1693
|
|
|
1707 1694 <span class="c"># Return sum of absolute value of subtraction of correponding ordered vector values...</span>
|
|
|
1708 1695 <span class="c">#</span>
|
|
|
1709 <a name="_GetSumOfAbsoluteValueOfSubtractionOfFingerprintsOrderedValues-"></a>1696 <span class="k">sub </span><span class="m">_GetSumOfAbsoluteValueOfSubtractionOfFingerprintsOrderedValues</span> <span class="s">{</span>
|
|
|
1710 1697 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1711 1698 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$SumAbsSubtractionXaiXbi</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1712 1699
|
|
|
1713 1700 <span class="i">$SumAbsSubtractionXaiXbi</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
1714 1701 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$FingerprintsVectorA</span>->{<span class="w">OrderedValuesRef</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
1715 1702 <span class="i">$SumAbsSubtractionXaiXbi</span> += <span class="k">abs</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span>->{<span class="w">OrderedValuesRef</span>}[<span class="i">$Index</span>] - <span class="i">$FingerprintsVectorB</span>->{<span class="w">OrderedValuesRef</span>}[<span class="i">$Index</span>]<span class="s">)</span><span class="sc">;</span>
|
|
|
1716 1703 <span class="s">}</span>
|
|
|
1717 1704 <span class="k">return</span> <span class="i">$SumAbsSubtractionXaiXbi</span><span class="sc">;</span>
|
|
|
1718 1705 <span class="s">}</span>
|
|
|
1719 1706
|
|
|
1720 1707 <span class="c"># Return sum of squares of subtraction of correponding ordered vector values...</span>
|
|
|
1721 1708 <span class="c">#</span>
|
|
|
1722 <a name="_GetSumOfSquaresOfSubtractionOfFingerprintsOrderedValues-"></a>1709 <span class="k">sub </span><span class="m">_GetSumOfSquaresOfSubtractionOfFingerprintsOrderedValues</span> <span class="s">{</span>
|
|
|
1723 1710 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1724 1711 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$SumSquaresSubtractionXaiXbi</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1725 1712
|
|
|
1726 1713 <span class="i">$SumSquaresSubtractionXaiXbi</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
1727 1714 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$FingerprintsVectorA</span>->{<span class="w">OrderedValuesRef</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
1728 1715 <span class="i">$SumSquaresSubtractionXaiXbi</span> += <span class="s">(</span><span class="i">$FingerprintsVectorA</span>->{<span class="w">OrderedValuesRef</span>}[<span class="i">$Index</span>] - <span class="i">$FingerprintsVectorB</span>->{<span class="w">OrderedValuesRef</span>}[<span class="i">$Index</span>]<span class="s">)</span>**<span class="n">2</span><span class="sc">;</span>
|
|
|
1729 1716 <span class="s">}</span>
|
|
|
1730 1717 <span class="k">return</span> <span class="i">$SumSquaresSubtractionXaiXbi</span><span class="sc">;</span>
|
|
|
1731 1718 <span class="s">}</span>
|
|
|
1732 1719
|
|
|
1733 1720 <span class="c"># Return sum of minimum of correponding ordered vector values...</span>
|
|
|
1734 1721 <span class="c">#</span>
|
|
|
1735 <a name="_GetSumOfMinimumOfFingerprintsOrderdedValues-"></a>1722 <span class="k">sub </span><span class="m">_GetSumOfMinimumOfFingerprintsOrderdedValues</span> <span class="s">{</span>
|
|
|
1736 1723 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1737 1724 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$SumMinXaiXbi</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1738 1725
|
|
|
1739 1726 <span class="i">$SumMinXaiXbi</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
1740 1727 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$FingerprintsVectorA</span>->{<span class="w">OrderedValuesRef</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
1741 1728 <span class="i">$SumMinXaiXbi</span> += <span class="i">MathUtil::min</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span>->{<span class="w">OrderedValuesRef</span>}[<span class="i">$Index</span>]<span class="cm">,</span> <span class="i">$FingerprintsVectorB</span>->{<span class="w">OrderedValuesRef</span>}[<span class="i">$Index</span>]<span class="s">)</span><span class="sc">;</span>
|
|
|
1742 1729 <span class="s">}</span>
|
|
|
1743 1730 <span class="k">return</span> <span class="i">$SumMinXaiXbi</span><span class="sc">;</span>
|
|
|
1744 1731 <span class="s">}</span>
|
|
|
1745 1732
|
|
|
1746 1733 <span class="c"># Return sum of maximum of correponding ordered vector values...</span>
|
|
|
1747 1734 <span class="c">#</span>
|
|
|
1748 <a name="_GetSumOfMaximumOfFingerprintsOrderdedValues-"></a>1735 <span class="k">sub </span><span class="m">_GetSumOfMaximumOfFingerprintsOrderdedValues</span> <span class="s">{</span>
|
|
|
1749 1736 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1750 1737 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$SumMaxXaiXbi</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1751 1738
|
|
|
1752 1739 <span class="i">$SumMaxXaiXbi</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
1753 1740 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$FingerprintsVectorA</span>->{<span class="w">OrderedValuesRef</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
1754 1741 <span class="i">$SumMaxXaiXbi</span> += <span class="i">MathUtil::max</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span>->{<span class="w">OrderedValuesRef</span>}[<span class="i">$Index</span>]<span class="cm">,</span> <span class="i">$FingerprintsVectorB</span>->{<span class="w">OrderedValuesRef</span>}[<span class="i">$Index</span>]<span class="s">)</span><span class="sc">;</span>
|
|
|
1755 1742 <span class="s">}</span>
|
|
|
1756 1743 <span class="k">return</span> <span class="i">$SumMaxXaiXbi</span><span class="sc">;</span>
|
|
|
1757 1744 <span class="s">}</span>
|
|
|
1758 1745
|
|
|
1759 1746 <span class="c"># Get number of Na, Nb and Nc bits in vector A and B for BinaryForm calculation...</span>
|
|
|
1760 1747 <span class="c">#</span>
|
|
|
1761 <a name="_GetNumOfIndividualAndCommonSetBits-"></a>1748 <span class="k">sub </span><span class="m">_GetNumOfIndividualAndCommonSetBits ($$)</span> <span class="s">{</span>
|
|
|
1762 1749 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsVectorB</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1763 1750 <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">$FingerprintsBitVectorA</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorB</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1764 1751
|
|
|
1765 1752 <span class="i">$FingerprintsBitVectorA</span> = <span class="i">$FingerprintsVectorA</span>->{<span class="w">BitVector</span>}<span class="sc">;</span>
|
|
|
1766 1753 <span class="i">$FingerprintsBitVectorB</span> = <span class="i">$FingerprintsVectorB</span>->{<span class="w">BitVector</span>}<span class="sc">;</span>
|
|
|
1767 1754
|
|
|
1768 1755 <span class="c"># Number of bits set to "1" in A</span>
|
|
|
1769 1756 <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>
|
|
|
1770 1757
|
|
|
1771 1758 <span class="c"># Number of bits set to "1" in B</span>
|
|
|
1772 1759 <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>
|
|
|
1773 1760
|
|
|
1774 1761 <span class="c"># Number of bits set to "1" in both A and B</span>
|
|
|
1775 1762 <span class="k">my</span><span class="s">(</span><span class="i">$NcBitVector</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1776 1763 <span class="i">$NcBitVector</span> = <span class="i">$FingerprintsBitVectorA</span> & <span class="i">$FingerprintsBitVectorB</span><span class="sc">;</span>
|
|
|
1777 1764 <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>
|
|
|
1778 1765
|
|
|
1779 1766 <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>
|
|
|
1780 1767 <span class="s">}</span>
|
|
|
1781 1768
|
|
|
1782 1769 <span class="c"># Return a list of supported distance coefficients...</span>
|
|
|
1783 1770 <span class="c">#</span>
|
|
|
1784 <a name="GetSupportedDistanceCoefficients-"></a>1771 <span class="k">sub </span><span class="m">GetSupportedDistanceCoefficients ()</span> <span class="s">{</span>
|
|
|
1785 1772
|
|
|
1786 1773 <span class="k">return</span> <span class="i">@DistanceCoefficients</span><span class="sc">;</span>
|
|
|
1787 1774 <span class="s">}</span>
|
|
|
1788 1775
|
|
|
1789 1776 <span class="c"># Return a list of supported similarity coefficients...</span>
|
|
|
1790 1777 <span class="c">#</span>
|
|
|
1791 <a name="GetSupportedSimilarityCoefficients-"></a>1778 <span class="k">sub </span><span class="m">GetSupportedSimilarityCoefficients ()</span> <span class="s">{</span>
|
|
|
1792 1779
|
|
|
1793 1780 <span class="k">return</span> <span class="i">@SimilarityCoefficients</span><span class="sc">;</span>
|
|
|
1794 1781 <span class="s">}</span>
|
|
|
1795 1782
|
|
|
1796 1783 <span class="c"># Return a list of supported distance and similarity coefficients...</span>
|
|
|
1797 1784 <span class="c">#</span>
|
|
|
1798 <a name="GetSupportedDistanceAndSimilarityCoefficients-"></a>1785 <span class="k">sub </span><span class="m">GetSupportedDistanceAndSimilarityCoefficients ()</span> <span class="s">{</span>
|
|
|
1799 1786 <span class="k">my</span><span class="s">(</span><span class="i">@DistanceAndSimilarityCoefficients</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1800 1787
|
|
|
1801 1788 <span class="i">@DistanceAndSimilarityCoefficients</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1802 1789 <span class="k">push</span> <span class="i">@DistanceAndSimilarityCoefficients</span><span class="cm">,</span> <span class="i">@DistanceCoefficients</span><span class="sc">;</span>
|
|
|
1803 1790 <span class="k">push</span> <span class="i">@DistanceAndSimilarityCoefficients</span><span class="cm">,</span> <span class="i">@SimilarityCoefficients</span><span class="sc">;</span>
|
|
|
1804 1791
|
|
|
1805 1792 <span class="k">return</span> <span class="k">sort</span> <span class="i">@DistanceAndSimilarityCoefficients</span><span class="sc">;</span>
|
|
|
1806 1793 <span class="s">}</span>
|
|
|
1807 1794
|
|
|
1808 1795 <span class="c"># Is it a fingerprints vector object?</span>
|
|
|
1809 <a name="IsFingerprintsVector-"></a>1796 <span class="k">sub </span><span class="m">IsFingerprintsVector ($)</span> <span class="s">{</span>
|
|
|
1810 1797 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1811 1798
|
|
|
1812 1799 <span class="k">return</span> <span class="i">_IsFingerprintsVector</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1813 1800 <span class="s">}</span>
|
|
|
1814 1801
|
|
|
1815 1802 <span class="c"># Is it a fingerprints vector object?</span>
|
|
|
1816 <a name="_IsFingerprintsVector-"></a>1803 <span class="k">sub </span><span class="m">_IsFingerprintsVector</span> <span class="s">{</span>
|
|
|
1817 1804 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1818 1805
|
|
|
1819 1806 <span class="k">return</span> <span class="s">(</span><span class="i">Scalar::Util::blessed</span><span class="s">(</span><span class="i">$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>
|
|
|
1820 1807 <span class="s">}</span>
|
|
|
1821 1808
|
|
|
1822 1809 <span class="c"># Return a string containing vector values...</span>
|
|
|
1823 <a name="StringifyFingerprintsVector-"></a>1810 <span class="k">sub </span><span class="m">StringifyFingerprintsVector</span> <span class="s">{</span>
|
|
|
1824 1811 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1825 1812 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsVectorString</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1826 1813
|
|
|
1827 1814 <span class="c"># Set type, values and value IDs...</span>
|
|
|
1828 1815 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfValues</span><span class="cm">,</span> <span class="i">$ValuesString</span><span class="cm">,</span> <span class="i">$NumOfValueIDs</span><span class="cm">,</span> <span class="i">$ValueIDsString</span><span class="cm">,</span> <span class="i">$MaxValuesToStringify</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1829 1816
|
|
|
1830 1817 <span class="i">$NumOfValues</span> = <span class="i">$This</span><span class="i">->GetNumOfValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1831 1818 <span class="i">$MaxValuesToStringify</span> = <span class="n">500</span><span class="sc">;</span>
|
|
|
1832 1819
|
|
|
1833 1820 <span class="k">if</span> <span class="s">(</span><span class="i">$NumOfValues</span> < <span class="i">$MaxValuesToStringify</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1834 1821 <span class="c"># Append all values...</span>
|
|
|
1835 1822 <span class="i">$ValuesString</span> = <span class="i">$NumOfValues</span> ? <span class="k">join</span> <span class="q">' '</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Values</span>}} <span class="co">:</span> <span class="q">'None'</span><span class="sc">;</span>
|
|
|
1836 1823 <span class="s">}</span>
|
|
|
1837 1824 <span class="k">else</span> <span class="s">{</span>
|
|
|
1838 1825 <span class="c"># Truncate values...</span>
|
|
|
1839 1826 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1840 1827 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$MaxValuesToStringify</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1841 1828 <span class="k">push</span> <span class="i">@Values</span><span class="cm">,</span> <span class="i">$This</span>->{<span class="w">Values</span>}[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
1842 1829 <span class="s">}</span>
|
|
|
1843 1830 <span class="i">$ValuesString</span> = <span class="k">join</span><span class="s">(</span><span class="q">' '</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> . <span class="q">" ..."</span><span class="sc">;</span>
|
|
|
1844 1831 <span class="s">}</span>
|
|
|
1845 1832
|
|
|
1846 1833 <span class="i">$NumOfValueIDs</span> = <span class="i">$This</span><span class="i">->GetNumOfValueIDs</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1847 1834 <span class="k">if</span> <span class="s">(</span><span class="i">$NumOfValueIDs</span> < <span class="i">$MaxValuesToStringify</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1848 1835 <span class="c"># Append all valueIDs...</span>
|
|
|
1849 1836 <span class="i">$ValueIDsString</span> = <span class="i">$NumOfValueIDs</span> ? <span class="k">join</span> <span class="q">' '</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">ValueIDs</span>}} <span class="co">:</span> <span class="q">'None'</span><span class="sc">;</span>
|
|
|
1850 1837 <span class="s">}</span>
|
|
|
1851 1838 <span class="k">else</span> <span class="s">{</span>
|
|
|
1852 1839 <span class="c"># Truncate value IDs...</span>
|
|
|
1853 1840 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">@ValueIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1854 1841 <span class="i">@ValueIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1855 1842 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$MaxValuesToStringify</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1856 1843 <span class="k">push</span> <span class="i">@ValueIDs</span><span class="cm">,</span> <span class="i">$This</span>->{<span class="w">ValueIDs</span>}[<span class="i">$Index</span>]<span class="sc">;</span>
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1857 1844 <span class="s">}</span>
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1858 1845 <span class="i">$ValueIDsString</span> = <span class="k">join</span><span class="s">(</span><span class="q">' '</span><span class="cm">,</span> <span class="i">@ValueIDs</span><span class="s">)</span> . <span class="q">" ..."</span><span class="sc">;</span>
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1859 1846 <span class="s">}</span>
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1860 1847
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1861 1848 <span class="i">$FingerprintsVectorString</span> = <span class="q">"Type: $This->{Type}; NumOfValues: $NumOfValues"</span><span class="sc">;</span>
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1862 1849 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>} =~ <span class="q">/^(OrderedNumericalValues|NumericalValues)$/i</span><span class="s">)</span> <span class="s">{</span>
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1863 1850 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfNonZeroValues</span><span class="s">)</span><span class="sc">;</span>
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1864 1851 <span class="i">$NumOfNonZeroValues</span> = <span class="i">$This</span><span class="i">->GetNumOfNonZeroValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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1865 1852 <span class="i">$FingerprintsVectorString</span> .= <span class="q">"; NumOfNonZeroValues: $NumOfNonZeroValues"</span><span class="sc">;</span>
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1866 1853 <span class="s">}</span>
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1867 1854
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1868 1855 <span class="c"># Append all the values and value IDs...</span>
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1869 1856 <span class="k">if</span> <span class="s">(</span><span class="i">$NumOfValues</span> < <span class="i">$MaxValuesToStringify</span><span class="s">)</span> <span class="s">{</span>
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1870 1857 <span class="i">$FingerprintsVectorString</span> .= <span class="q">"; Values: <$ValuesString>; NumOfValueIDs: $NumOfValueIDs; ValueIDs: <$ValueIDsString>"</span><span class="sc">;</span>
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1871 1858 <span class="s">}</span>
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1872 1859 <span class="k">else</span> <span class="s">{</span>
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1873 1860 <span class="i">$FingerprintsVectorString</span> .= <span class="q">"; Values (Truncated after $MaxValuesToStringify): <$ValuesString>; NumOfValueIDs: $NumOfValueIDs; ValueIDs (Truncated after $MaxValuesToStringify): <$ValueIDsString>"</span><span class="sc">;</span>
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1874 1861 <span class="s">}</span>
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1875 1862
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1876 1863 <span class="k">return</span> <span class="i">$FingerprintsVectorString</span><span class="sc">;</span>
|
|
|
1877 1864 <span class="s">}</span>
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1878 1865
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1879 <a name="EOF-"></a></pre>
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1880 <p> </p>
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1881 <br />
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1882 <center>
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1883 <img src="../../../images/h2o2.png">
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1884 </center>
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1885 </body>
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1886 </html>
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