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| author | deepakjadmin |
|---|---|
| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/docs/scripts/html/code/SimilarityMatricesFingerprints.html Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,1005 @@ +<html> +<head> +<title>MayaChemTools:Code:SimilarityMatricesFingerprints.pl</title> +<meta http-equiv="content-type" content="text/html;charset=utf-8"> +<link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> +</head> +<body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> +<br/> +<center> +<a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> +</center> +<br/> +<pre> + 1 #!/usr/bin/perl -w + 2 <span class="c">#</span> + 3 <span class="c"># $RCSfile: SimilarityMatricesFingerprints.pl,v $</span> + 4 <span class="c"># $Date: 2015/02/28 20:46:20 $</span> + 5 <span class="c"># $Revision: 1.21 $</span> + 6 <span class="c">#</span> + 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> + 8 <span class="c">#</span> + 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> + 10 <span class="c">#</span> + 11 <span class="c"># This file is part of MayaChemTools.</span> + 12 <span class="c">#</span> + 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> + 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> + 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> + 16 <span class="c"># later version.</span> + 17 <span class="c">#</span> + 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> + 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> + 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> + 21 <span class="c"># details.</span> + 22 <span class="c">#</span> + 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> + 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> + 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> + 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> + 27 <span class="c">#</span> + 28 + 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> + 30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">"$FindBin::Bin/../lib"</span><span class="sc">;</span> + 31 <span class="k">use</span> <span class="w">Getopt::Long</span><span class="sc">;</span> + 32 <span class="k">use</span> <span class="w">File::Basename</span><span class="sc">;</span> + 33 <span class="k">use</span> <span class="w">File::Copy</span><span class="sc">;</span> + 34 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span> + 35 <span class="k">use</span> <span class="w">Benchmark</span><span class="sc">;</span> + 36 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span> + 37 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span> + 38 <span class="k">use</span> <span class="w">Fingerprints::FingerprintsFileUtil</span><span class="sc">;</span> + 39 <span class="k">use</span> <span class="w">Fingerprints::FingerprintsBitVector</span><span class="sc">;</span> + 40 <span class="k">use</span> <span class="w">Fingerprints::FingerprintsVector</span><span class="sc">;</span> + 41 + 42 <span class="k">my</span><span class="s">(</span><span class="i">$ScriptName</span><span class="cm">,</span> <span class="i">%Options</span><span class="cm">,</span> <span class="i">$StartTime</span><span class="cm">,</span> <span class="i">$EndTime</span><span class="cm">,</span> <span class="i">$TotalTime</span><span class="s">)</span><span class="sc">;</span> + 43 + 44 <span class="c"># Autoflush STDOUT</span> + 45 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span> + 46 + 47 <span class="c"># Starting message...</span> + 48 <span class="i">$ScriptName</span> = <span class="i">basename</span><span class="s">(</span><span class="i">$0</span><span class="s">)</span><span class="sc">;</span> + 49 <span class="k">print</span> <span class="q">"\n$ScriptName: Starting...\n\n"</span><span class="sc">;</span> + 50 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span> + 51 + 52 <span class="c"># Get the options and setup script...</span> + 53 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 54 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">help</span>} || <span class="i">@ARGV</span> < <span class="n">1</span><span class="s">)</span> <span class="s">{</span> + 55 <span class="k">die</span> <span class="i">GetUsageFromPod</span><span class="s">(</span><span class="q">"$FindBin::Bin/$ScriptName"</span><span class="s">)</span><span class="sc">;</span> + 56 <span class="s">}</span> + 57 + 58 <span class="k">my</span><span class="s">(</span><span class="i">@FingerprintsFilesList</span><span class="s">)</span><span class="sc">;</span> + 59 <span class="i">@FingerprintsFilesList</span> = <span class="i">ExpandFileNames</span><span class="s">(</span>\<span class="i">@ARGV</span><span class="cm">,</span> <span class="q">"sdf sd fpf fp csv tsv"</span><span class="s">)</span><span class="sc">;</span> + 60 + 61 <span class="c"># Process options...</span> + 62 <span class="k">print</span> <span class="q">"Processing options...\n"</span><span class="sc">;</span> + 63 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span> + 64 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 65 + 66 <span class="c"># Setup information about input files...</span> + 67 <span class="k">print</span> <span class="q">"Checking input fingerprints file(s)...\n"</span><span class="sc">;</span> + 68 <span class="k">my</span><span class="s">(</span><span class="i">%FingerprintsFilesInfo</span><span class="s">)</span><span class="sc">;</span> + 69 <span class="i">RetrieveFingerprintsFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 70 + 71 <span class="c"># Process input files..</span> + 72 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span> + 73 <span class="k">if</span> <span class="s">(</span><span class="i">@FingerprintsFilesList</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span> + 74 <span class="k">print</span> <span class="q">"\nProcessing fingerprints files...\n"</span><span class="sc">;</span> + 75 <span class="s">}</span> + 76 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#FingerprintsFilesList</span><span class="s">)</span> <span class="s">{</span> + 77 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span> + 78 <span class="k">print</span> <span class="q">"\nProcessing file $FingerprintsFilesList[$FileIndex]...\n"</span><span class="sc">;</span> + 79 <span class="i">GenerateSimilarityMatrices</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span> + 80 <span class="s">}</span> + 81 <span class="s">}</span> + 82 <span class="k">print</span> <span class="q">"\n$ScriptName:Done...\n\n"</span><span class="sc">;</span> + 83 + 84 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span> + 85 <span class="i">$TotalTime</span> = <span class="w">timediff</span> <span class="s">(</span><span class="i">$EndTime</span><span class="cm">,</span> <span class="i">$StartTime</span><span class="s">)</span><span class="sc">;</span> + 86 <span class="k">print</span> <span class="q">"Total time: "</span><span class="cm">,</span> <span class="i">timestr</span><span class="s">(</span><span class="i">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 87 + 88 <span class="c">###############################################################################</span> + 89 + 90 <span class="c"># Generate similarity matrices using fingerprints data in text file...</span> + 91 <span class="c">#</span> +<a name="GenerateSimilarityMatrices-"></a> 92 <span class="k">sub </span><span class="m">GenerateSimilarityMatrices</span> <span class="s">{</span> + 93 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 94 + 95 <span class="i">ProcessFingerprintsData</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span> + 96 + 97 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">FingerprintsBitVectorStringMode</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span> + 98 <span class="i">GenerateSimilarityMatricesForFingerprintsBitVectors</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span> + 99 <span class="s">}</span> + 100 <span class="k">elsif</span> <span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">FingerprintsVectorStringMode</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span> + 101 <span class="i">GenerateSimilarityMatricesForFingerprintsVectors</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span> + 102 <span class="s">}</span> + 103 + 104 <span class="i">CleanupFingerprintsData</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span> + 105 <span class="s">}</span> + 106 + 107 <span class="c"># Generate bit vector similarity matrices...</span> + 108 <span class="c">#</span> +<a name="GenerateSimilarityMatricesForFingerprintsBitVectors-"></a> 109 <span class="k">sub </span><span class="m">GenerateSimilarityMatricesForFingerprintsBitVectors</span> <span class="s">{</span> + 110 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 111 <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedComparisonMeasure</span><span class="cm">,</span> <span class="i">$ComparisonMeasure</span><span class="cm">,</span> <span class="i">$NewTextFile</span><span class="cm">,</span> <span class="i">$SimilarityMatrixRef</span><span class="cm">,</span> <span class="i">$MethodName</span><span class="cm">,</span> <span class="i">@MethodParameters</span><span class="s">)</span><span class="sc">;</span> + 112 + 113 <span class="k">for</span> <span class="i">$SpecifiedComparisonMeasure</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedBitVectorComparisonsRef</span>}}<span class="s">)</span> <span class="s">{</span> + 114 <span class="i">$ComparisonMeasure</span> = <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedBitVectorComparisonsNameRef</span>}->{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedComparisonMeasure</span><span class="s">)</span>}<span class="sc">;</span> + 115 <span class="i">$NewTextFile</span> = <span class="i">$FingerprintsFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$FileIndex</span>] . <span class="q">"${ComparisonMeasure}."</span> . <span class="i">$FingerprintsFilesInfo</span>{<span class="w">OutFileExt</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span> + 116 + 117 <span class="i">$MethodName</span> = <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedBitVectorComparisonsMethodRef</span>}->{<span class="k">lc</span><span class="s">(</span><span class="i">$ComparisonMeasure</span><span class="s">)</span>}<span class="sc">;</span> + 118 + 119 <span class="i">@MethodParameters</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 120 <span class="i">@MethodParameters</span> = <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedBitVectorComparisonsParameterRef</span>}->{<span class="k">lc</span><span class="s">(</span><span class="i">$ComparisonMeasure</span><span class="s">)</span>}}<span class="sc">;</span> + 121 + 122 <span class="i">GenerateSimilarityMatrix</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$NewTextFile</span><span class="cm">,</span> <span class="i">$MethodName</span><span class="cm">,</span> \<span class="i">@MethodParameters</span><span class="s">)</span><span class="sc">;</span> + 123 <span class="s">}</span> + 124 <span class="s">}</span> + 125 + 126 <span class="c"># Generate vector similarity and/or distance matrices...</span> + 127 <span class="c">#</span> +<a name="GenerateSimilarityMatricesForFingerprintsVectors-"></a> 128 <span class="k">sub </span><span class="m">GenerateSimilarityMatricesForFingerprintsVectors</span> <span class="s">{</span> + 129 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 130 <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedComparisonMeasure</span><span class="cm">,</span> <span class="i">$ComparisonMode</span><span class="cm">,</span> <span class="i">$ComparisonMeasure</span><span class="cm">,</span> <span class="i">$NewTextFile</span><span class="cm">,</span> <span class="i">$MethodName</span><span class="cm">,</span> <span class="i">@MethodParameters</span><span class="s">)</span><span class="sc">;</span> + 131 + 132 <span class="k">for</span> <span class="i">$SpecifiedComparisonMeasure</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedVectorComparisonsRef</span>}}<span class="s">)</span> <span class="s">{</span> + 133 <span class="i">$ComparisonMeasure</span> = <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedVectorComparisonsNameRef</span>}->{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedComparisonMeasure</span><span class="s">)</span>}<span class="sc">;</span> + 134 + 135 <span class="k">for</span> <span class="i">$ComparisonMode</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedVectorComparisonModesRef</span>}}<span class="s">)</span> <span class="s">{</span> + 136 <span class="i">$NewTextFile</span> = <span class="i">$FingerprintsFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$FileIndex</span>] . <span class="q">"${ComparisonMeasure}${ComparisonMode}."</span> . <span class="i">$FingerprintsFilesInfo</span>{<span class="w">OutFileExt</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span> + 137 + 138 <span class="i">$MethodName</span> = <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedVectorComparisonsMethodRef</span>}->{<span class="k">lc</span><span class="s">(</span><span class="i">$ComparisonMeasure</span><span class="s">)</span>}<span class="sc">;</span> + 139 + 140 <span class="i">@MethodParameters</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 141 <span class="k">push</span> <span class="i">@MethodParameters</span><span class="cm">,</span> <span class="i">$ComparisonMode</span><span class="sc">;</span> + 142 <span class="k">push</span> <span class="i">@MethodParameters</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedVectorComparisonsParameterRef</span>}->{<span class="k">lc</span><span class="s">(</span><span class="i">$ComparisonMeasure</span><span class="s">)</span>}}<span class="sc">;</span> + 143 + 144 <span class="i">GenerateSimilarityMatrix</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$NewTextFile</span><span class="cm">,</span> <span class="i">$MethodName</span><span class="cm">,</span> \<span class="i">@MethodParameters</span><span class="s">)</span><span class="sc">;</span> + 145 <span class="s">}</span> + 146 <span class="s">}</span> + 147 <span class="s">}</span> + 148 + 149 <span class="c"># Calculate similarity matrix and write it out...</span> + 150 <span class="c">#</span> +<a name="GenerateSimilarityMatrix-"></a> 151 <span class="k">sub </span><span class="m">GenerateSimilarityMatrix</span> <span class="s">{</span> + 152 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$NewTextFile</span><span class="cm">,</span> <span class="i">$MethodName</span><span class="cm">,</span> <span class="i">$MethodParametersRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 153 + 154 <span class="k">print</span> <span class="q">"\nGenerating $NewTextFile...\n"</span><span class="sc">;</span> + 155 + 156 <span class="c"># Open new file and write out column labels...</span> + 157 <span class="k">open</span> <span class="w">NEWTEXTFILE</span><span class="cm">,</span> <span class="q">">$NewTextFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $NewTextFile: $! \n"</span><span class="sc">;</span> + 158 <span class="i">WriteColumnLabels</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> \<span class="i">*NEWTEXTFILE</span><span class="s">)</span><span class="sc">;</span> + 159 + 160 <span class="c"># Calculate and write out similarity matrix values...</span> + 161 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">InputDataMode</span>} =~ <span class="q">/^LoadInMemory$/i</span><span class="s">)</span> <span class="s">{</span> + 162 <span class="i">GenerateSimilarityMatrixUsingMemoryData</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> \<span class="i">*NEWTEXTFILE</span><span class="cm">,</span> <span class="i">$MethodName</span><span class="cm">,</span> <span class="i">$MethodParametersRef</span><span class="s">)</span><span class="sc">;</span> + 163 <span class="s">}</span> + 164 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">InputDataMode</span>} =~ <span class="q">/^ScanFile$/i</span><span class="s">)</span> <span class="s">{</span> + 165 <span class="i">GenerateSimilarityMatrixUsingFileData</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> \<span class="i">*NEWTEXTFILE</span><span class="cm">,</span> <span class="i">$MethodName</span><span class="cm">,</span> <span class="i">$MethodParametersRef</span><span class="s">)</span><span class="sc">;</span> + 166 <span class="s">}</span> + 167 <span class="k">else</span> <span class="s">{</span> + 168 <span class="k">warn</span> <span class="q">"Warning: Input data mode, $OptionsInfo{InputDataMode}, is not supported.\n"</span><span class="sc">;</span> + 169 <span class="s">}</span> + 170 + 171 <span class="c"># Close new text file...</span> + 172 <span class="k">close</span> <span class="w">NEWTEXTFILE</span><span class="sc">;</span> + 173 + 174 <span class="s">}</span> + 175 + 176 <span class="c"># Calculate and write out similarity values using fingerprints data already loaded in</span> + 177 <span class="c"># memory...</span> + 178 <span class="c">#</span> +<a name="GenerateSimilarityMatrixUsingMemoryData-"></a> 179 <span class="k">sub </span><span class="m">GenerateSimilarityMatrixUsingMemoryData</span> <span class="s">{</span> + 180 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$NewTextFileRef</span><span class="cm">,</span> <span class="i">$MethodName</span><span class="cm">,</span> <span class="i">$MethodParametersRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 181 <span class="k">my</span><span class="s">(</span><span class="i">$RowIndex</span><span class="cm">,</span> <span class="i">$ColIndex</span><span class="cm">,</span> <span class="i">$CmpdID1</span><span class="cm">,</span> <span class="i">$CmpdID2</span><span class="cm">,</span> <span class="i">$FingerprintsObject1</span><span class="cm">,</span> <span class="i">$FingerprintsObject2</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">$Line</span><span class="cm">,</span> <span class="i">@LineWords</span><span class="s">)</span><span class="sc">;</span> + 182 + 183 <span class="k">for</span> <span class="i">$RowIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">FingerprintsObjectsRef</span>}}<span class="s">)</span> <span class="s">{</span> + 184 <span class="i">$FingerprintsObject1</span> = <span class="i">$FingerprintsFilesInfo</span>{<span class="w">FingerprintsObjectsRef</span>}->[<span class="i">$RowIndex</span>]<span class="sc">;</span> + 185 <span class="i">$CmpdID1</span> = <span class="i">$FingerprintsFilesInfo</span>{<span class="w">CompundIDsRef</span>}->[<span class="i">$RowIndex</span>]<span class="sc">;</span> + 186 + 187 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">WriteRowsAndColumns</span>}<span class="s">)</span> <span class="s">{</span> + 188 <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="q">"$OptionsInfo{OutQuoteValue}${CmpdID1}$OptionsInfo{OutQuoteValue}"</span><span class="sc">;</span> + 189 <span class="s">}</span> + 190 + 191 <span class="j">COLINDEX:</span> <span class="k">for</span> <span class="i">$ColIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">FingerprintsObjectsRef</span>}}<span class="s">)</span> <span class="s">{</span> + 192 <span class="k">if</span> <span class="s">(</span><span class="i">SkipMatrixData</span><span class="s">(</span><span class="i">$RowIndex</span><span class="cm">,</span> <span class="i">$ColIndex</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 193 <span class="k">next</span> <span class="j">COLINDEX</span><span class="sc">;</span> + 194 <span class="s">}</span> + 195 + 196 <span class="i">$FingerprintsObject2</span> = <span class="i">$FingerprintsFilesInfo</span>{<span class="w">FingerprintsObjectsRef</span>}->[<span class="i">$ColIndex</span>]<span class="sc">;</span> + 197 + 198 <span class="i">$Value</span> = <span class="i">$FingerprintsObject1</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$FingerprintsObject2</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$MethodParametersRef</span>}<span class="s">)</span><span class="sc">;</span> + 199 <span class="i">$Value</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> && <span class="k">length</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> ? <span class="s">(</span><span class="k">sprintf</span><span class="s">(</span><span class="q">"%.$OptionsInfo{Precision}f"</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> + <span class="n">0</span><span class="s">)</span> <span class="co">:</span> <span class="q">''</span><span class="sc">;</span> + 200 + 201 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">WriteRowsAndColumns</span>}<span class="s">)</span> <span class="s">{</span> + 202 <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="q">"$OptionsInfo{OutDelim}$OptionsInfo{OutQuoteValue}${Value}$OptionsInfo{OutQuoteValue}"</span><span class="sc">;</span> + 203 <span class="s">}</span> + 204 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">WriteIDPairsAndValue</span>}<span class="s">)</span> <span class="s">{</span> + 205 <span class="i">$CmpdID2</span> = <span class="i">$FingerprintsFilesInfo</span>{<span class="w">CompundIDsRef</span>}->[<span class="i">$ColIndex</span>]<span class="sc">;</span> + 206 + 207 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 208 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="s">(</span><span class="i">$CmpdID1</span><span class="cm">,</span> <span class="i">$CmpdID2</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> + 209 <span class="i">$Line</span> = <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>}<span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span> + 210 <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="q">"$Line\n"</span><span class="sc">;</span> + 211 <span class="s">}</span> + 212 <span class="s">}</span> + 213 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">WriteRowsAndColumns</span>}<span class="s">)</span> <span class="s">{</span> + 214 <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="q">"\n"</span><span class="sc">;</span> + 215 <span class="s">}</span> + 216 <span class="s">}</span> + 217 <span class="s">}</span> + 218 + 219 <span class="c"># Calculate and write out similarity values by retrieving and prcessing data</span> + 220 <span class="c"># from fingerprint file...</span> + 221 <span class="c">#</span> +<a name="GenerateSimilarityMatrixUsingFileData-"></a> 222 <span class="k">sub </span><span class="m">GenerateSimilarityMatrixUsingFileData</span> <span class="s">{</span> + 223 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$NewTextFileRef</span><span class="cm">,</span> <span class="i">$MethodName</span><span class="cm">,</span> <span class="i">$MethodParametersRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 224 <span class="k">my</span><span class="s">(</span><span class="i">$RowIndex</span><span class="cm">,</span> <span class="i">$ColIndex</span><span class="cm">,</span> <span class="i">$FingerprintsFileIO</span><span class="cm">,</span> <span class="i">$TmpFingerprintsFileIO</span><span class="cm">,</span> <span class="i">$FingerprintsObject1</span><span class="cm">,</span> <span class="i">$FingerprintsObject2</span><span class="cm">,</span> <span class="i">$CmpdID1</span><span class="cm">,</span> <span class="i">$CmpdID2</span><span class="cm">,</span> <span class="i">$FingerprintsCount</span><span class="cm">,</span> <span class="i">$IgnoredFingerprintsCount</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">$Line</span><span class="cm">,</span> <span class="i">@LineWords</span><span class="s">)</span><span class="sc">;</span> + 225 + 226 <span class="k">print</span> <span class="q">"\nReading and processing fingerprints data...\n"</span><span class="sc">;</span> + 227 + 228 <span class="i">$FingerprintsFileIO</span> = <span class="i">Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO</span><span class="s">(</span><span class="i">%</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">FingerprintsFileIOParameters</span>}[<span class="i">$FileIndex</span>]}<span class="s">)</span><span class="sc">;</span> + 229 <span class="i">$FingerprintsFileIO</span><span class="i">->Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 230 + 231 <span class="i">$RowIndex</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$ColIndex</span> = <span class="n">0</span><span class="sc">;</span> + 232 <span class="i">$FingerprintsCount</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$IgnoredFingerprintsCount</span> = <span class="n">0</span><span class="sc">;</span> + 233 + 234 <span class="j">FINGERPRINTSFILEIO:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$FingerprintsFileIO</span><span class="i">->Read</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 235 <span class="i">$FingerprintsCount</span>++<span class="sc">;</span> + 236 + 237 <span class="k">if</span> <span class="s">(</span>!<span class="i">$FingerprintsFileIO</span><span class="i">->IsFingerprintsDataValid</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 238 <span class="i">$IgnoredFingerprintsCount</span>++<span class="sc">;</span> + 239 <span class="k">next</span> <span class="j">FINGERPRINTSFILEIO</span><span class="sc">;</span> + 240 <span class="s">}</span> + 241 <span class="i">$RowIndex</span>++<span class="sc">;</span> + 242 <span class="i">$FingerprintsObject1</span> = <span class="i">$FingerprintsFileIO</span><span class="i">->GetFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 243 <span class="i">$CmpdID1</span> = <span class="i">$FingerprintsFileIO</span><span class="i">->GetCompoundID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 244 + 245 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">WriteRowsAndColumns</span>}<span class="s">)</span> <span class="s">{</span> + 246 <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="q">"$OptionsInfo{OutQuoteValue}${CmpdID1}$OptionsInfo{OutQuoteValue}"</span><span class="sc">;</span> + 247 <span class="s">}</span> + 248 + 249 <span class="c"># Force detail level of 1 to avoid duplicate printing of diagnostic messages for invalid</span> + 250 <span class="c"># fingerprints data...</span> + 251 <span class="i">$TmpFingerprintsFileIO</span> = <span class="i">Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO</span><span class="s">(</span><span class="i">%</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">TmpFingerprintsFileIOParameters</span>}[<span class="i">$FileIndex</span>]}<span class="cm">,</span> <span class="q">"DetailLevel"</span> <span class="cm">=></span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span> + 252 <span class="i">$TmpFingerprintsFileIO</span><span class="i">->Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 253 + 254 <span class="i">$ColIndex</span> = <span class="n">0</span><span class="sc">;</span> + 255 <span class="j">TMPFINGERPRINTSFILEIO:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$TmpFingerprintsFileIO</span><span class="i">->Read</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 256 <span class="k">if</span> <span class="s">(</span>!<span class="i">$TmpFingerprintsFileIO</span><span class="i">->IsFingerprintsDataValid</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 257 <span class="k">next</span> <span class="j">TMPFINGERPRINTSFILEIO</span><span class="sc">;</span> + 258 <span class="s">}</span> + 259 <span class="i">$ColIndex</span>++<span class="sc">;</span> + 260 + 261 <span class="k">if</span> <span class="s">(</span><span class="i">SkipMatrixData</span><span class="s">(</span><span class="i">$RowIndex</span><span class="cm">,</span> <span class="i">$ColIndex</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 262 <span class="k">next</span> <span class="j">TMPFINGERPRINTSFILEIO</span><span class="sc">;</span> + 263 <span class="s">}</span> + 264 + 265 <span class="i">$FingerprintsObject2</span> = <span class="i">$TmpFingerprintsFileIO</span><span class="i">->GetFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 266 + 267 <span class="i">$Value</span> = <span class="i">$FingerprintsObject1</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$FingerprintsObject2</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$MethodParametersRef</span>}<span class="s">)</span><span class="sc">;</span> + 268 <span class="i">$Value</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> && <span class="k">length</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> ? <span class="s">(</span><span class="k">sprintf</span><span class="s">(</span><span class="q">"%.$OptionsInfo{Precision}f"</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> + <span class="n">0</span><span class="s">)</span> <span class="co">:</span> <span class="q">''</span><span class="sc">;</span> + 269 + 270 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">WriteRowsAndColumns</span>}<span class="s">)</span> <span class="s">{</span> + 271 <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="q">"$OptionsInfo{OutDelim}$OptionsInfo{OutQuoteValue}${Value}$OptionsInfo{OutQuoteValue}"</span><span class="sc">;</span> + 272 <span class="s">}</span> + 273 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">WriteIDPairsAndValue</span>}<span class="s">)</span> <span class="s">{</span> + 274 <span class="i">$CmpdID2</span> = <span class="i">$TmpFingerprintsFileIO</span><span class="i">->GetCompoundID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 275 + 276 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 277 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="s">(</span><span class="i">$CmpdID1</span><span class="cm">,</span> <span class="i">$CmpdID2</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> + 278 <span class="i">$Line</span> = <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>}<span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span> + 279 <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="q">"$Line\n"</span><span class="sc">;</span> + 280 <span class="s">}</span> + 281 <span class="s">}</span> + 282 <span class="i">$TmpFingerprintsFileIO</span><span class="i">->Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 283 + 284 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">WriteRowsAndColumns</span>}<span class="s">)</span> <span class="s">{</span> + 285 <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="q">"\n"</span><span class="sc">;</span> + 286 <span class="s">}</span> + 287 <span class="s">}</span> + 288 + 289 <span class="i">$FingerprintsFileIO</span><span class="i">->Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 290 + 291 <span class="k">print</span> <span class="q">"Number of fingerprints data entries in database fingerprints file: $FingerprintsCount\n"</span><span class="sc">;</span> + 292 <span class="k">print</span> <span class="q">"Number of fingerprints date entries processed successfully: "</span><span class="cm">,</span> <span class="s">(</span><span class="i">$FingerprintsCount</span> - <span class="i">$IgnoredFingerprintsCount</span><span class="s">)</span> <span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 293 <span class="k">print</span> <span class="q">"Number of fingerprints data entries ignored due to missing/invalid data: $IgnoredFingerprintsCount\n\n"</span><span class="sc">;</span> + 294 <span class="s">}</span> + 295 + 296 <span class="c"># Check whether matrix data need to be skipped...</span> + 297 <span class="c">#</span> +<a name="SkipMatrixData-"></a> 298 <span class="k">sub </span><span class="m">SkipMatrixData</span> <span class="s">{</span> + 299 <span class="k">my</span><span class="s">(</span><span class="i">$RowIndex</span><span class="cm">,</span> <span class="i">$ColIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 300 + 301 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">WriteFullMatrix</span>}<span class="s">)</span> <span class="s">{</span> + 302 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> + 303 <span class="s">}</span> + 304 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">WriteUpperTriangularMatrix</span>}<span class="s">)</span> <span class="s">{</span> + 305 <span class="k">return</span> <span class="s">(</span><span class="i">$RowIndex</span> > <span class="i">$ColIndex</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 306 <span class="s">}</span> + 307 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">WriteLowerTriangularMatrix</span>}<span class="s">)</span> <span class="s">{</span> + 308 <span class="k">return</span> <span class="s">(</span><span class="i">$RowIndex</span> < <span class="i">$ColIndex</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 309 <span class="s">}</span> + 310 + 311 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> + 312 <span class="s">}</span> + 313 + 314 <span class="c"># Write out column labels...</span> + 315 <span class="c">#</span> +<a name="WriteColumnLabels-"></a> 316 <span class="k">sub </span><span class="m">WriteColumnLabels</span> <span class="s">{</span> + 317 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$NewTextFileRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 318 <span class="k">my</span><span class="s">(</span><span class="i">$Line</span><span class="cm">,</span> <span class="i">@LineWords</span><span class="s">)</span><span class="sc">;</span> + 319 + 320 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutMatrixFormat</span>} =~ <span class="q">/^IDPairsAndValue$/i</span><span class="s">)</span> <span class="s">{</span> + 321 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 322 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="s">(</span><span class="q">'CmpdID1'</span><span class="cm">,</span> <span class="q">'CmpdID2'</span><span class="cm">,</span> <span class="q">'Coefficient Value'</span><span class="s">)</span><span class="sc">;</span> + 323 <span class="i">$Line</span> = <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>}<span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span> + 324 <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="q">"$Line\n"</span><span class="sc">;</span> + 325 <span class="s">}</span> + 326 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutMatrixFormat</span>} =~ <span class="q">/^RowsAndColumns$/i</span><span class="s">)</span> <span class="s">{</span> + 327 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">InputDataMode</span>} =~ <span class="q">/^LoadInMemory$/i</span><span class="s">)</span> <span class="s">{</span> + 328 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 329 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="q">''</span><span class="sc">;</span> + 330 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">CompundIDsRef</span>}}<span class="sc">;</span> + 331 <span class="i">$Line</span> = <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@LineWords</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>}<span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span> + 332 <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="q">"$Line\n"</span><span class="sc">;</span> + 333 <span class="s">}</span> + 334 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">InputDataMode</span>} =~ <span class="q">/^ScanFile$/i</span><span class="s">)</span> <span class="s">{</span> + 335 <span class="k">my</span><span class="s">(</span> <span class="i">$FingerprintsFileIO</span><span class="cm">,</span> <span class="i">$CmpdID</span><span class="s">)</span><span class="sc">;</span> + 336 + 337 <span class="c"># Scan file to retrieve compound IDs...</span> + 338 <span class="c">#</span> + 339 <span class="k">print</span> <span class="q">"\nProcessing fingerprints file to generate compound IDs...\n"</span><span class="sc">;</span> + 340 + 341 <span class="c"># Force detail level of 1 to avoid diagnostics messages for invalid fingeprints data during</span> + 342 <span class="c"># retrieval of compound IDs as these get printed out during calculation of matrix...</span> + 343 <span class="c">#</span> + 344 <span class="i">$FingerprintsFileIO</span> = <span class="i">Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO</span><span class="s">(</span><span class="i">%</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">FingerprintsFileIOParameters</span>}[<span class="i">$FileIndex</span>]}<span class="cm">,</span> <span class="q">"DetailLevel"</span> <span class="cm">=></span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span> + 345 <span class="i">$FingerprintsFileIO</span><span class="i">->Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 346 + 347 <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="q">"$OptionsInfo{OutQuoteValue}$OptionsInfo{OutQuoteValue}"</span><span class="sc">;</span> + 348 + 349 <span class="j">FINGERPRINTSFILEIO:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$FingerprintsFileIO</span><span class="i">->Read</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 350 <span class="k">if</span> <span class="s">(</span>!<span class="i">$FingerprintsFileIO</span><span class="i">->IsFingerprintsDataValid</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 351 <span class="k">next</span> <span class="j">FINGERPRINTSFILEIO</span><span class="sc">;</span> + 352 <span class="s">}</span> + 353 <span class="i">$CmpdID</span> = <span class="i">$FingerprintsFileIO</span><span class="i">->GetCompoundID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 354 <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="q">"$OptionsInfo{OutDelim}$OptionsInfo{OutQuoteValue}${CmpdID}$OptionsInfo{OutQuoteValue}"</span><span class="sc">;</span> + 355 <span class="s">}</span> + 356 <span class="i">$FingerprintsFileIO</span><span class="i">->Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 357 + 358 <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="q">"\n"</span><span class="sc">;</span> + 359 + 360 <span class="k">print</span> <span class="q">"Processing fingerprints file to generate matrix...\n"</span><span class="sc">;</span> + 361 <span class="s">}</span> + 362 <span class="s">}</span> + 363 <span class="k">else</span> <span class="s">{</span> + 364 <span class="k">warn</span> <span class="q">"Warning: Output matrix format, $OptionsInfo{OutMatrixFormat}, is not supported.\n"</span><span class="sc">;</span> + 365 <span class="s">}</span> + 366 <span class="s">}</span> + 367 + 368 <span class="c"># Process fingerprints data...</span> + 369 <span class="c">#</span> +<a name="ProcessFingerprintsData-"></a> 370 <span class="k">sub </span><span class="m">ProcessFingerprintsData</span> <span class="s">{</span> + 371 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 372 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsFileIO</span><span class="s">)</span><span class="sc">;</span> + 373 + 374 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">CompundIDsRef</span>} = <span class="k">undef</span><span class="sc">;</span> + 375 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">FingerprintsObjectsRef</span>} = <span class="k">undef</span><span class="sc">;</span> + 376 + 377 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">InputDataMode</span>} =~ <span class="q">/^LoadInMemory$/i</span><span class="s">)</span> <span class="s">{</span> + 378 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsFileIO</span><span class="s">)</span><span class="sc">;</span> + 379 + 380 <span class="i">$FingerprintsFileIO</span> = <span class="i">Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO</span><span class="s">(</span><span class="i">%</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">FingerprintsFileIOParameters</span>}[<span class="i">$FileIndex</span>]}<span class="s">)</span><span class="sc">;</span> + 381 <span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">CompundIDsRef</span>}<span class="cm">,</span> <span class="i">$FingerprintsFilesInfo</span>{<span class="w">FingerprintsObjectsRef</span>}<span class="s">)</span> = <span class="i">Fingerprints::FingerprintsFileUtil::ReadAndProcessFingerpritsData</span><span class="s">(</span><span class="i">$FingerprintsFileIO</span><span class="s">)</span><span class="sc">;</span> + 382 <span class="s">}</span> + 383 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">InputDataMode</span>} =~ <span class="q">/^ScanFile$/i</span><span class="s">)</span> <span class="s">{</span> + 384 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsFile</span><span class="cm">,</span> <span class="i">$TmpFingerprintsFile</span><span class="s">)</span><span class="sc">;</span> + 385 + 386 <span class="i">$FingerprintsFile</span> = <span class="i">$FingerprintsFilesList</span>[<span class="i">$FileIndex</span>]<span class="sc">;</span> + 387 <span class="i">$TmpFingerprintsFile</span> = <span class="i">$FingerprintsFilesInfo</span>{<span class="w">TmpFingerprintsFile</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span> + 388 + 389 <span class="c"># Copy fingerprints file to a tmp file for calculating similarity matrix...</span> + 390 <span class="k">print</span> <span class="q">"\nCopying fingerprints file, $FingerprintsFile, to temporary fingperints file, $TmpFingerprintsFile...\n"</span><span class="sc">;</span> + 391 <span class="w">copy</span> <span class="i">$FingerprintsFile</span><span class="cm">,</span> <span class="i">$TmpFingerprintsFile</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't copy $FingerprintsFile to $TmpFingerprintsFile: $! \n"</span><span class="sc">;</span> + 392 <span class="s">}</span> + 393 <span class="s">}</span> + 394 + 395 <span class="c"># Clean up fingerprints data...</span> + 396 <span class="c">#</span> +<a name="CleanupFingerprintsData-"></a> 397 <span class="k">sub </span><span class="m">CleanupFingerprintsData</span> <span class="s">{</span> + 398 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 399 + 400 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">InputDataMode</span>} =~ <span class="q">/^LoadInMemory$/i</span><span class="s">)</span> <span class="s">{</span> + 401 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">CompundIDsRef</span>} = <span class="k">undef</span><span class="sc">;</span> + 402 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">FingerprintsObjectsRef</span>} = <span class="k">undef</span><span class="sc">;</span> + 403 <span class="s">}</span> + 404 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">InputDataMode</span>} =~ <span class="q">/^ScanFile$/i</span><span class="s">)</span> <span class="s">{</span> + 405 <span class="k">my</span><span class="s">(</span><span class="i">$TmpFingerprintsFile</span><span class="s">)</span><span class="sc">;</span> + 406 + 407 <span class="c"># Delete temporary fingerprints file...</span> + 408 <span class="i">$TmpFingerprintsFile</span> = <span class="i">$FingerprintsFilesInfo</span>{<span class="w">TmpFingerprintsFile</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span> + 409 + 410 <span class="k">print</span> <span class="q">"\nDeleting temporary fingerprints file $TmpFingerprintsFile...\n"</span><span class="sc">;</span> + 411 <span class="k">unlink</span> <span class="i">$TmpFingerprintsFile</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't unlink $TmpFingerprintsFile: $! \n"</span><span class="sc">;</span> + 412 <span class="s">}</span> + 413 <span class="s">}</span> + 414 + 415 <span class="c"># Retrieve information about fingerprints files...</span> + 416 <span class="c">#</span> +<a name="RetrieveFingerprintsFilesInfo-"></a> 417 <span class="k">sub </span><span class="m">RetrieveFingerprintsFilesInfo</span> <span class="s">{</span> + 418 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsFile</span><span class="cm">,</span> <span class="i">$TmpFingerprintsFile</span><span class="cm">,</span> <span class="i">$FingerprintsFileIO</span><span class="cm">,</span> <span class="i">$FingerprintsBitVectorStringMode</span><span class="cm">,</span> <span class="i">$FingerprintsVectorStringMode</span><span class="cm">,</span> <span class="i">$FileType</span><span class="cm">,</span> <span class="i">$Index</span><span class="cm">,</span> <span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$InDelim</span><span class="cm">,</span> <span class="i">$OutFileRoot</span><span class="cm">,</span> <span class="i">$OutFileExt</span><span class="cm">,</span> <span class="i">%FingerprintsFileIOParameters</span><span class="s">)</span><span class="sc">;</span> + 419 + 420 <span class="i">%FingerprintsFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 421 <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">FileOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 422 <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">FileType</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 423 <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">InDelim</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 424 <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">OutFileRoot</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 425 <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">OutFileExt</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 426 + 427 <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">TmpFingerprintsFile</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 428 + 429 <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">FingerprintsFileIOParameters</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 430 <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">TmpFingerprintsFileIOParameters</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 431 + 432 <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">FingerprintsBitVectorStringMode</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 433 <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">FingerprintsVectorStringMode</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 434 + 435 <span class="j">FILELIST:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#FingerprintsFilesList</span><span class="s">)</span> <span class="s">{</span> + 436 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span> + 437 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">FileType</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span> + 438 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">InDelim</span>}[<span class="i">$Index</span>] = <span class="q">""</span><span class="sc">;</span> + 439 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span> + 440 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">OutFileExt</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span> + 441 + 442 <span class="i">%</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">FingerprintsFileIOParameters</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 443 + 444 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">TmpFingerprintsFile</span>}[<span class="i">$Index</span>] = <span class="q">""</span><span class="sc">;</span> + 445 <span class="i">%</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">TmpFingerprintsFileIOParameters</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 446 + 447 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">FingerprintsBitVectorStringMode</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span> + 448 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">FingerprintsVectorStringMode</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span> + 449 + 450 <span class="i">$FingerprintsFile</span> = <span class="i">$FingerprintsFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span> + 451 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">-e</span> <span class="i">$FingerprintsFile</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 452 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $FingerprintsFile: It doesn't exist\n"</span><span class="sc">;</span> + 453 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> + 454 <span class="s">}</span> + 455 + 456 <span class="i">$FileType</span> = <span class="i">Fingerprints::FingerprintsFileUtil::GetFingerprintsFileType</span><span class="s">(</span><span class="i">$FingerprintsFile</span><span class="s">)</span><span class="sc">;</span> + 457 <span class="k">if</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$FileType</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 458 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $FingerprintsFile: It's not a fingerprints file\n"</span><span class="sc">;</span> + 459 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> + 460 <span class="s">}</span> + 461 + 462 <span class="i">$FileDir</span> = <span class="q">""</span><span class="sc">;</span> <span class="i">$FileName</span> = <span class="q">""</span><span class="sc">;</span> <span class="i">$FileExt</span> = <span class="q">""</span><span class="sc">;</span> + 463 <span class="s">(</span><span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="s">)</span> = <span class="i">ParseFileName</span><span class="s">(</span><span class="i">$FingerprintsFile</span><span class="s">)</span><span class="sc">;</span> + 464 + 465 <span class="c"># Setup temporary fingerprints file name for scan file mode...</span> + 466 <span class="i">$TmpFingerprintsFile</span> = <span class="q">"${FileName}Tmp.${FileExt}"</span><span class="sc">;</span> + 467 + 468 <span class="i">$InDelim</span> = <span class="s">(</span><span class="i">$FileExt</span> =~ <span class="q">/^tsv$/i</span><span class="s">)</span> ? <span class="q">'Tab'</span> <span class="co">:</span> <span class="i">$OptionsInfo</span>{<span class="w">InDelim</span>}<span class="sc">;</span> + 469 + 470 <span class="c"># Setup output file names...</span> + 471 <span class="i">$OutFileExt</span> = <span class="q">"csv"</span><span class="sc">;</span> + 472 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/^tab$/i</span><span class="s">)</span> <span class="s">{</span> + 473 <span class="i">$OutFileExt</span> = <span class="q">"tsv"</span><span class="sc">;</span> + 474 <span class="s">}</span> + 475 + 476 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span> + 477 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} && <span class="s">(</span><span class="i">@FingerprintsFilesList</span> == <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 478 <span class="k">my</span> <span class="s">(</span><span class="i">$RootFileDir</span><span class="cm">,</span> <span class="i">$RootFileName</span><span class="cm">,</span> <span class="i">$RootFileExt</span><span class="s">)</span> = <span class="i">ParseFileName</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="s">)</span><span class="sc">;</span> + 479 <span class="k">if</span> <span class="s">(</span><span class="i">$RootFileName</span> && <span class="i">$RootFileExt</span><span class="s">)</span> <span class="s">{</span> + 480 <span class="i">$FileName</span> = <span class="i">$RootFileName</span><span class="sc">;</span> + 481 <span class="s">}</span> + 482 <span class="k">else</span> <span class="s">{</span> + 483 <span class="i">$FileName</span> = <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="sc">;</span> + 484 <span class="s">}</span> + 485 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span> + 486 <span class="s">}</span> + 487 + 488 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">overwrite</span>}<span class="s">)</span> <span class="s">{</span> + 489 <span class="c"># Similarity matrices output file names for bit-vector strings...</span> + 490 <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedComparisonMeasure</span><span class="cm">,</span> <span class="i">$ComparisonMeasure</span><span class="s">)</span><span class="sc">;</span> + 491 <span class="k">for</span> <span class="i">$SpecifiedComparisonMeasure</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedBitVectorComparisonsRef</span>}}<span class="s">)</span> <span class="s">{</span> + 492 <span class="i">$ComparisonMeasure</span> = <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedBitVectorComparisonsNameRef</span>}->{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedComparisonMeasure</span><span class="s">)</span>}<span class="sc">;</span> + 493 <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="q">"${OutFileRoot}${ComparisonMeasure}.${OutFileExt}"</span><span class="s">)</span> <span class="s">{</span> + 494 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $FingerprintsFile: The file ${OutFileRoot}${ComparisonMeasure}.${OutFileExt} already exists.\n"</span><span class="sc">;</span> + 495 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> + 496 <span class="s">}</span> + 497 <span class="s">}</span> + 498 <span class="c"># Similarity matrices output file names for vector strings...</span> + 499 <span class="k">my</span><span class="s">(</span><span class="i">$ComparisonMode</span><span class="s">)</span><span class="sc">;</span> + 500 <span class="k">for</span> <span class="i">$SpecifiedComparisonMeasure</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedVectorComparisonsRef</span>}}<span class="s">)</span> <span class="s">{</span> + 501 <span class="i">$ComparisonMeasure</span> = <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedVectorComparisonsNameRef</span>}->{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedComparisonMeasure</span><span class="s">)</span>}<span class="sc">;</span> + 502 <span class="k">for</span> <span class="i">$ComparisonMode</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedVectorComparisonModesRef</span>}}<span class="s">)</span> <span class="s">{</span> + 503 <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="q">"${OutFileRoot}${ComparisonMeasure}${ComparisonMode}.${OutFileExt}"</span><span class="s">)</span> <span class="s">{</span> + 504 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $FingerprintsFile: The file ${OutFileRoot}${ComparisonMeasure}${ComparisonMode}.${OutFileExt} already exists.\n"</span><span class="sc">;</span> + 505 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> + 506 <span class="s">}</span> + 507 <span class="s">}</span> + 508 <span class="s">}</span> + 509 <span class="s">}</span> + 510 + 511 <span class="c"># Setup FingerprintsFileIO parameters...</span> + 512 <span class="i">%FingerprintsFileIOParameters</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 513 <span class="j">FILEIOPARAMETERS:</span> <span class="s">{</span> + 514 <span class="k">if</span> <span class="s">(</span><span class="i">$FileType</span> =~ <span class="q">/^SD$/i</span><span class="s">)</span> <span class="s">{</span> + 515 <span class="i">%FingerprintsFileIOParameters</span> = <span class="s">(</span><span class="q">'Name'</span> <span class="cm">=></span> <span class="i">$FingerprintsFile</span><span class="cm">,</span> <span class="q">'Mode'</span> <span class="cm">=></span> <span class="q">'Read'</span><span class="cm">,</span> <span class="q">'FingerprintsStringMode'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>}<span class="cm">,</span> <span class="q">'ValidateData'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">ValidateData</span>}<span class="cm">,</span> <span class="q">'DetailLevel'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">Detail</span>}<span class="cm">,</span> <span class="q">'FingerprintsFieldLabel'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsField</span>}<span class="cm">,</span> <span class="q">'CompoundIDMode'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>}<span class="cm">,</span> <span class="q">'CompoundIDFieldLabel'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDField</span>}<span class="cm">,</span> <span class="q">'CompoundIDPrefix'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDPrefix</span>}<span class="s">)</span><span class="sc">;</span> + 516 <span class="k">last</span> <span class="j">FILEIOPARAMETERS</span><span class="sc">;</span> + 517 <span class="s">}</span> + 518 <span class="k">if</span> <span class="s">(</span><span class="i">$FileType</span> =~ <span class="q">/^FP$/i</span><span class="s">)</span> <span class="s">{</span> + 519 <span class="i">%FingerprintsFileIOParameters</span> = <span class="s">(</span><span class="q">'Name'</span> <span class="cm">=></span> <span class="i">$FingerprintsFile</span><span class="cm">,</span> <span class="q">'Mode'</span> <span class="cm">=></span> <span class="q">'Read'</span><span class="cm">,</span> <span class="q">'FingerprintsStringMode'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>}<span class="cm">,</span> <span class="q">'ValidateData'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">ValidateData</span>}<span class="cm">,</span> <span class="q">'DetailLevel'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">Detail</span>}<span class="s">)</span><span class="sc">;</span> + 520 <span class="k">last</span> <span class="j">FILEIOPARAMETERS</span><span class="sc">;</span> + 521 <span class="s">}</span> + 522 <span class="k">if</span> <span class="s">(</span><span class="i">$FileType</span> =~ <span class="q">/^Text$/i</span><span class="s">)</span> <span class="s">{</span> + 523 <span class="i">%FingerprintsFileIOParameters</span> = <span class="s">(</span><span class="q">'Name'</span> <span class="cm">=></span> <span class="i">$FingerprintsFile</span><span class="cm">,</span> <span class="q">'Mode'</span> <span class="cm">=></span> <span class="q">'Read'</span><span class="cm">,</span> <span class="q">'FingerprintsStringMode'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>}<span class="cm">,</span> <span class="q">'ValidateData'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">ValidateData</span>}<span class="cm">,</span> <span class="q">'DetailLevel'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">Detail</span>}<span class="cm">,</span> <span class="q">'FingerprintsCol'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsCol</span>}<span class="cm">,</span> <span class="q">'ColMode'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">ColMode</span>}<span class="cm">,</span> <span class="q">'CompoundIDCol'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDCol</span>}<span class="cm">,</span> <span class="q">'CompoundIDPrefix'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDPrefix</span>}<span class="cm">,</span> <span class="q">'InDelim'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">InDelim</span>}<span class="s">)</span><span class="sc">;</span> + 524 <span class="k">last</span> <span class="j">FILEIOPARAMETERS</span><span class="sc">;</span> + 525 <span class="s">}</span> + 526 <span class="k">warn</span> <span class="q">"Warning: File type for fingerprints file, $FingerprintsFile, is not valid. Supported file types: SD, FP or Text\n"</span><span class="sc">;</span> + 527 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> + 528 <span class="s">}</span> + 529 + 530 <span class="c"># Retrieve fingerints file string mode information...</span> + 531 <span class="i">$FingerprintsFileIO</span> = <span class="i">Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO</span><span class="s">(</span><span class="i">%FingerprintsFileIOParameters</span><span class="s">)</span><span class="sc">;</span> + 532 + 533 <span class="k">if</span> <span class="s">(</span>!<span class="i">$FingerprintsFileIO</span><span class="s">)</span> <span class="s">{</span> + 534 <span class="k">warn</span> <span class="q">"Warning: Ignoring fingerprints file $FingerprintsFile: It contains invalid fingerprints data\n"</span><span class="sc">;</span> + 535 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> + 536 <span class="s">}</span> + 537 <span class="k">if</span> <span class="s">(</span>!<span class="i">$FingerprintsFileIO</span><span class="i">->IsFingerprintsFileDataValid</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 538 <span class="k">warn</span> <span class="q">"Warning: Ignoring fingerprints file $FingerprintsFile: It contains invalid fingerprints data\n"</span><span class="sc">;</span> + 539 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> + 540 <span class="s">}</span> + 541 <span class="i">$FingerprintsBitVectorStringMode</span> = <span class="i">$FingerprintsFileIO</span><span class="i">->GetFingerprintsBitVectorStringMode</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 542 <span class="i">$FingerprintsVectorStringMode</span> = <span class="i">$FingerprintsFileIO</span><span class="i">->GetFingerprintsVectorStringMode</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 543 + 544 + 545 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span> + 546 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">FileType</span>}[<span class="i">$Index</span>] = <span class="i">$FileType</span><span class="sc">;</span> + 547 + 548 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">InDelim</span>}[<span class="i">$Index</span>] = <span class="i">$InDelim</span><span class="sc">;</span> + 549 + 550 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="i">$OutFileRoot</span><span class="sc">;</span> + 551 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">OutFileExt</span>}[<span class="i">$Index</span>] = <span class="i">$OutFileExt</span><span class="sc">;</span> + 552 + 553 <span class="i">%</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">FingerprintsFileIOParameters</span>}[<span class="i">$Index</span>]} = <span class="i">%FingerprintsFileIOParameters</span><span class="sc">;</span> + 554 + 555 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">TmpFingerprintsFile</span>}[<span class="i">$Index</span>] = <span class="i">$TmpFingerprintsFile</span><span class="sc">;</span> + 556 + 557 <span class="i">$FingerprintsFileIOParameters</span>{<span class="w">Name</span>} = <span class="i">$TmpFingerprintsFile</span><span class="sc">;</span> + 558 <span class="i">%</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">TmpFingerprintsFileIOParameters</span>}[<span class="i">$Index</span>]} = <span class="i">%FingerprintsFileIOParameters</span><span class="sc">;</span> + 559 + 560 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">FingerprintsBitVectorStringMode</span>}[<span class="i">$Index</span>] = <span class="i">$FingerprintsBitVectorStringMode</span><span class="sc">;</span> + 561 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">FingerprintsVectorStringMode</span>}[<span class="i">$Index</span>] = <span class="i">$FingerprintsVectorStringMode</span><span class="sc">;</span> + 562 <span class="s">}</span> + 563 <span class="s">}</span> + 564 + 565 <span class="c"># Process option values...</span> +<a name="ProcessOptions-"></a> 566 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span> + 567 <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 568 + 569 <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span> + 570 + 571 <span class="i">$OptionsInfo</span>{<span class="w">InputDataMode</span>} = <span class="i">$Options</span>{<span class="w">inputdatamode</span>}<span class="sc">;</span> + 572 + 573 <span class="i">ProcessBitVectorComparisonOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 574 <span class="i">ProcessVectorComparisonOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 575 + 576 <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDPrefix</span>} = <span class="i">$Options</span>{<span class="w">compoundidprefix</span>} ? <span class="i">$Options</span>{<span class="w">compoundidprefix</span>} <span class="co">:</span> <span class="q">'Cmpd'</span><span class="sc">;</span> + 577 + 578 <span class="c"># Compound ID and fingerprints column options for text files...</span> + 579 <span class="i">$OptionsInfo</span>{<span class="w">ColMode</span>} = <span class="i">$Options</span>{<span class="w">colmode</span>}<span class="sc">;</span> + 580 + 581 <span class="k">if</span> <span class="s">(</span><span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidcol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 582 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">colmode</span>} =~ <span class="q">/^ColNum$/i</span><span class="s">)</span> <span class="s">{</span> + 583 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidcol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 584 <span class="k">die</span> <span class="q">"Error: Column value, $Options{compoundidcol}, specified using \"--CompoundIDCol\" is not valid: Allowed integer values: > 0\n"</span><span class="sc">;</span> + 585 <span class="s">}</span> + 586 <span class="s">}</span> + 587 <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDCol</span>} = <span class="i">$Options</span>{<span class="w">compoundidcol</span>}<span class="sc">;</span> + 588 <span class="s">}</span> + 589 <span class="k">else</span> <span class="s">{</span> + 590 <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDCol</span>} = <span class="q">'AutoDetect'</span><span class="sc">;</span> + 591 <span class="s">}</span> + 592 + 593 <span class="k">if</span> <span class="s">(</span><span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">fingerprintscol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 594 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">colmode</span>} =~ <span class="q">/^ColNum$/i</span><span class="s">)</span> <span class="s">{</span> + 595 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">fingerprintscol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 596 <span class="k">die</span> <span class="q">"Error: Column value, $Options{fingerprintscol}, specified using \"--FingerprintsCol\" is not valid: Allowed integer values: > 0\n"</span><span class="sc">;</span> + 597 <span class="s">}</span> + 598 <span class="s">}</span> + 599 <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsCol</span>} = <span class="i">$Options</span>{<span class="w">fingerprintscol</span>}<span class="sc">;</span> + 600 <span class="s">}</span> + 601 <span class="k">else</span> <span class="s">{</span> + 602 <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsCol</span>} = <span class="q">'AutoDetect'</span><span class="sc">;</span> + 603 <span class="s">}</span> + 604 + 605 <span class="k">if</span> <span class="s">(</span><span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidcol</span>}<span class="s">)</span> && <span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">fingerprintscol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 606 <span class="k">if</span> <span class="s">(</span><span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidcol</span>}<span class="s">)</span> && <span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">fingerprintscol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 607 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidcol</span>} == <span class="i">$Options</span>{<span class="w">fingerprintscol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 608 <span class="k">die</span> <span class="q">"Error: Values specified using \"--CompoundIDCol\" and \"--FingerprintsCol\", $Options{compoundidcol}, must be different.\n"</span><span class="sc">;</span> + 609 <span class="s">}</span> + 610 <span class="s">}</span> + 611 <span class="k">else</span> <span class="s">{</span> + 612 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidcol</span>} <span class="k">eq</span> <span class="i">$Options</span>{<span class="w">fingerprintscol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 613 <span class="k">die</span> <span class="q">"Error: Values specified using \"--CompoundIDCol\" and \"--FingerprintsCol\", $Options{compoundidcol}, must be different.\n"</span><span class="sc">;</span> + 614 <span class="s">}</span> + 615 <span class="s">}</span> + 616 <span class="s">}</span> + 617 + 618 <span class="c"># Compound ID and fingerprints field options for SD files...</span> + 619 <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} = <span class="i">$Options</span>{<span class="w">compoundidmode</span>}<span class="sc">;</span> + 620 <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDField</span>} = <span class="q">''</span><span class="sc">;</span> + 621 + 622 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidmode</span>} =~ <span class="q">/^DataField$/i</span><span class="s">)</span> <span class="s">{</span> + 623 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">compoundidfield</span>}<span class="s">)</span> <span class="s">{</span> + 624 <span class="k">die</span> <span class="q">"Error: You must specify a value for \"--CompoundIDField\" option in \"DataField\" \"--CompoundIDMode\". \n"</span><span class="sc">;</span> + 625 <span class="s">}</span> + 626 <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDField</span>} = <span class="i">$Options</span>{<span class="w">compoundidfield</span>}<span class="sc">;</span> + 627 <span class="s">}</span> + 628 + 629 + 630 <span class="k">if</span> <span class="s">(</span><span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">fingerprintsfield</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 631 <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsField</span>} = <span class="i">$Options</span>{<span class="w">fingerprintsfield</span>}<span class="sc">;</span> + 632 <span class="s">}</span> + 633 <span class="k">else</span> <span class="s">{</span> + 634 <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsField</span>} = <span class="q">'AutoDetect'</span><span class="sc">;</span> + 635 <span class="s">}</span> + 636 + 637 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidfield</span>} && <span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">fingerprintsfield</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 638 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidfield</span>} <span class="k">eq</span> <span class="i">$Options</span>{<span class="w">fingerprintsfield</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 639 <span class="k">die</span> <span class="q">"Error: Values specified using \"--CompoundIDField\" and \"--Fingerprintsfield\", $Options{compoundidfield}, must be different.\n"</span><span class="sc">;</span> + 640 <span class="s">}</span> + 641 <span class="s">}</span> + 642 + 643 <span class="i">$OptionsInfo</span>{<span class="w">Detail</span>} = <span class="i">$Options</span>{<span class="w">detail</span>}<span class="sc">;</span> + 644 + 645 <span class="i">$OptionsInfo</span>{<span class="w">InDelim</span>} = <span class="i">$Options</span>{<span class="w">indelim</span>}<span class="sc">;</span> + 646 <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/tab/i</span> <span class="s">)</span> ? <span class="q">"\t"</span> <span class="co">:</span> <span class="s">(</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/semicolon/i</span><span class="s">)</span> ? <span class="q">"\;"</span> <span class="co">:</span> <span class="q">"\,"</span><span class="s">)</span><span class="sc">;</span> + 647 <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">quote</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 648 <span class="i">$OptionsInfo</span>{<span class="w">OutQuoteValue</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">quote</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="q">'"'</span> <span class="co">:</span> <span class="q">''</span><span class="sc">;</span> + 649 + 650 <span class="i">$OptionsInfo</span>{<span class="w">OutMatrixFormat</span>} = <span class="i">$Options</span>{<span class="w">outmatrixformat</span>}<span class="sc">;</span> + 651 + 652 <span class="i">$OptionsInfo</span>{<span class="w">WriteRowsAndColumns</span>} = <span class="n">0</span><span class="sc">;</span> <span class="i">$OptionsInfo</span>{<span class="w">WriteIDPairsAndValue</span>} = <span class="n">0</span><span class="sc">;</span> + 653 <span class="j">OUTMATRIXFORMAT:</span> <span class="s">{</span> + 654 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutMatrixFormat</span>} =~ <span class="q">/^RowsAndColumns$/i</span><span class="s">)</span> <span class="s">{</span> + 655 <span class="i">$OptionsInfo</span>{<span class="w">WriteRowsAndColumns</span>} = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">OUTMATRIXFORMAT</span><span class="sc">;</span> + 656 <span class="s">}</span> + 657 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutMatrixFormat</span>} =~ <span class="q">/^IDPairsAndValue$/i</span><span class="s">)</span> <span class="s">{</span> + 658 <span class="i">$OptionsInfo</span>{<span class="w">WriteIDPairsAndValue</span>} = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">OUTMATRIXFORMAT</span><span class="sc">;</span> + 659 <span class="s">}</span> + 660 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{outmatrixformat}, for option \"--OutMatrixFormat\" is not valid. Allowed values: RowsAndColumns or IDPairsAndValue\n"</span><span class="sc">;</span> + 661 <span class="s">}</span> + 662 + 663 <span class="i">$OptionsInfo</span>{<span class="w">OutMatrixType</span>} = <span class="i">$Options</span>{<span class="w">outmatrixtype</span>}<span class="sc">;</span> + 664 + 665 <span class="i">$OptionsInfo</span>{<span class="w">WriteFullMatrix</span>} = <span class="n">0</span><span class="sc">;</span> + 666 <span class="i">$OptionsInfo</span>{<span class="w">WriteUpperTriangularMatrix</span>} = <span class="n">0</span><span class="sc">;</span> <span class="i">$OptionsInfo</span>{<span class="w">WriteLowerTriangularMatrix</span>} = <span class="n">0</span><span class="sc">;</span> + 667 <span class="j">OUTMATRIXTYPE:</span> <span class="s">{</span> + 668 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutMatrixType</span>} =~ <span class="q">/^FullMatrix$/i</span><span class="s">)</span> <span class="s">{</span> + 669 <span class="i">$OptionsInfo</span>{<span class="w">WriteFullMatrix</span>} = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">OUTMATRIXTYPE</span><span class="sc">;</span> + 670 <span class="s">}</span> + 671 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutMatrixType</span>} =~ <span class="q">/^UpperTriangularMatrix$/i</span><span class="s">)</span> <span class="s">{</span> + 672 <span class="i">$OptionsInfo</span>{<span class="w">WriteUpperTriangularMatrix</span>} = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">OUTMATRIXTYPE</span><span class="sc">;</span> + 673 <span class="s">}</span> + 674 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutMatrixType</span>} =~ <span class="q">/^LowerTriangularMatrix$/i</span><span class="s">)</span> <span class="s">{</span> + 675 <span class="i">$OptionsInfo</span>{<span class="w">WriteLowerTriangularMatrix</span>} = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">OUTMATRIXTYPE</span><span class="sc">;</span> + 676 <span class="s">}</span> + 677 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{outmatrixtype}, for option \"--OutMatrixType\" is not valid. Allowed values: FullMatrix, UpperTriangularMatrix or LowerTriangularMatrix\n"</span><span class="sc">;</span> + 678 <span class="s">}</span> + 679 + 680 <span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>} = <span class="i">$Options</span>{<span class="w">overwrite</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 681 <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} = <span class="i">$Options</span>{<span class="w">root</span>} ? <span class="i">$Options</span>{<span class="w">root</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 682 + 683 <span class="i">$OptionsInfo</span>{<span class="w">Fast</span>} = <span class="i">$Options</span>{<span class="w">fast</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 684 <span class="i">$OptionsInfo</span>{<span class="w">ValidateData</span>} = <span class="i">$Options</span>{<span class="w">fast</span>} ? <span class="n">0</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span> + 685 + 686 <span class="i">$OptionsInfo</span>{<span class="w">Precision</span>} = <span class="i">$Options</span>{<span class="w">precision</span>}<span class="sc">;</span> + 687 + 688 <span class="s">}</span> + 689 + 690 <span class="c"># Process options related to comparion of bit vector strings...</span> + 691 <span class="c">#</span> +<a name="ProcessBitVectorComparisonOptions-"></a> 692 <span class="k">sub </span><span class="m">ProcessBitVectorComparisonOptions</span> <span class="s">{</span> + 693 <span class="c"># Setup supported bit vector similarity coefficients for bit vector strings...</span> + 694 <span class="k">my</span><span class="s">(</span><span class="i">$ComparisonMeasure</span><span class="cm">,</span> <span class="i">$SupportedComparisonMeasure</span><span class="cm">,</span> <span class="i">@SupportedComparisonMeasures</span><span class="cm">,</span> <span class="i">%SupportedComparisonMeasuresNameMap</span><span class="cm">,</span> <span class="i">%SupportedComparisonMeasuresMethodMap</span><span class="s">)</span><span class="sc">;</span> + 695 + 696 <span class="i">@SupportedComparisonMeasures</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 697 <span class="i">%SupportedComparisonMeasuresNameMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 698 <span class="i">%SupportedComparisonMeasuresMethodMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 699 + 700 <span class="k">for</span> <span class="i">$SupportedComparisonMeasure</span> <span class="s">(</span><span class="i">Fingerprints::FingerprintsBitVector::GetSupportedSimilarityCoefficients</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 701 <span class="c"># Similarity coefficient function/method names contain "Coefficient" in their names.</span> + 702 <span class="c"># So take 'em out and setup a map to original function/method name...</span> + 703 <span class="i">$ComparisonMeasure</span> = <span class="i">$SupportedComparisonMeasure</span><span class="sc">;</span> + 704 <span class="i">$ComparisonMeasure</span> =~ <span class="q">s/Coefficient$//</span><span class="sc">;</span> + 705 + 706 <span class="k">push</span> <span class="i">@SupportedComparisonMeasures</span><span class="cm">,</span> <span class="i">$ComparisonMeasure</span><span class="sc">;</span> + 707 <span class="i">$SupportedComparisonMeasuresNameMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ComparisonMeasure</span><span class="s">)</span>} = <span class="i">$ComparisonMeasure</span><span class="sc">;</span> + 708 <span class="i">$SupportedComparisonMeasuresMethodMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ComparisonMeasure</span><span class="s">)</span>} = <span class="i">$SupportedComparisonMeasure</span><span class="sc">;</span> + 709 <span class="s">}</span> + 710 + 711 <span class="c"># Setup a list of similarity coefficients to use for calculating similarity matrices for bit vector strings...</span> + 712 <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedMeasure</span><span class="cm">,</span> <span class="i">@SpecifiedComparisonMeasures</span><span class="cm">,</span> <span class="i">%SpecifiedComparisonMeasuresNameMap</span><span class="cm">,</span> <span class="i">%SpecifiedComparisonMeasuresMethodMap</span><span class="cm">,</span> <span class="i">%SpecifiedComparisonMeasuresParameterMap</span><span class="s">)</span><span class="sc">;</span> + 713 + 714 <span class="i">@SpecifiedComparisonMeasures</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 715 <span class="i">%SpecifiedComparisonMeasuresNameMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 716 <span class="i">%SpecifiedComparisonMeasuresMethodMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 717 <span class="i">%SpecifiedComparisonMeasuresParameterMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 718 + 719 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">bitvectorcomparisonmode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span> + 720 <span class="k">push</span> <span class="i">@SpecifiedComparisonMeasures</span><span class="cm">,</span> <span class="i">@SupportedComparisonMeasures</span><span class="sc">;</span> + 721 <span class="s">}</span> + 722 <span class="k">else</span> <span class="s">{</span> + 723 <span class="c"># Comma delimited list of similarity coefficients...</span> + 724 <span class="k">my</span><span class="s">(</span><span class="i">$BitVectorComparisonMode</span><span class="cm">,</span> <span class="i">@SpecifiedMeasures</span><span class="cm">,</span> <span class="i">@UnsupportedSpecifiedMeasures</span><span class="s">)</span><span class="sc">;</span> + 725 + 726 <span class="i">$BitVectorComparisonMode</span> = <span class="i">$Options</span>{<span class="w">bitvectorcomparisonmode</span>}<span class="sc">;</span> + 727 <span class="i">$BitVectorComparisonMode</span> =~ <span class="q">s/ //g</span><span class="sc">;</span> + 728 <span class="i">@SpecifiedMeasures</span> = <span class="k">split</span> <span class="q">","</span><span class="cm">,</span> <span class="i">$BitVectorComparisonMode</span><span class="sc">;</span> + 729 <span class="i">@UnsupportedSpecifiedMeasures</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 730 + 731 <span class="k">for</span> <span class="i">$SpecifiedMeasure</span> <span class="s">(</span><span class="i">@SpecifiedMeasures</span><span class="s">)</span> <span class="s">{</span> + 732 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$SupportedComparisonMeasuresMethodMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedMeasure</span><span class="s">)</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 733 <span class="k">push</span> <span class="i">@SpecifiedComparisonMeasures</span><span class="cm">,</span> <span class="i">$SpecifiedMeasure</span><span class="sc">;</span> + 734 <span class="s">}</span> + 735 <span class="k">else</span> <span class="s">{</span> + 736 <span class="k">push</span> <span class="i">@UnsupportedSpecifiedMeasures</span><span class="cm">,</span> <span class="i">$SpecifiedMeasure</span><span class="sc">;</span> + 737 <span class="s">}</span> + 738 <span class="s">}</span> + 739 <span class="k">if</span> <span class="s">(</span><span class="i">@UnsupportedSpecifiedMeasures</span><span class="s">)</span> <span class="s">{</span> + 740 <span class="k">if</span> <span class="s">(</span><span class="i">@UnsupportedSpecifiedMeasures</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span> + 741 <span class="k">warn</span> <span class="q">"Error: The values specified - "</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@UnsupportedSpecifiedMeasures</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span><span class="q">" - for option \"-b --BitVectorComparisonMode\" are not valid.\n"</span><span class="sc">;</span> + 742 <span class="s">}</span> + 743 <span class="k">else</span> <span class="s">{</span> + 744 <span class="k">warn</span> <span class="q">"Error: The value specified, @UnsupportedSpecifiedMeasures, for option \"-b --BitVectorComparisonMode\" is not valid.\n"</span><span class="sc">;</span> + 745 <span class="s">}</span> + 746 <span class="k">die</span> <span class="q">"Allowed values:"</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@SupportedComparisonMeasures</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 747 <span class="s">}</span> + 748 <span class="s">}</span> + 749 <span class="k">for</span> <span class="i">$SpecifiedMeasure</span> <span class="s">(</span><span class="i">@SpecifiedComparisonMeasures</span><span class="s">)</span> <span class="s">{</span> + 750 <span class="i">$SpecifiedComparisonMeasuresMethodMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedMeasure</span><span class="s">)</span>} = <span class="i">$SupportedComparisonMeasuresMethodMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedMeasure</span><span class="s">)</span>}<span class="sc">;</span> + 751 <span class="i">$SpecifiedComparisonMeasuresNameMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedMeasure</span><span class="s">)</span>} = <span class="i">$SupportedComparisonMeasuresNameMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedMeasure</span><span class="s">)</span>}<span class="sc">;</span> + 752 <span class="s">}</span> + 753 + 754 <span class="i">$OptionsInfo</span>{<span class="w">BitVectorComparisonMode</span>} = <span class="i">$Options</span>{<span class="w">bitvectorcomparisonmode</span>}<span class="sc">;</span> + 755 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedBitVectorComparisonsRef</span>} = \<span class="i">@SpecifiedComparisonMeasures</span><span class="sc">;</span> + 756 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedBitVectorComparisonsNameRef</span>} = \<span class="i">%SpecifiedComparisonMeasuresNameMap</span><span class="sc">;</span> + 757 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedBitVectorComparisonsMethodRef</span>} = \<span class="i">%SpecifiedComparisonMeasuresMethodMap</span><span class="sc">;</span> + 758 + 759 <span class="c"># Make sure valid alpha parameter is specified for Tversky calculation...</span> + 760 <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedMeasure1</span><span class="cm">,</span> <span class="i">$SpecifiedMeasure2</span><span class="s">)</span><span class="sc">;</span> + 761 <span class="i">$OptionsInfo</span>{<span class="w">Alpha</span>} = <span class="q">''</span><span class="sc">;</span> + 762 <span class="i">$SpecifiedMeasure1</span> = <span class="q">'TverskySimilarity'</span><span class="sc">;</span> + 763 <span class="i">$SpecifiedMeasure2</span> = <span class="q">'WeightedTverskySimilarity'</span><span class="sc">;</span> + 764 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedComparisonMeasuresNameMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedMeasure1</span><span class="s">)</span>} || <span class="i">$SpecifiedComparisonMeasuresNameMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedMeasure2</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span> + 765 <span class="k">if</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">alpha</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 766 <span class="k">die</span> <span class="q">"Error: You must specify a value for \"-a, --alpha\" option in \"$SpecifiedMeasure1, $SpecifiedMeasure2, or All\" \"-m --mode\". \n"</span><span class="sc">;</span> + 767 <span class="s">}</span> + 768 <span class="k">my</span><span class="s">(</span><span class="i">$Alpha</span><span class="s">)</span><span class="sc">;</span> + 769 <span class="i">$Alpha</span> = <span class="i">$Options</span>{<span class="w">alpha</span>}<span class="sc">;</span> + 770 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">IsFloat</span><span class="s">(</span><span class="i">$Alpha</span><span class="s">)</span> && <span class="i">$Alpha</span> >=<span class="n">0</span> && <span class="i">$Alpha</span> <= <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 771 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{alpha}, for option \"-a, --alpha\" is not valid. Allowed values: >= 0 and <= 1\n"</span><span class="sc">;</span> + 772 <span class="s">}</span> + 773 <span class="i">$OptionsInfo</span>{<span class="w">Alpha</span>} = <span class="i">$Alpha</span><span class="sc">;</span> + 774 <span class="s">}</span> + 775 + 776 <span class="c"># Make sure valid beta parameter is specified for WeightedTanimoto and WeightedTversky</span> + 777 <span class="c"># calculations...</span> + 778 <span class="i">$OptionsInfo</span>{<span class="w">Beta</span>} = <span class="q">''</span><span class="sc">;</span> + 779 <span class="i">$SpecifiedMeasure1</span> = <span class="q">'WeightedTverskySimilarity'</span><span class="sc">;</span> + 780 <span class="i">$SpecifiedMeasure2</span> = <span class="q">'WeightedTanimotoSimilarity'</span><span class="sc">;</span> + 781 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedComparisonMeasuresNameMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedMeasure1</span><span class="s">)</span>} || <span class="i">$SpecifiedComparisonMeasuresNameMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedMeasure2</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span> + 782 <span class="k">if</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">beta</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 783 <span class="k">die</span> <span class="q">"Error: You must specify a value for \"-b, --beta\" option in \"$SpecifiedMeasure1, $SpecifiedMeasure2, or All\" \"-m --mode\". \n"</span><span class="sc">;</span> + 784 <span class="s">}</span> + 785 <span class="k">my</span><span class="s">(</span><span class="i">$Beta</span><span class="s">)</span><span class="sc">;</span> + 786 <span class="i">$Beta</span> = <span class="i">$Options</span>{<span class="w">beta</span>}<span class="sc">;</span> + 787 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">IsFloat</span><span class="s">(</span><span class="i">$Beta</span><span class="s">)</span> && <span class="i">$Beta</span> >=<span class="n">0</span> && <span class="i">$Beta</span> <= <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 788 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{beta}, for option \"-b, --beta\" is not valid. Allowed values: >= 0 and <= 1\n"</span><span class="sc">;</span> + 789 <span class="s">}</span> + 790 <span class="i">$OptionsInfo</span>{<span class="w">Beta</span>} = <span class="i">$Beta</span><span class="sc">;</span> + 791 <span class="s">}</span> + 792 + 793 <span class="c"># Setup any parameters required for specified comparison menthod...</span> + 794 <span class="k">for</span> <span class="i">$SpecifiedMeasure</span> <span class="s">(</span><span class="i">@SpecifiedComparisonMeasures</span><span class="s">)</span> <span class="s">{</span> + 795 <span class="i">@</span>{<span class="i">$SpecifiedComparisonMeasuresParameterMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedMeasure</span><span class="s">)</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 796 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedMeasure</span> =~ <span class="q">/^TverskySimilarity$/i</span><span class="s">)</span> <span class="s">{</span> + 797 <span class="k">push</span> <span class="i">@</span>{<span class="i">$SpecifiedComparisonMeasuresParameterMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedMeasure</span><span class="s">)</span>}}<span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">Alpha</span>}<span class="sc">;</span> + 798 <span class="s">}</span> + 799 <span class="k">elsif</span> <span class="s">(</span><span class="i">$SpecifiedMeasure</span> =~ <span class="q">/^WeightedTverskySimilarity$/i</span><span class="s">)</span> <span class="s">{</span> + 800 <span class="k">push</span> <span class="i">@</span>{<span class="i">$SpecifiedComparisonMeasuresParameterMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedMeasure</span><span class="s">)</span>}}<span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">Alpha</span>}<span class="sc">;</span> + 801 <span class="k">push</span> <span class="i">@</span>{<span class="i">$SpecifiedComparisonMeasuresParameterMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedMeasure</span><span class="s">)</span>}}<span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">Beta</span>}<span class="sc">;</span> + 802 <span class="s">}</span> + 803 <span class="k">elsif</span> <span class="s">(</span><span class="i">$SpecifiedMeasure</span> =~ <span class="q">/^WeightedTanimotoSimilarity$/i</span><span class="s">)</span> <span class="s">{</span> + 804 <span class="k">push</span> <span class="i">@</span>{<span class="i">$SpecifiedComparisonMeasuresParameterMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedMeasure</span><span class="s">)</span>}}<span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">Beta</span>}<span class="sc">;</span> + 805 <span class="s">}</span> + 806 <span class="s">}</span> + 807 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedBitVectorComparisonsParameterRef</span>} = \<span class="i">%SpecifiedComparisonMeasuresParameterMap</span><span class="sc">;</span> + 808 <span class="s">}</span> + 809 + 810 <span class="c"># Process options related to comparion of vector strings...</span> + 811 <span class="c">#</span> +<a name="ProcessVectorComparisonOptions-"></a> 812 <span class="k">sub </span><span class="m">ProcessVectorComparisonOptions</span> <span class="s">{</span> + 813 <span class="c"># Setup specified similarity coefficients for vector strings..</span> + 814 <span class="k">my</span><span class="s">(</span><span class="i">$ComparisonMeasure</span><span class="cm">,</span> <span class="i">$SupportedComparisonMeasure</span><span class="cm">,</span> <span class="i">@SupportedComparisonMeasures</span><span class="cm">,</span> <span class="i">%SupportedComparisonMeasuresNameMap</span><span class="cm">,</span> <span class="i">%SupportedComparisonMeasuresMethodMap</span><span class="s">)</span><span class="sc">;</span> + 815 + 816 <span class="i">@SupportedComparisonMeasures</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 817 <span class="i">%SupportedComparisonMeasuresNameMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 818 <span class="i">%SupportedComparisonMeasuresMethodMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 819 <span class="k">for</span> <span class="i">$SupportedComparisonMeasure</span> <span class="s">(</span><span class="i">Fingerprints::FingerprintsVector::GetSupportedDistanceAndSimilarityCoefficients</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 820 <span class="c"># Similarity and distance coefficient function/method names contain "Coefficient" in their names.</span> + 821 <span class="c"># So take 'em out and setup a map to original function/method name...</span> + 822 <span class="i">$ComparisonMeasure</span> = <span class="i">$SupportedComparisonMeasure</span><span class="sc">;</span> + 823 <span class="k">if</span> <span class="s">(</span><span class="i">$ComparisonMeasure</span> =~ <span class="q">/Coefficient$/i</span><span class="s">)</span> <span class="s">{</span> + 824 <span class="i">$ComparisonMeasure</span> =~ <span class="q">s/Coefficient$//i</span><span class="sc">;</span> + 825 <span class="s">}</span> + 826 <span class="k">push</span> <span class="i">@SupportedComparisonMeasures</span><span class="cm">,</span> <span class="i">$ComparisonMeasure</span><span class="sc">;</span> + 827 <span class="i">$SupportedComparisonMeasuresNameMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ComparisonMeasure</span><span class="s">)</span>} = <span class="i">$ComparisonMeasure</span><span class="sc">;</span> + 828 <span class="i">$SupportedComparisonMeasuresMethodMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ComparisonMeasure</span><span class="s">)</span>} = <span class="i">$SupportedComparisonMeasure</span><span class="sc">;</span> + 829 <span class="s">}</span> + 830 + 831 <span class="c"># Setup a list of similarity coefficients to use for calculating similarity matrices for bit vector strings...</span> + 832 <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedMeasure</span><span class="cm">,</span> <span class="i">@SpecifiedComparisonMeasures</span><span class="cm">,</span> <span class="i">%SpecifiedComparisonMeasuresNameMap</span><span class="cm">,</span> <span class="i">%SpecifiedComparisonMeasuresMethodMap</span><span class="cm">,</span> <span class="i">%SpecifiedComparisonMeasuresParameterMap</span><span class="s">)</span><span class="sc">;</span> + 833 + 834 <span class="i">@SpecifiedComparisonMeasures</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 835 <span class="i">%SpecifiedComparisonMeasuresNameMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 836 <span class="i">%SpecifiedComparisonMeasuresMethodMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 837 + 838 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">vectorcomparisonmode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span> + 839 <span class="k">push</span> <span class="i">@SpecifiedComparisonMeasures</span><span class="cm">,</span> <span class="i">@SupportedComparisonMeasures</span><span class="sc">;</span> + 840 <span class="s">}</span> + 841 <span class="k">else</span> <span class="s">{</span> + 842 <span class="c"># Comma delimited list of similarity coefficients...</span> + 843 <span class="k">my</span><span class="s">(</span><span class="i">$VectorComparisonMode</span><span class="cm">,</span> <span class="i">@SpecifiedMeasures</span><span class="cm">,</span> <span class="i">@UnsupportedSpecifiedMeasures</span><span class="s">)</span><span class="sc">;</span> + 844 + 845 <span class="i">$VectorComparisonMode</span> = <span class="i">$Options</span>{<span class="w">vectorcomparisonmode</span>}<span class="sc">;</span> + 846 <span class="i">$VectorComparisonMode</span> =~ <span class="q">s/ //g</span><span class="sc">;</span> + 847 <span class="i">@SpecifiedMeasures</span> = <span class="k">split</span> <span class="q">","</span><span class="cm">,</span> <span class="i">$VectorComparisonMode</span><span class="sc">;</span> + 848 <span class="i">@UnsupportedSpecifiedMeasures</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 849 + 850 <span class="k">for</span> <span class="i">$SpecifiedMeasure</span> <span class="s">(</span><span class="i">@SpecifiedMeasures</span><span class="s">)</span> <span class="s">{</span> + 851 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$SupportedComparisonMeasuresMethodMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedMeasure</span><span class="s">)</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 852 <span class="k">push</span> <span class="i">@SpecifiedComparisonMeasures</span><span class="cm">,</span> <span class="i">$SpecifiedMeasure</span><span class="sc">;</span> + 853 <span class="s">}</span> + 854 <span class="k">else</span> <span class="s">{</span> + 855 <span class="k">push</span> <span class="i">@UnsupportedSpecifiedMeasures</span><span class="cm">,</span> <span class="i">$SpecifiedMeasure</span><span class="sc">;</span> + 856 <span class="s">}</span> + 857 <span class="s">}</span> + 858 <span class="k">if</span> <span class="s">(</span><span class="i">@UnsupportedSpecifiedMeasures</span><span class="s">)</span> <span class="s">{</span> + 859 <span class="k">if</span> <span class="s">(</span><span class="i">@UnsupportedSpecifiedMeasures</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span> + 860 <span class="k">warn</span> <span class="q">"Error: The values specified - "</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@UnsupportedSpecifiedMeasures</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span><span class="q">" - for option \"-v --VectorComparisonMode\" are not valid.\n"</span><span class="sc">;</span> + 861 <span class="s">}</span> + 862 <span class="k">else</span> <span class="s">{</span> + 863 <span class="k">warn</span> <span class="q">"Error: The value specified, @UnsupportedSpecifiedMeasures, for option \"-v --VectorComparisonMode\" is not valid.\n"</span><span class="sc">;</span> + 864 <span class="s">}</span> + 865 <span class="k">die</span> <span class="q">"Allowed values:"</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@SupportedComparisonMeasures</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 866 <span class="s">}</span> + 867 <span class="s">}</span> + 868 <span class="k">for</span> <span class="i">$SpecifiedMeasure</span> <span class="s">(</span><span class="i">@SpecifiedComparisonMeasures</span><span class="s">)</span> <span class="s">{</span> + 869 <span class="i">$SpecifiedComparisonMeasuresMethodMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedMeasure</span><span class="s">)</span>} = <span class="i">$SupportedComparisonMeasuresMethodMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedMeasure</span><span class="s">)</span>}<span class="sc">;</span> + 870 <span class="i">$SpecifiedComparisonMeasuresNameMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedMeasure</span><span class="s">)</span>} = <span class="i">$SupportedComparisonMeasuresNameMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedMeasure</span><span class="s">)</span>}<span class="sc">;</span> + 871 <span class="s">}</span> + 872 + 873 <span class="i">$OptionsInfo</span>{<span class="w">VectorComparisonMode</span>} = <span class="i">$Options</span>{<span class="w">vectorcomparisonmode</span>}<span class="sc">;</span> + 874 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedVectorComparisonsRef</span>} = \<span class="i">@SpecifiedComparisonMeasures</span><span class="sc">;</span> + 875 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedVectorComparisonsNameRef</span>} = \<span class="i">%SpecifiedComparisonMeasuresNameMap</span><span class="sc">;</span> + 876 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedVectorComparisonsMethodRef</span>} = \<span class="i">%SpecifiedComparisonMeasuresMethodMap</span><span class="sc">;</span> + 877 + 878 <span class="c"># Setup specified vector comparison calculation modes...</span> + 879 <span class="k">my</span><span class="s">(</span><span class="i">@SpecifiedVectorComparisonModes</span><span class="s">)</span><span class="sc">;</span> + 880 <span class="i">@SpecifiedVectorComparisonModes</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 881 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">vectorcomparisonformulism</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span> + 882 <span class="k">push</span> <span class="i">@SpecifiedVectorComparisonModes</span><span class="cm">,</span> <span class="s">(</span><span class="q">"AlgebraicForm"</span><span class="cm">,</span> <span class="q">"BinaryForm"</span><span class="cm">,</span> <span class="q">"SetTheoreticForm"</span><span class="s">)</span><span class="sc">;</span> + 883 <span class="s">}</span> + 884 <span class="k">else</span> <span class="s">{</span> + 885 <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedFormulism</span><span class="cm">,</span> <span class="i">@SpecifiedFormulismWords</span><span class="s">)</span><span class="sc">;</span> + 886 + 887 <span class="i">@SpecifiedFormulismWords</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">vectorcomparisonformulism</span>}<span class="sc">;</span> + 888 <span class="k">for</span> <span class="i">$SpecifiedFormulism</span> <span class="s">(</span><span class="i">@SpecifiedFormulismWords</span><span class="s">)</span> <span class="s">{</span> + 889 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedFormulism</span> !~ <span class="q">/^(AlgebraicForm|BinaryForm|SetTheoreticForm)$/i</span><span class="s">)</span> <span class="s">{</span> + 890 <span class="k">die</span> <span class="q">"Error: The value specified, $SpecifiedFormulism, for option \"--VectorComparisonFormulism\" is not valid. Allowed values: AlgebraicForm, BinaryForm or SetTheoreticForm\n"</span><span class="sc">;</span> + 891 <span class="s">}</span> + 892 <span class="k">push</span> <span class="i">@SpecifiedVectorComparisonModes</span><span class="cm">,</span> <span class="i">$SpecifiedFormulism</span><span class="sc">;</span> + 893 <span class="s">}</span> + 894 <span class="s">}</span> + 895 <span class="i">$OptionsInfo</span>{<span class="w">VectorComparisonFormulism</span>} = <span class="i">$Options</span>{<span class="w">vectorcomparisonformulism</span>}<span class="sc">;</span> + 896 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedVectorComparisonModesRef</span>} = \<span class="i">@SpecifiedVectorComparisonModes</span><span class="sc">;</span> + 897 + 898 <span class="c"># Setup any parameters required for specified comparison menthod...</span> + 899 <span class="k">for</span> <span class="i">$SpecifiedMeasure</span> <span class="s">(</span><span class="i">@SpecifiedComparisonMeasures</span><span class="s">)</span> <span class="s">{</span> + 900 <span class="i">@</span>{<span class="i">$SpecifiedComparisonMeasuresParameterMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedMeasure</span><span class="s">)</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 901 <span class="k">push</span> <span class="i">@</span>{<span class="i">$SpecifiedComparisonMeasuresParameterMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedMeasure</span><span class="s">)</span>}}<span class="cm">,</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">fast</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span> + 902 <span class="s">}</span> + 903 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedVectorComparisonsParameterRef</span>} = \<span class="i">%SpecifiedComparisonMeasuresParameterMap</span><span class="sc">;</span> + 904 <span class="s">}</span> + 905 + 906 <span class="c"># Setup script usage and retrieve command line arguments specified using various options...</span> +<a name="SetupScriptUsage-"></a> 907 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span> + 908 + 909 <span class="c"># Retrieve all the options...</span> + 910 <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 911 + 912 <span class="i">$Options</span>{<span class="w">alpha</span>} = <span class="n">0.5</span><span class="sc">;</span> + 913 <span class="i">$Options</span>{<span class="w">beta</span>} = <span class="n">1</span><span class="sc">;</span> + 914 + 915 <span class="i">$Options</span>{<span class="w">bitvectorcomparisonmode</span>} = <span class="q">"TanimotoSimilarity"</span><span class="sc">;</span> + 916 + 917 <span class="i">$Options</span>{<span class="w">colmode</span>} = <span class="q">'colnum'</span><span class="sc">;</span> + 918 + 919 <span class="i">$Options</span>{<span class="w">compoundidprefix</span>} = <span class="q">'Cmpd'</span><span class="sc">;</span> + 920 <span class="i">$Options</span>{<span class="w">compoundidmode</span>} = <span class="q">'LabelPrefix'</span><span class="sc">;</span> + 921 + 922 <span class="i">$Options</span>{<span class="w">detail</span>} = <span class="n">1</span><span class="sc">;</span> + 923 + 924 <span class="i">$Options</span>{<span class="w">indelim</span>} = <span class="q">'comma'</span><span class="sc">;</span> + 925 <span class="i">$Options</span>{<span class="w">outdelim</span>} = <span class="q">'comma'</span><span class="sc">;</span> + 926 + 927 <span class="i">$Options</span>{<span class="w">inputdatamode</span>} = <span class="q">'LoadInMemory'</span><span class="sc">;</span> + 928 + 929 <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">'AutoDetect'</span><span class="sc">;</span> + 930 + 931 <span class="i">$Options</span>{<span class="w">outmatrixformat</span>} = <span class="q">'RowsAndColumns'</span><span class="sc">;</span> + 932 + 933 <span class="i">$Options</span>{<span class="w">outmatrixtype</span>} = <span class="q">'FullMatrix'</span><span class="sc">;</span> + 934 + 935 <span class="i">$Options</span>{<span class="w">quote</span>} = <span class="q">'yes'</span><span class="sc">;</span> + 936 <span class="i">$Options</span>{<span class="w">precision</span>} = <span class="n">2</span><span class="sc">;</span> + 937 + 938 <span class="i">$Options</span>{<span class="w">vectorcomparisonmode</span>} = <span class="q">"TanimotoSimilarity"</span><span class="sc">;</span> + 939 <span class="i">$Options</span>{<span class="w">vectorcomparisonformulism</span>} = <span class="q">"AlgebraicForm"</span><span class="sc">;</span> + 940 + 941 <span class="k">if</span> <span class="s">(</span>!<span class="i">GetOptions</span><span class="s">(</span>\<span class="i">%Options</span><span class="cm">,</span> <span class="q">"alpha=f"</span><span class="cm">,</span> <span class="q">"beta=f"</span><span class="cm">,</span> <span class="q">"bitvectorcomparisonmode|b=s"</span><span class="cm">,</span> <span class="q">"colmode|c=s"</span><span class="cm">,</span> <span class="q">"compoundidcol=s"</span><span class="cm">,</span> <span class="q">"compoundidprefix=s"</span><span class="cm">,</span> <span class="q">"compoundidfield=s"</span><span class="cm">,</span> <span class="q">"compoundidmode=s"</span><span class="cm">,</span> <span class="q">"detail|d=i"</span><span class="cm">,</span> <span class="q">"fast|f"</span><span class="cm">,</span> <span class="q">"fingerprintscol=s"</span><span class="cm">,</span> <span class="q">"fingerprintsfield=s"</span><span class="cm">,</span> <span class="q">"help|h"</span><span class="cm">,</span> <span class="q">"indelim=s"</span><span class="cm">,</span> <span class="q">"inputdatamode=s"</span><span class="cm">,</span> <span class="q">"mode|m=s"</span><span class="cm">,</span> <span class="q">"outdelim=s"</span><span class="cm">,</span> <span class="q">"overwrite|o"</span><span class="cm">,</span> <span class="q">"outmatrixformat=s"</span><span class="cm">,</span> <span class="q">"outmatrixtype=s"</span><span class="cm">,</span> <span class="q">"precision|p=s"</span><span class="cm">,</span> <span class="q">"quote|q=s"</span><span class="cm">,</span> <span class="q">"root|r=s"</span><span class="cm">,</span> <span class="q">"vectorcomparisonmode|v=s"</span><span class="cm">,</span> <span class="q">"vectorcomparisonformulism=s"</span><span class="cm">,</span> <span class="q">"workingdir|w=s"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 942 <span class="k">die</span> <span class="q">"\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n"</span><span class="sc">;</span> + 943 <span class="s">}</span> + 944 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span> + 945 <span class="k">if</span> <span class="s">(</span>! <span class="k">-d</span> <span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span> + 946 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"</span><span class="sc">;</span> + 947 <span class="s">}</span> + 948 <span class="k">chdir</span> <span class="i">$Options</span>{<span class="w">workingdir</span>} <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't chdir $Options{workingdir}: $! \n"</span><span class="sc">;</span> + 949 <span class="s">}</span> + 950 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">colmode</span>} !~ <span class="q">/^(ColNum|ColLabel)$/i</span><span class="s">)</span> <span class="s">{</span> + 951 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{colmode}, for option \"-c, --ColMode\" is not valid. Allowed values: ColNum, or ColLabel\n"</span><span class="sc">;</span> + 952 <span class="s">}</span> + 953 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidmode</span>} !~ <span class="q">/^(DataField|MolName|LabelPrefix|MolNameOrLabelPrefix)$/i</span><span class="s">)</span> <span class="s">{</span> + 954 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{compoundidmode}, for option \"--CompoundIDMode\" is not valid. Allowed values: DataField, MolName, LabelPrefix or MolNameOrLabelPrefix\n"</span><span class="sc">;</span> + 955 <span class="s">}</span> + 956 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">detail</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 957 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{detail}, for option \"-d, --detail\" is not valid. Allowed values: > 0 \n"</span><span class="sc">;</span> + 958 <span class="s">}</span> + 959 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">inputdatamode</span>} !~ <span class="q">/^(LoadInMemory|ScanFile)$/i</span><span class="s">)</span> <span class="s">{</span> + 960 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{inputdatamode}, for option \"--InputDataMode\" is not valid. Allowed values: LoadInMemory or ScanFile\n"</span><span class="sc">;</span> + 961 <span class="s">}</span> + 962 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} !~ <span class="q">/^(AutoDetect|FingerprintsBitVectorString|FingerprintsVectorString)$/i</span><span class="s">)</span> <span class="s">{</span> + 963 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{mode}, for option \"-m, --mode\" is not valid. Allowed values: AutoDetect, FingerprintsBitVectorString or FingerprintsVectorString \n"</span><span class="sc">;</span> + 964 <span class="s">}</span> + 965 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">indelim</span>} !~ <span class="q">/^(comma|semicolon)$/i</span><span class="s">)</span> <span class="s">{</span> + 966 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{indelim}, for option \"--InDelim\" is not valid. Allowed values: comma, or semicolon\n"</span><span class="sc">;</span> + 967 <span class="s">}</span> + 968 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} !~ <span class="q">/^(comma|semicolon|tab)$/i</span><span class="s">)</span> <span class="s">{</span> + 969 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{outdelim}, for option \"--OutDelim\" is not valid. Allowed values: comma, tab, or semicolon\n"</span><span class="sc">;</span> + 970 <span class="s">}</span> + 971 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outmatrixformat</span>} !~ <span class="q">/^(RowsAndColumns|IDPairsAndValue)$/i</span><span class="s">)</span> <span class="s">{</span> + 972 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{outmatrixformat}, for option \"--OutMatrixFormat\" is not valid. Allowed values: RowsAndColumns or IDPairsAndValue\n"</span><span class="sc">;</span> + 973 <span class="s">}</span> + 974 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outmatrixtype</span>} !~ <span class="q">/^(FullMatrix|UpperTriangularMatrix|LowerTriangularMatrix)$/i</span><span class="s">)</span> <span class="s">{</span> + 975 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{outmatrixtype}, for option \"--OutMatrixType\" is not valid. Allowed values: FullMatrix, UpperTriangularMatrix or LowerTriangularMatrix\n"</span><span class="sc">;</span> + 976 <span class="s">}</span> + 977 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">quote</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span> + 978 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: Yes or No\n"</span><span class="sc">;</span> + 979 <span class="s">}</span> + 980 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">precision</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 981 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{precision}, for option \"--precision\" is not valid. Allowed values: > 0 \n"</span><span class="sc">;</span> + 982 <span class="s">}</span> + 983 <span class="s">}</span> + 984 +<a name="EOF-"></a></pre> +<p> </p> +<br /> +<center> +<img src="../../../images/h2o2.png"> +</center> +</body> +</html>