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<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>