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+<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">
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+<br/>
+<center>
+<a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a>
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+<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 $</span>
+6 <span class="c">#</span>
+7 <span class="c"># Author: Manish Sud &lt;msud@san.rr.com&gt;</span>
+8 <span class="c">#</span>
+9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
+10 <span class="c">#</span>
+11 <span class="c"># This file is part of MayaChemTools.</span>
+12 <span class="c">#</span>
+13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
+14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
+15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
+16 <span class="c"># later version.</span>
+17 <span class="c">#</span>
+18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
+19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
+20 <span class="c"># for a particular purpose.  See the GNU Lesser General Public License for more</span>
+21 <span class="c"># details.</span>
+22 <span class="c">#</span>
+23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
+24 <span class="c"># along with MayaChemTools; if not, see &lt;http://www.gnu.org/licenses/&gt; or</span>
+25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
+26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
+27 <span class="c">#</span>
+28
+29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
+30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">&quot;$FindBin::Bin/../lib&quot;</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">$0</span><span class="s">)</span><span class="sc">;</span>
+49 <span class="k">print</span> <span class="q">&quot;\n$ScriptName: Starting...\n\n&quot;</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> &lt; <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">&quot;$FindBin::Bin/$ScriptName&quot;</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">&quot;sdf sd fpf fp csv tsv&quot;</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">&quot;Processing options...\n&quot;</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">&quot;Checking input fingerprints file(s)...\n&quot;</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">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
+73 <span class="k">if</span> <span class="s">(</span><span class="i">@FingerprintsFilesList</span> &gt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
+74   <span class="k">print</span> <span class="q">&quot;\nProcessing fingerprints files...\n&quot;</span><span class="sc">;</span>
+75 <span class="s">}</span>
+76 <span class="k">for</span> <span class="i">$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">&quot;\nProcessing file $FingerprintsFilesList[$FileIndex]...\n&quot;</span><span class="sc">;</span>
+79     <span class="i">GenerateSimilarityMatrices</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
+80   <span class="s">}</span>
+81 <span class="s">}</span>
+82 <span class="k">print</span> <span class="q">&quot;\n$ScriptName:Done...\n\n&quot;</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">&quot;Total time: &quot;</span><span class="cm">,</span> <span class="i">timestr</span><span class="s">(</span><span class="i">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+87
+88 <span class="c">###############################################################################</span>
+89
+90 <span class="c"># Generate similarity matrices using fingerprints data in text file...</span>
+91 <span class="c">#</span>
+<a name="GenerateSimilarityMatrices-"></a>  92 <span class="k">sub </span><span class="m">GenerateSimilarityMatrices</span> <span class="s">{</span>
+93   <span class="k">my</span><span class="s">(</span><span class="i">$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>}-&gt;{<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">&quot;${ComparisonMeasure}.&quot;</span> . <span class="i">$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">$OptionsInfo</span>{<span class="w">SpecifiedBitVectorComparisonsMethodRef</span>}-&gt;{<span class="k">lc</span><span class="s">(</span><span class="i">$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">$OptionsInfo</span>{<span class="w">SpecifiedBitVectorComparisonsParameterRef</span>}-&gt;{<span class="k">lc</span><span class="s">(</span><span class="i">$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">$OptionsInfo</span>{<span class="w">SpecifiedVectorComparisonsNameRef</span>}-&gt;{<span class="k">lc</span><span class="s">(</span><span class="i">$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">$FileIndex</span>] . <span class="q">&quot;${ComparisonMeasure}${ComparisonMode}.&quot;</span> . <span class="i">$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">$OptionsInfo</span>{<span class="w">SpecifiedVectorComparisonsMethodRef</span>}-&gt;{<span class="k">lc</span><span class="s">(</span><span class="i">$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>}-&gt;{<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">&quot;\nGenerating $NewTextFile...\n&quot;</span><span class="sc">;</span>
+155
+156   <span class="c"># Open new file and write out column labels...</span>
+157   <span class="k">open</span> <span class="w">NEWTEXTFILE</span><span class="cm">,</span> <span class="q">&quot;&gt;$NewTextFile&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Can&#39;t open $NewTextFile: $! \n&quot;</span><span class="sc">;</span>
+158   <span class="i">WriteColumnLabels</span><span class="s">(</span><span class="i">$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">&quot;Warning: Input data mode, $OptionsInfo{InputDataMode}, is not supported.\n&quot;</span><span class="sc">;</span>
+169   <span class="s">}</span>
+170
+171   <span class="c"># Close new text file...</span>
+172   <span class="k">close</span> <span class="w">NEWTEXTFILE</span><span class="sc">;</span>
+173
+174 <span class="s">}</span>
+175
+176 <span class="c"># Calculate and write out similarity values using fingerprints data already loaded in</span>
+177 <span class="c"># memory...</span>
+178 <span class="c">#</span>
+<a name="GenerateSimilarityMatrixUsingMemoryData-"></a> 179 <span class="k">sub </span><span class="m">GenerateSimilarityMatrixUsingMemoryData</span> <span class="s">{</span>
+180   <span class="k">my</span><span class="s">(</span><span class="i">$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>}-&gt;[<span class="i">$RowIndex</span>]<span class="sc">;</span>
+185     <span class="i">$CmpdID1</span> = <span class="i">$FingerprintsFilesInfo</span>{<span class="w">CompundIDsRef</span>}-&gt;[<span class="i">$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">&quot;$OptionsInfo{OutQuoteValue}${CmpdID1}$OptionsInfo{OutQuoteValue}&quot;</span><span class="sc">;</span>
+189     <span class="s">}</span>
+190
+191     <span class="j">COLINDEX:</span> <span class="k">for</span> <span class="i">$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>}-&gt;[<span class="i">$ColIndex</span>]<span class="sc">;</span>
+197
+198       <span class="i">$Value</span> = <span class="i">$FingerprintsObject1</span><span class="i">-&gt;$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> &amp;&amp; <span class="k">length</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> ? <span class="s">(</span><span class="k">sprintf</span><span class="s">(</span><span class="q">&quot;%.$OptionsInfo{Precision}f&quot;</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> + <span class="n">0</span><span class="s">)</span> <span class="co">:</span> <span class="q">&#39;&#39;</span><span class="sc">;</span>
+200
+201       <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">WriteRowsAndColumns</span>}<span class="s">)</span> <span class="s">{</span>
+202         <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="q">&quot;$OptionsInfo{OutDelim}$OptionsInfo{OutQuoteValue}${Value}$OptionsInfo{OutQuoteValue}&quot;</span><span class="sc">;</span>
+203       <span class="s">}</span>
+204       <span class="k">elsif</span> <span class="s">(</span><span class="i">$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>}-&gt;[<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">&quot;$Line\n&quot;</span><span class="sc">;</span>
+211       <span class="s">}</span>
+212     <span class="s">}</span>
+213     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">WriteRowsAndColumns</span>}<span class="s">)</span> <span class="s">{</span>
+214       <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+215     <span class="s">}</span>
+216   <span class="s">}</span>
+217 <span class="s">}</span>
+218
+219 <span class="c"># Calculate and write out similarity values by retrieving and prcessing data</span>
+220 <span class="c"># from fingerprint file...</span>
+221 <span class="c">#</span>
+<a name="GenerateSimilarityMatrixUsingFileData-"></a> 222 <span class="k">sub </span><span class="m">GenerateSimilarityMatrixUsingFileData</span> <span class="s">{</span>
+223   <span class="k">my</span><span class="s">(</span><span class="i">$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">$Line</span><span class="cm">,</span> <span class="i">@LineWords</span><span class="s">)</span><span class="sc">;</span>
+225
+226   <span class="k">print</span> <span class="q">&quot;\nReading and processing fingerprints data...\n&quot;</span><span class="sc">;</span>
+227
+228   <span class="i">$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">$FingerprintsFileIO</span><span class="i">-&gt;Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+230
+231   <span class="i">$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">-&gt;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">-&gt;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">-&gt;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">-&gt;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">&quot;$OptionsInfo{OutQuoteValue}${CmpdID1}$OptionsInfo{OutQuoteValue}&quot;</span><span class="sc">;</span>
+247     <span class="s">}</span>
+248
+249     <span class="c"># Force detail level of 1 to avoid duplicate printing of diagnostic messages for invalid</span>
+250     <span class="c"># fingerprints data...</span>
+251     <span class="i">$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">&quot;DetailLevel&quot;</span> <span class="cm">=&gt;</span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span>
+252     <span class="i">$TmpFingerprintsFileIO</span><span class="i">-&gt;Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+253
+254     <span class="i">$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">$TmpFingerprintsFileIO</span><span class="i">-&gt;Read</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+256       <span class="k">if</span> <span class="s">(</span>!<span class="i">$TmpFingerprintsFileIO</span><span class="i">-&gt;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">$TmpFingerprintsFileIO</span><span class="i">-&gt;GetFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+266
+267       <span class="i">$Value</span> = <span class="i">$FingerprintsObject1</span><span class="i">-&gt;$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> &amp;&amp; <span class="k">length</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> ? <span class="s">(</span><span class="k">sprintf</span><span class="s">(</span><span class="q">&quot;%.$OptionsInfo{Precision}f&quot;</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> + <span class="n">0</span><span class="s">)</span> <span class="co">:</span> <span class="q">&#39;&#39;</span><span class="sc">;</span>
+269
+270       <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">WriteRowsAndColumns</span>}<span class="s">)</span> <span class="s">{</span>
+271         <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="q">&quot;$OptionsInfo{OutDelim}$OptionsInfo{OutQuoteValue}${Value}$OptionsInfo{OutQuoteValue}&quot;</span><span class="sc">;</span>
+272       <span class="s">}</span>
+273       <span class="k">elsif</span> <span class="s">(</span><span class="i">$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">-&gt;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">$NewTextFileRef</span> <span class="q">&quot;$Line\n&quot;</span><span class="sc">;</span>
+280       <span class="s">}</span>
+281     <span class="s">}</span>
+282     <span class="i">$TmpFingerprintsFileIO</span><span class="i">-&gt;Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+283
+284     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">WriteRowsAndColumns</span>}<span class="s">)</span> <span class="s">{</span>
+285       <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+286     <span class="s">}</span>
+287   <span class="s">}</span>
+288
+289   <span class="i">$FingerprintsFileIO</span><span class="i">-&gt;Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+290
+291   <span class="k">print</span> <span class="q">&quot;Number of fingerprints data entries in database fingerprints file: $FingerprintsCount\n&quot;</span><span class="sc">;</span>
+292   <span class="k">print</span> <span class="q">&quot;Number of fingerprints date entries processed successfully: &quot;</span><span class="cm">,</span> <span class="s">(</span><span class="i">$FingerprintsCount</span> - <span class="i">$IgnoredFingerprintsCount</span><span class="s">)</span>  <span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+293   <span class="k">print</span> <span class="q">&quot;Number of fingerprints data entries ignored due to missing/invalid data: $IgnoredFingerprintsCount\n\n&quot;</span><span class="sc">;</span>
+294 <span class="s">}</span>
+295
+296 <span class="c"># Check whether matrix data need to be skipped...</span>
+297 <span class="c">#</span>
+<a name="SkipMatrixData-"></a> 298 <span class="k">sub </span><span class="m">SkipMatrixData</span> <span class="s">{</span>
+299   <span class="k">my</span><span class="s">(</span><span class="i">$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> &gt; <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">$RowIndex</span> &lt; <span class="i">$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$/i</span><span class="s">)</span> <span class="s">{</span>
+321     <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+322     <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="s">(</span><span class="q">&#39;CmpdID1&#39;</span><span class="cm">,</span> <span class="q">&#39;CmpdID2&#39;</span><span class="cm">,</span> <span class="q">&#39;Coefficient Value&#39;</span><span class="s">)</span><span class="sc">;</span>
+323     <span class="i">$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">$NewTextFileRef</span> <span class="q">&quot;$Line\n&quot;</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">&#39;&#39;</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">$NewTextFileRef</span> <span class="q">&quot;$Line\n&quot;</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">&quot;\nProcessing fingerprints file to generate compound IDs...\n&quot;</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">$FileIndex</span>]}<span class="cm">,</span> <span class="q">&quot;DetailLevel&quot;</span> <span class="cm">=&gt;</span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span>
+345       <span class="i">$FingerprintsFileIO</span><span class="i">-&gt;Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+346
+347       <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="q">&quot;$OptionsInfo{OutQuoteValue}$OptionsInfo{OutQuoteValue}&quot;</span><span class="sc">;</span>
+348
+349       <span class="j">FINGERPRINTSFILEIO:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$FingerprintsFileIO</span><span class="i">-&gt;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">$FingerprintsFileIO</span><span class="i">-&gt;IsFingerprintsDataValid</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+351           <span class="k">next</span> <span class="j">FINGERPRINTSFILEIO</span><span class="sc">;</span>
+352         <span class="s">}</span>
+353         <span class="i">$CmpdID</span> = <span class="i">$FingerprintsFileIO</span><span class="i">-&gt;GetCompoundID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+354         <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="q">&quot;$OptionsInfo{OutDelim}$OptionsInfo{OutQuoteValue}${CmpdID}$OptionsInfo{OutQuoteValue}&quot;</span><span class="sc">;</span>
+355       <span class="s">}</span>
+356       <span class="i">$FingerprintsFileIO</span><span class="i">-&gt;Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+357
+358       <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+359
+360       <span class="k">print</span> <span class="q">&quot;Processing fingerprints file to generate matrix...\n&quot;</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">&quot;Warning: Output matrix format, $OptionsInfo{OutMatrixFormat}, is not supported.\n&quot;</span><span class="sc">;</span>
+365   <span class="s">}</span>
+366 <span class="s">}</span>
+367
+368 <span class="c"># Process fingerprints data...</span>
+369 <span class="c">#</span>
+<a name="ProcessFingerprintsData-"></a> 370 <span class="k">sub </span><span class="m">ProcessFingerprintsData</span> <span class="s">{</span>
+371   <span class="k">my</span><span class="s">(</span><span class="i">$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">&quot;\nCopying fingerprints file, $FingerprintsFile, to temporary fingperints file, $TmpFingerprintsFile...\n&quot;</span><span class="sc">;</span>
+391     <span class="w">copy</span> <span class="i">$FingerprintsFile</span><span class="cm">,</span> <span class="i">$TmpFingerprintsFile</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Couldn&#39;t copy $FingerprintsFile to $TmpFingerprintsFile: $! \n&quot;</span><span class="sc">;</span>
+392   <span class="s">}</span>
+393 <span class="s">}</span>
+394
+395 <span class="c"># Clean up fingerprints data...</span>
+396 <span class="c">#</span>
+<a name="CleanupFingerprintsData-"></a> 397 <span class="k">sub </span><span class="m">CleanupFingerprintsData</span> <span class="s">{</span>
+398   <span class="k">my</span><span class="s">(</span><span class="i">$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">&quot;\nDeleting temporary fingerprints file $TmpFingerprintsFile...\n&quot;</span><span class="sc">;</span>
+411     <span class="k">unlink</span> <span class="i">$TmpFingerprintsFile</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Couldn&#39;t unlink $TmpFingerprintsFile: $! \n&quot;</span><span class="sc">;</span>
+412   <span class="s">}</span>
+413 <span class="s">}</span>
+414
+415 <span class="c"># Retrieve information about fingerprints files...</span>
+416 <span class="c">#</span>
+<a name="RetrieveFingerprintsFilesInfo-"></a> 417 <span class="k">sub </span><span class="m">RetrieveFingerprintsFilesInfo</span> <span class="s">{</span>
+418   <span class="k">my</span><span class="s">(</span><span class="i">$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">&#39;&#39;</span><span class="sc">;</span>
+438     <span class="i">$FingerprintsFilesInfo</span>{<span class="w">InDelim</span>}[<span class="i">$Index</span>] = <span class="q">&quot;&quot;</span><span class="sc">;</span>
+439     <span class="i">$FingerprintsFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+440     <span class="i">$FingerprintsFilesInfo</span>{<span class="w">OutFileExt</span>}[<span class="i">$Index</span>] = <span class="q">&#39;&#39;</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">&quot;&quot;</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">&quot;Warning: Ignoring file $FingerprintsFile: It doesn&#39;t exist\n&quot;</span><span class="sc">;</span>
+453       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+454     <span class="s">}</span>
+455
+456     <span class="i">$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">&quot;Warning: Ignoring file $FingerprintsFile: It&#39;s not a fingerprints file\n&quot;</span><span class="sc">;</span>
+459       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+460     <span class="s">}</span>
+461
+462     <span class="i">$FileDir</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span> <span class="i">$FileName</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span> <span class="i">$FileExt</span> = <span class="q">&quot;&quot;</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">$TmpFingerprintsFile</span> = <span class="q">&quot;${FileName}Tmp.${FileExt}&quot;</span><span class="sc">;</span>
+467
+468     <span class="i">$InDelim</span> = <span class="s">(</span><span class="i">$FileExt</span> =~ <span class="q">/^tsv$/i</span><span class="s">)</span> ? <span class="q">&#39;Tab&#39;</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">&quot;csv&quot;</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">$OutFileExt</span> = <span class="q">&quot;tsv&quot;</span><span class="sc">;</span>
+474     <span class="s">}</span>
+475
+476     <span class="i">$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>} &amp;&amp; <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">$RootFileName</span> &amp;&amp; <span class="i">$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">$OptionsInfo</span>{<span class="w">SpecifiedBitVectorComparisonsNameRef</span>}-&gt;{<span class="k">lc</span><span class="s">(</span><span class="i">$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">&quot;${OutFileRoot}${ComparisonMeasure}.${OutFileExt}&quot;</span><span class="s">)</span> <span class="s">{</span>
+494           <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $FingerprintsFile: The file ${OutFileRoot}${ComparisonMeasure}.${OutFileExt} already exists.\n&quot;</span><span class="sc">;</span>
+495           <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+496         <span class="s">}</span>
+497       <span class="s">}</span>
+498       <span class="c"># Similarity matrices output file names for vector strings...</span>
+499       <span class="k">my</span><span class="s">(</span><span class="i">$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>}-&gt;{<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">$OptionsInfo</span>{<span class="w">SpecifiedVectorComparisonModesRef</span>}}<span class="s">)</span> <span class="s">{</span>
+503           <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="q">&quot;${OutFileRoot}${ComparisonMeasure}${ComparisonMode}.${OutFileExt}&quot;</span><span class="s">)</span> <span class="s">{</span>
+504             <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $FingerprintsFile: The file ${OutFileRoot}${ComparisonMeasure}${ComparisonMode}.${OutFileExt} already exists.\n&quot;</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">&#39;Name&#39;</span> <span class="cm">=&gt;</span> <span class="i">$FingerprintsFile</span><span class="cm">,</span> <span class="q">&#39;Mode&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;Read&#39;</span><span class="cm">,</span> <span class="q">&#39;FingerprintsStringMode&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>}<span class="cm">,</span> <span class="q">&#39;ValidateData&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">ValidateData</span>}<span class="cm">,</span> <span class="q">&#39;DetailLevel&#39;</span> <span class="cm">=&gt;</span>  <span class="i">$OptionsInfo</span>{<span class="w">Detail</span>}<span class="cm">,</span> <span class="q">&#39;FingerprintsFieldLabel&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsField</span>}<span class="cm">,</span> <span class="q">&#39;CompoundIDMode&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>}<span class="cm">,</span> <span class="q">&#39;CompoundIDFieldLabel&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDField</span>}<span class="cm">,</span> <span class="q">&#39;CompoundIDPrefix&#39;</span> <span class="cm">=&gt;</span> <span class="i">$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">&#39;Name&#39;</span> <span class="cm">=&gt;</span> <span class="i">$FingerprintsFile</span><span class="cm">,</span> <span class="q">&#39;Mode&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;Read&#39;</span><span class="cm">,</span> <span class="q">&#39;FingerprintsStringMode&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>}<span class="cm">,</span> <span class="q">&#39;ValidateData&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">ValidateData</span>}<span class="cm">,</span> <span class="q">&#39;DetailLevel&#39;</span> <span class="cm">=&gt;</span>  <span class="i">$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">&#39;Name&#39;</span> <span class="cm">=&gt;</span> <span class="i">$FingerprintsFile</span><span class="cm">,</span> <span class="q">&#39;Mode&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;Read&#39;</span><span class="cm">,</span> <span class="q">&#39;FingerprintsStringMode&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>}<span class="cm">,</span> <span class="q">&#39;ValidateData&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">ValidateData</span>}<span class="cm">,</span> <span class="q">&#39;DetailLevel&#39;</span> <span class="cm">=&gt;</span>  <span class="i">$OptionsInfo</span>{<span class="w">Detail</span>}<span class="cm">,</span> <span class="q">&#39;FingerprintsCol&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsCol</span>}<span class="cm">,</span> <span class="q">&#39;ColMode&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">ColMode</span>}<span class="cm">,</span> <span class="q">&#39;CompoundIDCol&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDCol</span>}<span class="cm">,</span> <span class="q">&#39;CompoundIDPrefix&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDPrefix</span>}<span class="cm">,</span> <span class="q">&#39;InDelim&#39;</span> <span class="cm">=&gt;</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">&quot;Warning: File type for fingerprints file, $FingerprintsFile, is not valid. Supported file types: SD, FP or Text\n&quot;</span><span class="sc">;</span>
+527       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+528     <span class="s">}</span>
+529
+530     <span class="c"># Retrieve fingerints file string mode information...</span>
+531     <span class="i">$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">&quot;Warning: Ignoring fingerprints file $FingerprintsFile: It contains invalid fingerprints data\n&quot;</span><span class="sc">;</span>
+535       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+536     <span class="s">}</span>
+537     <span class="k">if</span> <span class="s">(</span>!<span class="i">$FingerprintsFileIO</span><span class="i">-&gt;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">&quot;Warning: Ignoring fingerprints file $FingerprintsFile: It contains invalid fingerprints data\n&quot;</span><span class="sc">;</span>
+539       <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
+540     <span class="s">}</span>
+541     <span class="i">$FingerprintsBitVectorStringMode</span> = <span class="i">$FingerprintsFileIO</span><span class="i">-&gt;GetFingerprintsBitVectorStringMode</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+542     <span class="i">$FingerprintsVectorStringMode</span> = <span class="i">$FingerprintsFileIO</span><span class="i">-&gt;GetFingerprintsVectorStringMode</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+543
+544
+545     <span class="i">$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">$Options</span>{<span class="w">compoundidprefix</span>} <span class="co">:</span> <span class="q">&#39;Cmpd&#39;</span><span class="sc">;</span>
+577
+578   <span class="c"># Compound ID and fingerprints column options for text files...</span>
+579   <span class="i">$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">&quot;Error: Column value, $Options{compoundidcol}, specified using \&quot;--CompoundIDCol\&quot; is not valid: Allowed integer values: &gt; 0\n&quot;</span><span class="sc">;</span>
+585       <span class="s">}</span>
+586     <span class="s">}</span>
+587     <span class="i">$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">&#39;AutoDetect&#39;</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">&quot;Error: Column value, $Options{fingerprintscol}, specified using \&quot;--FingerprintsCol\&quot; is not valid: Allowed integer values: &gt; 0\n&quot;</span><span class="sc">;</span>
+597       <span class="s">}</span>
+598     <span class="s">}</span>
+599     <span class="i">$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">&#39;AutoDetect&#39;</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">$Options</span>{<span class="w">compoundidcol</span>}<span class="s">)</span> &amp;&amp; <span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$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">$Options</span>{<span class="w">compoundidcol</span>}<span class="s">)</span> &amp;&amp; <span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$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">&quot;Error: Values specified using \&quot;--CompoundIDCol\&quot; and \&quot;--FingerprintsCol\&quot;, $Options{compoundidcol}, must be different.\n&quot;</span><span class="sc">;</span>
+609       <span class="s">}</span>
+610     <span class="s">}</span>
+611     <span class="k">else</span> <span class="s">{</span>
+612       <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">$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">&quot;Error: Values specified using \&quot;--CompoundIDCol\&quot; and \&quot;--FingerprintsCol\&quot;, $Options{compoundidcol}, must be different.\n&quot;</span><span class="sc">;</span>
+614       <span class="s">}</span>
+615     <span class="s">}</span>
+616   <span class="s">}</span>
+617
+618   <span class="c"># Compound ID and fingerprints field options for SD files...</span>
+619   <span class="i">$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">&#39;&#39;</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">$Options</span>{<span class="w">compoundidfield</span>}<span class="s">)</span> <span class="s">{</span>
+624       <span class="k">die</span> <span class="q">&quot;Error: You must specify a value for \&quot;--CompoundIDField\&quot; option in \&quot;DataField\&quot; \&quot;--CompoundIDMode\&quot;. \n&quot;</span><span class="sc">;</span>
+625     <span class="s">}</span>
+626     <span class="i">$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">$OptionsInfo</span>{<span class="w">FingerprintsField</span>} = <span class="q">&#39;AutoDetect&#39;</span><span class="sc">;</span>
+635   <span class="s">}</span>
+636
+637   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidfield</span>} &amp;&amp; <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">&quot;Error: Values specified using \&quot;--CompoundIDField\&quot; and \&quot;--Fingerprintsfield\&quot;, $Options{compoundidfield}, must be different.\n&quot;</span><span class="sc">;</span>
+640     <span class="s">}</span>
+641   <span class="s">}</span>
+642
+643   <span class="i">$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">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/tab/i</span> <span class="s">)</span> ? <span class="q">&quot;\t&quot;</span> <span class="co">:</span> <span class="s">(</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/semicolon/i</span><span class="s">)</span> ? <span class="q">&quot;\;&quot;</span> <span class="co">:</span> <span class="q">&quot;\,&quot;</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">&#39;&quot;&#39;</span> <span class="co">:</span> <span class="q">&#39;&#39;</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">&quot;Error: The value specified, $Options{outmatrixformat}, for option \&quot;--OutMatrixFormat\&quot; is not valid. Allowed values: RowsAndColumns or IDPairsAndValue\n&quot;</span><span class="sc">;</span>
+661   <span class="s">}</span>
+662
+663   <span class="i">$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">&quot;Error: The value specified, $Options{outmatrixtype}, for option \&quot;--OutMatrixType\&quot; is not valid. Allowed values: FullMatrix, UpperTriangularMatrix or LowerTriangularMatrix\n&quot;</span><span class="sc">;</span>
+678   <span class="s">}</span>
+679
+680   <span class="i">$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">$SupportedComparisonMeasure</span> <span class="s">(</span><span class="i">Fingerprints::FingerprintsBitVector::GetSupportedSimilarityCoefficients</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+701     <span class="c"># Similarity coefficient function/method names contain &quot;Coefficient&quot; in their names.</span>
+702     <span class="c"># So take &#39;em out and setup a map to original function/method name...</span>
+703     <span class="i">$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">$BitVectorComparisonMode</span> =~ <span class="q">s/ //g</span><span class="sc">;</span>
+728     <span class="i">@SpecifiedMeasures</span> = <span class="k">split</span> <span class="q">&quot;,&quot;</span><span class="cm">,</span> <span class="i">$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">$SpecifiedMeasure</span><span class="sc">;</span>
+737       <span class="s">}</span>
+738     <span class="s">}</span>
+739     <span class="k">if</span> <span class="s">(</span><span class="i">@UnsupportedSpecifiedMeasures</span><span class="s">)</span> <span class="s">{</span>
+740       <span class="k">if</span> <span class="s">(</span><span class="i">@UnsupportedSpecifiedMeasures</span> &gt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
+741         <span class="k">warn</span> <span class="q">&quot;Error: The values specified - &quot;</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@UnsupportedSpecifiedMeasures</span><span class="cm">,</span> <span class="q">&quot;, &quot;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span><span class="q">&quot; - for option \&quot;-b --BitVectorComparisonMode\&quot; are not valid.\n&quot;</span><span class="sc">;</span>
+742       <span class="s">}</span>
+743       <span class="k">else</span> <span class="s">{</span>
+744         <span class="k">warn</span> <span class="q">&quot;Error: The value specified, @UnsupportedSpecifiedMeasures, for option \&quot;-b --BitVectorComparisonMode\&quot; is not valid.\n&quot;</span><span class="sc">;</span>
+745       <span class="s">}</span>
+746       <span class="k">die</span> <span class="q">&quot;Allowed values:&quot;</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@SupportedComparisonMeasures</span><span class="cm">,</span> <span class="q">&quot;, &quot;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+747     <span class="s">}</span>
+748   <span class="s">}</span>
+749   <span class="k">for</span> <span class="i">$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">&#39;&#39;</span><span class="sc">;</span>
+762   <span class="i">$SpecifiedMeasure1</span> = <span class="q">&#39;TverskySimilarity&#39;</span><span class="sc">;</span>
+763   <span class="i">$SpecifiedMeasure2</span> = <span class="q">&#39;WeightedTverskySimilarity&#39;</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">$Options</span>{<span class="w">alpha</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+766       <span class="k">die</span> <span class="q">&quot;Error: You must specify a value for \&quot;-a, --alpha\&quot; option in \&quot;$SpecifiedMeasure1, $SpecifiedMeasure2, or All\&quot; \&quot;-m --mode\&quot;. \n&quot;</span><span class="sc">;</span>
+767     <span class="s">}</span>
+768     <span class="k">my</span><span class="s">(</span><span class="i">$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">$Alpha</span><span class="s">)</span> &amp;&amp; <span class="i">$Alpha</span> &gt;=<span class="n">0</span> &amp;&amp; <span class="i">$Alpha</span> &lt;= <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+771       <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{alpha}, for option \&quot;-a, --alpha\&quot; is not valid. Allowed values: &gt;= 0 and &lt;= 1\n&quot;</span><span class="sc">;</span>
+772     <span class="s">}</span>
+773     <span class="i">$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">&#39;&#39;</span><span class="sc">;</span>
+779   <span class="i">$SpecifiedMeasure1</span> = <span class="q">&#39;WeightedTverskySimilarity&#39;</span><span class="sc">;</span>
+780   <span class="i">$SpecifiedMeasure2</span> = <span class="q">&#39;WeightedTanimotoSimilarity&#39;</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">$Options</span>{<span class="w">beta</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+783       <span class="k">die</span> <span class="q">&quot;Error: You must specify a value for \&quot;-b, --beta\&quot; option in \&quot;$SpecifiedMeasure1, $SpecifiedMeasure2, or All\&quot; \&quot;-m --mode\&quot;. \n&quot;</span><span class="sc">;</span>
+784     <span class="s">}</span>
+785     <span class="k">my</span><span class="s">(</span><span class="i">$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">$Beta</span><span class="s">)</span> &amp;&amp; <span class="i">$Beta</span> &gt;=<span class="n">0</span> &amp;&amp; <span class="i">$Beta</span> &lt;= <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+788       <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{beta}, for option \&quot;-b, --beta\&quot; is not valid. Allowed values: &gt;= 0 and &lt;= 1\n&quot;</span><span class="sc">;</span>
+789     <span class="s">}</span>
+790     <span class="i">$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 &quot;Coefficient&quot; in their names.</span>
+821     <span class="c"># So take &#39;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">&quot;,&quot;</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> &gt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
+860         <span class="k">warn</span> <span class="q">&quot;Error: The values specified - &quot;</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">&quot;, &quot;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span><span class="q">&quot; - for option \&quot;-v --VectorComparisonMode\&quot; are not valid.\n&quot;</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">&quot;Error: The value specified, @UnsupportedSpecifiedMeasures, for option \&quot;-v --VectorComparisonMode\&quot; is not valid.\n&quot;</span><span class="sc">;</span>
+864       <span class="s">}</span>
+865       <span class="k">die</span> <span class="q">&quot;Allowed values:&quot;</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">&quot;, &quot;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</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">&quot;AlgebraicForm&quot;</span><span class="cm">,</span> <span class="q">&quot;BinaryForm&quot;</span><span class="cm">,</span> <span class="q">&quot;SetTheoreticForm&quot;</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">&quot;Error: The value specified, $SpecifiedFormulism, for option \&quot;--VectorComparisonFormulism\&quot; is not valid. Allowed values: AlgebraicForm, BinaryForm or SetTheoreticForm\n&quot;</span><span class="sc">;</span>
+891       <span class="s">}</span>
+892       <span class="k">push</span> <span class="i">@SpecifiedVectorComparisonModes</span><span class="cm">,</span> <span class="i">$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">$Options</span>{<span class="w">bitvectorcomparisonmode</span>} = <span class="q">&quot;TanimotoSimilarity&quot;</span><span class="sc">;</span>
+916
+917   <span class="i">$Options</span>{<span class="w">colmode</span>} = <span class="q">&#39;colnum&#39;</span><span class="sc">;</span>
+918
+919   <span class="i">$Options</span>{<span class="w">compoundidprefix</span>} = <span class="q">&#39;Cmpd&#39;</span><span class="sc">;</span>
+920   <span class="i">$Options</span>{<span class="w">compoundidmode</span>} = <span class="q">&#39;LabelPrefix&#39;</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">&#39;comma&#39;</span><span class="sc">;</span>
+925   <span class="i">$Options</span>{<span class="w">outdelim</span>} = <span class="q">&#39;comma&#39;</span><span class="sc">;</span>
+926
+927   <span class="i">$Options</span>{<span class="w">inputdatamode</span>} = <span class="q">&#39;LoadInMemory&#39;</span><span class="sc">;</span>
+928
+929   <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">&#39;AutoDetect&#39;</span><span class="sc">;</span>
+930
+931   <span class="i">$Options</span>{<span class="w">outmatrixformat</span>} = <span class="q">&#39;RowsAndColumns&#39;</span><span class="sc">;</span>
+932
+933   <span class="i">$Options</span>{<span class="w">outmatrixtype</span>} = <span class="q">&#39;FullMatrix&#39;</span><span class="sc">;</span>
+934
+935   <span class="i">$Options</span>{<span class="w">quote</span>} = <span class="q">&#39;yes&#39;</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">&quot;TanimotoSimilarity&quot;</span><span class="sc">;</span>
+939   <span class="i">$Options</span>{<span class="w">vectorcomparisonformulism</span>} = <span class="q">&quot;AlgebraicForm&quot;</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">&quot;alpha=f&quot;</span><span class="cm">,</span> <span class="q">&quot;beta=f&quot;</span><span class="cm">,</span> <span class="q">&quot;bitvectorcomparisonmode|b=s&quot;</span><span class="cm">,</span> <span class="q">&quot;colmode|c=s&quot;</span><span class="cm">,</span> <span class="q">&quot;compoundidcol=s&quot;</span><span class="cm">,</span> <span class="q">&quot;compoundidprefix=s&quot;</span><span class="cm">,</span> <span class="q">&quot;compoundidfield=s&quot;</span><span class="cm">,</span> <span class="q">&quot;compoundidmode=s&quot;</span><span class="cm">,</span> <span class="q">&quot;detail|d=i&quot;</span><span class="cm">,</span> <span class="q">&quot;fast|f&quot;</span><span class="cm">,</span> <span class="q">&quot;fingerprintscol=s&quot;</span><span class="cm">,</span> <span class="q">&quot;fingerprintsfield=s&quot;</span><span class="cm">,</span> <span class="q">&quot;help|h&quot;</span><span class="cm">,</span> <span class="q">&quot;indelim=s&quot;</span><span class="cm">,</span> <span class="q">&quot;inputdatamode=s&quot;</span><span class="cm">,</span> <span class="q">&quot;mode|m=s&quot;</span><span class="cm">,</span> <span class="q">&quot;outdelim=s&quot;</span><span class="cm">,</span> <span class="q">&quot;overwrite|o&quot;</span><span class="cm">,</span> <span class="q">&quot;outmatrixformat=s&quot;</span><span class="cm">,</span> <span class="q">&quot;outmatrixtype=s&quot;</span><span class="cm">,</span> <span class="q">&quot;precision|p=s&quot;</span><span class="cm">,</span> <span class="q">&quot;quote|q=s&quot;</span><span class="cm">,</span> <span class="q">&quot;root|r=s&quot;</span><span class="cm">,</span> <span class="q">&quot;vectorcomparisonmode|v=s&quot;</span><span class="cm">,</span> <span class="q">&quot;vectorcomparisonformulism=s&quot;</span><span class="cm">,</span> <span class="q">&quot;workingdir|w=s&quot;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+942     <span class="k">die</span> <span class="q">&quot;\nTo get a list of valid options and their values, use \&quot;$ScriptName -h\&quot; or\n\&quot;perl -S $ScriptName -h\&quot; command and try again...\n&quot;</span><span class="sc">;</span>
+943   <span class="s">}</span>
+944   <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{workingdir}, for option \&quot;-w --workingdir\&quot; is not a directory name.\n&quot;</span><span class="sc">;</span>
+947     <span class="s">}</span>
+948     <span class="k">chdir</span> <span class="i">$Options</span>{<span class="w">workingdir</span>} <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Couldn&#39;t chdir $Options{workingdir}: $! \n&quot;</span><span class="sc">;</span>
+949   <span class="s">}</span>
+950   <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{colmode}, for option \&quot;-c, --ColMode\&quot; is not valid. Allowed values: ColNum, or ColLabel\n&quot;</span><span class="sc">;</span>
+952   <span class="s">}</span>
+953   <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{compoundidmode}, for option \&quot;--CompoundIDMode\&quot; is not valid. Allowed values: DataField, MolName, LabelPrefix or MolNameOrLabelPrefix\n&quot;</span><span class="sc">;</span>
+955   <span class="s">}</span>
+956   <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{detail}, for option \&quot;-d, --detail\&quot; is not valid. Allowed values: &gt; 0 \n&quot;</span><span class="sc">;</span>
+958   <span class="s">}</span>
+959   <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{inputdatamode}, for option \&quot;--InputDataMode\&quot; is not valid. Allowed values: LoadInMemory or ScanFile\n&quot;</span><span class="sc">;</span>
+961   <span class="s">}</span>
+962   <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{mode}, for option \&quot;-m, --mode\&quot; is not valid. Allowed values: AutoDetect, FingerprintsBitVectorString or FingerprintsVectorString \n&quot;</span><span class="sc">;</span>
+964   <span class="s">}</span>
+965   <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{indelim}, for option \&quot;--InDelim\&quot; is not valid. Allowed values: comma, or semicolon\n&quot;</span><span class="sc">;</span>
+967   <span class="s">}</span>
+968   <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{outdelim}, for option \&quot;--OutDelim\&quot; is not valid. Allowed values: comma, tab, or semicolon\n&quot;</span><span class="sc">;</span>
+970   <span class="s">}</span>
+971   <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{outmatrixformat}, for option \&quot;--OutMatrixFormat\&quot; is not valid. Allowed values: RowsAndColumns or IDPairsAndValue\n&quot;</span><span class="sc">;</span>
+973   <span class="s">}</span>
+974   <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{outmatrixtype}, for option \&quot;--OutMatrixType\&quot; is not valid. Allowed values: FullMatrix, UpperTriangularMatrix or LowerTriangularMatrix\n&quot;</span><span class="sc">;</span>
+976   <span class="s">}</span>
+977   <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{quote}, for option \&quot;-q --quote\&quot; is not valid. Allowed values: Yes or No\n&quot;</span><span class="sc">;</span>
+979   <span class="s">}</span>
+980   <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$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">&quot;Error: The value specified, $Options{precision}, for option \&quot;--precision\&quot; is not valid. Allowed values: &gt; 0 \n&quot;</span><span class="sc">;</span>
+982   <span class="s">}</span>
+983 <span class="s">}</span>
+984
+<a name="EOF-"></a></pre>
+<p>&nbsp;</p>
+<br />
+<center>
+<img src="../../../images/h2o2.png">
+</center>
+</body>
+</html>

Mercurial > repos > deepakjadmin > mayatool3_test3

comparison mayachemtools/docs/scripts/html/code/SimilarityMatricesFingerprints.html @ 0:73ae111cf86f draft