mayatool3_test3: mayachemtools/docs/scripts/html/code/SimilarityMatricesFingerprints.html annotate

annotate mayachemtools/docs/scripts/html/code/SimilarityMatricesFingerprints.html @ 3:e420415a1799 draft

Uploaded

author	deepakjadmin
date	Wed, 20 Jan 2016 12:16:47 -0500
parents	73ae111cf86f
children

rev	line source
0 73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1 <html>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	2 <head>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	3 <title>MayaChemTools:Code:SimilarityMatricesFingerprints.pl</title>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	4 <meta http-equiv="content-type" content="text/html;charset=utf-8">
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	5 <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css">
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	6 </head>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10">
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	8 <br/>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	9 <center>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	11 </center>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	12 <br/>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	13 <pre>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	14 1 #!/usr/bin/perl -w
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	15 2 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	16 3 <span class="c"># $RCSfile: SimilarityMatricesFingerprints.pl,v $</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	17 4 <span class="c"># $Date: 2015/02/28 20:46:20 $</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	18 5 <span class="c"># $Revision: 1.21 $</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	19 6 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	21 8 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	23 10 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	24 11 <span class="c"># This file is part of MayaChemTools.</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	25 12 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	29 16 <span class="c"># later version.</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	30 17 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	34 21 <span class="c"># details.</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	35 22 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	40 27 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	41 28
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	43 30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">"$FindBin::Bin/../lib"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	44 31 <span class="k">use</span> <span class="w">Getopt::Long</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	45 32 <span class="k">use</span> <span class="w">File::Basename</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	46 33 <span class="k">use</span> <span class="w">File::Copy</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	47 34 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	48 35 <span class="k">use</span> <span class="w">Benchmark</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	49 36 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	50 37 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	51 38 <span class="k">use</span> <span class="w">Fingerprints::FingerprintsFileUtil</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	52 39 <span class="k">use</span> <span class="w">Fingerprints::FingerprintsBitVector</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	53 40 <span class="k">use</span> <span class="w">Fingerprints::FingerprintsVector</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	54 41
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	55 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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	56 43
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	57 44 <span class="c"># Autoflush STDOUT</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	58 45 <span class="i">$\|</span> = <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	59 46
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	60 47 <span class="c"># Starting message...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	61 48 <span class="i">$ScriptName</span> = <span class="i">basename</span><span class="s">(</span><span class="i">$0</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	62 49 <span class="k">print</span> <span class="q">"\n$ScriptName: Starting...\n\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	63 50 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	64 51
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	65 52 <span class="c"># Get the options and setup script...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	66 53 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	67 54 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">help</span>} \|\| <span class="i">@ARGV</span> < <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	68 55 <span class="k">die</span> <span class="i">GetUsageFromPod</span><span class="s">(</span><span class="q">"$FindBin::Bin/$ScriptName"</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	69 56 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	70 57
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	71 58 <span class="k">my</span><span class="s">(</span><span class="i">@FingerprintsFilesList</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	72 59 <span class="i">@FingerprintsFilesList</span> = <span class="i">ExpandFileNames</span><span class="s">(</span>\<span class="i">@ARGV</span><span class="cm">,</span> <span class="q">"sdf sd fpf fp csv tsv"</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	73 60
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	74 61 <span class="c"># Process options...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	75 62 <span class="k">print</span> <span class="q">"Processing options...\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	76 63 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	77 64 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	78 65
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	79 66 <span class="c"># Setup information about input files...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	80 67 <span class="k">print</span> <span class="q">"Checking input fingerprints file(s)...\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	81 68 <span class="k">my</span><span class="s">(</span><span class="i">%FingerprintsFilesInfo</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	82 69 <span class="i">RetrieveFingerprintsFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	83 70
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	84 71 <span class="c"># Process input files..</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	85 72 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	86 73 <span class="k">if</span> <span class="s">(</span><span class="i">@FingerprintsFilesList</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	87 74 <span class="k">print</span> <span class="q">"\nProcessing fingerprints files...\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	88 75 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	89 76 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#FingerprintsFilesList</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	90 77 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	91 78 <span class="k">print</span> <span class="q">"\nProcessing file $FingerprintsFilesList[$FileIndex]...\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	92 79 <span class="i">GenerateSimilarityMatrices</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	93 80 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	94 81 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	95 82 <span class="k">print</span> <span class="q">"\n$ScriptName:Done...\n\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	96 83
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	97 84 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	98 85 <span class="i">$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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	99 86 <span class="k">print</span> <span class="q">"Total time: "</span><span class="cm">,</span> <span class="i">timestr</span><span class="s">(</span><span class="i">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	100 87
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	101 88 <span class="c">###############################################################################</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	102 89
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	103 90 <span class="c"># Generate similarity matrices using fingerprints data in text file...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	104 91 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	105 <a name="GenerateSimilarityMatrices-"></a> 92 <span class="k">sub </span><span class="m">GenerateSimilarityMatrices</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	106 93 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	107 94
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	108 95 <span class="i">ProcessFingerprintsData</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	109 96
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	110 97 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsFilesInfo</span>{<span class="w">FingerprintsBitVectorStringMode</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	111 98 <span class="i">GenerateSimilarityMatricesForFingerprintsBitVectors</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	112 99 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	113 100 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	114 101 <span class="i">GenerateSimilarityMatricesForFingerprintsVectors</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	115 102 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	116 103
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	117 104 <span class="i">CleanupFingerprintsData</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	118 105 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	119 106
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	120 107 <span class="c"># Generate bit vector similarity matrices...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	121 108 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	122 <a name="GenerateSimilarityMatricesForFingerprintsBitVectors-"></a> 109 <span class="k">sub </span><span class="m">GenerateSimilarityMatricesForFingerprintsBitVectors</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	123 110 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	124 111 <span class="k">my</span><span class="s">(</span><span class="i">$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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	125 112
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	126 113 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	127 114 <span class="i">$ComparisonMeasure</span> = <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedBitVectorComparisonsNameRef</span>}->{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedComparisonMeasure</span><span class="s">)</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	128 115 <span class="i">$NewTextFile</span> = <span class="i">$FingerprintsFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$FileIndex</span>] . <span class="q">"${ComparisonMeasure}."</span> . <span class="i">$FingerprintsFilesInfo</span>{<span class="w">OutFileExt</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	129 116
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	130 117 <span class="i">$MethodName</span> = <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedBitVectorComparisonsMethodRef</span>}->{<span class="k">lc</span><span class="s">(</span><span class="i">$ComparisonMeasure</span><span class="s">)</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	131 118
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	132 119 <span class="i">@MethodParameters</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	133 120 <span class="i">@MethodParameters</span> = <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedBitVectorComparisonsParameterRef</span>}->{<span class="k">lc</span><span class="s">(</span><span class="i">$ComparisonMeasure</span><span class="s">)</span>}}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	134 121
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	135 122 <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">$MethodName</span><span class="cm">,</span> \<span class="i">@MethodParameters</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	136 123 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	137 124 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	138 125
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	139 126 <span class="c"># Generate vector similarity and/or distance matrices...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	140 127 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	141 <a name="GenerateSimilarityMatricesForFingerprintsVectors-"></a> 128 <span class="k">sub </span><span class="m">GenerateSimilarityMatricesForFingerprintsVectors</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	142 129 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	143 130 <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">$MethodName</span><span class="cm">,</span> <span class="i">@MethodParameters</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	144 131
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	145 132 <span class="k">for</span> <span class="i">$SpecifiedComparisonMeasure</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedVectorComparisonsRef</span>}}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	146 133 <span class="i">$ComparisonMeasure</span> = <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedVectorComparisonsNameRef</span>}->{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedComparisonMeasure</span><span class="s">)</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	147 134
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	148 135 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	149 136 <span class="i">$NewTextFile</span> = <span class="i">$FingerprintsFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$FileIndex</span>] . <span class="q">"${ComparisonMeasure}${ComparisonMode}."</span> . <span class="i">$FingerprintsFilesInfo</span>{<span class="w">OutFileExt</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	150 137
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	151 138 <span class="i">$MethodName</span> = <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedVectorComparisonsMethodRef</span>}->{<span class="k">lc</span><span class="s">(</span><span class="i">$ComparisonMeasure</span><span class="s">)</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	152 139
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	153 140 <span class="i">@MethodParameters</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	154 141 <span class="k">push</span> <span class="i">@MethodParameters</span><span class="cm">,</span> <span class="i">$ComparisonMode</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	155 142 <span class="k">push</span> <span class="i">@MethodParameters</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedVectorComparisonsParameterRef</span>}->{<span class="k">lc</span><span class="s">(</span><span class="i">$ComparisonMeasure</span><span class="s">)</span>}}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	156 143
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	157 144 <span class="i">GenerateSimilarityMatrix</span><span class="s">(</span><span class="i">$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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	158 145 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	159 146 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	160 147 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	161 148
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	162 149 <span class="c"># Calculate similarity matrix and write it out...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	163 150 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	164 <a name="GenerateSimilarityMatrix-"></a> 151 <span class="k">sub </span><span class="m">GenerateSimilarityMatrix</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	165 152 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	166 153
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	167 154 <span class="k">print</span> <span class="q">"\nGenerating $NewTextFile...\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	168 155
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	169 156 <span class="c"># Open new file and write out column labels...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	170 157 <span class="k">open</span> <span class="w">NEWTEXTFILE</span><span class="cm">,</span> <span class="q">">$NewTextFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $NewTextFile: $! \n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	171 158 <span class="i">WriteColumnLabels</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> \<span class="i">*NEWTEXTFILE</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	172 159
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	173 160 <span class="c"># Calculate and write out similarity matrix values...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	174 161 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	175 162 <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">$MethodParametersRef</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	176 163 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	177 164 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">InputDataMode</span>} =~ <span class="q">/^ScanFile$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	178 165 <span class="i">GenerateSimilarityMatrixUsingFileData</span><span class="s">(</span><span class="i">$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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	179 166 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	180 167 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	181 168 <span class="k">warn</span> <span class="q">"Warning: Input data mode, $OptionsInfo{InputDataMode}, is not supported.\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	182 169 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	183 170
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	184 171 <span class="c"># Close new text file...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	185 172 <span class="k">close</span> <span class="w">NEWTEXTFILE</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	186 173
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	187 174 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	188 175
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	189 176 <span class="c"># Calculate and write out similarity values using fingerprints data already loaded in</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	190 177 <span class="c"># memory...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	191 178 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	192 <a name="GenerateSimilarityMatrixUsingMemoryData-"></a> 179 <span class="k">sub </span><span class="m">GenerateSimilarityMatrixUsingMemoryData</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	193 180 <span class="k">my</span><span class="s">(</span><span class="i">$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">$MethodParametersRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	194 181 <span class="k">my</span><span class="s">(</span><span class="i">$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">$Line</span><span class="cm">,</span> <span class="i">@LineWords</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	195 182
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	196 183 <span class="k">for</span> <span class="i">$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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	197 184 <span class="i">$FingerprintsObject1</span> = <span class="i">$FingerprintsFilesInfo</span>{<span class="w">FingerprintsObjectsRef</span>}->[<span class="i">$RowIndex</span>]<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	198 185 <span class="i">$CmpdID1</span> = <span class="i">$FingerprintsFilesInfo</span>{<span class="w">CompundIDsRef</span>}->[<span class="i">$RowIndex</span>]<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	199 186
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	200 187 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">WriteRowsAndColumns</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	201 188 <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="q">"$OptionsInfo{OutQuoteValue}${CmpdID1}$OptionsInfo{OutQuoteValue}"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	202 189 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	203 190
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	204 191 <span class="j">COLINDEX:</span> <span class="k">for</span> <span class="i">$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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	205 192 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	206 193 <span class="k">next</span> <span class="j">COLINDEX</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	207 194 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	208 195
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	209 196 <span class="i">$FingerprintsObject2</span> = <span class="i">$FingerprintsFilesInfo</span>{<span class="w">FingerprintsObjectsRef</span>}->[<span class="i">$ColIndex</span>]<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	210 197
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	211 198 <span class="i">$Value</span> = <span class="i">$FingerprintsObject1</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$FingerprintsObject2</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$MethodParametersRef</span>}<span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	212 199 <span class="i">$Value</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> && <span class="k">length</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> ? <span class="s">(</span><span class="k">sprintf</span><span class="s">(</span><span class="q">"%.$OptionsInfo{Precision}f"</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> + <span class="n">0</span><span class="s">)</span> <span class="co">:</span> <span class="q">''</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	213 200
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	214 201 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">WriteRowsAndColumns</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	215 202 <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="q">"$OptionsInfo{OutDelim}$OptionsInfo{OutQuoteValue}${Value}$OptionsInfo{OutQuoteValue}"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	216 203 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	217 204 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">WriteIDPairsAndValue</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	218 205 <span class="i">$CmpdID2</span> = <span class="i">$FingerprintsFilesInfo</span>{<span class="w">CompundIDsRef</span>}->[<span class="i">$ColIndex</span>]<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	219 206
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	220 207 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	221 208 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="s">(</span><span class="i">$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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	222 209 <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">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	223 210 <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="q">"$Line\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	224 211 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	225 212 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	226 213 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">WriteRowsAndColumns</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	227 214 <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="q">"\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	228 215 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	229 216 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	230 217 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	231 218
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	232 219 <span class="c"># Calculate and write out similarity values by retrieving and prcessing data</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	233 220 <span class="c"># from fingerprint file...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	234 221 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	235 <a name="GenerateSimilarityMatrixUsingFileData-"></a> 222 <span class="k">sub </span><span class="m">GenerateSimilarityMatrixUsingFileData</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	236 223 <span class="k">my</span><span class="s">(</span><span class="i">$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">$MethodParametersRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	237 224 <span class="k">my</span><span class="s">(</span><span class="i">$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">$Line</span><span class="cm">,</span> <span class="i">@LineWords</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	238 225
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	239 226 <span class="k">print</span> <span class="q">"\nReading and processing fingerprints data...\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	240 227
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	241 228 <span class="i">$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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	242 229 <span class="i">$FingerprintsFileIO</span><span class="i">->Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	243 230
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	244 231 <span class="i">$RowIndex</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$ColIndex</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	245 232 <span class="i">$FingerprintsCount</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$IgnoredFingerprintsCount</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	246 233
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	247 234 <span class="j">FINGERPRINTSFILEIO:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$FingerprintsFileIO</span><span class="i">->Read</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	248 235 <span class="i">$FingerprintsCount</span>++<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	249 236
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	250 237 <span class="k">if</span> <span class="s">(</span>!<span class="i">$FingerprintsFileIO</span><span class="i">->IsFingerprintsDataValid</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	251 238 <span class="i">$IgnoredFingerprintsCount</span>++<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	252 239 <span class="k">next</span> <span class="j">FINGERPRINTSFILEIO</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	253 240 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	254 241 <span class="i">$RowIndex</span>++<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	255 242 <span class="i">$FingerprintsObject1</span> = <span class="i">$FingerprintsFileIO</span><span class="i">->GetFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	256 243 <span class="i">$CmpdID1</span> = <span class="i">$FingerprintsFileIO</span><span class="i">->GetCompoundID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	257 244
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	258 245 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">WriteRowsAndColumns</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	259 246 <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="q">"$OptionsInfo{OutQuoteValue}${CmpdID1}$OptionsInfo{OutQuoteValue}"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	260 247 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	261 248
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	262 249 <span class="c"># Force detail level of 1 to avoid duplicate printing of diagnostic messages for invalid</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	263 250 <span class="c"># fingerprints data...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	264 251 <span class="i">$TmpFingerprintsFileIO</span> = <span class="i">Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO</span><span class="s">(</span><span class="i">%</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">TmpFingerprintsFileIOParameters</span>}[<span class="i">$FileIndex</span>]}<span class="cm">,</span> <span class="q">"DetailLevel"</span> <span class="cm">=></span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	265 252 <span class="i">$TmpFingerprintsFileIO</span><span class="i">->Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	266 253
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	267 254 <span class="i">$ColIndex</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	268 255 <span class="j">TMPFINGERPRINTSFILEIO:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$TmpFingerprintsFileIO</span><span class="i">->Read</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	269 256 <span class="k">if</span> <span class="s">(</span>!<span class="i">$TmpFingerprintsFileIO</span><span class="i">->IsFingerprintsDataValid</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	270 257 <span class="k">next</span> <span class="j">TMPFINGERPRINTSFILEIO</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	271 258 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	272 259 <span class="i">$ColIndex</span>++<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	273 260
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	274 261 <span class="k">if</span> <span class="s">(</span><span class="i">SkipMatrixData</span><span class="s">(</span><span class="i">$RowIndex</span><span class="cm">,</span> <span class="i">$ColIndex</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	275 262 <span class="k">next</span> <span class="j">TMPFINGERPRINTSFILEIO</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	276 263 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	277 264
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	278 265 <span class="i">$FingerprintsObject2</span> = <span class="i">$TmpFingerprintsFileIO</span><span class="i">->GetFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	279 266
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	280 267 <span class="i">$Value</span> = <span class="i">$FingerprintsObject1</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$FingerprintsObject2</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$MethodParametersRef</span>}<span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	281 268 <span class="i">$Value</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> && <span class="k">length</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> ? <span class="s">(</span><span class="k">sprintf</span><span class="s">(</span><span class="q">"%.$OptionsInfo{Precision}f"</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> + <span class="n">0</span><span class="s">)</span> <span class="co">:</span> <span class="q">''</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	282 269
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	283 270 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">WriteRowsAndColumns</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	284 271 <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="q">"$OptionsInfo{OutDelim}$OptionsInfo{OutQuoteValue}${Value}$OptionsInfo{OutQuoteValue}"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	285 272 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	286 273 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">WriteIDPairsAndValue</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	287 274 <span class="i">$CmpdID2</span> = <span class="i">$TmpFingerprintsFileIO</span><span class="i">->GetCompoundID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	288 275
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	289 276 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	290 277 <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">$Value</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	291 278 <span class="i">$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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	292 279 <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="q">"$Line\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	293 280 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	294 281 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	295 282 <span class="i">$TmpFingerprintsFileIO</span><span class="i">->Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	296 283
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	297 284 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">WriteRowsAndColumns</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	298 285 <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="q">"\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	299 286 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	300 287 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	301 288
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	302 289 <span class="i">$FingerprintsFileIO</span><span class="i">->Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	303 290
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	304 291 <span class="k">print</span> <span class="q">"Number of fingerprints data entries in database fingerprints file: $FingerprintsCount\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	305 292 <span class="k">print</span> <span class="q">"Number of fingerprints date entries processed successfully: "</span><span class="cm">,</span> <span class="s">(</span><span class="i">$FingerprintsCount</span> - <span class="i">$IgnoredFingerprintsCount</span><span class="s">)</span> <span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	306 293 <span class="k">print</span> <span class="q">"Number of fingerprints data entries ignored due to missing/invalid data: $IgnoredFingerprintsCount\n\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	307 294 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	308 295
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	309 296 <span class="c"># Check whether matrix data need to be skipped...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	310 297 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	311 <a name="SkipMatrixData-"></a> 298 <span class="k">sub </span><span class="m">SkipMatrixData</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	312 299 <span class="k">my</span><span class="s">(</span><span class="i">$RowIndex</span><span class="cm">,</span> <span class="i">$ColIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	313 300
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	314 301 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">WriteFullMatrix</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	315 302 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	316 303 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	317 304 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">WriteUpperTriangularMatrix</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	318 305 <span class="k">return</span> <span class="s">(</span><span class="i">$RowIndex</span> > <span class="i">$ColIndex</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	319 306 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	320 307 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">WriteLowerTriangularMatrix</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	321 308 <span class="k">return</span> <span class="s">(</span><span class="i">$RowIndex</span> < <span class="i">$ColIndex</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	322 309 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	323 310
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	324 311 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	325 312 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	326 313
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	327 314 <span class="c"># Write out column labels...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	328 315 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	329 <a name="WriteColumnLabels-"></a> 316 <span class="k">sub </span><span class="m">WriteColumnLabels</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	330 317 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	331 318 <span class="k">my</span><span class="s">(</span><span class="i">$Line</span><span class="cm">,</span> <span class="i">@LineWords</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	332 319
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	333 320 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutMatrixFormat</span>} =~ <span class="q">/^IDPairsAndValue$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	334 321 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	335 322 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="s">(</span><span class="q">'CmpdID1'</span><span class="cm">,</span> <span class="q">'CmpdID2'</span><span class="cm">,</span> <span class="q">'Coefficient Value'</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	336 323 <span class="i">$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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	337 324 <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="q">"$Line\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	338 325 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	339 326 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	340 327 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	341 328 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	342 329 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="q">''</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	343 330 <span class="k">push</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">CompundIDsRef</span>}}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	344 331 <span class="i">$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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	345 332 <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="q">"$Line\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	346 333 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	347 334 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	348 335 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	349 336
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	350 337 <span class="c"># Scan file to retrieve compound IDs...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	351 338 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	352 339 <span class="k">print</span> <span class="q">"\nProcessing fingerprints file to generate compound IDs...\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	353 340
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	354 341 <span class="c"># Force detail level of 1 to avoid diagnostics messages for invalid fingeprints data during</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	355 342 <span class="c"># retrieval of compound IDs as these get printed out during calculation of matrix...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	356 343 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	357 344 <span class="i">$FingerprintsFileIO</span> = <span class="i">Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO</span><span class="s">(</span><span class="i">%</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">FingerprintsFileIOParameters</span>}[<span class="i">$FileIndex</span>]}<span class="cm">,</span> <span class="q">"DetailLevel"</span> <span class="cm">=></span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	358 345 <span class="i">$FingerprintsFileIO</span><span class="i">->Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	359 346
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	360 347 <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="q">"$OptionsInfo{OutQuoteValue}$OptionsInfo{OutQuoteValue}"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	361 348
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	362 349 <span class="j">FINGERPRINTSFILEIO:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$FingerprintsFileIO</span><span class="i">->Read</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	363 350 <span class="k">if</span> <span class="s">(</span>!<span class="i">$FingerprintsFileIO</span><span class="i">->IsFingerprintsDataValid</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	364 351 <span class="k">next</span> <span class="j">FINGERPRINTSFILEIO</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	365 352 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	366 353 <span class="i">$CmpdID</span> = <span class="i">$FingerprintsFileIO</span><span class="i">->GetCompoundID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	367 354 <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="q">"$OptionsInfo{OutDelim}$OptionsInfo{OutQuoteValue}${CmpdID}$OptionsInfo{OutQuoteValue}"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	368 355 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	369 356 <span class="i">$FingerprintsFileIO</span><span class="i">->Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	370 357
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	371 358 <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="q">"\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	372 359
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	373 360 <span class="k">print</span> <span class="q">"Processing fingerprints file to generate matrix...\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	374 361 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	375 362 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	376 363 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	377 364 <span class="k">warn</span> <span class="q">"Warning: Output matrix format, $OptionsInfo{OutMatrixFormat}, is not supported.\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	378 365 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	379 366 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	380 367
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	381 368 <span class="c"># Process fingerprints data...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	382 369 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	383 <a name="ProcessFingerprintsData-"></a> 370 <span class="k">sub </span><span class="m">ProcessFingerprintsData</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	384 371 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	385 372 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsFileIO</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	386 373
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	387 374 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">CompundIDsRef</span>} = <span class="k">undef</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	388 375 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">FingerprintsObjectsRef</span>} = <span class="k">undef</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	389 376
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	390 377 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">InputDataMode</span>} =~ <span class="q">/^LoadInMemory$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	391 378 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsFileIO</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	392 379
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	393 380 <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">$FileIndex</span>]}<span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	394 381 <span class="s">(</span><span class="i">$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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	395 382 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	396 383 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	397 384 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	398 385
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	399 386 <span class="i">$FingerprintsFile</span> = <span class="i">$FingerprintsFilesList</span>[<span class="i">$FileIndex</span>]<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	400 387 <span class="i">$TmpFingerprintsFile</span> = <span class="i">$FingerprintsFilesInfo</span>{<span class="w">TmpFingerprintsFile</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	401 388
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	402 389 <span class="c"># Copy fingerprints file to a tmp file for calculating similarity matrix...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	403 390 <span class="k">print</span> <span class="q">"\nCopying fingerprints file, $FingerprintsFile, to temporary fingperints file, $TmpFingerprintsFile...\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	404 391 <span class="w">copy</span> <span class="i">$FingerprintsFile</span><span class="cm">,</span> <span class="i">$TmpFingerprintsFile</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't copy $FingerprintsFile to $TmpFingerprintsFile: $! \n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	405 392 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	406 393 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	407 394
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	408 395 <span class="c"># Clean up fingerprints data...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	409 396 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	410 <a name="CleanupFingerprintsData-"></a> 397 <span class="k">sub </span><span class="m">CleanupFingerprintsData</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	411 398 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	412 399
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	413 400 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	414 401 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">CompundIDsRef</span>} = <span class="k">undef</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	415 402 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">FingerprintsObjectsRef</span>} = <span class="k">undef</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	416 403 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	417 404 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	418 405 <span class="k">my</span><span class="s">(</span><span class="i">$TmpFingerprintsFile</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	419 406
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	420 407 <span class="c"># Delete temporary fingerprints file...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	421 408 <span class="i">$TmpFingerprintsFile</span> = <span class="i">$FingerprintsFilesInfo</span>{<span class="w">TmpFingerprintsFile</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	422 409
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	423 410 <span class="k">print</span> <span class="q">"\nDeleting temporary fingerprints file $TmpFingerprintsFile...\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	424 411 <span class="k">unlink</span> <span class="i">$TmpFingerprintsFile</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't unlink $TmpFingerprintsFile: $! \n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	425 412 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	426 413 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	427 414
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	428 415 <span class="c"># Retrieve information about fingerprints files...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	429 416 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	430 <a name="RetrieveFingerprintsFilesInfo-"></a> 417 <span class="k">sub </span><span class="m">RetrieveFingerprintsFilesInfo</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	431 418 <span class="k">my</span><span class="s">(</span><span class="i">$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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	432 419
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	433 420 <span class="i">%FingerprintsFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	434 421 <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">FileOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	435 422 <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">FileType</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	436 423 <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">InDelim</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	437 424 <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">OutFileRoot</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	438 425 <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">OutFileExt</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	439 426
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	440 427 <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">TmpFingerprintsFile</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	441 428
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	442 429 <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">FingerprintsFileIOParameters</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	443 430 <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">TmpFingerprintsFileIOParameters</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	444 431
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	445 432 <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">FingerprintsBitVectorStringMode</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	446 433 <span class="i">@</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">FingerprintsVectorStringMode</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	447 434
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	448 435 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	449 436 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	450 437 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">FileType</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	451 438 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">InDelim</span>}[<span class="i">$Index</span>] = <span class="q">""</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	452 439 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	453 440 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">OutFileExt</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	454 441
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	455 442 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	456 443
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	457 444 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">TmpFingerprintsFile</span>}[<span class="i">$Index</span>] = <span class="q">""</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	458 445 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	459 446
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	460 447 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">FingerprintsBitVectorStringMode</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	461 448 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">FingerprintsVectorStringMode</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	462 449
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	463 450 <span class="i">$FingerprintsFile</span> = <span class="i">$FingerprintsFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	464 451 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">-e</span> <span class="i">$FingerprintsFile</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	465 452 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $FingerprintsFile: It doesn't exist\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	466 453 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	467 454 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	468 455
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	469 456 <span class="i">$FileType</span> = <span class="i">Fingerprints::FingerprintsFileUtil::GetFingerprintsFileType</span><span class="s">(</span><span class="i">$FingerprintsFile</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	470 457 <span class="k">if</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$FileType</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	471 458 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $FingerprintsFile: It's not a fingerprints file\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	472 459 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	473 460 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	474 461
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	475 462 <span class="i">$FileDir</span> = <span class="q">""</span><span class="sc">;</span> <span class="i">$FileName</span> = <span class="q">""</span><span class="sc">;</span> <span class="i">$FileExt</span> = <span class="q">""</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	476 463 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	477 464
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	478 465 <span class="c"># Setup temporary fingerprints file name for scan file mode...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	479 466 <span class="i">$TmpFingerprintsFile</span> = <span class="q">"${FileName}Tmp.${FileExt}"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	480 467
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	481 468 <span class="i">$InDelim</span> = <span class="s">(</span><span class="i">$FileExt</span> =~ <span class="q">/^tsv$/i</span><span class="s">)</span> ? <span class="q">'Tab'</span> <span class="co">:</span> <span class="i">$OptionsInfo</span>{<span class="w">InDelim</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	482 469
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	483 470 <span class="c"># Setup output file names...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	484 471 <span class="i">$OutFileExt</span> = <span class="q">"csv"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	485 472 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	486 473 <span class="i">$OutFileExt</span> = <span class="q">"tsv"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	487 474 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	488 475
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	489 476 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	490 477 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} && <span class="s">(</span><span class="i">@FingerprintsFilesList</span> == <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	491 478 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	492 479 <span class="k">if</span> <span class="s">(</span><span class="i">$RootFileName</span> && <span class="i">$RootFileExt</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	493 480 <span class="i">$FileName</span> = <span class="i">$RootFileName</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	494 481 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	495 482 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	496 483 <span class="i">$FileName</span> = <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	497 484 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	498 485 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	499 486 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	500 487
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	501 488 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">overwrite</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	502 489 <span class="c"># Similarity matrices output file names for bit-vector strings...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	503 490 <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedComparisonMeasure</span><span class="cm">,</span> <span class="i">$ComparisonMeasure</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	504 491 <span class="k">for</span> <span class="i">$SpecifiedComparisonMeasure</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedBitVectorComparisonsRef</span>}}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	505 492 <span class="i">$ComparisonMeasure</span> = <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedBitVectorComparisonsNameRef</span>}->{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedComparisonMeasure</span><span class="s">)</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	506 493 <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="q">"${OutFileRoot}${ComparisonMeasure}.${OutFileExt}"</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	507 494 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $FingerprintsFile: The file ${OutFileRoot}${ComparisonMeasure}.${OutFileExt} already exists.\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	508 495 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	509 496 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	510 497 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	511 498 <span class="c"># Similarity matrices output file names for vector strings...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	512 499 <span class="k">my</span><span class="s">(</span><span class="i">$ComparisonMode</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	513 500 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	514 501 <span class="i">$ComparisonMeasure</span> = <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedVectorComparisonsNameRef</span>}->{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedComparisonMeasure</span><span class="s">)</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	515 502 <span class="k">for</span> <span class="i">$ComparisonMode</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedVectorComparisonModesRef</span>}}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	516 503 <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="q">"${OutFileRoot}${ComparisonMeasure}${ComparisonMode}.${OutFileExt}"</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	517 504 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $FingerprintsFile: The file ${OutFileRoot}${ComparisonMeasure}${ComparisonMode}.${OutFileExt} already exists.\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	518 505 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	519 506 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	520 507 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	521 508 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	522 509 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	523 510
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	524 511 <span class="c"># Setup FingerprintsFileIO parameters...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	525 512 <span class="i">%FingerprintsFileIOParameters</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	526 513 <span class="j">FILEIOPARAMETERS:</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	527 514 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	528 515 <span class="i">%FingerprintsFileIOParameters</span> = <span class="s">(</span><span class="q">'Name'</span> <span class="cm">=></span> <span class="i">$FingerprintsFile</span><span class="cm">,</span> <span class="q">'Mode'</span> <span class="cm">=></span> <span class="q">'Read'</span><span class="cm">,</span> <span class="q">'FingerprintsStringMode'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>}<span class="cm">,</span> <span class="q">'ValidateData'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">ValidateData</span>}<span class="cm">,</span> <span class="q">'DetailLevel'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">Detail</span>}<span class="cm">,</span> <span class="q">'FingerprintsFieldLabel'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsField</span>}<span class="cm">,</span> <span class="q">'CompoundIDMode'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>}<span class="cm">,</span> <span class="q">'CompoundIDFieldLabel'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDField</span>}<span class="cm">,</span> <span class="q">'CompoundIDPrefix'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDPrefix</span>}<span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	529 516 <span class="k">last</span> <span class="j">FILEIOPARAMETERS</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	530 517 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	531 518 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	532 519 <span class="i">%FingerprintsFileIOParameters</span> = <span class="s">(</span><span class="q">'Name'</span> <span class="cm">=></span> <span class="i">$FingerprintsFile</span><span class="cm">,</span> <span class="q">'Mode'</span> <span class="cm">=></span> <span class="q">'Read'</span><span class="cm">,</span> <span class="q">'FingerprintsStringMode'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>}<span class="cm">,</span> <span class="q">'ValidateData'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">ValidateData</span>}<span class="cm">,</span> <span class="q">'DetailLevel'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">Detail</span>}<span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	533 520 <span class="k">last</span> <span class="j">FILEIOPARAMETERS</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	534 521 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	535 522 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	536 523 <span class="i">%FingerprintsFileIOParameters</span> = <span class="s">(</span><span class="q">'Name'</span> <span class="cm">=></span> <span class="i">$FingerprintsFile</span><span class="cm">,</span> <span class="q">'Mode'</span> <span class="cm">=></span> <span class="q">'Read'</span><span class="cm">,</span> <span class="q">'FingerprintsStringMode'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>}<span class="cm">,</span> <span class="q">'ValidateData'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">ValidateData</span>}<span class="cm">,</span> <span class="q">'DetailLevel'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">Detail</span>}<span class="cm">,</span> <span class="q">'FingerprintsCol'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsCol</span>}<span class="cm">,</span> <span class="q">'ColMode'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">ColMode</span>}<span class="cm">,</span> <span class="q">'CompoundIDCol'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDCol</span>}<span class="cm">,</span> <span class="q">'CompoundIDPrefix'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDPrefix</span>}<span class="cm">,</span> <span class="q">'InDelim'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">InDelim</span>}<span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	537 524 <span class="k">last</span> <span class="j">FILEIOPARAMETERS</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	538 525 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	539 526 <span class="k">warn</span> <span class="q">"Warning: File type for fingerprints file, $FingerprintsFile, is not valid. Supported file types: SD, FP or Text\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	540 527 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	541 528 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	542 529
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	543 530 <span class="c"># Retrieve fingerints file string mode information...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	544 531 <span class="i">$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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	545 532
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	546 533 <span class="k">if</span> <span class="s">(</span>!<span class="i">$FingerprintsFileIO</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	547 534 <span class="k">warn</span> <span class="q">"Warning: Ignoring fingerprints file $FingerprintsFile: It contains invalid fingerprints data\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	548 535 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	549 536 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	550 537 <span class="k">if</span> <span class="s">(</span>!<span class="i">$FingerprintsFileIO</span><span class="i">->IsFingerprintsFileDataValid</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	551 538 <span class="k">warn</span> <span class="q">"Warning: Ignoring fingerprints file $FingerprintsFile: It contains invalid fingerprints data\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	552 539 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	553 540 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	554 541 <span class="i">$FingerprintsBitVectorStringMode</span> = <span class="i">$FingerprintsFileIO</span><span class="i">->GetFingerprintsBitVectorStringMode</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	555 542 <span class="i">$FingerprintsVectorStringMode</span> = <span class="i">$FingerprintsFileIO</span><span class="i">->GetFingerprintsVectorStringMode</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	556 543
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	557 544
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	558 545 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	559 546 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">FileType</span>}[<span class="i">$Index</span>] = <span class="i">$FileType</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	560 547
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	561 548 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">InDelim</span>}[<span class="i">$Index</span>] = <span class="i">$InDelim</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	562 549
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	563 550 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="i">$OutFileRoot</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	564 551 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">OutFileExt</span>}[<span class="i">$Index</span>] = <span class="i">$OutFileExt</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	565 552
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	566 553 <span class="i">%</span>{<span class="i">$FingerprintsFilesInfo</span>{<span class="w">FingerprintsFileIOParameters</span>}[<span class="i">$Index</span>]} = <span class="i">%FingerprintsFileIOParameters</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	567 554
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	568 555 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">TmpFingerprintsFile</span>}[<span class="i">$Index</span>] = <span class="i">$TmpFingerprintsFile</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	569 556
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	570 557 <span class="i">$FingerprintsFileIOParameters</span>{<span class="w">Name</span>} = <span class="i">$TmpFingerprintsFile</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	571 558 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	572 559
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	573 560 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">FingerprintsBitVectorStringMode</span>}[<span class="i">$Index</span>] = <span class="i">$FingerprintsBitVectorStringMode</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	574 561 <span class="i">$FingerprintsFilesInfo</span>{<span class="w">FingerprintsVectorStringMode</span>}[<span class="i">$Index</span>] = <span class="i">$FingerprintsVectorStringMode</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	575 562 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	576 563 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	577 564
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	578 565 <span class="c"># Process option values...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	579 <a name="ProcessOptions-"></a> 566 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	580 567 <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	581 568
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	582 569 <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	583 570
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	584 571 <span class="i">$OptionsInfo</span>{<span class="w">InputDataMode</span>} = <span class="i">$Options</span>{<span class="w">inputdatamode</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	585 572
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	586 573 <span class="i">ProcessBitVectorComparisonOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	587 574 <span class="i">ProcessVectorComparisonOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	588 575
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	589 576 <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDPrefix</span>} = <span class="i">$Options</span>{<span class="w">compoundidprefix</span>} ? <span class="i">$Options</span>{<span class="w">compoundidprefix</span>} <span class="co">:</span> <span class="q">'Cmpd'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	590 577
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	591 578 <span class="c"># Compound ID and fingerprints column options for text files...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	592 579 <span class="i">$OptionsInfo</span>{<span class="w">ColMode</span>} = <span class="i">$Options</span>{<span class="w">colmode</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	593 580
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	594 581 <span class="k">if</span> <span class="s">(</span><span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidcol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	595 582 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	596 583 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	597 584 <span class="k">die</span> <span class="q">"Error: Column value, $Options{compoundidcol}, specified using \"--CompoundIDCol\" is not valid: Allowed integer values: > 0\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	598 585 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	599 586 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	600 587 <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDCol</span>} = <span class="i">$Options</span>{<span class="w">compoundidcol</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	601 588 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	602 589 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	603 590 <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDCol</span>} = <span class="q">'AutoDetect'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	604 591 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	605 592
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	606 593 <span class="k">if</span> <span class="s">(</span><span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">fingerprintscol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	607 594 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">colmode</span>} =~ <span class="q">/^ColNum$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	608 595 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">fingerprintscol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	609 596 <span class="k">die</span> <span class="q">"Error: Column value, $Options{fingerprintscol}, specified using \"--FingerprintsCol\" is not valid: Allowed integer values: > 0\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	610 597 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	611 598 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	612 599 <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsCol</span>} = <span class="i">$Options</span>{<span class="w">fingerprintscol</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	613 600 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	614 601 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	615 602 <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsCol</span>} = <span class="q">'AutoDetect'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	616 603 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	617 604
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	618 605 <span class="k">if</span> <span class="s">(</span><span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidcol</span>}<span class="s">)</span> && <span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">fingerprintscol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	619 606 <span class="k">if</span> <span class="s">(</span><span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidcol</span>}<span class="s">)</span> && <span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">fingerprintscol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	620 607 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	621 608 <span class="k">die</span> <span class="q">"Error: Values specified using \"--CompoundIDCol\" and \"--FingerprintsCol\", $Options{compoundidcol}, must be different.\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	622 609 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	623 610 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	624 611 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	625 612 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">$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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	626 613 <span class="k">die</span> <span class="q">"Error: Values specified using \"--CompoundIDCol\" and \"--FingerprintsCol\", $Options{compoundidcol}, must be different.\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	627 614 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	628 615 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	629 616 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	630 617
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	631 618 <span class="c"># Compound ID and fingerprints field options for SD files...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	632 619 <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} = <span class="i">$Options</span>{<span class="w">compoundidmode</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	633 620 <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDField</span>} = <span class="q">''</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	634 621
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	635 622 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	636 623 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">compoundidfield</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	637 624 <span class="k">die</span> <span class="q">"Error: You must specify a value for \"--CompoundIDField\" option in \"DataField\" \"--CompoundIDMode\". \n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	638 625 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	639 626 <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDField</span>} = <span class="i">$Options</span>{<span class="w">compoundidfield</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	640 627 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	641 628
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	642 629
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	643 630 <span class="k">if</span> <span class="s">(</span><span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">fingerprintsfield</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	644 631 <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsField</span>} = <span class="i">$Options</span>{<span class="w">fingerprintsfield</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	645 632 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	646 633 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	647 634 <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsField</span>} = <span class="q">'AutoDetect'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	648 635 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	649 636
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	650 637 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidfield</span>} && <span class="i">IsNotEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">fingerprintsfield</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	651 638 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">$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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	652 639 <span class="k">die</span> <span class="q">"Error: Values specified using \"--CompoundIDField\" and \"--Fingerprintsfield\", $Options{compoundidfield}, must be different.\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	653 640 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	654 641 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	655 642
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	656 643 <span class="i">$OptionsInfo</span>{<span class="w">Detail</span>} = <span class="i">$Options</span>{<span class="w">detail</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	657 644
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	658 645 <span class="i">$OptionsInfo</span>{<span class="w">InDelim</span>} = <span class="i">$Options</span>{<span class="w">indelim</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	659 646 <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/tab/i</span> <span class="s">)</span> ? <span class="q">"\t"</span> <span class="co">:</span> <span class="s">(</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/semicolon/i</span><span class="s">)</span> ? <span class="q">"\;"</span> <span class="co">:</span> <span class="q">"\,"</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	660 647 <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$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	661 648 <span class="i">$OptionsInfo</span>{<span class="w">OutQuoteValue</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">quote</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="q">'"'</span> <span class="co">:</span> <span class="q">''</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	662 649
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	663 650 <span class="i">$OptionsInfo</span>{<span class="w">OutMatrixFormat</span>} = <span class="i">$Options</span>{<span class="w">outmatrixformat</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	664 651
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	665 652 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	666 653 <span class="j">OUTMATRIXFORMAT:</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	667 654 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	668 655 <span class="i">$OptionsInfo</span>{<span class="w">WriteRowsAndColumns</span>} = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">OUTMATRIXFORMAT</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	669 656 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	670 657 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutMatrixFormat</span>} =~ <span class="q">/^IDPairsAndValue$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	671 658 <span class="i">$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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	672 659 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	673 660 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{outmatrixformat}, for option \"--OutMatrixFormat\" is not valid. Allowed values: RowsAndColumns or IDPairsAndValue\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	674 661 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	675 662
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	676 663 <span class="i">$OptionsInfo</span>{<span class="w">OutMatrixType</span>} = <span class="i">$Options</span>{<span class="w">outmatrixtype</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	677 664
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	678 665 <span class="i">$OptionsInfo</span>{<span class="w">WriteFullMatrix</span>} = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	679 666 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	680 667 <span class="j">OUTMATRIXTYPE:</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	681 668 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	682 669 <span class="i">$OptionsInfo</span>{<span class="w">WriteFullMatrix</span>} = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">OUTMATRIXTYPE</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	683 670 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	684 671 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutMatrixType</span>} =~ <span class="q">/^UpperTriangularMatrix$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	685 672 <span class="i">$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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	686 673 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	687 674 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	688 675 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	689 676 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	690 677 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{outmatrixtype}, for option \"--OutMatrixType\" is not valid. Allowed values: FullMatrix, UpperTriangularMatrix or LowerTriangularMatrix\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	691 678 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	692 679
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	693 680 <span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>} = <span class="i">$Options</span>{<span class="w">overwrite</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	694 681 <span class="i">$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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	695 682
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	696 683 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	697 684 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	698 685
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	699 686 <span class="i">$OptionsInfo</span>{<span class="w">Precision</span>} = <span class="i">$Options</span>{<span class="w">precision</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	700 687
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	701 688 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	702 689
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	703 690 <span class="c"># Process options related to comparion of bit vector strings...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	704 691 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	705 <a name="ProcessBitVectorComparisonOptions-"></a> 692 <span class="k">sub </span><span class="m">ProcessBitVectorComparisonOptions</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	706 693 <span class="c"># Setup supported bit vector similarity coefficients for bit vector strings...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	707 694 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	708 695
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	709 696 <span class="i">@SupportedComparisonMeasures</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	710 697 <span class="i">%SupportedComparisonMeasuresNameMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	711 698 <span class="i">%SupportedComparisonMeasuresMethodMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	712 699
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	713 700 <span class="k">for</span> <span class="i">$SupportedComparisonMeasure</span> <span class="s">(</span><span class="i">Fingerprints::FingerprintsBitVector::GetSupportedSimilarityCoefficients</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	714 701 <span class="c"># Similarity coefficient function/method names contain "Coefficient" in their names.</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	715 702 <span class="c"># So take 'em out and setup a map to original function/method name...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	716 703 <span class="i">$ComparisonMeasure</span> = <span class="i">$SupportedComparisonMeasure</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	717 704 <span class="i">$ComparisonMeasure</span> =~ <span class="q">s/Coefficient$//</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	718 705
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	719 706 <span class="k">push</span> <span class="i">@SupportedComparisonMeasures</span><span class="cm">,</span> <span class="i">$ComparisonMeasure</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	720 707 <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">$ComparisonMeasure</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	721 708 <span class="i">$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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	722 709 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	723 710
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	724 711 <span class="c"># Setup a list of similarity coefficients to use for calculating similarity matrices for bit vector strings...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	725 712 <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedMeasure</span><span class="cm">,</span> <span class="i">@SpecifiedComparisonMeasures</span><span class="cm">,</span> <span class="i">%SpecifiedComparisonMeasuresNameMap</span><span class="cm">,</span> <span class="i">%SpecifiedComparisonMeasuresMethodMap</span><span class="cm">,</span> <span class="i">%SpecifiedComparisonMeasuresParameterMap</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	726 713
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	727 714 <span class="i">@SpecifiedComparisonMeasures</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	728 715 <span class="i">%SpecifiedComparisonMeasuresNameMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	729 716 <span class="i">%SpecifiedComparisonMeasuresMethodMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	730 717 <span class="i">%SpecifiedComparisonMeasuresParameterMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	731 718
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	732 719 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">bitvectorcomparisonmode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	733 720 <span class="k">push</span> <span class="i">@SpecifiedComparisonMeasures</span><span class="cm">,</span> <span class="i">@SupportedComparisonMeasures</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	734 721 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	735 722 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	736 723 <span class="c"># Comma delimited list of similarity coefficients...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	737 724 <span class="k">my</span><span class="s">(</span><span class="i">$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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	738 725
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	739 726 <span class="i">$BitVectorComparisonMode</span> = <span class="i">$Options</span>{<span class="w">bitvectorcomparisonmode</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	740 727 <span class="i">$BitVectorComparisonMode</span> =~ <span class="q">s/ //g</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	741 728 <span class="i">@SpecifiedMeasures</span> = <span class="k">split</span> <span class="q">","</span><span class="cm">,</span> <span class="i">$BitVectorComparisonMode</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	742 729 <span class="i">@UnsupportedSpecifiedMeasures</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	743 730
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	744 731 <span class="k">for</span> <span class="i">$SpecifiedMeasure</span> <span class="s">(</span><span class="i">@SpecifiedMeasures</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	745 732 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$SupportedComparisonMeasuresMethodMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$SpecifiedMeasure</span><span class="s">)</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	746 733 <span class="k">push</span> <span class="i">@SpecifiedComparisonMeasures</span><span class="cm">,</span> <span class="i">$SpecifiedMeasure</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	747 734 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	748 735 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	749 736 <span class="k">push</span> <span class="i">@UnsupportedSpecifiedMeasures</span><span class="cm">,</span> <span class="i">$SpecifiedMeasure</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	750 737 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	751 738 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	752 739 <span class="k">if</span> <span class="s">(</span><span class="i">@UnsupportedSpecifiedMeasures</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	753 740 <span class="k">if</span> <span class="s">(</span><span class="i">@UnsupportedSpecifiedMeasures</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	754 741 <span class="k">warn</span> <span class="q">"Error: The values specified - "</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@UnsupportedSpecifiedMeasures</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span><span class="q">" - for option \"-b --BitVectorComparisonMode\" are not valid.\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	755 742 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	756 743 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	757 744 <span class="k">warn</span> <span class="q">"Error: The value specified, @UnsupportedSpecifiedMeasures, for option \"-b --BitVectorComparisonMode\" is not valid.\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	758 745 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	759 746 <span class="k">die</span> <span class="q">"Allowed values:"</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@SupportedComparisonMeasures</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	760 747 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	761 748 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	762 749 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	763 750 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	764 751 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	765 752 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	766 753
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	767 754 <span class="i">$OptionsInfo</span>{<span class="w">BitVectorComparisonMode</span>} = <span class="i">$Options</span>{<span class="w">bitvectorcomparisonmode</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	768 755 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedBitVectorComparisonsRef</span>} = \<span class="i">@SpecifiedComparisonMeasures</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	769 756 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedBitVectorComparisonsNameRef</span>} = \<span class="i">%SpecifiedComparisonMeasuresNameMap</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	770 757 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedBitVectorComparisonsMethodRef</span>} = \<span class="i">%SpecifiedComparisonMeasuresMethodMap</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	771 758
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	772 759 <span class="c"># Make sure valid alpha parameter is specified for Tversky calculation...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	773 760 <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedMeasure1</span><span class="cm">,</span> <span class="i">$SpecifiedMeasure2</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	774 761 <span class="i">$OptionsInfo</span>{<span class="w">Alpha</span>} = <span class="q">''</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	775 762 <span class="i">$SpecifiedMeasure1</span> = <span class="q">'TverskySimilarity'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	776 763 <span class="i">$SpecifiedMeasure2</span> = <span class="q">'WeightedTverskySimilarity'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	777 764 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	778 765 <span class="k">if</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">alpha</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	779 766 <span class="k">die</span> <span class="q">"Error: You must specify a value for \"-a, --alpha\" option in \"$SpecifiedMeasure1, $SpecifiedMeasure2, or All\" \"-m --mode\". \n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	780 767 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	781 768 <span class="k">my</span><span class="s">(</span><span class="i">$Alpha</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	782 769 <span class="i">$Alpha</span> = <span class="i">$Options</span>{<span class="w">alpha</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	783 770 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">IsFloat</span><span class="s">(</span><span class="i">$Alpha</span><span class="s">)</span> && <span class="i">$Alpha</span> >=<span class="n">0</span> && <span class="i">$Alpha</span> <= <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	784 771 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{alpha}, for option \"-a, --alpha\" is not valid. Allowed values: >= 0 and <= 1\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	785 772 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	786 773 <span class="i">$OptionsInfo</span>{<span class="w">Alpha</span>} = <span class="i">$Alpha</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	787 774 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	788 775
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	789 776 <span class="c"># Make sure valid beta parameter is specified for WeightedTanimoto and WeightedTversky</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	790 777 <span class="c"># calculations...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	791 778 <span class="i">$OptionsInfo</span>{<span class="w">Beta</span>} = <span class="q">''</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	792 779 <span class="i">$SpecifiedMeasure1</span> = <span class="q">'WeightedTverskySimilarity'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	793 780 <span class="i">$SpecifiedMeasure2</span> = <span class="q">'WeightedTanimotoSimilarity'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	794 781 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	795 782 <span class="k">if</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">beta</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	796 783 <span class="k">die</span> <span class="q">"Error: You must specify a value for \"-b, --beta\" option in \"$SpecifiedMeasure1, $SpecifiedMeasure2, or All\" \"-m --mode\". \n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	797 784 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	798 785 <span class="k">my</span><span class="s">(</span><span class="i">$Beta</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	799 786 <span class="i">$Beta</span> = <span class="i">$Options</span>{<span class="w">beta</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	800 787 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">IsFloat</span><span class="s">(</span><span class="i">$Beta</span><span class="s">)</span> && <span class="i">$Beta</span> >=<span class="n">0</span> && <span class="i">$Beta</span> <= <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	801 788 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{beta}, for option \"-b, --beta\" is not valid. Allowed values: >= 0 and <= 1\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	802 789 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	803 790 <span class="i">$OptionsInfo</span>{<span class="w">Beta</span>} = <span class="i">$Beta</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	804 791 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	805 792
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	806 793 <span class="c"># Setup any parameters required for specified comparison menthod...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	807 794 <span class="k">for</span> <span class="i">$SpecifiedMeasure</span> <span class="s">(</span><span class="i">@SpecifiedComparisonMeasures</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	808 795 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	809 796 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	810 797 <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">$OptionsInfo</span>{<span class="w">Alpha</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	811 798 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	812 799 <span class="k">elsif</span> <span class="s">(</span><span class="i">$SpecifiedMeasure</span> =~ <span class="q">/^WeightedTverskySimilarity$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	813 800 <span class="k">push</span> <span class="i">@</span>{<span class="i">$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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	814 801 <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">$OptionsInfo</span>{<span class="w">Beta</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	815 802 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	816 803 <span class="k">elsif</span> <span class="s">(</span><span class="i">$SpecifiedMeasure</span> =~ <span class="q">/^WeightedTanimotoSimilarity$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	817 804 <span class="k">push</span> <span class="i">@</span>{<span class="i">$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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	818 805 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	819 806 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	820 807 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedBitVectorComparisonsParameterRef</span>} = \<span class="i">%SpecifiedComparisonMeasuresParameterMap</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	821 808 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	822 809
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	823 810 <span class="c"># Process options related to comparion of vector strings...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	824 811 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	825 <a name="ProcessVectorComparisonOptions-"></a> 812 <span class="k">sub </span><span class="m">ProcessVectorComparisonOptions</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	826 813 <span class="c"># Setup specified similarity coefficients for vector strings..</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	827 814 <span class="k">my</span><span class="s">(</span><span class="i">$ComparisonMeasure</span><span class="cm">,</span> <span class="i">$SupportedComparisonMeasure</span><span class="cm">,</span> <span class="i">@SupportedComparisonMeasures</span><span class="cm">,</span> <span class="i">%SupportedComparisonMeasuresNameMap</span><span class="cm">,</span> <span class="i">%SupportedComparisonMeasuresMethodMap</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	828 815
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	829 816 <span class="i">@SupportedComparisonMeasures</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	830 817 <span class="i">%SupportedComparisonMeasuresNameMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	831 818 <span class="i">%SupportedComparisonMeasuresMethodMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	832 819 <span class="k">for</span> <span class="i">$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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	833 820 <span class="c"># Similarity and distance coefficient function/method names contain "Coefficient" in their names.</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	834 821 <span class="c"># So take 'em out and setup a map to original function/method name...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	835 822 <span class="i">$ComparisonMeasure</span> = <span class="i">$SupportedComparisonMeasure</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	836 823 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	837 824 <span class="i">$ComparisonMeasure</span> =~ <span class="q">s/Coefficient$//i</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	838 825 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	839 826 <span class="k">push</span> <span class="i">@SupportedComparisonMeasures</span><span class="cm">,</span> <span class="i">$ComparisonMeasure</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	840 827 <span class="i">$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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	841 828 <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">$SupportedComparisonMeasure</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	842 829 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	843 830
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	844 831 <span class="c"># Setup a list of similarity coefficients to use for calculating similarity matrices for bit vector strings...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	845 832 <span class="k">my</span><span class="s">(</span><span class="i">$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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	846 833
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	847 834 <span class="i">@SpecifiedComparisonMeasures</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	848 835 <span class="i">%SpecifiedComparisonMeasuresNameMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	849 836 <span class="i">%SpecifiedComparisonMeasuresMethodMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	850 837
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	851 838 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	852 839 <span class="k">push</span> <span class="i">@SpecifiedComparisonMeasures</span><span class="cm">,</span> <span class="i">@SupportedComparisonMeasures</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	853 840 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	854 841 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	855 842 <span class="c"># Comma delimited list of similarity coefficients...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	856 843 <span class="k">my</span><span class="s">(</span><span class="i">$VectorComparisonMode</span><span class="cm">,</span> <span class="i">@SpecifiedMeasures</span><span class="cm">,</span> <span class="i">@UnsupportedSpecifiedMeasures</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	857 844
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	858 845 <span class="i">$VectorComparisonMode</span> = <span class="i">$Options</span>{<span class="w">vectorcomparisonmode</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	859 846 <span class="i">$VectorComparisonMode</span> =~ <span class="q">s/ //g</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	860 847 <span class="i">@SpecifiedMeasures</span> = <span class="k">split</span> <span class="q">","</span><span class="cm">,</span> <span class="i">$VectorComparisonMode</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	861 848 <span class="i">@UnsupportedSpecifiedMeasures</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	862 849
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	863 850 <span class="k">for</span> <span class="i">$SpecifiedMeasure</span> <span class="s">(</span><span class="i">@SpecifiedMeasures</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	864 851 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	865 852 <span class="k">push</span> <span class="i">@SpecifiedComparisonMeasures</span><span class="cm">,</span> <span class="i">$SpecifiedMeasure</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	866 853 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	867 854 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	868 855 <span class="k">push</span> <span class="i">@UnsupportedSpecifiedMeasures</span><span class="cm">,</span> <span class="i">$SpecifiedMeasure</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	869 856 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	870 857 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	871 858 <span class="k">if</span> <span class="s">(</span><span class="i">@UnsupportedSpecifiedMeasures</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	872 859 <span class="k">if</span> <span class="s">(</span><span class="i">@UnsupportedSpecifiedMeasures</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	873 860 <span class="k">warn</span> <span class="q">"Error: The values specified - "</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@UnsupportedSpecifiedMeasures</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span><span class="q">" - for option \"-v --VectorComparisonMode\" are not valid.\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	874 861 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	875 862 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	876 863 <span class="k">warn</span> <span class="q">"Error: The value specified, @UnsupportedSpecifiedMeasures, for option \"-v --VectorComparisonMode\" is not valid.\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	877 864 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	878 865 <span class="k">die</span> <span class="q">"Allowed values:"</span><span class="cm">,</span> <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@SupportedComparisonMeasures</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	879 866 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	880 867 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	881 868 <span class="k">for</span> <span class="i">$SpecifiedMeasure</span> <span class="s">(</span><span class="i">@SpecifiedComparisonMeasures</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	882 869 <span class="i">$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">$SpecifiedMeasure</span><span class="s">)</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	883 870 <span class="i">$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">$SpecifiedMeasure</span><span class="s">)</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	884 871 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	885 872
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	886 873 <span class="i">$OptionsInfo</span>{<span class="w">VectorComparisonMode</span>} = <span class="i">$Options</span>{<span class="w">vectorcomparisonmode</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	887 874 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedVectorComparisonsRef</span>} = \<span class="i">@SpecifiedComparisonMeasures</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	888 875 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedVectorComparisonsNameRef</span>} = \<span class="i">%SpecifiedComparisonMeasuresNameMap</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	889 876 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedVectorComparisonsMethodRef</span>} = \<span class="i">%SpecifiedComparisonMeasuresMethodMap</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	890 877
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	891 878 <span class="c"># Setup specified vector comparison calculation modes...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	892 879 <span class="k">my</span><span class="s">(</span><span class="i">@SpecifiedVectorComparisonModes</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	893 880 <span class="i">@SpecifiedVectorComparisonModes</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	894 881 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	895 882 <span class="k">push</span> <span class="i">@SpecifiedVectorComparisonModes</span><span class="cm">,</span> <span class="s">(</span><span class="q">"AlgebraicForm"</span><span class="cm">,</span> <span class="q">"BinaryForm"</span><span class="cm">,</span> <span class="q">"SetTheoreticForm"</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	896 883 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	897 884 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	898 885 <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedFormulism</span><span class="cm">,</span> <span class="i">@SpecifiedFormulismWords</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	899 886
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	900 887 <span class="i">@SpecifiedFormulismWords</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">vectorcomparisonformulism</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	901 888 <span class="k">for</span> <span class="i">$SpecifiedFormulism</span> <span class="s">(</span><span class="i">@SpecifiedFormulismWords</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	902 889 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedFormulism</span> !~ <span class="q">/^(AlgebraicForm\|BinaryForm\|SetTheoreticForm)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	903 890 <span class="k">die</span> <span class="q">"Error: The value specified, $SpecifiedFormulism, for option \"--VectorComparisonFormulism\" is not valid. Allowed values: AlgebraicForm, BinaryForm or SetTheoreticForm\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	904 891 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	905 892 <span class="k">push</span> <span class="i">@SpecifiedVectorComparisonModes</span><span class="cm">,</span> <span class="i">$SpecifiedFormulism</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	906 893 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	907 894 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	908 895 <span class="i">$OptionsInfo</span>{<span class="w">VectorComparisonFormulism</span>} = <span class="i">$Options</span>{<span class="w">vectorcomparisonformulism</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	909 896 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedVectorComparisonModesRef</span>} = \<span class="i">@SpecifiedVectorComparisonModes</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	910 897
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	911 898 <span class="c"># Setup any parameters required for specified comparison menthod...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	912 899 <span class="k">for</span> <span class="i">$SpecifiedMeasure</span> <span class="s">(</span><span class="i">@SpecifiedComparisonMeasures</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	913 900 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	914 901 <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">$Options</span>{<span class="w">fast</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	915 902 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	916 903 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedVectorComparisonsParameterRef</span>} = \<span class="i">%SpecifiedComparisonMeasuresParameterMap</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	917 904 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	918 905
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	919 906 <span class="c"># Setup script usage and retrieve command line arguments specified using various options...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	920 <a name="SetupScriptUsage-"></a> 907 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	921 908
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	922 909 <span class="c"># Retrieve all the options...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	923 910 <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	924 911
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	925 912 <span class="i">$Options</span>{<span class="w">alpha</span>} = <span class="n">0.5</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	926 913 <span class="i">$Options</span>{<span class="w">beta</span>} = <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	927 914
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	928 915 <span class="i">$Options</span>{<span class="w">bitvectorcomparisonmode</span>} = <span class="q">"TanimotoSimilarity"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	929 916
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	930 917 <span class="i">$Options</span>{<span class="w">colmode</span>} = <span class="q">'colnum'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	931 918
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	932 919 <span class="i">$Options</span>{<span class="w">compoundidprefix</span>} = <span class="q">'Cmpd'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	933 920 <span class="i">$Options</span>{<span class="w">compoundidmode</span>} = <span class="q">'LabelPrefix'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	934 921
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	935 922 <span class="i">$Options</span>{<span class="w">detail</span>} = <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	936 923
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	937 924 <span class="i">$Options</span>{<span class="w">indelim</span>} = <span class="q">'comma'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	938 925 <span class="i">$Options</span>{<span class="w">outdelim</span>} = <span class="q">'comma'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	939 926
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	940 927 <span class="i">$Options</span>{<span class="w">inputdatamode</span>} = <span class="q">'LoadInMemory'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	941 928
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	942 929 <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">'AutoDetect'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	943 930
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	944 931 <span class="i">$Options</span>{<span class="w">outmatrixformat</span>} = <span class="q">'RowsAndColumns'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	945 932
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	946 933 <span class="i">$Options</span>{<span class="w">outmatrixtype</span>} = <span class="q">'FullMatrix'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	947 934
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	948 935 <span class="i">$Options</span>{<span class="w">quote</span>} = <span class="q">'yes'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	949 936 <span class="i">$Options</span>{<span class="w">precision</span>} = <span class="n">2</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	950 937
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	951 938 <span class="i">$Options</span>{<span class="w">vectorcomparisonmode</span>} = <span class="q">"TanimotoSimilarity"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	952 939 <span class="i">$Options</span>{<span class="w">vectorcomparisonformulism</span>} = <span class="q">"AlgebraicForm"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	953 940
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	954 941 <span class="k">if</span> <span class="s">(</span>!<span class="i">GetOptions</span><span class="s">(</span>\<span class="i">%Options</span><span class="cm">,</span> <span class="q">"alpha=f"</span><span class="cm">,</span> <span class="q">"beta=f"</span><span class="cm">,</span> <span class="q">"bitvectorcomparisonmode\|b=s"</span><span class="cm">,</span> <span class="q">"colmode\|c=s"</span><span class="cm">,</span> <span class="q">"compoundidcol=s"</span><span class="cm">,</span> <span class="q">"compoundidprefix=s"</span><span class="cm">,</span> <span class="q">"compoundidfield=s"</span><span class="cm">,</span> <span class="q">"compoundidmode=s"</span><span class="cm">,</span> <span class="q">"detail\|d=i"</span><span class="cm">,</span> <span class="q">"fast\|f"</span><span class="cm">,</span> <span class="q">"fingerprintscol=s"</span><span class="cm">,</span> <span class="q">"fingerprintsfield=s"</span><span class="cm">,</span> <span class="q">"help\|h"</span><span class="cm">,</span> <span class="q">"indelim=s"</span><span class="cm">,</span> <span class="q">"inputdatamode=s"</span><span class="cm">,</span> <span class="q">"mode\|m=s"</span><span class="cm">,</span> <span class="q">"outdelim=s"</span><span class="cm">,</span> <span class="q">"overwrite\|o"</span><span class="cm">,</span> <span class="q">"outmatrixformat=s"</span><span class="cm">,</span> <span class="q">"outmatrixtype=s"</span><span class="cm">,</span> <span class="q">"precision\|p=s"</span><span class="cm">,</span> <span class="q">"quote\|q=s"</span><span class="cm">,</span> <span class="q">"root\|r=s"</span><span class="cm">,</span> <span class="q">"vectorcomparisonmode\|v=s"</span><span class="cm">,</span> <span class="q">"vectorcomparisonformulism=s"</span><span class="cm">,</span> <span class="q">"workingdir\|w=s"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	955 942 <span class="k">die</span> <span class="q">"\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	956 943 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	957 944 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	958 945 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	959 946 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	960 947 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	961 948 <span class="k">chdir</span> <span class="i">$Options</span>{<span class="w">workingdir</span>} <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't chdir $Options{workingdir}: $! \n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	962 949 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	963 950 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">colmode</span>} !~ <span class="q">/^(ColNum\|ColLabel)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	964 951 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{colmode}, for option \"-c, --ColMode\" is not valid. Allowed values: ColNum, or ColLabel\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	965 952 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	966 953 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidmode</span>} !~ <span class="q">/^(DataField\|MolName\|LabelPrefix\|MolNameOrLabelPrefix)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	967 954 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{compoundidmode}, for option \"--CompoundIDMode\" is not valid. Allowed values: DataField, MolName, LabelPrefix or MolNameOrLabelPrefix\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	968 955 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	969 956 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">detail</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	970 957 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{detail}, for option \"-d, --detail\" is not valid. Allowed values: > 0 \n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	971 958 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	972 959 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">inputdatamode</span>} !~ <span class="q">/^(LoadInMemory\|ScanFile)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	973 960 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{inputdatamode}, for option \"--InputDataMode\" is not valid. Allowed values: LoadInMemory or ScanFile\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	974 961 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	975 962 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} !~ <span class="q">/^(AutoDetect\|FingerprintsBitVectorString\|FingerprintsVectorString)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	976 963 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{mode}, for option \"-m, --mode\" is not valid. Allowed values: AutoDetect, FingerprintsBitVectorString or FingerprintsVectorString \n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	977 964 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	978 965 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">indelim</span>} !~ <span class="q">/^(comma\|semicolon)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	979 966 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{indelim}, for option \"--InDelim\" is not valid. Allowed values: comma, or semicolon\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	980 967 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	981 968 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} !~ <span class="q">/^(comma\|semicolon\|tab)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	982 969 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{outdelim}, for option \"--OutDelim\" is not valid. Allowed values: comma, tab, or semicolon\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	983 970 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	984 971 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outmatrixformat</span>} !~ <span class="q">/^(RowsAndColumns\|IDPairsAndValue)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	985 972 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{outmatrixformat}, for option \"--OutMatrixFormat\" is not valid. Allowed values: RowsAndColumns or IDPairsAndValue\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	986 973 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	987 974 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outmatrixtype</span>} !~ <span class="q">/^(FullMatrix\|UpperTriangularMatrix\|LowerTriangularMatrix)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	988 975 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{outmatrixtype}, for option \"--OutMatrixType\" is not valid. Allowed values: FullMatrix, UpperTriangularMatrix or LowerTriangularMatrix\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	989 976 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	990 977 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">quote</span>} !~ <span class="q">/^(Yes\|No)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	991 978 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: Yes or No\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	992 979 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	993 980 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">precision</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	994 981 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{precision}, for option \"--precision\" is not valid. Allowed values: > 0 \n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	995 982 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	996 983 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	997 984
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	998 <a name="EOF-"></a></pre>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	999 <p> </p>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1000 <br />
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1001 <center>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1002 <img src="../../../images/h2o2.png">
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1003 </center>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1004 </body>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1005 </html>

Mercurial > repos > deepakjadmin > mayatool3_test3

annotate mayachemtools/docs/scripts/html/code/SimilarityMatricesFingerprints.html @ 3:e420415a1799 draft