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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/docs/scripts/html/code/ElementalAnalysisTextFiles.html Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,633 @@ +<html> +<head> +<title>MayaChemTools:Code:ElementalAnalysisTextFiles.pl</title> +<meta http-equiv="content-type" content="text/html;charset=utf-8"> +<link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> +</head> +<body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> +<br/> +<center> +<a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> +</center> +<br/> +<pre> + 1 #!/usr/bin/perl -w + 2 <span class="c">#</span> + 3 <span class="c"># $RCSfile: ElementalAnalysisTextFiles.pl,v $</span> + 4 <span class="c"># $Date: 2015/02/28 20:46:19 $</span> + 5 <span class="c"># $Revision: 1.28 $</span> + 6 <span class="c">#</span> + 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> + 8 <span class="c">#</span> + 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> + 10 <span class="c">#</span> + 11 <span class="c"># This file is part of MayaChemTools.</span> + 12 <span class="c">#</span> + 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> + 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> + 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> + 16 <span class="c"># later version.</span> + 17 <span class="c">#</span> + 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> + 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> + 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> + 21 <span class="c"># details.</span> + 22 <span class="c">#</span> + 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> + 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> + 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> + 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> + 27 <span class="c">#</span> + 28 + 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> + 30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">"$FindBin::Bin/../lib"</span><span class="sc">;</span> + 31 <span class="k">use</span> <span class="w">Getopt::Long</span><span class="sc">;</span> + 32 <span class="k">use</span> <span class="w">File::Basename</span><span class="sc">;</span> + 33 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span> + 34 <span class="k">use</span> <span class="w">Benchmark</span><span class="sc">;</span> + 35 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span> + 36 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span> + 37 <span class="k">use</span> <span class="w">MolecularFormula</span><span class="sc">;</span> + 38 + 39 <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> + 40 + 41 <span class="c"># Autoflush STDOUT</span> + 42 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span> + 43 + 44 <span class="c"># Starting message...</span> + 45 <span class="i">$ScriptName</span> = <span class="i">basename</span><span class="s">(</span><span class="i">$0</span><span class="s">)</span><span class="sc">;</span> + 46 <span class="k">print</span> <span class="q">"\n$ScriptName: Starting...\n\n"</span><span class="sc">;</span> + 47 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span> + 48 + 49 <span class="c"># Get the options and setup script...</span> + 50 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 51 <span class="k">if</span> <span class="s">(</span><span class="i">$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> + 52 <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> + 53 <span class="s">}</span> + 54 + 55 <span class="k">my</span><span class="s">(</span><span class="i">@TextFilesList</span><span class="s">)</span><span class="sc">;</span> + 56 <span class="i">@TextFilesList</span> = <span class="i">ExpandFileNames</span><span class="s">(</span>\<span class="i">@ARGV</span><span class="cm">,</span> <span class="q">"csv tsv"</span><span class="s">)</span><span class="sc">;</span> + 57 + 58 <span class="c"># Process options...</span> + 59 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span> + 60 <span class="k">print</span> <span class="q">"Processing options...\n"</span><span class="sc">;</span> + 61 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 62 + 63 <span class="k">print</span> <span class="q">"Checking input text file(s)...\n"</span><span class="sc">;</span> + 64 <span class="k">my</span><span class="s">(</span><span class="i">%TextFilesInfo</span><span class="s">)</span><span class="sc">;</span> + 65 <span class="i">RetrieveTextFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 66 <span class="i">RetrieveColumnsAndLabelsInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 67 + 68 <span class="c"># Generate output files...</span> + 69 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span> + 70 <span class="k">if</span> <span class="s">(</span><span class="i">@TextFilesList</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span> + 71 <span class="k">print</span> <span class="q">"\nProcessing text files...\n"</span><span class="sc">;</span> + 72 <span class="s">}</span> + 73 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#TextFilesList</span><span class="s">)</span> <span class="s">{</span> + 74 <span class="k">if</span> <span class="s">(</span><span class="i">$TextFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span> + 75 <span class="k">print</span> <span class="q">"\nProcessing file $TextFilesList[$FileIndex]...\n"</span><span class="sc">;</span> + 76 <span class="i">PerformElementalAnalysis</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span> + 77 <span class="s">}</span> + 78 <span class="s">}</span> + 79 <span class="k">print</span> <span class="q">"\n$ScriptName:Done...\n\n"</span><span class="sc">;</span> + 80 + 81 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span> + 82 <span class="i">$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> + 83 <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">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> + 84 + 85 <span class="c">###############################################################################</span> + 86 + 87 <span class="c"># Perform elemental analysis...</span> +<a name="PerformElementalAnalysis-"></a> 88 <span class="k">sub </span><span class="m">PerformElementalAnalysis</span> <span class="s">{</span> + 89 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 90 <span class="k">my</span><span class="s">(</span><span class="i">$TextFile</span><span class="cm">,</span> <span class="i">$NewTextFile</span><span class="cm">,</span> <span class="i">$FormulaCol</span><span class="cm">,</span> <span class="i">$Line</span><span class="cm">,</span> <span class="i">$NewLine</span><span class="cm">,</span> <span class="i">$FormulaColValue</span><span class="cm">,</span> <span class="i">$InDelim</span><span class="cm">,</span> <span class="i">$ColNum</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">$Status</span><span class="cm">,</span> <span class="i">$ErrorMsg</span><span class="cm">,</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">@ColNumsBeforeNew</span><span class="cm">,</span> <span class="i">@ColNumsAfterNew</span><span class="s">)</span><span class="sc">;</span> + 91 + 92 <span class="i">$TextFile</span> = <span class="i">$TextFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span> + 93 <span class="i">$InDelim</span> = <span class="i">$TextFilesInfo</span>{<span class="w">InDelim</span>}[<span class="i">$Index</span>]<span class="sc">;</span> + 94 <span class="i">$NewTextFile</span> = <span class="i">$TextFilesInfo</span>{<span class="w">OutFile</span>}[<span class="i">$Index</span>]<span class="sc">;</span> + 95 <span class="i">$FormulaCol</span> = <span class="i">$TextFilesInfo</span>{<span class="w">FormulaColNum</span>}[<span class="i">$Index</span>]<span class="sc">;</span> + 96 + 97 <span class="i">@ColNumsBeforeNew</span> = <span class="i">@</span>{<span class="i">$TextFilesInfo</span>{<span class="w">ColNumsBeforeNew</span>}[<span class="i">$Index</span>]}<span class="sc">;</span> + 98 <span class="i">@ColNumsAfterNew</span> = <span class="i">@</span>{<span class="i">$TextFilesInfo</span>{<span class="w">ColNumsAfterNew</span>}[<span class="i">$Index</span>]}<span class="sc">;</span> + 99 + 100 <span class="k">print</span> <span class="q">"Generating new Text file $NewTextFile...\n"</span><span class="sc">;</span> + 101 <span class="k">open</span> <span class="w">NEWTEXTFILE</span><span class="cm">,</span> <span class="q">">$NewTextFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't open $NewTextFile: $! \n"</span><span class="sc">;</span> + 102 <span class="k">open</span> <span class="w">TEXTFILE</span><span class="cm">,</span> <span class="q">"$TextFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $TextFile: $! \n"</span><span class="sc">;</span> + 103 + 104 <span class="c"># Skip over column labels from old file...</span> + 105 <span class="i">$Line</span> = <span class="i">GetTextLine</span><span class="s">(</span>\<span class="i">*TEXTFILE</span><span class="s">)</span><span class="sc">;</span> + 106 + 107 <span class="c"># Add column lablels in new file...</span> + 108 <span class="i">@ColLabels</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 109 <span class="k">for</span> <span class="i">$ColNum</span> <span class="s">(</span><span class="i">@ColNumsBeforeNew</span><span class="s">)</span> <span class="s">{</span> + 110 <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">$TextFilesInfo</span>{<span class="w">ColLabels</span>}[<span class="i">$Index</span>][<span class="i">$ColNum</span>]<span class="sc">;</span> + 111 <span class="s">}</span> + 112 <span class="k">for</span> <span class="i">$Value</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedCalculations</span>}}<span class="s">)</span> <span class="s">{</span> + 113 <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">$TextFilesInfo</span>{<span class="w">ValueLabelsMap</span>}[<span class="i">$Index</span>]{<span class="i">$Value</span>}<span class="sc">;</span> + 114 <span class="s">}</span> + 115 <span class="k">for</span> <span class="i">$ColNum</span> <span class="s">(</span><span class="i">@ColNumsAfterNew</span><span class="s">)</span> <span class="s">{</span> + 116 <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">$TextFilesInfo</span>{<span class="w">ColLabels</span>}[<span class="i">$Index</span>][<span class="i">$ColNum</span>]<span class="sc">;</span> + 117 <span class="s">}</span> + 118 <span class="i">$NewLine</span> = <span class="q">''</span><span class="sc">;</span> + 119 <span class="i">$NewLine</span> = <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>}<span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span> + 120 <span class="k">print</span> <span class="i">NEWTEXTFILE</span> <span class="q">"$NewLine\n"</span><span class="sc">;</span> + 121 + 122 <span class="c"># Go over all rows...</span> + 123 <span class="k">my</span><span class="s">(</span><span class="i">$LineCount</span><span class="cm">,</span> <span class="i">$ElementsRef</span><span class="cm">,</span> <span class="i">$ElementCompositionRef</span><span class="cm">,</span> <span class="i">$CalculationType</span><span class="cm">,</span> <span class="i">$CalculatedValue</span><span class="cm">,</span> <span class="i">@CalculatedValues</span><span class="s">)</span><span class="sc">;</span> + 124 + 125 <span class="i">$LineCount</span> = <span class="n">1</span><span class="sc">;</span> + 126 <span class="j">TEXTLINE:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$Line</span> = <span class="i">GetTextLine</span><span class="s">(</span>\<span class="i">*TEXTFILE</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 127 <span class="i">@LineWords</span> = <span class="i">quotewords</span><span class="s">(</span><span class="i">$InDelim</span><span class="cm">,</span> <span class="n">0</span><span class="cm">,</span> <span class="i">$Line</span><span class="s">)</span><span class="sc">;</span> + 128 <span class="i">$LineCount</span>++<span class="sc">;</span> + 129 + 130 <span class="i">@CalculatedValues</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 131 <span class="k">for</span> <span class="i">$Value</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedCalculations</span>}}<span class="s">)</span> <span class="s">{</span> + 132 <span class="k">push</span> <span class="i">@CalculatedValues</span><span class="cm">,</span> <span class="q">''</span><span class="sc">;</span> + 133 <span class="s">}</span> + 134 <span class="k">if</span> <span class="s">(</span><span class="i">$FormulaCol</span> > <span class="i">@LineWords</span><span class="s">)</span> <span class="s">{</span> + 135 <span class="i">$ErrorMsg</span> = <span class="q">"Ignoring line $LineCount: Formula column $ColLabels[$FormulaCol] not found"</span><span class="sc">;</span> + 136 <span class="i">PrintErrorMsg</span><span class="s">(</span><span class="i">$Line</span><span class="cm">,</span> <span class="i">$ErrorMsg</span><span class="s">)</span><span class="sc">;</span> + 137 <span class="i">ComposeAndWriteNewLine</span><span class="s">(</span>\<span class="i">*NEWTEXTFILE</span><span class="cm">,</span> \<span class="i">@LineWords</span><span class="cm">,</span> \<span class="i">@ColNumsBeforeNew</span><span class="cm">,</span> \<span class="i">@ColNumsAfterNew</span><span class="cm">,</span> \<span class="i">@CalculatedValues</span><span class="s">)</span><span class="sc">;</span> + 138 <span class="k">next</span> <span class="j">TEXTLINE</span><span class="sc">;</span> + 139 <span class="s">}</span> + 140 + 141 <span class="c"># Make sure it's a valid molecular formula...</span> + 142 <span class="i">$FormulaColValue</span> = <span class="i">$LineWords</span>[<span class="i">$FormulaCol</span>]<span class="sc">;</span> + 143 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CheckFormula</span>}<span class="s">)</span> <span class="s">{</span> + 144 <span class="s">(</span><span class="i">$Status</span><span class="cm">,</span> <span class="i">$ErrorMsg</span><span class="s">)</span> = <span class="i">MolecularFormula::IsMolecularFormula</span><span class="s">(</span><span class="i">$FormulaColValue</span><span class="s">)</span><span class="sc">;</span> + 145 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Status</span><span class="s">)</span> <span class="s">{</span> + 146 <span class="i">$ErrorMsg</span> = <span class="q">"Ignoring line $LineCount: Formula column $ColLabels[$FormulaCol] value is not valid: $ErrorMsg"</span><span class="sc">;</span> + 147 <span class="i">PrintErrorMsg</span><span class="s">(</span><span class="i">$Line</span><span class="cm">,</span> <span class="i">$ErrorMsg</span><span class="s">)</span><span class="sc">;</span> + 148 <span class="i">ComposeAndWriteNewLine</span><span class="s">(</span>\<span class="i">*NEWTEXTFILE</span><span class="cm">,</span> \<span class="i">@LineWords</span><span class="cm">,</span> \<span class="i">@ColNumsBeforeNew</span><span class="cm">,</span> \<span class="i">@ColNumsAfterNew</span><span class="cm">,</span> \<span class="i">@CalculatedValues</span><span class="s">)</span><span class="sc">;</span> + 149 <span class="k">next</span> <span class="j">TEXTLINE</span><span class="sc">;</span> + 150 <span class="s">}</span> + 151 <span class="s">}</span> + 152 + 153 <span class="c"># Calculate appropriate values and write 'em out...</span> + 154 <span class="i">@CalculatedValues</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 155 <span class="k">for</span> <span class="i">$CalculationType</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedCalculations</span>}}<span class="s">)</span> <span class="s">{</span> + 156 <span class="k">if</span> <span class="s">(</span><span class="i">$CalculationType</span> =~ <span class="q">/^ElementalAnalysis$/i</span><span class="s">)</span> <span class="s">{</span> + 157 <span class="s">(</span><span class="i">$ElementsRef</span><span class="cm">,</span> <span class="i">$ElementCompositionRef</span><span class="s">)</span> = <span class="i">MolecularFormula::CalculateElementalComposition</span><span class="s">(</span><span class="i">$FormulaColValue</span><span class="s">)</span><span class="sc">;</span> + 158 <span class="i">$CalculatedValue</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$ElementsRef</span><span class="s">)</span> && <span class="k">defined</span><span class="s">(</span><span class="i">$ElementCompositionRef</span><span class="s">)</span><span class="s">)</span> ? <span class="i">MolecularFormula::FormatCompositionInfomation</span><span class="s">(</span><span class="i">$ElementsRef</span><span class="cm">,</span> <span class="i">$ElementCompositionRef</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">Precision</span>}<span class="s">)</span> <span class="co">:</span> <span class="q">''</span><span class="sc">;</span> + 159 <span class="s">}</span> + 160 <span class="k">elsif</span> <span class="s">(</span><span class="i">$CalculationType</span> =~ <span class="q">/^MolecularWeight$/i</span><span class="s">)</span> <span class="s">{</span> + 161 <span class="i">$CalculatedValue</span> = <span class="i">MolecularFormula::CalculateMolecularWeight</span><span class="s">(</span><span class="i">$FormulaColValue</span><span class="s">)</span><span class="sc">;</span> + 162 <span class="i">$CalculatedValue</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$CalculatedValue</span><span class="s">)</span> && <span class="k">length</span><span class="s">(</span><span class="i">$CalculatedValue</span><span class="s">)</span><span class="s">)</span> ? <span class="s">(</span><span class="k">sprintf</span><span class="s">(</span><span class="q">"%.$OptionsInfo{Precision}f"</span><span class="cm">,</span> <span class="i">$CalculatedValue</span><span class="s">)</span><span class="s">)</span> <span class="co">:</span> <span class="q">""</span><span class="sc">;</span> + 163 <span class="s">}</span> + 164 <span class="k">elsif</span> <span class="s">(</span><span class="i">$CalculationType</span> =~ <span class="q">/^ExactMass$/i</span><span class="s">)</span> <span class="s">{</span> + 165 <span class="i">$CalculatedValue</span> = <span class="i">MolecularFormula::CalculateExactMass</span><span class="s">(</span><span class="i">$FormulaColValue</span><span class="s">)</span><span class="sc">;</span> + 166 <span class="i">$CalculatedValue</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$CalculatedValue</span><span class="s">)</span> && <span class="k">length</span><span class="s">(</span><span class="i">$CalculatedValue</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">"%.$OptionsInfo{Precision}f"</span><span class="cm">,</span> <span class="i">$CalculatedValue</span><span class="s">)</span><span class="s">)</span> <span class="co">:</span> <span class="q">""</span><span class="sc">;</span> + 167 <span class="s">}</span> + 168 <span class="k">else</span> <span class="s">{</span> + 169 <span class="i">$CalculatedValue</span> = <span class="q">''</span><span class="sc">;</span> + 170 <span class="s">}</span> + 171 <span class="k">push</span> <span class="i">@CalculatedValues</span><span class="cm">,</span> <span class="i">$CalculatedValue</span><span class="sc">;</span> + 172 <span class="s">}</span> + 173 + 174 <span class="i">ComposeAndWriteNewLine</span><span class="s">(</span>\<span class="i">*NEWTEXTFILE</span><span class="cm">,</span> \<span class="i">@LineWords</span><span class="cm">,</span> \<span class="i">@ColNumsBeforeNew</span><span class="cm">,</span> \<span class="i">@ColNumsAfterNew</span><span class="cm">,</span> \<span class="i">@CalculatedValues</span><span class="s">)</span><span class="sc">;</span> + 175 <span class="s">}</span> + 176 <span class="k">close</span> <span class="w">NEWTEXTFILE</span><span class="sc">;</span> + 177 <span class="k">close</span> <span class="w">TEXTFILE</span><span class="sc">;</span> + 178 + 179 <span class="s">}</span> + 180 + 181 <span class="c"># Write out new line using old and new calculated data...</span> +<a name="ComposeAndWriteNewLine-"></a> 182 <span class="k">sub </span><span class="m">ComposeAndWriteNewLine</span> <span class="s">{</span> + 183 <span class="k">my</span><span class="s">(</span><span class="i">$NewTextFileRef</span><span class="cm">,</span> <span class="i">$OldLineWordsRef</span><span class="cm">,</span> <span class="i">$ColNumsBeforeNewRef</span><span class="cm">,</span> <span class="i">$ColNumsAfterNewRef</span><span class="cm">,</span> <span class="i">$CalculatedValuesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 184 <span class="k">my</span><span class="s">(</span><span class="i">$NewLine</span><span class="cm">,</span> <span class="i">$ColNum</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">@NewLineWords</span><span class="s">)</span><span class="sc">;</span> + 185 + 186 <span class="i">@NewLineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 187 <span class="k">for</span> <span class="i">$ColNum</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ColNumsBeforeNewRef</span>}<span class="s">)</span> <span class="s">{</span> + 188 <span class="k">push</span> <span class="i">@NewLineWords</span><span class="cm">,</span> <span class="i">$OldLineWordsRef</span>->[<span class="i">$ColNum</span>]<span class="sc">;</span> + 189 <span class="s">}</span> + 190 <span class="k">for</span> <span class="i">$Value</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$CalculatedValuesRef</span>}<span class="s">)</span> <span class="s">{</span> + 191 <span class="k">push</span> <span class="i">@NewLineWords</span><span class="cm">,</span> <span class="i">$Value</span><span class="sc">;</span> + 192 <span class="s">}</span> + 193 <span class="k">for</span> <span class="i">$ColNum</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ColNumsAfterNewRef</span>}<span class="s">)</span> <span class="s">{</span> + 194 <span class="k">push</span> <span class="i">@NewLineWords</span><span class="cm">,</span> <span class="i">$OldLineWordsRef</span>->[<span class="i">$ColNum</span>]<span class="sc">;</span> + 195 <span class="s">}</span> + 196 <span class="i">$NewLine</span> = <span class="i">JoinWords</span><span class="s">(</span>\<span class="i">@NewLineWords</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> + 197 <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="q">"$NewLine\n"</span><span class="sc">;</span> + 198 <span class="s">}</span> + 199 + 200 <span class="c"># Print out error message...</span> +<a name="PrintErrorMsg-"></a> 201 <span class="k">sub </span><span class="m">PrintErrorMsg</span> <span class="s">{</span> + 202 <span class="k">my</span><span class="s">(</span><span class="i">$Line</span><span class="cm">,</span> <span class="i">$ErrorMsg</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 203 + 204 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} >= <span class="n">2</span> <span class="s">)</span> <span class="s">{</span> + 205 <span class="k">print</span> <span class="q">"$ErrorMsg: $Line\n"</span><span class="sc">;</span> + 206 <span class="s">}</span> + 207 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} >= <span class="n">1</span><span class="s">)</span> <span class="s">{</span> + 208 <span class="k">print</span> <span class="q">"$ErrorMsg\n"</span><span class="sc">;</span> + 209 <span class="s">}</span> + 210 <span class="s">}</span> + 211 + 212 <span class="c"># Process formula columns and other information...</span> +<a name="RetrieveColumnsAndLabelsInfo-"></a> 213 <span class="k">sub </span><span class="m">RetrieveColumnsAndLabelsInfo</span> <span class="s">{</span> + 214 <span class="i">RetrieveFormulaColumnsInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 215 <span class="i">RetrieveStartColumnsAndValueLabelsInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 216 <span class="s">}</span> + 217 + 218 <span class="c"># Make sure specified formula column are okay...</span> +<a name="RetrieveFormulaColumnsInfo-"></a> 219 <span class="k">sub </span><span class="m">RetrieveFormulaColumnsInfo</span> <span class="s">{</span> + 220 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$TextFile</span><span class="s">)</span><span class="sc">;</span> + 221 + 222 <span class="i">@</span>{<span class="i">$TextFilesInfo</span>{<span class="w">FormulaColNum</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 223 + 224 <span class="j">FILELIST:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#TextFilesList</span><span class="s">)</span> <span class="s">{</span> + 225 <span class="i">$TextFile</span> = <span class="i">$TextFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span> + 226 + 227 <span class="i">$TextFilesInfo</span>{<span class="w">FormulaColNum</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span> + 228 + 229 <span class="k">if</span> <span class="s">(</span><span class="i">$TextFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>]<span class="s">)</span> <span class="s">{</span> + 230 <span class="k">my</span><span class="s">(</span><span class="i">$FormulaColNum</span><span class="cm">,</span> <span class="i">$FormulaColValid</span><span class="s">)</span><span class="sc">;</span> + 231 + 232 <span class="i">$FormulaColNum</span> = <span class="n">0</span><span class="sc">;</span> + 233 <span class="i">$FormulaColValid</span> = <span class="n">0</span><span class="sc">;</span> + 234 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SpecifiedFormulaCol</span>}<span class="s">)</span> <span class="s">{</span> + 235 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ColMode</span>} =~ <span class="q">/^colnum$/i</span><span class="s">)</span> <span class="s">{</span> + 236 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SpecifiedFormulaCol</span>} <= <span class="i">$TextFilesInfo</span>{<span class="w">ColCount</span>}[<span class="i">$Index</span>]<span class="s">)</span> <span class="s">{</span> + 237 <span class="i">$FormulaColNum</span> = <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedFormulaCol</span>} - <span class="n">1</span><span class="sc">;</span> + 238 <span class="i">$FormulaColValid</span> = <span class="n">1</span><span class="sc">;</span> + 239 <span class="s">}</span> + 240 <span class="s">}</span> + 241 <span class="k">else</span> <span class="s">{</span> + 242 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$TextFilesInfo</span>{<span class="w">ColLabelToNumMap</span>}[<span class="i">$Index</span>]{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedFormulaCol</span>}}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 243 <span class="i">$FormulaColNum</span> = <span class="i">$TextFilesInfo</span>{<span class="w">ColLabelToNumMap</span>}[<span class="i">$Index</span>]{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedFormulaCol</span>}}<span class="sc">;</span> + 244 <span class="i">$FormulaColValid</span> = <span class="n">1</span><span class="sc">;</span> + 245 <span class="s">}</span> + 246 <span class="s">}</span> + 247 <span class="s">}</span> + 248 <span class="k">else</span> <span class="s">{</span> + 249 <span class="c"># Grab the first column with the word Formula in its label...</span> + 250 <span class="k">my</span><span class="s">(</span><span class="i">$ColLabel</span><span class="s">)</span><span class="sc">;</span> + 251 <span class="j">LABEL:</span> <span class="k">for</span> <span class="i">$ColLabel</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$TextFilesInfo</span>{<span class="w">ColLabels</span>}[<span class="i">$Index</span>]}<span class="s">)</span> <span class="s">{</span> + 252 <span class="k">if</span> <span class="s">(</span><span class="i">$ColLabel</span> =~ <span class="q">/Formula/i</span><span class="s">)</span> <span class="s">{</span> + 253 <span class="i">$FormulaColNum</span> = <span class="i">$TextFilesInfo</span>{<span class="w">ColLabelToNumMap</span>}[<span class="i">$Index</span>]{<span class="i">$ColLabel</span>}<span class="sc">;</span> + 254 <span class="i">$FormulaColValid</span> = <span class="n">1</span><span class="sc">;</span> + 255 <span class="k">last</span> <span class="j">LABEL</span><span class="sc">;</span> + 256 <span class="s">}</span> + 257 <span class="s">}</span> + 258 <span class="s">}</span> + 259 <span class="k">if</span> <span class="s">(</span><span class="i">$FormulaColValid</span><span class="s">)</span> <span class="s">{</span> + 260 <span class="i">$TextFilesInfo</span>{<span class="w">FormulaColNum</span>}[<span class="i">$Index</span>] = <span class="i">$FormulaColNum</span><span class="sc">;</span> + 261 <span class="s">}</span> + 262 <span class="k">else</span> <span class="s">{</span> + 263 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SpecifiedFormulaCol</span>}<span class="s">)</span> <span class="s">{</span> + 264 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $TextFile: Formula column specified, $OptionsInfo{SpecifiedFormulaCol}, using \"f --formulacol\" option doesn't exist\n"</span><span class="sc">;</span> + 265 <span class="s">}</span> + 266 <span class="k">else</span> <span class="s">{</span> + 267 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $TextFile: Column label containing the word Formula doesn't exist\n"</span><span class="sc">;</span> + 268 <span class="s">}</span> + 269 <span class="i">$TextFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span> + 270 <span class="s">}</span> + 271 <span class="s">}</span> + 272 <span class="s">}</span> + 273 <span class="s">}</span> + 274 + 275 <span class="c"># Setup starting column number for adding calculated values and</span> + 276 <span class="c"># column lables to use for these values...</span> +<a name="RetrieveStartColumnsAndValueLabelsInfo-"></a> 277 <span class="k">sub </span><span class="m">RetrieveStartColumnsAndValueLabelsInfo</span> <span class="s">{</span> + 278 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$TextFile</span><span class="cm">,</span> <span class="i">$SpecifiedStartColNum</span><span class="cm">,</span> <span class="i">$StartColNum</span><span class="cm">,</span> <span class="i">$Label</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">$NewLabel</span><span class="cm">,</span> <span class="i">$Count</span><span class="cm">,</span> <span class="i">$BeforeStartColNum</span><span class="cm">,</span> <span class="i">$AfterStartColNum</span><span class="cm">,</span> <span class="i">$FirstColNum</span><span class="cm">,</span> <span class="i">$LastColNum</span><span class="cm">,</span> <span class="i">$ColNum</span><span class="cm">,</span> <span class="i">$Part1StartColNum</span><span class="cm">,</span> <span class="i">$Part1EndColNum</span><span class="cm">,</span> <span class="i">$Part2StartColNum</span><span class="cm">,</span> <span class="i">$Part2EndColNum</span><span class="cm">,</span> <span class="i">@Part1ColNums</span><span class="cm">,</span> <span class="i">@Part2ColNums</span><span class="s">)</span><span class="sc">;</span> + 279 + 280 <span class="c"># Start column number for inserting new values...</span> + 281 <span class="i">$SpecifiedStartColNum</span> = <span class="q">"last"</span><span class="sc">;</span> + 282 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">StartCol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 283 <span class="k">if</span> <span class="s">(</span><span class="k">length</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">StartCol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 284 <span class="i">$SpecifiedStartColNum</span> = <span class="i">$OptionsInfo</span>{<span class="w">StartCol</span>} + 285 <span class="s">}</span> + 286 <span class="s">}</span> + 287 + 288 <span class="c"># Column labels for for new calculated values...</span> + 289 <span class="k">my</span><span class="s">(</span><span class="i">%NewValueLabels</span><span class="s">)</span> = <span class="s">(</span><span class="w">ElementalAnalysis</span> <span class="cm">=></span> <span class="q">'ElementalAnalysis'</span><span class="cm">,</span> <span class="w">MolecularWeight</span> <span class="cm">=></span> <span class="q">'MolecularWeight'</span><span class="cm">,</span> <span class="w">ExactMass</span> <span class="cm">=></span> <span class="q">'ExactMass'</span><span class="s">)</span><span class="sc">;</span> + 290 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedValueLabels</span>}}<span class="s">)</span> <span class="s">{</span> + 291 <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$Index</span> < <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedValueLabels</span>}}<span class="sc">;</span> <span class="i">$Index</span> +=<span class="n">2</span><span class="s">)</span> <span class="s">{</span> + 292 <span class="i">$Value</span> = <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedValueLabels</span>}[<span class="i">$Index</span>]<span class="sc">;</span> + 293 <span class="i">$Label</span> = <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedValueLabels</span>}[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span> + 294 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$NewValueLabels</span>{<span class="i">$Value</span>}<span class="s">)</span> <span class="s">{</span> + 295 <span class="i">$NewValueLabels</span>{<span class="i">$Value</span>} = <span class="i">$Label</span><span class="sc">;</span> + 296 <span class="s">}</span> + 297 <span class="s">}</span> + 298 <span class="s">}</span> + 299 + 300 <span class="i">@</span>{<span class="i">$TextFilesInfo</span>{<span class="w">ColNumsBeforeNew</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 301 <span class="i">@</span>{<span class="i">$TextFilesInfo</span>{<span class="w">ColNumsAfterNew</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 302 <span class="i">@</span>{<span class="i">$TextFilesInfo</span>{<span class="w">ValueLabelsMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 303 + 304 <span class="j">FILELIST:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#TextFilesList</span><span class="s">)</span> <span class="s">{</span> + 305 <span class="i">$TextFile</span> = <span class="i">$TextFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span> + 306 + 307 <span class="i">@</span>{<span class="i">$TextFilesInfo</span>{<span class="w">ColNumsBeforeNew</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 308 <span class="i">@</span>{<span class="i">$TextFilesInfo</span>{<span class="w">ColNumsAfterNew</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 309 <span class="i">%</span>{<span class="i">$TextFilesInfo</span>{<span class="w">ValueLabelsMap</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 310 + 311 <span class="k">if</span> <span class="s">(</span>!<span class="i">$TextFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>]<span class="s">)</span> <span class="s">{</span> + 312 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> + 313 <span class="s">}</span> + 314 + 315 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedStartColNum</span> !~ <span class="q">/^last$/i</span><span class="s">)</span> <span class="s">{</span> + 316 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ColMode</span>} =~ <span class="q">/^collabel$/i</span><span class="s">)</span> <span class="s">{</span> + 317 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$TextFilesInfo</span>{<span class="w">ColLabelToNumMap</span>}[<span class="i">$Index</span>]{<span class="i">$SpecifiedStartColNum</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 318 <span class="i">$StartColNum</span> = <span class="i">$TextFilesInfo</span>{<span class="w">ColLabelToNumMap</span>}[<span class="i">$Index</span>]{<span class="i">$SpecifiedStartColNum</span>}<span class="sc">;</span> + 319 <span class="s">}</span> + 320 <span class="k">else</span> <span class="s">{</span> + 321 <span class="k">die</span> <span class="q">"Error: Invalid value $SpecifiedStartColNum specified using \"-s --startcol\" option: column name doesn't exist in $TextFile \n"</span><span class="sc">;</span> + 322 <span class="s">}</span> + 323 <span class="s">}</span> + 324 <span class="k">else</span> <span class="s">{</span> + 325 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedStartColNum</span> > <span class="n">0</span> && <span class="i">$SpecifiedStartColNum</span> <= <span class="i">$TextFilesInfo</span>{<span class="w">ColCount</span>}[<span class="i">$Index</span>]<span class="s">)</span> <span class="s">{</span> + 326 <span class="i">$StartColNum</span> -= <span class="n">1</span><span class="sc">;</span> + 327 <span class="s">}</span> + 328 <span class="k">else</span> <span class="s">{</span> + 329 <span class="k">die</span> <span class="q">"Error: Invalid value $SpecifiedStartColNum specified using \"-s --startcol\" option: column number doesn't exist in $TextFile \n"</span><span class="sc">;</span> + 330 <span class="s">}</span> + 331 <span class="s">}</span> + 332 <span class="s">}</span> + 333 <span class="k">else</span> <span class="s">{</span> + 334 <span class="i">$StartColNum</span> = <span class="i">$TextFilesInfo</span>{<span class="w">ColCount</span>}[<span class="i">$Index</span>] - <span class="n">1</span><span class="sc">;</span> + 335 <span class="s">}</span> + 336 <span class="c"># Set up columns lists for before and after the addition of calculated column values</span> + 337 <span class="c"># for each text file...</span> + 338 <span class="k">my</span><span class="s">(</span><span class="i">$BeforeStartColNum</span><span class="cm">,</span> <span class="i">$AfterStartColNum</span><span class="cm">,</span> <span class="i">$FirstColNum</span><span class="cm">,</span> <span class="i">$LastColNum</span><span class="cm">,</span> <span class="i">$ColNum</span><span class="cm">,</span> <span class="i">$Part1StartColNum</span><span class="cm">,</span> <span class="i">$Part1EndColNum</span><span class="cm">,</span> <span class="i">$Part2StartColNum</span><span class="cm">,</span> <span class="i">$Part2EndColNum</span><span class="cm">,</span> <span class="i">@Part1ColNums</span><span class="cm">,</span> <span class="i">@Part2ColNums</span><span class="s">)</span><span class="sc">;</span> + 339 + 340 <span class="i">$FirstColNum</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$LastColNum</span> = <span class="i">$TextFilesInfo</span>{<span class="w">ColCount</span>}[<span class="i">$Index</span>] - <span class="n">1</span><span class="sc">;</span> + 341 + 342 <span class="i">$BeforeStartColNum</span> = <span class="i">$StartColNum</span> - <span class="n">1</span><span class="sc">;</span> + 343 <span class="i">$AfterStartColNum</span> = <span class="i">$StartColNum</span> + <span class="n">1</span><span class="sc">;</span> + 344 + 345 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">StartColMode</span>} =~ <span class="q">/^after$/i</span><span class="s">)</span> <span class="s">{</span> + 346 <span class="i">$Part1StartColNum</span> = <span class="i">$FirstColNum</span><span class="sc">;</span> <span class="i">$Part1EndColNum</span> = <span class="i">$StartColNum</span><span class="sc">;</span> + 347 <span class="i">$Part2StartColNum</span> = <span class="i">$AfterStartColNum</span><span class="sc">;</span> <span class="i">$Part2EndColNum</span> = <span class="i">$LastColNum</span><span class="sc">;</span> + 348 <span class="s">}</span> + 349 <span class="k">else</span> <span class="s">{</span> + 350 <span class="i">$Part1StartColNum</span> = <span class="i">$FirstColNum</span><span class="sc">;</span> <span class="i">$Part1EndColNum</span> = <span class="i">$BeforeStartColNum</span><span class="sc">;</span> + 351 <span class="i">$Part2StartColNum</span> = <span class="i">$StartColNum</span><span class="sc">;</span> <span class="i">$Part2EndColNum</span> = <span class="i">$LastColNum</span><span class="sc">;</span> + 352 <span class="s">}</span> + 353 <span class="i">@Part1ColNums</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@Part2ColNums</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 354 <span class="k">for</span> <span class="i">$ColNum</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$TextFilesInfo</span>{<span class="w">ColCount</span>}[<span class="i">$Index</span>]<span class="s">)</span> <span class="s">{</span> + 355 <span class="k">if</span> <span class="s">(</span><span class="i">$ColNum</span> >= <span class="i">$Part1StartColNum</span> && <span class="i">$ColNum</span> <= <span class="i">$Part1EndColNum</span><span class="s">)</span> <span class="s">{</span> + 356 <span class="k">push</span> <span class="i">@Part1ColNums</span><span class="cm">,</span> <span class="i">$ColNum</span><span class="sc">;</span> + 357 <span class="s">}</span> + 358 <span class="s">}</span> + 359 <span class="k">for</span> <span class="i">$ColNum</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$TextFilesInfo</span>{<span class="w">ColCount</span>}[<span class="i">$Index</span>]<span class="s">)</span> <span class="s">{</span> + 360 <span class="k">if</span> <span class="s">(</span><span class="i">$ColNum</span> >= <span class="i">$Part2StartColNum</span> && <span class="i">$ColNum</span> <= <span class="i">$Part2EndColNum</span><span class="s">)</span> <span class="s">{</span> + 361 <span class="k">push</span> <span class="i">@Part2ColNums</span><span class="cm">,</span> <span class="i">$ColNum</span><span class="sc">;</span> + 362 <span class="s">}</span> + 363 <span class="s">}</span> + 364 <span class="k">push</span> <span class="i">@</span>{<span class="i">$TextFilesInfo</span>{<span class="w">ColNumsBeforeNew</span>}[<span class="i">$Index</span>]}<span class="cm">,</span> <span class="i">@Part1ColNums</span><span class="sc">;</span> + 365 <span class="k">push</span> <span class="i">@</span>{<span class="i">$TextFilesInfo</span>{<span class="w">ColNumsAfterNew</span>}[<span class="i">$Index</span>]}<span class="cm">,</span> <span class="i">@Part2ColNums</span><span class="sc">;</span> + 366 + 367 <span class="c"># Setup column labels for calculated values...</span> + 368 <span class="k">for</span> <span class="i">$Value</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%NewValueLabels</span><span class="s">)</span> <span class="s">{</span> + 369 <span class="i">$Label</span> = <span class="i">$NewValueLabels</span>{<span class="i">$Value</span>}<span class="sc">;</span> + 370 + 371 <span class="c"># Make sure it doesn't already exists...</span> + 372 <span class="i">$Count</span> = <span class="n">1</span><span class="sc">;</span> + 373 <span class="i">$NewLabel</span> = <span class="i">$Label</span><span class="sc">;</span> + 374 <span class="k">while</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$TextFilesInfo</span>{<span class="w">ColLabelToNumMap</span>}[<span class="i">$Index</span>]{<span class="i">$NewLabel</span>}<span class="s">)</span> <span class="s">{</span> + 375 <span class="i">$Count</span>++<span class="sc">;</span> + 376 <span class="i">$NewLabel</span> = <span class="i">$Label</span> . <span class="i">$Count</span><span class="sc">;</span> + 377 <span class="s">}</span> + 378 <span class="i">$TextFilesInfo</span>{<span class="w">ValueLabelsMap</span>}[<span class="i">$Index</span>]{<span class="i">$Value</span>} = <span class="i">$NewLabel</span><span class="sc">;</span> + 379 <span class="s">}</span> + 380 <span class="s">}</span> + 381 <span class="s">}</span> + 382 + 383 <span class="c"># Retrieve information about input text files...</span> +<a name="RetrieveTextFilesInfo-"></a> 384 <span class="k">sub </span><span class="m">RetrieveTextFilesInfo</span> <span class="s">{</span> + 385 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$TextFile</span><span class="cm">,</span> <span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="cm">,</span> <span class="i">$InDelim</span><span class="cm">,</span> <span class="i">$Line</span><span class="cm">,</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">$OutFileRoot</span><span class="cm">,</span> <span class="i">$OutFile</span><span class="cm">,</span> <span class="i">$ColNum</span><span class="cm">,</span> <span class="i">$ColLabel</span><span class="s">)</span><span class="sc">;</span> + 386 + 387 <span class="i">%TextFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 388 + 389 <span class="i">@</span>{<span class="i">$TextFilesInfo</span>{<span class="w">FileOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 390 <span class="i">@</span>{<span class="i">$TextFilesInfo</span>{<span class="w">ColCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 391 <span class="i">@</span>{<span class="i">$TextFilesInfo</span>{<span class="w">ColLabels</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 392 <span class="i">@</span>{<span class="i">$TextFilesInfo</span>{<span class="w">ColLabelToNumMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 393 <span class="i">@</span>{<span class="i">$TextFilesInfo</span>{<span class="w">InDelim</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 394 <span class="i">@</span>{<span class="i">$TextFilesInfo</span>{<span class="w">OutFile</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 395 + 396 <span class="j">FILELIST:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#TextFilesList</span><span class="s">)</span> <span class="s">{</span> + 397 <span class="i">$TextFile</span> = <span class="i">$TextFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span> + 398 + 399 <span class="i">$TextFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span> + 400 <span class="i">$TextFilesInfo</span>{<span class="w">ColCount</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span> + 401 <span class="i">$TextFilesInfo</span>{<span class="w">InDelim</span>}[<span class="i">$Index</span>] = <span class="q">""</span><span class="sc">;</span> + 402 <span class="i">$TextFilesInfo</span>{<span class="w">OutFile</span>}[<span class="i">$Index</span>] = <span class="q">""</span><span class="sc">;</span> + 403 + 404 <span class="i">@</span>{<span class="i">$TextFilesInfo</span>{<span class="w">ColLabels</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 405 <span class="i">%</span>{<span class="i">$TextFilesInfo</span>{<span class="w">ColLabelToNumMap</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 406 + 407 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">-e</span> <span class="i">$TextFile</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 408 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $TextFile: It doesn't exist\n"</span><span class="sc">;</span> + 409 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> + 410 <span class="s">}</span> + 411 <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckFileType</span><span class="s">(</span><span class="i">$TextFile</span><span class="cm">,</span> <span class="q">"csv tsv"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 412 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $TextFile: It's not a csv or tsv file\n"</span><span class="sc">;</span> + 413 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> + 414 <span class="s">}</span> + 415 <span class="s">(</span><span class="i">$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">$TextFile</span><span class="s">)</span><span class="sc">;</span> + 416 <span class="k">if</span> <span class="s">(</span><span class="i">$FileExt</span> =~ <span class="q">/^tsv$/i</span><span class="s">)</span> <span class="s">{</span> + 417 <span class="i">$InDelim</span> = <span class="q">"\t"</span><span class="sc">;</span> + 418 <span class="s">}</span> + 419 <span class="k">else</span> <span class="s">{</span> + 420 <span class="i">$InDelim</span> = <span class="q">"\,"</span><span class="sc">;</span> + 421 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">indelim</span>} !~ <span class="q">/^(comma|semicolon)$/i</span><span class="s">)</span> <span class="s">{</span> + 422 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $TextFile: The value specified, $Options{indelim}, for option \"--indelim\" is not valid for csv files\n"</span><span class="sc">;</span> + 423 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> + 424 <span class="s">}</span> + 425 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">indelim</span>} =~ <span class="q">/^semicolon$/i</span><span class="s">)</span> <span class="s">{</span> + 426 <span class="i">$InDelim</span> = <span class="q">"\;"</span><span class="sc">;</span> + 427 <span class="s">}</span> + 428 <span class="s">}</span> + 429 + 430 <span class="k">if</span> <span class="s">(</span>!<span class="k">open</span> <span class="w">TEXTFILE</span><span class="cm">,</span> <span class="q">"$TextFile"</span><span class="s">)</span> <span class="s">{</span> + 431 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $TextFile: Couldn't open it: $! \n"</span><span class="sc">;</span> + 432 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> + 433 <span class="s">}</span> + 434 + 435 <span class="i">$Line</span> = <span class="i">GetTextLine</span><span class="s">(</span>\<span class="i">*TEXTFILE</span><span class="s">)</span><span class="sc">;</span> + 436 <span class="i">@ColLabels</span> = <span class="i">quotewords</span><span class="s">(</span><span class="i">$InDelim</span><span class="cm">,</span> <span class="n">0</span><span class="cm">,</span> <span class="i">$Line</span><span class="s">)</span><span class="sc">;</span> + 437 <span class="k">close</span> <span class="w">TEXTFILE</span><span class="sc">;</span> + 438 + 439 <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">$FileExt</span> = <span class="q">""</span><span class="sc">;</span> + 440 <span class="s">(</span><span class="i">$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">$TextFile</span><span class="s">)</span><span class="sc">;</span> + 441 <span class="i">$FileExt</span> = <span class="q">"csv"</span><span class="sc">;</span> + 442 <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> + 443 <span class="i">$FileExt</span> = <span class="q">"tsv"</span><span class="sc">;</span> + 444 <span class="s">}</span> + 445 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">root</span>} && <span class="s">(</span><span class="i">@TextFilesList</span> == <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 446 <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">$RootFileExt</span><span class="s">)</span> = <span class="i">ParseFileName</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">root</span>}<span class="s">)</span><span class="sc">;</span> + 447 <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> + 448 <span class="i">$FileName</span> = <span class="i">$RootFileName</span><span class="sc">;</span> + 449 <span class="s">}</span> + 450 <span class="k">else</span> <span class="s">{</span> + 451 <span class="i">$FileName</span> = <span class="i">$Options</span>{<span class="w">root</span>}<span class="sc">;</span> + 452 <span class="s">}</span> + 453 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span> + 454 <span class="s">}</span> + 455 <span class="k">else</span> <span class="s">{</span> + 456 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span> . <span class="q">"ElementalAnalysis"</span><span class="sc">;</span> + 457 <span class="s">}</span> + 458 + 459 <span class="i">$OutFile</span> = <span class="i">$OutFileRoot</span> . <span class="q">".$FileExt"</span><span class="sc">;</span> + 460 <span class="k">if</span> <span class="s">(</span><span class="k">lc</span><span class="s">(</span><span class="i">$OutFile</span><span class="s">)</span> <span class="k">eq</span> <span class="k">lc</span><span class="s">(</span><span class="i">$TextFile</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 461 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $TextFile:Output file name, $OutFile, is same as input text file name, $TextFile\n"</span><span class="sc">;</span> + 462 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> + 463 <span class="s">}</span> + 464 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">overwrite</span>}<span class="s">)</span> <span class="s">{</span> + 465 <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="i">$OutFile</span><span class="s">)</span> <span class="s">{</span> + 466 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $TextFile: The file $OutFile already exists\n"</span><span class="sc">;</span> + 467 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> + 468 <span class="s">}</span> + 469 <span class="s">}</span> + 470 + 471 <span class="i">$TextFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span> + 472 <span class="i">$TextFilesInfo</span>{<span class="w">InDelim</span>}[<span class="i">$Index</span>] = <span class="i">$InDelim</span><span class="sc">;</span> + 473 <span class="i">$TextFilesInfo</span>{<span class="w">OutFile</span>}[<span class="i">$Index</span>] = <span class="q">"$OutFile"</span><span class="sc">;</span> + 474 + 475 <span class="i">$TextFilesInfo</span>{<span class="w">ColCount</span>}[<span class="i">$Index</span>] = <span class="i">@ColLabels</span><span class="sc">;</span> + 476 <span class="k">push</span> <span class="i">@</span>{<span class="i">$TextFilesInfo</span>{<span class="w">ColLabels</span>}[<span class="i">$Index</span>]}<span class="cm">,</span> <span class="i">@ColLabels</span><span class="sc">;</span> + 477 <span class="k">for</span> <span class="i">$ColNum</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#ColLabels</span><span class="s">)</span> <span class="s">{</span> + 478 <span class="i">$ColLabel</span> = <span class="i">$ColLabels</span>[<span class="i">$ColNum</span>]<span class="sc">;</span> + 479 <span class="i">$TextFilesInfo</span>{<span class="w">ColLabelToNumMap</span>}[<span class="i">$Index</span>]{<span class="i">$ColLabel</span>} = <span class="i">$ColNum</span><span class="sc">;</span> + 480 <span class="s">}</span> + 481 <span class="s">}</span> + 482 + 483 <span class="s">}</span> + 484 + 485 <span class="c"># Process option values...</span> +<a name="ProcessOptions-"></a> 486 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span> + 487 <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 488 + 489 <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span> + 490 + 491 <span class="i">$OptionsInfo</span>{<span class="w">ColMode</span>} = <span class="i">$Options</span>{<span class="w">colmode</span>}<span class="sc">;</span> + 492 <span class="i">$OptionsInfo</span>{<span class="w">StartColMode</span>} = <span class="i">$Options</span>{<span class="w">startcolmode</span>}<span class="sc">;</span> + 493 + 494 <span class="i">$OptionsInfo</span>{<span class="w">Fast</span>} = <span class="k">defined</span> <span class="i">$Options</span>{<span class="w">fast</span>} ? <span class="i">$Options</span>{<span class="w">fast</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span> + 495 + 496 <span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} = <span class="i">$Options</span>{<span class="w">detail</span>}<span class="sc">;</span> + 497 <span class="i">$OptionsInfo</span>{<span class="w">CheckFormula</span>} = <span class="i">$Options</span>{<span class="w">fast</span>} ? <span class="n">0</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span> + 498 <span class="i">$OptionsInfo</span>{<span class="w">Precision</span>} = <span class="i">$Options</span>{<span class="w">precision</span>}<span class="sc">;</span> + 499 + 500 <span class="i">$OptionsInfo</span>{<span class="w">InDelim</span>} = <span class="i">$Options</span>{<span class="w">indelim</span>}<span class="sc">;</span> + 501 + 502 <span class="i">$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> + 503 <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$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 504 + 505 <span class="i">$OptionsInfo</span>{<span class="w">Overwrite</span>} = <span class="k">defined</span> <span class="i">$Options</span>{<span class="w">overwrite</span>} ? <span class="i">$Options</span>{<span class="w">overwrite</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span> + 506 <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} = <span class="k">defined</span> <span class="i">$Options</span>{<span class="w">root</span>} ? <span class="i">$Options</span>{<span class="w">root</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span> + 507 + 508 <span class="i">$OptionsInfo</span>{<span class="w">StartCol</span>} = <span class="k">defined</span> <span class="i">$Options</span>{<span class="w">startcol</span>} ? <span class="i">$Options</span>{<span class="w">startcol</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span> + 509 + 510 <span class="i">$OptionsInfo</span>{<span class="w">FormulaCol</span>} = <span class="k">defined</span> <span class="i">$Options</span>{<span class="w">formulacol</span>} ? <span class="i">$Options</span>{<span class="w">formulacol</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span> + 511 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedFormulaCol</span>} = <span class="q">""</span><span class="sc">;</span> + 512 + 513 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$Options</span>{<span class="w">formulacol</span>}<span class="s">)</span> <span class="s">{</span> + 514 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedFormulaCol</span>} = <span class="i">$Options</span>{<span class="w">formulacol</span>}<span class="sc">;</span> + 515 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">colmode</span>} =~ <span class="q">/^colnum$/i</span><span class="s">)</span> <span class="s">{</span> + 516 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SpecifiedFormulaCol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 517 <span class="k">die</span> <span class="q">"Error: Invalid value $Options{formulacol} specified using \"-f -formulacol\" option: Allowed values: > 0\n"</span><span class="sc">;</span> + 518 <span class="s">}</span> + 519 <span class="s">}</span> + 520 <span class="s">}</span> + 521 + 522 <span class="c"># Setup what to calculate...</span> + 523 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedCalculations</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 524 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span> + 525 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedCalculations</span>}} = <span class="q">qw(ElementalAnalysis MolecularWeight ExactMass)</span><span class="sc">;</span> + 526 <span class="s">}</span> + 527 <span class="k">else</span> <span class="s">{</span> + 528 <span class="k">my</span><span class="s">(</span><span class="i">$Mode</span><span class="cm">,</span> <span class="i">$ModeValue</span><span class="cm">,</span> <span class="i">@SpecifiedModeValues</span><span class="s">)</span><span class="sc">;</span> + 529 <span class="i">$Mode</span> = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span> + 530 <span class="i">$Mode</span> =~ <span class="q">s/ //g</span><span class="sc">;</span> + 531 <span class="i">@SpecifiedModeValues</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Mode</span><span class="sc">;</span> + 532 <span class="k">for</span> <span class="i">$ModeValue</span> <span class="s">(</span><span class="i">@SpecifiedModeValues</span><span class="s">)</span> <span class="s">{</span> + 533 <span class="k">if</span> <span class="s">(</span><span class="i">$ModeValue</span> !~ <span class="q">/^(ElementalAnalysis|MolecularWeight|ExactMass)$/i</span><span class="s">)</span> <span class="s">{</span> + 534 <span class="k">if</span> <span class="s">(</span><span class="i">$ModeValue</span> =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span> + 535 <span class="k">die</span> <span class="q">"Error: All value for option \"-m --mode\" is not allowed with other valid values.\n"</span><span class="sc">;</span> + 536 <span class="s">}</span> + 537 <span class="k">else</span> <span class="s">{</span> + 538 <span class="k">die</span> <span class="q">"Error: The value specified, $ModeValue, for option \"-m --mode\" is not valid. Allowed values: ElementalAnalysis, MolecularWeight, or ExactMass\n"</span><span class="sc">;</span> + 539 <span class="s">}</span> + 540 <span class="s">}</span> + 541 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedCalculations</span>}}<span class="cm">,</span> <span class="i">$ModeValue</span><span class="sc">;</span> + 542 <span class="s">}</span> + 543 <span class="s">}</span> + 544 + 545 <span class="i">$OptionsInfo</span>{<span class="w">ValueColLabels</span>} = <span class="k">defined</span> <span class="i">$Options</span>{<span class="w">valuecollabels</span>} ? <span class="i">$Options</span>{<span class="w">valuecollabels</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span> + 546 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedValueLabels</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 547 + 548 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">valuecollabels</span>}<span class="s">)</span> <span class="s">{</span> + 549 <span class="k">my</span><span class="s">(</span><span class="i">$Value</span><span class="cm">,</span> <span class="i">$Label</span><span class="cm">,</span> <span class="i">@ValueLabels</span><span class="s">)</span><span class="sc">;</span> + 550 <span class="i">@ValueLabels</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">valuecollabels</span>}<span class="sc">;</span> + 551 <span class="k">if</span> <span class="s">(</span><span class="i">@ValueLabels</span> % <span class="n">2</span><span class="s">)</span> <span class="s">{</span> + 552 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{valuecollabels}, for option \"-v --valuecollabels\" is not valid: It must contain even number of comma delimited values\n"</span><span class="sc">;</span> + 553 <span class="s">}</span> + 554 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="s">)</span><span class="sc">;</span> + 555 <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$Index</span> < <span class="i">@ValueLabels</span><span class="sc">;</span> <span class="i">$Index</span> +=<span class="n">2</span><span class="s">)</span> <span class="s">{</span> + 556 <span class="i">$Value</span> = <span class="i">$ValueLabels</span>[<span class="i">$Index</span>]<span class="sc">;</span> + 557 <span class="i">$Value</span> =~ <span class="q">s/ //g</span><span class="sc">;</span> + 558 <span class="i">$Label</span> = <span class="i">$ValueLabels</span>[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span> + 559 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(ElementalAnalysis|MolecularWeight|ExactMass)$/i</span><span class="s">)</span> <span class="s">{</span> + 560 <span class="k">die</span> <span class="q">"Error: The value specified, $Value, using option \"-v --valuecollabels\" is not valid. Allowed values: ElementalAnalysis, MolecularWeight, or ExactMass\n"</span><span class="sc">;</span> + 561 <span class="s">}</span> + 562 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedValueLabels</span>}}<span class="cm">,</span> <span class="s">(</span><span class="i">$Value</span><span class="cm">,</span> <span class="i">$Label</span><span class="s">)</span><span class="sc">;</span> + 563 <span class="s">}</span> + 564 <span class="s">}</span> + 565 <span class="s">}</span> + 566 + 567 <span class="c"># Setup script usage and retrieve command line arguments specified using various options...</span> +<a name="SetupScriptUsage-"></a> 568 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span> + 569 + 570 <span class="c"># Retrieve all the options...</span> + 571 <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 572 <span class="i">$Options</span>{<span class="w">colmode</span>} = <span class="q">"colnum"</span><span class="sc">;</span> + 573 <span class="i">$Options</span>{<span class="w">detail</span>} = <span class="n">1</span><span class="sc">;</span> + 574 <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">"All"</span><span class="sc">;</span> + 575 <span class="i">$Options</span>{<span class="w">indelim</span>} = <span class="q">"comma"</span><span class="sc">;</span> + 576 <span class="i">$Options</span>{<span class="w">outdelim</span>} = <span class="q">"comma"</span><span class="sc">;</span> + 577 <span class="i">$Options</span>{<span class="w">precision</span>} = <span class="n">2</span><span class="sc">;</span> + 578 <span class="i">$Options</span>{<span class="w">quote</span>} = <span class="q">"yes"</span><span class="sc">;</span> + 579 <span class="i">$Options</span>{<span class="w">startcolmode</span>} = <span class="q">"after"</span><span class="sc">;</span> + 580 + 581 <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">"colmode|c=s"</span><span class="cm">,</span> <span class="q">"detail|d=i"</span><span class="cm">,</span> <span class="q">"fast"</span><span class="cm">,</span> <span class="q">"formulacol|f=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">"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">"precision|p=i"</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">"startcol|s=s"</span><span class="cm">,</span> <span class="q">"startcolmode=s"</span><span class="cm">,</span> <span class="q">"valuecollabels|v=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> + 582 <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 $ScriptName -h\" command and try again...\n"</span><span class="sc">;</span> + 583 <span class="s">}</span> + 584 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span> + 585 <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> + 586 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"</span><span class="sc">;</span> + 587 <span class="s">}</span> + 588 <span class="k">chdir</span> <span class="i">$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}: $! \n"</span><span class="sc">;</span> + 589 <span class="s">}</span> + 590 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">colmode</span>} !~ <span class="q">/^(colnum|collabel)$/i</span><span class="s">)</span> <span class="s">{</span> + 591 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{colmode}, for option \"-c --colmode\" is not valid. Allowed values: colnum or collabel\n"</span><span class="sc">;</span> + 592 <span class="s">}</span> + 593 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">indelim</span>} !~ <span class="q">/^(comma|semicolon)$/i</span><span class="s">)</span> <span class="s">{</span> + 594 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{indelim}, for option \"--indelim\" is not valid. Allowed values: comma or semicolon\n"</span><span class="sc">;</span> + 595 <span class="s">}</span> + 596 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} !~ <span class="q">/^(comma|semicolon|tab)$/i</span><span class="s">)</span> <span class="s">{</span> + 597 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n"</span><span class="sc">;</span> + 598 <span class="s">}</span> + 599 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">precision</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 600 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{precision}, for option \"-p --precision\" is not valid. Allowed values: > 0 \n"</span><span class="sc">;</span> + 601 <span class="s">}</span> + 602 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">quote</span>} !~ <span class="q">/^(yes|no)$/i</span><span class="s">)</span> <span class="s">{</span> + 603 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: yes or no\n"</span><span class="sc">;</span> + 604 <span class="s">}</span> + 605 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">startcolmode</span>} !~ <span class="q">/^(before|after)$/i</span><span class="s">)</span> <span class="s">{</span> + 606 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{quote}, for option \"--startcolmode\" is not valid. Allowed values: before or after\n"</span><span class="sc">;</span> + 607 <span class="s">}</span> + 608 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">detail</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 609 <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> + 610 <span class="s">}</span> + 611 <span class="s">}</span> + 612 +<a name="EOF-"></a></pre> +<p> </p> +<br /> +<center> +<img src="../../../images/h2o2.png"> +</center> +</body> +</html>