diff docs/scripts/html/code/ElementalAnalysis.html @ 0:4816e4a8ae95 draft default tip

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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/ElementalAnalysis.html	Wed Jan 20 09:23:18 2016 -0500
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+<html>
+<head>
+<title>MayaChemTools:Code:ElementalAnalysis.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>
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+<br/>
+<pre>
+   1 #!/usr/bin/perl -w
+   2 <span class="c">#</span>
+   3 <span class="c"># $RCSfile: ElementalAnalysis.pl,v $</span>
+   4 <span class="c"># $Date: 2015/02/28 20:46:19 $</span>
+   5 <span class="c"># $Revision: 1.19 $</span>
+   6 <span class="c">#</span>
+   7 <span class="c"># Author: Manish Sud &lt;msud@san.rr.com&gt;</span>
+   8 <span class="c">#</span>
+   9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
+  10 <span class="c">#</span>
+  11 <span class="c"># This file is part of MayaChemTools.</span>
+  12 <span class="c">#</span>
+  13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
+  14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
+  15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
+  16 <span class="c"># later version.</span>
+  17 <span class="c">#</span>
+  18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
+  19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
+  20 <span class="c"># for a particular purpose.  See the GNU Lesser General Public License for more</span>
+  21 <span class="c"># details.</span>
+  22 <span class="c">#</span>
+  23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
+  24 <span class="c"># along with MayaChemTools; if not, see &lt;http://www.gnu.org/licenses/&gt; or</span>
+  25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
+  26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
+  27 <span class="c">#</span>
+  28 
+  29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
+  30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">&quot;$FindBin::Bin/../lib&quot;</span><span class="sc">;</span>
+  31 <span class="k">use</span> <span class="w">Getopt::Long</span><span class="sc">;</span>
+  32 <span class="k">use</span> <span class="w">File::Basename</span><span class="sc">;</span>
+  33 <span class="k">use</span> <span class="w">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">$0</span><span class="s">)</span><span class="sc">;</span>
+  46 <span class="k">print</span> <span class="q">&quot;\n$ScriptName: Starting...\n\n&quot;</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="s">)</span> <span class="s">{</span>
+  52   <span class="k">die</span> <span class="i">GetUsageFromPod</span><span class="s">(</span><span class="q">&quot;$FindBin::Bin/$ScriptName&quot;</span><span class="s">)</span><span class="sc">;</span>
+  53 <span class="s">}</span>
+  54 
+  55 <span class="k">print</span> <span class="q">&quot;Processing options...\n&quot;</span><span class="sc">;</span>
+  56 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span>
+  57 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  58 
+  59 <span class="i">PerformElementalAnalysis</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  60 
+  61 <span class="k">print</span> <span class="q">&quot;\n$ScriptName:Done...\n\n&quot;</span><span class="sc">;</span>
+  62 
+  63 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
+  64 <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">$StartTime</span><span class="s">)</span><span class="sc">;</span>
+  65 <span class="k">print</span> <span class="q">&quot;Total time: &quot;</span><span class="cm">,</span> <span class="i">timestr</span><span class="s">(</span><span class="i">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+  66 
+  67 <span class="c">###############################################################################</span>
+  68 
+  69 <span class="c"># Elemental analysis...</span>
+<a name="PerformElementalAnalysis-"></a>  70 <span class="k">sub </span><span class="m">PerformElementalAnalysis</span> <span class="s">{</span>
+  71   <span class="k">my</span><span class="s">(</span><span class="i">$Formula</span><span class="cm">,</span> <span class="i">$FormulaDataRef</span><span class="cm">,</span> <span class="i">$ValueLabel</span><span class="cm">,</span> <span class="i">$CalculationType</span><span class="cm">,</span> <span class="i">$CalculatedValue</span><span class="cm">,</span> <span class="i">$ElementsRef</span><span class="cm">,</span> <span class="i">$ElementCompositionRef</span><span class="cm">,</span> <span class="i">$Status</span><span class="cm">,</span> <span class="i">$ErrorMsg</span><span class="cm">,</span> <span class="i">@ValueLabels</span><span class="cm">,</span> <span class="i">@CalculatedValues</span><span class="s">)</span><span class="sc">;</span>
+  72 
+  73   <span class="k">print</span> <span class="q">&quot;Performing elemental analysis...\n&quot;</span><span class="sc">;</span>
+  74 
+  75   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FileOutput</span>}<span class="s">)</span> <span class="s">{</span>
+  76     <span class="k">print</span> <span class="q">&quot;Generating file $OptionsInfo{OutFileName}...\n&quot;</span><span class="sc">;</span>
+  77     <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">&quot;&gt;$OptionsInfo{OutFileName}&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Couldn&#39;t open $OptionsInfo{OutFileName}: $!\n&quot;</span><span class="sc">;</span>
+  78   <span class="s">}</span>
+  79 
+  80   <span class="c"># Setup value labels...</span>
+  81   <span class="i">@ValueLabels</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  82   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RowsOutput</span>}<span class="s">)</span> <span class="s">{</span>
+  83     <span class="k">push</span> <span class="i">@ValueLabels</span><span class="cm">,</span> <span class="q">&quot;Formula&quot;</span><span class="sc">;</span>
+  84   <span class="s">}</span>
+  85   <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>
+  86     <span class="k">push</span> <span class="i">@ValueLabels</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">ValueLabelsMap</span>}{<span class="i">$CalculationType</span>}<span class="sc">;</span>
+  87   <span class="s">}</span>
+  88 
+  89   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RowsOutput</span>}<span class="s">)</span> <span class="s">{</span>
+  90     <span class="i">ListHeaderRowData</span><span class="s">(</span>\<span class="i">@ValueLabels</span><span class="s">)</span><span class="sc">;</span>
+  91   <span class="s">}</span>
+  92 
+  93   <span class="c"># Go over specified properties...</span>
+  94   <span class="j">FORMULA:</span> <span class="k">for</span> <span class="i">$Formula</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedFormulas</span>}}<span class="s">)</span> <span class="s">{</span>
+  95     <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">RowsOutput</span>}<span class="s">)</span> <span class="s">{</span>
+  96       <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FileOutput</span>}<span class="s">)</span> <span class="s">{</span>
+  97         <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;\nPerforming elemental analysis using formula $Formula...\n\n&quot;</span><span class="sc">;</span>
+  98       <span class="s">}</span>
+  99       <span class="k">else</span> <span class="s">{</span>
+ 100         <span class="k">print</span> <span class="q">&quot;\nPerforming elemental analysis using formula  $Formula...\n\n&quot;</span><span class="sc">;</span>
+ 101       <span class="s">}</span>
+ 102     <span class="s">}</span>
+ 103     <span class="c"># Calculate appropriate values and write &#39;em out...</span>
+ 104     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CheckFormula</span>}<span class="s">)</span> <span class="s">{</span>
+ 105       <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">$Formula</span><span class="s">)</span><span class="sc">;</span>
+ 106       <span class="k">if</span> <span class="s">(</span>!<span class="i">$Status</span><span class="s">)</span> <span class="s">{</span>
+ 107         <span class="k">warn</span><span class="s">(</span><span class="q">&quot;Warning: Ignoring formula $Formula: It&#39;s not a valid value: $ErrorMsg\n&quot;</span><span class="s">)</span><span class="sc">;</span>
+ 108         <span class="k">next</span> <span class="j">FORMULA</span><span class="sc">;</span>
+ 109       <span class="s">}</span>
+ 110     <span class="s">}</span>
+ 111     <span class="i">@CalculatedValues</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 112     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RowsOutput</span>}<span class="s">)</span> <span class="s">{</span>
+ 113       <span class="k">push</span> <span class="i">@CalculatedValues</span><span class="cm">,</span> <span class="i">$Formula</span><span class="sc">;</span>
+ 114     <span class="s">}</span>
+ 115     <span class="k">for</span> <span class="i">$CalculationType</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedCalculations</span>}}<span class="s">)</span> <span class="s">{</span>
+ 116       <span class="k">if</span> <span class="s">(</span><span class="i">$CalculationType</span> =~ <span class="q">/^ElementalAnalysis$/i</span><span class="s">)</span> <span class="s">{</span>
+ 117         <span class="s">(</span><span class="i">$ElementsRef</span><span class="cm">,</span> <span class="i">$ElementCompositionRef</span><span class="s">)</span> = <span class="i">MolecularFormula::CalculateElementalComposition</span><span class="s">(</span><span class="i">$Formula</span><span class="s">)</span><span class="sc">;</span>
+ 118         <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> &amp;&amp; <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">&#39;&#39;</span><span class="sc">;</span>
+ 119       <span class="s">}</span>
+ 120       <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>
+ 121         <span class="i">$CalculatedValue</span> = <span class="i">MolecularFormula::CalculateMolecularWeight</span><span class="s">(</span><span class="i">$Formula</span><span class="s">)</span><span class="sc">;</span>
+ 122         <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> &amp;&amp; <span class="k">length</span><span class="s">(</span><span class="i">$CalculatedValue</span><span class="s">)</span><span class="s">)</span> ? <span class="s">(</span><span class="k">sprintf</span><span class="s">(</span><span class="q">&quot;%.$OptionsInfo{Precision}f&quot;</span><span class="cm">,</span> <span class="i">$CalculatedValue</span><span class="s">)</span><span class="s">)</span> <span class="co">:</span> <span class="q">&quot;&quot;</span><span class="sc">;</span>
+ 123       <span class="s">}</span>
+ 124       <span class="k">elsif</span> <span class="s">(</span><span class="i">$CalculationType</span> =~ <span class="q">/^ExactMass$/i</span><span class="s">)</span> <span class="s">{</span>
+ 125         <span class="i">$CalculatedValue</span> = <span class="i">MolecularFormula::CalculateExactMass</span><span class="s">(</span><span class="i">$Formula</span><span class="s">)</span><span class="sc">;</span>
+ 126         <span class="i">$CalculatedValue</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$CalculatedValue</span><span class="s">)</span> &amp;&amp; <span class="k">length</span><span class="s">(</span><span class="i">$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">&quot;%.$OptionsInfo{Precision}f&quot;</span><span class="cm">,</span> <span class="i">$CalculatedValue</span><span class="s">)</span><span class="s">)</span> <span class="co">:</span> <span class="q">&quot;&quot;</span><span class="sc">;</span>
+ 127       <span class="s">}</span>
+ 128       <span class="k">else</span> <span class="s">{</span>
+ 129         <span class="i">$CalculatedValue</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+ 130       <span class="s">}</span>
+ 131       <span class="k">push</span> <span class="i">@CalculatedValues</span><span class="cm">,</span> <span class="i">$CalculatedValue</span><span class="sc">;</span>
+ 132     <span class="s">}</span>
+ 133     <span class="c"># List data...</span>
+ 134     <span class="i">ListFormulaData</span><span class="s">(</span>\<span class="i">@ValueLabels</span><span class="cm">,</span> \<span class="i">@CalculatedValues</span><span class="s">)</span><span class="sc">;</span>
+ 135   <span class="s">}</span>
+ 136   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FileOutput</span>}<span class="s">)</span> <span class="s">{</span>
+ 137     <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span>
+ 138   <span class="s">}</span>
+ 139   <span class="k">print</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+ 140 <span class="s">}</span>
+ 141 
+ 142 <span class="c"># List calculated data values...</span>
+<a name="ListFormulaData-"></a> 143 <span class="k">sub </span><span class="m">ListFormulaData</span> <span class="s">{</span>
+ 144   <span class="k">my</span><span class="s">(</span><span class="i">$DataLabelRef</span><span class="cm">,</span> <span class="i">$DataValueRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 145   <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$Line</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
+ 146 
+ 147   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">RowsOutput</span>}<span class="s">)</span> <span class="s">{</span>
+ 148     <span class="i">$Line</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+ 149     <span class="c"># Format data...</span>
+ 150     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>} || <span class="i">$Options</span>{<span class="w">outdelim</span>} !~ <span class="q">/^comma$/i</span><span class="s">)</span> <span class="s">{</span>
+ 151       <span class="i">$Line</span> = <span class="i">JoinWords</span><span class="s">(</span><span class="i">$DataValueRef</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>}<span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span>
+ 152     <span class="s">}</span>
+ 153     <span class="k">else</span> <span class="s">{</span>
+ 154       <span class="c"># Always quote values containing commas...</span>
+ 155       <span class="i">$Line</span> = <span class="s">(</span><span class="i">$DataValueRef</span>-&gt;[<span class="n">0</span>] =~ <span class="q">/\,/</span><span class="s">)</span> ? <span class="q">qq(&quot;$DataValueRef-&gt;[0]&quot;)</span> <span class="co">:</span> <span class="i">$DataValueRef</span>-&gt;[<span class="n">0</span>]<span class="sc">;</span>
+ 156       <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">1</span> .. <span class="i">$#</span>{<span class="i">$DataValueRef</span>} <span class="s">)</span> <span class="s">{</span>
+ 157         <span class="i">$Value</span> = <span class="i">$DataValueRef</span>-&gt;[<span class="i">$Index</span>]<span class="sc">;</span>
+ 158         <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> =~ <span class="q">/\,/</span><span class="s">)</span> <span class="s">{</span>
+ 159           <span class="i">$Value</span> = <span class="q">qq(&quot;$Value&quot;)</span><span class="sc">;</span>
+ 160         <span class="s">}</span>
+ 161         <span class="i">$Line</span> .= <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>} . <span class="i">$Value</span><span class="sc">;</span>
+ 162       <span class="s">}</span>
+ 163     <span class="s">}</span>
+ 164     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FileOutput</span>}<span class="s">)</span> <span class="s">{</span>
+ 165       <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$Line\n&quot;</span><span class="sc">;</span>
+ 166     <span class="s">}</span>
+ 167     <span class="k">else</span> <span class="s">{</span>
+ 168       <span class="k">print</span> <span class="q">&quot;$Line\n&quot;</span><span class="sc">;</span>
+ 169     <span class="s">}</span>
+ 170   <span class="s">}</span>
+ 171   <span class="k">else</span> <span class="s">{</span>
+ 172     <span class="c"># Format and list data...</span>
+ 173     <span class="i">$Line</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+ 174     <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$DataLabelRef</span>} <span class="s">)</span> <span class="s">{</span>
+ 175       <span class="i">$Line</span> = <span class="i">$DataLabelRef</span>-&gt;[<span class="i">$Index</span>] . <span class="q">&#39;: &#39;</span> . <span class="i">$DataValueRef</span>-&gt;[<span class="i">$Index</span>]<span class="sc">;</span>
+ 176       <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FileOutput</span>}<span class="s">)</span> <span class="s">{</span>
+ 177         <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$Line\n&quot;</span><span class="sc">;</span>
+ 178       <span class="s">}</span>
+ 179       <span class="k">else</span> <span class="s">{</span>
+ 180         <span class="k">print</span> <span class="q">&quot;$Line\n&quot;</span><span class="sc">;</span>
+ 181       <span class="s">}</span>
+ 182     <span class="s">}</span>
+ 183   <span class="s">}</span>
+ 184 <span class="s">}</span>
+ 185 
+ 186 <span class="c"># List calculated data for a formula...</span>
+<a name="ListHeaderRowData-"></a> 187 <span class="k">sub </span><span class="m">ListHeaderRowData</span> <span class="s">{</span>
+ 188   <span class="k">my</span><span class="s">(</span><span class="i">$DataLabelRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 189   <span class="k">my</span><span class="s">(</span><span class="i">$Line</span><span class="s">)</span><span class="sc">;</span>
+ 190 
+ 191   <span class="c"># Format data...</span>
+ 192   <span class="i">$Line</span> = <span class="i">JoinWords</span><span class="s">(</span><span class="i">$DataLabelRef</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>
+ 193   <span class="i">$Line</span> =~ <span class="q">s/\://g</span><span class="sc">;</span>
+ 194   <span class="c"># List data...</span>
+ 195   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FileOutput</span>}<span class="s">)</span> <span class="s">{</span>
+ 196     <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$Line\n&quot;</span><span class="sc">;</span>
+ 197   <span class="s">}</span>
+ 198   <span class="k">else</span> <span class="s">{</span>
+ 199     <span class="k">print</span> <span class="q">&quot;$Line\n&quot;</span><span class="sc">;</span>
+ 200   <span class="s">}</span>
+ 201 <span class="s">}</span>
+ 202 
+ 203 <span class="c"># Process option values...</span>
+<a name="ProcessOptions-"></a> 204 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span>
+ 205   <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 206 
+ 207   <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span>
+ 208 
+ 209   <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/^tab$/i</span> <span class="s">)</span> ? <span class="q">&quot;\t&quot;</span> <span class="co">:</span> <span class="s">(</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/^semicolon$/i</span><span class="s">)</span> ? <span class="q">&quot;\;&quot;</span> <span class="co">:</span> <span class="q">&quot;\,&quot;</span><span class="s">)</span><span class="sc">;</span>
+ 210   <span class="i">$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>
+ 211 
+ 212   <span class="i">$OptionsInfo</span>{<span class="w">Output</span>} = <span class="i">$Options</span>{<span class="w">output</span>}<span class="sc">;</span>
+ 213   <span class="i">$OptionsInfo</span>{<span class="w">OutputStyle</span>} = <span class="i">$Options</span>{<span class="w">outputstyle</span>}<span class="sc">;</span>
+ 214 
+ 215   <span class="i">$OptionsInfo</span>{<span class="w">RowsOutput</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">outputstyle</span>} =~ <span class="q">/^FormulaRows$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+ 216   <span class="i">$OptionsInfo</span>{<span class="w">FileOutput</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">output</span>} =~ <span class="q">/^File$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+ 217   <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>
+ 218 
+ 219   <span class="i">$OptionsInfo</span>{<span class="w">Precision</span>} = <span class="i">$Options</span>{<span class="w">precision</span>}<span class="sc">;</span>
+ 220 
+ 221   <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">$Options</span>{<span class="w">root</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
+ 222   <span class="i">$OptionsInfo</span>{<span class="w">ValueLabels</span>} = <span class="k">defined</span> <span class="i">$Options</span>{<span class="w">valuelabels</span>} ? <span class="i">$Options</span>{<span class="w">valuelabels</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
+ 223 
+ 224   <span class="c"># Setup formulas...</span>
+ 225   <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedFormulas</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 226   <span class="k">if</span> <span class="s">(</span><span class="i">@ARGV</span> &gt;= <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
+ 227     <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedFormulas</span>}}<span class="cm">,</span> <span class="i">@ARGV</span><span class="sc">;</span>
+ 228   <span class="s">}</span>
+ 229   <span class="k">else</span> <span class="s">{</span>
+ 230     <span class="c"># Setup mode specified default values...</span>
+ 231     <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedFormulas</span>}}<span class="cm">,</span> <span class="q">&#39;H2O&#39;</span><span class="sc">;</span>
+ 232   <span class="s">}</span>
+ 233 
+ 234   <span class="c"># Setup what to calculate...</span>
+ 235   <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedCalculations</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 236   <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>
+ 237     <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedCalculations</span>}} = <span class="q">qw(ElementalAnalysis MolecularWeight ExactMass)</span><span class="sc">;</span>
+ 238   <span class="s">}</span>
+ 239   <span class="k">else</span> <span class="s">{</span>
+ 240     <span class="k">my</span><span class="s">(</span><span class="i">$Mode</span><span class="cm">,</span> <span class="i">$ModeValue</span><span class="cm">,</span> <span class="i">@SpecifiedModeValues</span><span class="s">)</span><span class="sc">;</span>
+ 241     <span class="i">$Mode</span> = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span>
+ 242     <span class="i">$Mode</span> =~ <span class="q">s/ //g</span><span class="sc">;</span>
+ 243     <span class="i">@SpecifiedModeValues</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Mode</span><span class="sc">;</span>
+ 244     <span class="k">for</span> <span class="i">$ModeValue</span> <span class="s">(</span><span class="i">@SpecifiedModeValues</span><span class="s">)</span> <span class="s">{</span>
+ 245       <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>
+ 246         <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>
+ 247           <span class="k">die</span> <span class="q">&quot;Error: All value for option \&quot;-m --mode\&quot; is not allowed with other valid values.\n&quot;</span><span class="sc">;</span>
+ 248         <span class="s">}</span>
+ 249         <span class="k">else</span> <span class="s">{</span>
+ 250           <span class="k">die</span> <span class="q">&quot;Error: The value specified, $ModeValue, for option \&quot;-m --mode\&quot; is not valid. Allowed values: ElementalAnalysis, MolecularWeight, or ExactMass\n&quot;</span><span class="sc">;</span>
+ 251         <span class="s">}</span>
+ 252       <span class="s">}</span>
+ 253       <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedCalculations</span>}}<span class="cm">,</span> <span class="i">$ModeValue</span><span class="sc">;</span>
+ 254     <span class="s">}</span>
+ 255   <span class="s">}</span>
+ 256   <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">$Label</span><span class="s">)</span><span class="sc">;</span>
+ 257   <span class="c"># Set up labels for calculated values...</span>
+ 258   <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedValueLabels</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 259   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">valuelabels</span>}<span class="s">)</span> <span class="s">{</span>
+ 260     <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>
+ 261     <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">valuelabels</span>}<span class="sc">;</span>
+ 262     <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>
+ 263       <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{valuelabels}, for option \&quot;-v --valuelabels\&quot; is not valid: It must contain even number of comma delimited values\n&quot;</span><span class="sc">;</span>
+ 264     <span class="s">}</span>
+ 265     <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$Index</span> &lt; <span class="i">@ValueLabels</span><span class="sc">;</span> <span class="i">$Index</span> +=<span class="n">2</span><span class="s">)</span> <span class="s">{</span>
+ 266       <span class="i">$Value</span> = <span class="i">$ValueLabels</span>[<span class="i">$Index</span>]<span class="sc">;</span>
+ 267       <span class="i">$Value</span> =~ <span class="q">s/ //g</span><span class="sc">;</span>
+ 268       <span class="i">$Label</span> = <span class="i">$ValueLabels</span>[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span>
+ 269       <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(ElementalAnalysis|MolecularWeight|ExactMass)$/i</span><span class="s">)</span> <span class="s">{</span>
+ 270         <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Value, using option \&quot;-v --valuelabels\&quot; is not valid. Allowed values: ElementalAnalysis, MolecularWeight, or ExactMass\n&quot;</span><span class="sc">;</span>
+ 271       <span class="s">}</span>
+ 272       <span class="k">push</span> <span class="i">@</span>{<span class="i">$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>
+ 273     <span class="s">}</span>
+ 274   <span class="s">}</span>
+ 275 
+ 276   <span class="c"># Set up calculation type to label map...</span>
+ 277   <span class="i">%</span>{<span class="i">$OptionsInfo</span>{<span class="w">ValueLabelsMap</span>}} = <span class="s">(</span><span class="w">ElementalAnalysis</span> <span class="cm">=&gt;</span> <span class="q">&#39;ElementalAnalysis&#39;</span><span class="cm">,</span> <span class="w">MolecularWeight</span> <span class="cm">=&gt;</span> <span class="q">&#39;MolecularWeight&#39;</span><span class="cm">,</span> <span class="w">ExactMass</span> <span class="cm">=&gt;</span> <span class="q">&#39;ExactMass&#39;</span><span class="s">)</span><span class="sc">;</span>
+ 278   <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedValueLabels</span>}}<span class="s">)</span> <span class="s">{</span>
+ 279     <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> &lt; <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>
+ 280       <span class="i">$Value</span> = <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedValueLabels</span>}[<span class="i">$Index</span>]<span class="sc">;</span>
+ 281       <span class="i">$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>
+ 282       <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$OptionsInfo</span>{<span class="w">ValueLabelsMap</span>}{<span class="i">$Value</span>}<span class="s">)</span> <span class="s">{</span>
+ 283         <span class="i">$OptionsInfo</span>{<span class="w">ValueLabelsMap</span>}{<span class="i">$Value</span>} = <span class="i">$Label</span><span class="sc">;</span>
+ 284       <span class="s">}</span>
+ 285     <span class="s">}</span>
+ 286   <span class="s">}</span>
+ 287 
+ 288   <span class="c"># Setup output file name...</span>
+ 289   <span class="i">$OptionsInfo</span>{<span class="w">OutFileName</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+ 290   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FileOutput</span>}<span class="s">)</span> <span class="s">{</span>
+ 291     <span class="k">my</span><span class="s">(</span><span class="i">$OutFileRoot</span><span class="cm">,</span> <span class="i">$OutFileExt</span><span class="s">)</span><span class="sc">;</span>
+ 292 
+ 293     <span class="i">$OutFileRoot</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+ 294     <span class="i">$OutFileExt</span> = <span class="q">&quot;csv&quot;</span><span class="sc">;</span>
+ 295     <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/^tab$/i</span><span class="s">)</span> <span class="s">{</span>
+ 296       <span class="i">$OutFileExt</span> = <span class="q">&quot;tsv&quot;</span><span class="sc">;</span>
+ 297     <span class="s">}</span>
+ 298     <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">root</span>}<span class="s">)</span> <span class="s">{</span>
+ 299       <span class="k">my</span> <span class="s">(</span><span class="i">$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">$Options</span>{<span class="w">root</span>}<span class="s">)</span><span class="sc">;</span>
+ 300       <span class="k">if</span> <span class="s">(</span><span class="i">$RootFileName</span> &amp;&amp; <span class="i">$RootFileExt</span><span class="s">)</span> <span class="s">{</span>
+ 301         <span class="i">$OutFileRoot</span> = <span class="i">$RootFileName</span><span class="sc">;</span>
+ 302       <span class="s">}</span>
+ 303       <span class="k">else</span> <span class="s">{</span>
+ 304         <span class="i">$OutFileRoot</span> = <span class="i">$Options</span>{<span class="w">root</span>}<span class="sc">;</span>
+ 305       <span class="s">}</span>
+ 306     <span class="s">}</span>
+ 307     <span class="k">else</span> <span class="s">{</span>
+ 308       <span class="i">$OutFileRoot</span> = <span class="q">&#39;FormulasElementalAnalysis&#39;</span><span class="sc">;</span>
+ 309     <span class="s">}</span>
+ 310     <span class="i">$OptionsInfo</span>{<span class="w">OutFileName</span>} = <span class="i">$OutFileRoot</span> . <span class="q">&#39;.&#39;</span> . <span class="i">$OutFileExt</span><span class="sc">;</span>
+ 311     <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">overwrite</span>}<span class="s">)</span> <span class="s">{</span>
+ 312       <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="i">$OptionsInfo</span>{<span class="w">OutFileName</span>}<span class="s">)</span> <span class="s">{</span>
+ 313         <span class="k">die</span> <span class="q">&quot;Error: Output file, $OptionsInfo{OutFileName}, already exists.\nUse \-o --overwrite\ option or specify a different name using \&quot;-r --root\&quot; option.\n&quot;</span><span class="sc">;</span>
+ 314       <span class="s">}</span>
+ 315     <span class="s">}</span>
+ 316   <span class="s">}</span>
+ 317 <span class="s">}</span>
+ 318 
+ 319 
+ 320 <span class="c"># Setup script usage  and retrieve command line arguments specified using various options...</span>
+<a name="SetupScriptUsage-"></a> 321 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span>
+ 322 
+ 323   <span class="c"># Retrieve all the options...</span>
+ 324   <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 325   <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">&quot;All&quot;</span><span class="sc">;</span>
+ 326   <span class="i">$Options</span>{<span class="w">outdelim</span>} = <span class="q">&quot;comma&quot;</span><span class="sc">;</span>
+ 327   <span class="i">$Options</span>{<span class="w">output</span>} = <span class="q">&quot;STDOUT&quot;</span><span class="sc">;</span>
+ 328   <span class="i">$Options</span>{<span class="w">outputstyle</span>} = <span class="q">&quot;FormulaBlock&quot;</span><span class="sc">;</span>
+ 329   <span class="i">$Options</span>{<span class="w">precision</span>} = <span class="n">2</span><span class="sc">;</span>
+ 330   <span class="i">$Options</span>{<span class="w">quote</span>} = <span class="q">&quot;yes&quot;</span><span class="sc">;</span>
+ 331 
+ 332   <span class="k">if</span> <span class="s">(</span>!<span class="i">GetOptions</span><span class="s">(</span>\<span class="i">%Options</span><span class="cm">,</span> <span class="q">&quot;help|h&quot;</span><span class="cm">,</span> <span class="q">&quot;fast&quot;</span><span class="cm">,</span> <span class="q">&quot;mode|m=s&quot;</span><span class="cm">,</span> <span class="q">&quot;outdelim=s&quot;</span><span class="cm">,</span> <span class="q">&quot;output=s&quot;</span><span class="cm">,</span> <span class="q">&quot;outputstyle=s&quot;</span><span class="cm">,</span> <span class="q">&quot;overwrite|o&quot;</span><span class="cm">,</span> <span class="q">&quot;precision=i&quot;</span><span class="cm">,</span> <span class="q">&quot;quote|q=s&quot;</span><span class="cm">,</span> <span class="q">&quot;root|r=s&quot;</span><span class="cm">,</span> <span class="q">&quot;valuelabels|v=s&quot;</span><span class="cm">,</span> <span class="q">&quot;workingdir|w=s&quot;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 333     <span class="k">die</span> <span class="q">&quot;\nTo get a list of valid options and their values, use \&quot;$ScriptName -h\&quot; or\n\&quot;perl -S $ScriptName -h\&quot; command and try again...\n&quot;</span><span class="sc">;</span>
+ 334   <span class="s">}</span>
+ 335   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
+ 336     <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>
+ 337       <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{workingdir}, for option \&quot;-w --workingdir\&quot; is not a directory name.\n&quot;</span><span class="sc">;</span>
+ 338     <span class="s">}</span>
+ 339     <span class="k">chdir</span> <span class="i">$Options</span>{<span class="w">workingdir</span>} <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Couldn&#39;t chdir $Options{workingdir}: $! \n&quot;</span><span class="sc">;</span>
+ 340   <span class="s">}</span>
+ 341   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} !~ <span class="q">/^(comma|semicolon|tab)$/i</span><span class="s">)</span> <span class="s">{</span>
+ 342     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{outdelim}, for option \&quot;--outdelim\&quot; is not valid. Allowed values: comma, tab, or semicolon\n&quot;</span><span class="sc">;</span>
+ 343   <span class="s">}</span>
+ 344   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">output</span>} !~ <span class="q">/^(STDOUT|File)$/i</span><span class="s">)</span> <span class="s">{</span>
+ 345     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{output}, for option \&quot;--output\&quot; is not valid. Allowed values: STDOUT or File\n&quot;</span><span class="sc">;</span>
+ 346   <span class="s">}</span>
+ 347   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outputstyle</span>} !~ <span class="q">/^(FormulaBlock|FormulaRows)$/i</span><span class="s">)</span> <span class="s">{</span>
+ 348     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{outputstyle}, for option \&quot;--outputstyle\&quot; is not valid. Allowed values: FormulaBlock or FormulaRows\n&quot;</span><span class="sc">;</span>
+ 349   <span class="s">}</span>
+ 350   <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">precision</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 351     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{precision}, for option \&quot;-p --precision\&quot; is not valid. Allowed values: &gt; 0 \n&quot;</span><span class="sc">;</span>
+ 352   <span class="s">}</span>
+ 353   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">quote</span>} !~ <span class="q">/^(yes|no)$/i</span><span class="s">)</span> <span class="s">{</span>
+ 354     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{quote}, for option \&quot;-q --quote\&quot; is not valid. Allowed values: yes or no\n&quot;</span><span class="sc">;</span>
+ 355   <span class="s">}</span>
+ 356 <span class="s">}</span>
+ 357 
+<a name="EOF-"></a></pre>
+<p>&nbsp;</p>
+<br />
+<center>
+<img src="../../../images/h2o2.png">
+</center>
+</body>
+</html>