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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> </center> <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 $</span> 6 <span class="c">#</span> 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> 8 <span class="c">#</span> 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> 10 <span class="c">#</span> 11 <span class="c"># This file is part of MayaChemTools.</span> 12 <span class="c">#</span> 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> 16 <span class="c"># later version.</span> 17 <span class="c">#</span> 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> 21 <span class="c"># details.</span> 22 <span class="c">#</span> 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> 27 <span class="c">#</span> 28 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> 30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">"$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="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">print</span> <span class="q">"Processing options...\n"</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">"\n$ScriptName:Done...\n\n"</span><span class="sc">;</span> 62 63 <span class="i">$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">$StartTime</span><span class="s">)</span><span class="sc">;</span> 65 <span class="k">print</span> <span class="q">"Total time: "</span><span class="cm">,</span> <span class="i">timestr</span><span class="s">(</span><span class="i">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> 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">$ErrorMsg</span><span class="cm">,</span> <span class="i">@ValueLabels</span><span class="cm">,</span> <span class="i">@CalculatedValues</span><span class="s">)</span><span class="sc">;</span> 72 73 <span class="k">print</span> <span class="q">"Performing elemental analysis...\n"</span><span class="sc">;</span> 74 75 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FileOutput</span>}<span class="s">)</span> <span class="s">{</span> 76 <span class="k">print</span> <span class="q">"Generating file $OptionsInfo{OutFileName}...\n"</span><span class="sc">;</span> 77 <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">">$OptionsInfo{OutFileName}"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Couldn't open $OptionsInfo{OutFileName}: $!\n"</span><span class="sc">;</span> 78 <span class="s">}</span> 79 80 <span class="c"># Setup value labels...</span> 81 <span class="i">@ValueLabels</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 82 <span class="k">if</span> <span class="s">(</span><span class="i">$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">"Formula"</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">"\nPerforming elemental analysis using formula $Formula...\n\n"</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">"\nPerforming elemental analysis using formula $Formula...\n\n"</span><span class="sc">;</span> 101 <span class="s">}</span> 102 <span class="s">}</span> 103 <span class="c"># Calculate appropriate values and write 'em out...</span> 104 <span class="k">if</span> <span class="s">(</span><span class="i">$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">"Warning: Ignoring formula $Formula: It's not a valid value: $ErrorMsg\n"</span><span class="s">)</span><span class="sc">;</span> 108 <span class="k">next</span> <span class="j">FORMULA</span><span class="sc">;</span> 109 <span class="s">}</span> 110 <span class="s">}</span> 111 <span class="i">@CalculatedValues</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 112 <span class="k">if</span> <span class="s">(</span><span class="i">$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> && <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> 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> && <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">$CalculatedValue</span><span class="s">)</span><span class="s">)</span> <span class="co">:</span> <span class="q">""</span><span class="sc">;</span> 123 <span class="s">}</span> 124 <span class="k">elsif</span> <span class="s">(</span><span class="i">$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">$CalculatedValue</span><span class="s">)</span> && <span class="k">length</span><span class="s">(</span><span class="i">$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> 127 <span class="s">}</span> 128 <span class="k">else</span> <span class="s">{</span> 129 <span class="i">$CalculatedValue</span> = <span class="q">''</span><span class="sc">;</span> 130 <span class="s">}</span> 131 <span class="k">push</span> <span class="i">@CalculatedValues</span><span class="cm">,</span> <span class="i">$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">$OptionsInfo</span>{<span class="w">FileOutput</span>}<span class="s">)</span> <span class="s">{</span> 137 <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span> 138 <span class="s">}</span> 139 <span class="k">print</span> <span class="q">"\n"</span><span class="sc">;</span> 140 <span class="s">}</span> 141 142 <span class="c"># List calculated data values...</span> <a name="ListFormulaData-"></a> 143 <span class="k">sub </span><span class="m">ListFormulaData</span> <span class="s">{</span> 144 <span class="k">my</span><span class="s">(</span><span class="i">$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">''</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">$DataValueRef</span>->[<span class="n">0</span>] =~ <span class="q">/\,/</span><span class="s">)</span> ? <span class="q">qq("$DataValueRef->[0]")</span> <span class="co">:</span> <span class="i">$DataValueRef</span>->[<span class="n">0</span>]<span class="sc">;</span> 156 <span class="k">for</span> <span class="i">$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>->[<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">$Value</span> = <span class="q">qq("$Value")</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">"$Line\n"</span><span class="sc">;</span> 166 <span class="s">}</span> 167 <span class="k">else</span> <span class="s">{</span> 168 <span class="k">print</span> <span class="q">"$Line\n"</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">$Line</span> = <span class="q">''</span><span class="sc">;</span> 174 <span class="k">for</span> <span class="i">$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>->[<span class="i">$Index</span>] . <span class="q">': '</span> . <span class="i">$DataValueRef</span>->[<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">"$Line\n"</span><span class="sc">;</span> 178 <span class="s">}</span> 179 <span class="k">else</span> <span class="s">{</span> 180 <span class="k">print</span> <span class="q">"$Line\n"</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">"$Line\n"</span><span class="sc">;</span> 197 <span class="s">}</span> 198 <span class="k">else</span> <span class="s">{</span> 199 <span class="k">print</span> <span class="q">"$Line\n"</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$/i</span> <span class="s">)</span> ? <span class="q">"\t"</span> <span class="co">:</span> <span class="s">(</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/^semicolon$/i</span><span class="s">)</span> ? <span class="q">"\;"</span> <span class="co">:</span> <span class="q">"\,"</span><span class="s">)</span><span class="sc">;</span> 210 <span class="i">$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">$OptionsInfo</span>{<span class="w">SpecifiedFormulas</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 226 <span class="k">if</span> <span class="s">(</span><span class="i">@ARGV</span> >= <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 227 <span class="k">push</span> <span class="i">@</span>{<span class="i">$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">$OptionsInfo</span>{<span class="w">SpecifiedFormulas</span>}}<span class="cm">,</span> <span class="q">'H2O'</span><span class="sc">;</span> 232 <span class="s">}</span> 233 234 <span class="c"># Setup what to calculate...</span> 235 <span class="i">@</span>{<span class="i">$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">"Error: All value for option \"-m --mode\" is not allowed with other valid values.\n"</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">"Error: The value specified, $ModeValue, for option \"-m --mode\" is not valid. Allowed values: ElementalAnalysis, MolecularWeight, or ExactMass\n"</span><span class="sc">;</span> 251 <span class="s">}</span> 252 <span class="s">}</span> 253 <span class="k">push</span> <span class="i">@</span>{<span class="i">$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">"Error: The value specified, $Options{valuelabels}, for option \"-v --valuelabels\" is not valid: It must contain even number of comma delimited values\n"</span><span class="sc">;</span> 264 <span class="s">}</span> 265 <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$Index</span> < <span class="i">@ValueLabels</span><span class="sc">;</span> <span class="i">$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">"Error: The value specified, $Value, using option \"-v --valuelabels\" is not valid. Allowed values: ElementalAnalysis, MolecularWeight, or ExactMass\n"</span><span class="sc">;</span> 271 <span class="s">}</span> 272 <span class="k">push</span> <span class="i">@</span>{<span class="i">$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">$OptionsInfo</span>{<span class="w">ValueLabelsMap</span>}} = <span class="s">(</span><span class="w">ElementalAnalysis</span> <span class="cm">=></span> <span class="q">'ElementalAnalysis'</span><span class="cm">,</span> <span class="w">MolecularWeight</span> <span class="cm">=></span> <span class="q">'MolecularWeight'</span><span class="cm">,</span> <span class="w">ExactMass</span> <span class="cm">=></span> <span class="q">'ExactMass'</span><span class="s">)</span><span class="sc">;</span> 278 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$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> < <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">''</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">''</span><span class="sc">;</span> 294 <span class="i">$OutFileExt</span> = <span class="q">"csv"</span><span class="sc">;</span> 295 <span class="k">if</span> <span class="s">(</span><span class="i">$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">"tsv"</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> && <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">'FormulasElementalAnalysis'</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">'.'</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">"Error: Output file, $OptionsInfo{OutFileName}, already exists.\nUse \-o --overwrite\ option or specify a different name using \"-r --root\" option.\n"</span><span class="sc">;</span> 314 <span class="s">}</span> 315 <span class="s">}</span> 316 <span class="s">}</span> 317 <span class="s">}</span> 318 319 320 <span class="c"># Setup script usage and retrieve command line arguments specified using various options...</span> <a name="SetupScriptUsage-"></a> 321 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span> 322 323 <span class="c"># Retrieve all the options...</span> 324 <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 325 <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">"All"</span><span class="sc">;</span> 326 <span class="i">$Options</span>{<span class="w">outdelim</span>} = <span class="q">"comma"</span><span class="sc">;</span> 327 <span class="i">$Options</span>{<span class="w">output</span>} = <span class="q">"STDOUT"</span><span class="sc">;</span> 328 <span class="i">$Options</span>{<span class="w">outputstyle</span>} = <span class="q">"FormulaBlock"</span><span class="sc">;</span> 329 <span class="i">$Options</span>{<span class="w">precision</span>} = <span class="n">2</span><span class="sc">;</span> 330 <span class="i">$Options</span>{<span class="w">quote</span>} = <span class="q">"yes"</span><span class="sc">;</span> 331 332 <span class="k">if</span> <span class="s">(</span>!<span class="i">GetOptions</span><span class="s">(</span>\<span class="i">%Options</span><span class="cm">,</span> <span class="q">"help|h"</span><span class="cm">,</span> <span class="q">"fast"</span><span class="cm">,</span> <span class="q">"mode|m=s"</span><span class="cm">,</span> <span class="q">"outdelim=s"</span><span class="cm">,</span> <span class="q">"output=s"</span><span class="cm">,</span> <span class="q">"outputstyle=s"</span><span class="cm">,</span> <span class="q">"overwrite|o"</span><span class="cm">,</span> <span class="q">"precision=i"</span><span class="cm">,</span> <span class="q">"quote|q=s"</span><span class="cm">,</span> <span class="q">"root|r=s"</span><span class="cm">,</span> <span class="q">"valuelabels|v=s"</span><span class="cm">,</span> <span class="q">"workingdir|w=s"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 333 <span class="k">die</span> <span class="q">"\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n"</span><span class="sc">;</span> 334 <span class="s">}</span> 335 <span class="k">if</span> <span class="s">(</span><span class="i">$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">"Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"</span><span class="sc">;</span> 338 <span class="s">}</span> 339 <span class="k">chdir</span> <span class="i">$Options</span>{<span class="w">workingdir</span>} <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't chdir $Options{workingdir}: $! \n"</span><span class="sc">;</span> 340 <span class="s">}</span> 341 <span class="k">if</span> <span class="s">(</span><span class="i">$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">"Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n"</span><span class="sc">;</span> 343 <span class="s">}</span> 344 <span class="k">if</span> <span class="s">(</span><span class="i">$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">"Error: The value specified, $Options{output}, for option \"--output\" is not valid. Allowed values: STDOUT or File\n"</span><span class="sc">;</span> 346 <span class="s">}</span> 347 <span class="k">if</span> <span class="s">(</span><span class="i">$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">"Error: The value specified, $Options{outputstyle}, for option \"--outputstyle\" is not valid. Allowed values: FormulaBlock or FormulaRows\n"</span><span class="sc">;</span> 349 <span class="s">}</span> 350 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$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">"Error: The value specified, $Options{precision}, for option \"-p --precision\" is not valid. Allowed values: > 0 \n"</span><span class="sc">;</span> 352 <span class="s">}</span> 353 <span class="k">if</span> <span class="s">(</span><span class="i">$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">"Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: yes or no\n"</span><span class="sc">;</span> 355 <span class="s">}</span> 356 <span class="s">}</span> 357 <a name="EOF-"></a></pre> <p> </p> <br /> <center> <img src="../../../images/h2o2.png"> </center> </body> </html>