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1 <html>
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2 <head>
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3 <title>MayaChemTools:Code:ElementalAnalysisTextFiles.pl</title>
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4 <meta http-equiv="content-type" content="text/html;charset=utf-8">
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5 <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css">
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8 <br/>
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12 <br/>
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13 <pre>
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14 1 #!/usr/bin/perl -w
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15 2 <span class="c">#</span>
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16 3 <span class="c"># $RCSfile: ElementalAnalysisTextFiles.pl,v $</span>
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17 4 <span class="c"># $Date: 2015/02/28 20:46:19 $</span>
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18 5 <span class="c"># $Revision: 1.28 $</span>
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19 6 <span class="c">#</span>
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20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span>
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21 8 <span class="c">#</span>
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22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
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23 10 <span class="c">#</span>
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24 11 <span class="c"># This file is part of MayaChemTools.</span>
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25 12 <span class="c">#</span>
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26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
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27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
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28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
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29 16 <span class="c"># later version.</span>
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30 17 <span class="c">#</span>
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31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
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32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
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33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span>
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34 21 <span class="c"># details.</span>
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35 22 <span class="c">#</span>
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36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
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37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span>
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38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
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39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
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40 27 <span class="c">#</span>
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41 28
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42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
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43 30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">"$FindBin::Bin/../lib"</span><span class="sc">;</span>
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44 31 <span class="k">use</span> <span class="w">Getopt::Long</span><span class="sc">;</span>
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45 32 <span class="k">use</span> <span class="w">File::Basename</span><span class="sc">;</span>
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46 33 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span>
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47 34 <span class="k">use</span> <span class="w">Benchmark</span><span class="sc">;</span>
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48 35 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span>
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49 36 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span>
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50 37 <span class="k">use</span> <span class="w">MolecularFormula</span><span class="sc">;</span>
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51 38
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52 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>
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53 40
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54 41 <span class="c"># Autoflush STDOUT</span>
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55 42 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span>
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56 43
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57 44 <span class="c"># Starting message...</span>
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58 45 <span class="i">$ScriptName</span> = <span class="i">basename</span><span class="s">(</span><span class="i">$0</span><span class="s">)</span><span class="sc">;</span>
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59 46 <span class="k">print</span> <span class="q">"\n$ScriptName: Starting...\n\n"</span><span class="sc">;</span>
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60 47 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
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61 48
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62 49 <span class="c"># Get the options and setup script...</span>
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63 50 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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64 51 <span class="k">if</span> <span class="s">(</span><span class="i">$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>
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65 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>
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66 53 <span class="s">}</span>
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67 54
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68 55 <span class="k">my</span><span class="s">(</span><span class="i">@TextFilesList</span><span class="s">)</span><span class="sc">;</span>
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69 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>
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70 57
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71 58 <span class="c"># Process options...</span>
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72 59 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span>
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73 60 <span class="k">print</span> <span class="q">"Processing options...\n"</span><span class="sc">;</span>
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74 61 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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75 62
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76 63 <span class="k">print</span> <span class="q">"Checking input text file(s)...\n"</span><span class="sc">;</span>
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77 64 <span class="k">my</span><span class="s">(</span><span class="i">%TextFilesInfo</span><span class="s">)</span><span class="sc">;</span>
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78 65 <span class="i">RetrieveTextFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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79 66 <span class="i">RetrieveColumnsAndLabelsInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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80 67
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81 68 <span class="c"># Generate output files...</span>
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82 69 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
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83 70 <span class="k">if</span> <span class="s">(</span><span class="i">@TextFilesList</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
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84 71 <span class="k">print</span> <span class="q">"\nProcessing text files...\n"</span><span class="sc">;</span>
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85 72 <span class="s">}</span>
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86 73 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#TextFilesList</span><span class="s">)</span> <span class="s">{</span>
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87 74 <span class="k">if</span> <span class="s">(</span><span class="i">$TextFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span>
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88 75 <span class="k">print</span> <span class="q">"\nProcessing file $TextFilesList[$FileIndex]...\n"</span><span class="sc">;</span>
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89 76 <span class="i">PerformElementalAnalysis</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
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90 77 <span class="s">}</span>
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91 78 <span class="s">}</span>
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92 79 <span class="k">print</span> <span class="q">"\n$ScriptName:Done...\n\n"</span><span class="sc">;</span>
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93 80
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94 81 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
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95 82 <span class="i">$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>
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96 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">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
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97 84
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98 85 <span class="c">###############################################################################</span>
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99 86
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100 87 <span class="c"># Perform elemental analysis...</span>
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101 <a name="PerformElementalAnalysis-"></a> 88 <span class="k">sub </span><span class="m">PerformElementalAnalysis</span> <span class="s">{</span>
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102 89 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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103 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">$ErrorMsg</span><span class="cm">,</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">@ColNumsBeforeNew</span><span class="cm">,</span> <span class="i">@ColNumsAfterNew</span><span class="s">)</span><span class="sc">;</span>
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104 91
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105 92 <span class="i">$TextFile</span> = <span class="i">$TextFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
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106 93 <span class="i">$InDelim</span> = <span class="i">$TextFilesInfo</span>{<span class="w">InDelim</span>}[<span class="i">$Index</span>]<span class="sc">;</span>
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107 94 <span class="i">$NewTextFile</span> = <span class="i">$TextFilesInfo</span>{<span class="w">OutFile</span>}[<span class="i">$Index</span>]<span class="sc">;</span>
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108 95 <span class="i">$FormulaCol</span> = <span class="i">$TextFilesInfo</span>{<span class="w">FormulaColNum</span>}[<span class="i">$Index</span>]<span class="sc">;</span>
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109 96
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110 97 <span class="i">@ColNumsBeforeNew</span> = <span class="i">@</span>{<span class="i">$TextFilesInfo</span>{<span class="w">ColNumsBeforeNew</span>}[<span class="i">$Index</span>]}<span class="sc">;</span>
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111 98 <span class="i">@ColNumsAfterNew</span> = <span class="i">@</span>{<span class="i">$TextFilesInfo</span>{<span class="w">ColNumsAfterNew</span>}[<span class="i">$Index</span>]}<span class="sc">;</span>
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112 99
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113 100 <span class="k">print</span> <span class="q">"Generating new Text file $NewTextFile...\n"</span><span class="sc">;</span>
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114 101 <span class="k">open</span> <span class="w">NEWTEXTFILE</span><span class="cm">,</span> <span class="q">">$NewTextFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't open $NewTextFile: $! \n"</span><span class="sc">;</span>
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115 102 <span class="k">open</span> <span class="w">TEXTFILE</span><span class="cm">,</span> <span class="q">"$TextFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $TextFile: $! \n"</span><span class="sc">;</span>
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116 103
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117 104 <span class="c"># Skip over column labels from old file...</span>
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118 105 <span class="i">$Line</span> = <span class="i">GetTextLine</span><span class="s">(</span>\<span class="i">*TEXTFILE</span><span class="s">)</span><span class="sc">;</span>
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119 106
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120 107 <span class="c"># Add column lablels in new file...</span>
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121 108 <span class="i">@ColLabels</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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122 109 <span class="k">for</span> <span class="i">$ColNum</span> <span class="s">(</span><span class="i">@ColNumsBeforeNew</span><span class="s">)</span> <span class="s">{</span>
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123 110 <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">$TextFilesInfo</span>{<span class="w">ColLabels</span>}[<span class="i">$Index</span>][<span class="i">$ColNum</span>]<span class="sc">;</span>
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124 111 <span class="s">}</span>
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125 112 <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>
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126 113 <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">$Value</span>}<span class="sc">;</span>
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127 114 <span class="s">}</span>
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128 115 <span class="k">for</span> <span class="i">$ColNum</span> <span class="s">(</span><span class="i">@ColNumsAfterNew</span><span class="s">)</span> <span class="s">{</span>
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129 116 <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">$ColNum</span>]<span class="sc">;</span>
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130 117 <span class="s">}</span>
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131 118 <span class="i">$NewLine</span> = <span class="q">''</span><span class="sc">;</span>
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132 119 <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">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span>
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133 120 <span class="k">print</span> <span class="i">NEWTEXTFILE</span> <span class="q">"$NewLine\n"</span><span class="sc">;</span>
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134 121
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135 122 <span class="c"># Go over all rows...</span>
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136 123 <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">$CalculatedValue</span><span class="cm">,</span> <span class="i">@CalculatedValues</span><span class="s">)</span><span class="sc">;</span>
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137 124
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138 125 <span class="i">$LineCount</span> = <span class="n">1</span><span class="sc">;</span>
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139 126 <span class="j">TEXTLINE:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$Line</span> = <span class="i">GetTextLine</span><span class="s">(</span>\<span class="i">*TEXTFILE</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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140 127 <span class="i">@LineWords</span> = <span class="i">quotewords</span><span class="s">(</span><span class="i">$InDelim</span><span class="cm">,</span> <span class="n">0</span><span class="cm">,</span> <span class="i">$Line</span><span class="s">)</span><span class="sc">;</span>
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141 128 <span class="i">$LineCount</span>++<span class="sc">;</span>
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142 129
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143 130 <span class="i">@CalculatedValues</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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144 131 <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>
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145 132 <span class="k">push</span> <span class="i">@CalculatedValues</span><span class="cm">,</span> <span class="q">''</span><span class="sc">;</span>
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146 133 <span class="s">}</span>
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147 134 <span class="k">if</span> <span class="s">(</span><span class="i">$FormulaCol</span> > <span class="i">@LineWords</span><span class="s">)</span> <span class="s">{</span>
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148 135 <span class="i">$ErrorMsg</span> = <span class="q">"Ignoring line $LineCount: Formula column $ColLabels[$FormulaCol] not found"</span><span class="sc">;</span>
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149 136 <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>
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150 137 <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>
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151 138 <span class="k">next</span> <span class="j">TEXTLINE</span><span class="sc">;</span>
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152 139 <span class="s">}</span>
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153 140
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154 141 <span class="c"># Make sure it's a valid molecular formula...</span>
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155 142 <span class="i">$FormulaColValue</span> = <span class="i">$LineWords</span>[<span class="i">$FormulaCol</span>]<span class="sc">;</span>
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156 143 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CheckFormula</span>}<span class="s">)</span> <span class="s">{</span>
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157 144 <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">$FormulaColValue</span><span class="s">)</span><span class="sc">;</span>
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158 145 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Status</span><span class="s">)</span> <span class="s">{</span>
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159 146 <span class="i">$ErrorMsg</span> = <span class="q">"Ignoring line $LineCount: Formula column $ColLabels[$FormulaCol] value is not valid: $ErrorMsg"</span><span class="sc">;</span>
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160 147 <span class="i">PrintErrorMsg</span><span class="s">(</span><span class="i">$Line</span><span class="cm">,</span> <span class="i">$ErrorMsg</span><span class="s">)</span><span class="sc">;</span>
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161 148 <span class="i">ComposeAndWriteNewLine</span><span class="s">(</span>\<span class="i">*NEWTEXTFILE</span><span class="cm">,</span> \<span class="i">@LineWords</span><span class="cm">,</span> \<span class="i">@ColNumsBeforeNew</span><span class="cm">,</span> \<span class="i">@ColNumsAfterNew</span><span class="cm">,</span> \<span class="i">@CalculatedValues</span><span class="s">)</span><span class="sc">;</span>
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162 149 <span class="k">next</span> <span class="j">TEXTLINE</span><span class="sc">;</span>
|
|
|
163 150 <span class="s">}</span>
|
|
|
164 151 <span class="s">}</span>
|
|
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165 152
|
|
|
166 153 <span class="c"># Calculate appropriate values and write 'em out...</span>
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|
|
167 154 <span class="i">@CalculatedValues</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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|
168 155 <span class="k">for</span> <span class="i">$CalculationType</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedCalculations</span>}}<span class="s">)</span> <span class="s">{</span>
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|
|
169 156 <span class="k">if</span> <span class="s">(</span><span class="i">$CalculationType</span> =~ <span class="q">/^ElementalAnalysis$/i</span><span class="s">)</span> <span class="s">{</span>
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|
170 157 <span class="s">(</span><span class="i">$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>
|
|
|
171 158 <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>
|
|
|
172 159 <span class="s">}</span>
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|
|
173 160 <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>
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|
174 161 <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>
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|
175 162 <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">$CalculatedValue</span><span class="s">)</span><span class="s">)</span> <span class="co">:</span> <span class="q">""</span><span class="sc">;</span>
|
|
|
176 163 <span class="s">}</span>
|
|
|
177 164 <span class="k">elsif</span> <span class="s">(</span><span class="i">$CalculationType</span> =~ <span class="q">/^ExactMass$/i</span><span class="s">)</span> <span class="s">{</span>
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|
|
178 165 <span class="i">$CalculatedValue</span> = <span class="i">MolecularFormula::CalculateExactMass</span><span class="s">(</span><span class="i">$FormulaColValue</span><span class="s">)</span><span class="sc">;</span>
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|
|
179 166 <span class="i">$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>
|
|
|
180 167 <span class="s">}</span>
|
|
|
181 168 <span class="k">else</span> <span class="s">{</span>
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|
|
182 169 <span class="i">$CalculatedValue</span> = <span class="q">''</span><span class="sc">;</span>
|
|
|
183 170 <span class="s">}</span>
|
|
|
184 171 <span class="k">push</span> <span class="i">@CalculatedValues</span><span class="cm">,</span> <span class="i">$CalculatedValue</span><span class="sc">;</span>
|
|
|
185 172 <span class="s">}</span>
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186 173
|
|
|
187 174 <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>
|
|
|
188 175 <span class="s">}</span>
|
|
|
189 176 <span class="k">close</span> <span class="w">NEWTEXTFILE</span><span class="sc">;</span>
|
|
|
190 177 <span class="k">close</span> <span class="w">TEXTFILE</span><span class="sc">;</span>
|
|
|
191 178
|
|
|
192 179 <span class="s">}</span>
|
|
|
193 180
|
|
|
194 181 <span class="c"># Write out new line using old and new calculated data...</span>
|
|
|
195 <a name="ComposeAndWriteNewLine-"></a> 182 <span class="k">sub </span><span class="m">ComposeAndWriteNewLine</span> <span class="s">{</span>
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|
|
196 183 <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">$CalculatedValuesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
197 184 <span class="k">my</span><span class="s">(</span><span class="i">$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>
|
|
|
198 185
|
|
|
199 186 <span class="i">@NewLineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
200 187 <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>
|
|
|
201 188 <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>
|
|
|
202 189 <span class="s">}</span>
|
|
|
203 190 <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>
|
|
|
204 191 <span class="k">push</span> <span class="i">@NewLineWords</span><span class="cm">,</span> <span class="i">$Value</span><span class="sc">;</span>
|
|
|
205 192 <span class="s">}</span>
|
|
|
206 193 <span class="k">for</span> <span class="i">$ColNum</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ColNumsAfterNewRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
207 194 <span class="k">push</span> <span class="i">@NewLineWords</span><span class="cm">,</span> <span class="i">$OldLineWordsRef</span>->[<span class="i">$ColNum</span>]<span class="sc">;</span>
|
|
|
208 195 <span class="s">}</span>
|
|
|
209 196 <span class="i">$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>
|
|
|
210 197 <span class="k">print</span> <span class="i">$NewTextFileRef</span> <span class="q">"$NewLine\n"</span><span class="sc">;</span>
|
|
|
211 198 <span class="s">}</span>
|
|
|
212 199
|
|
|
213 200 <span class="c"># Print out error message...</span>
|
|
|
214 <a name="PrintErrorMsg-"></a> 201 <span class="k">sub </span><span class="m">PrintErrorMsg</span> <span class="s">{</span>
|
|
|
215 202 <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>
|
|
|
216 203
|
|
|
217 204 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} >= <span class="n">2</span> <span class="s">)</span> <span class="s">{</span>
|
|
|
218 205 <span class="k">print</span> <span class="q">"$ErrorMsg: $Line\n"</span><span class="sc">;</span>
|
|
|
219 206 <span class="s">}</span>
|
|
|
220 207 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} >= <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
|
|
|
221 208 <span class="k">print</span> <span class="q">"$ErrorMsg\n"</span><span class="sc">;</span>
|
|
|
222 209 <span class="s">}</span>
|
|
|
223 210 <span class="s">}</span>
|
|
|
224 211
|
|
|
225 212 <span class="c"># Process formula columns and other information...</span>
|
|
|
226 <a name="RetrieveColumnsAndLabelsInfo-"></a> 213 <span class="k">sub </span><span class="m">RetrieveColumnsAndLabelsInfo</span> <span class="s">{</span>
|
|
|
227 214 <span class="i">RetrieveFormulaColumnsInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
228 215 <span class="i">RetrieveStartColumnsAndValueLabelsInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
229 216 <span class="s">}</span>
|
|
|
230 217
|
|
|
231 218 <span class="c"># Make sure specified formula column are okay...</span>
|
|
|
232 <a name="RetrieveFormulaColumnsInfo-"></a> 219 <span class="k">sub </span><span class="m">RetrieveFormulaColumnsInfo</span> <span class="s">{</span>
|
|
|
233 220 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$TextFile</span><span class="s">)</span><span class="sc">;</span>
|
|
|
234 221
|
|
|
235 222 <span class="i">@</span>{<span class="i">$TextFilesInfo</span>{<span class="w">FormulaColNum</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
236 223
|
|
|
237 224 <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>
|
|
|
238 225 <span class="i">$TextFile</span> = <span class="i">$TextFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
239 226
|
|
|
240 227 <span class="i">$TextFilesInfo</span>{<span class="w">FormulaColNum</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
|
|
|
241 228
|
|
|
242 229 <span class="k">if</span> <span class="s">(</span><span class="i">$TextFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>]<span class="s">)</span> <span class="s">{</span>
|
|
|
243 230 <span class="k">my</span><span class="s">(</span><span class="i">$FormulaColNum</span><span class="cm">,</span> <span class="i">$FormulaColValid</span><span class="s">)</span><span class="sc">;</span>
|
|
|
244 231
|
|
|
245 232 <span class="i">$FormulaColNum</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
246 233 <span class="i">$FormulaColValid</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
247 234 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SpecifiedFormulaCol</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
248 235 <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>
|
|
|
249 236 <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">$Index</span>]<span class="s">)</span> <span class="s">{</span>
|
|
|
250 237 <span class="i">$FormulaColNum</span> = <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedFormulaCol</span>} - <span class="n">1</span><span class="sc">;</span>
|
|
|
251 238 <span class="i">$FormulaColValid</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
252 239 <span class="s">}</span>
|
|
|
253 240 <span class="s">}</span>
|
|
|
254 241 <span class="k">else</span> <span class="s">{</span>
|
|
|
255 242 <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">$OptionsInfo</span>{<span class="w">SpecifiedFormulaCol</span>}}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
256 243 <span class="i">$FormulaColNum</span> = <span class="i">$TextFilesInfo</span>{<span class="w">ColLabelToNumMap</span>}[<span class="i">$Index</span>]{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedFormulaCol</span>}}<span class="sc">;</span>
|
|
|
257 244 <span class="i">$FormulaColValid</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
258 245 <span class="s">}</span>
|
|
|
259 246 <span class="s">}</span>
|
|
|
260 247 <span class="s">}</span>
|
|
|
261 248 <span class="k">else</span> <span class="s">{</span>
|
|
|
262 249 <span class="c"># Grab the first column with the word Formula in its label...</span>
|
|
|
263 250 <span class="k">my</span><span class="s">(</span><span class="i">$ColLabel</span><span class="s">)</span><span class="sc">;</span>
|
|
|
264 251 <span class="j">LABEL:</span> <span class="k">for</span> <span class="i">$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>
|
|
|
265 252 <span class="k">if</span> <span class="s">(</span><span class="i">$ColLabel</span> =~ <span class="q">/Formula/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
266 253 <span class="i">$FormulaColNum</span> = <span class="i">$TextFilesInfo</span>{<span class="w">ColLabelToNumMap</span>}[<span class="i">$Index</span>]{<span class="i">$ColLabel</span>}<span class="sc">;</span>
|
|
|
267 254 <span class="i">$FormulaColValid</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
268 255 <span class="k">last</span> <span class="j">LABEL</span><span class="sc">;</span>
|
|
|
269 256 <span class="s">}</span>
|
|
|
270 257 <span class="s">}</span>
|
|
|
271 258 <span class="s">}</span>
|
|
|
272 259 <span class="k">if</span> <span class="s">(</span><span class="i">$FormulaColValid</span><span class="s">)</span> <span class="s">{</span>
|
|
|
273 260 <span class="i">$TextFilesInfo</span>{<span class="w">FormulaColNum</span>}[<span class="i">$Index</span>] = <span class="i">$FormulaColNum</span><span class="sc">;</span>
|
|
|
274 261 <span class="s">}</span>
|
|
|
275 262 <span class="k">else</span> <span class="s">{</span>
|
|
|
276 263 <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>
|
|
|
277 264 <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>
|
|
|
278 265 <span class="s">}</span>
|
|
|
279 266 <span class="k">else</span> <span class="s">{</span>
|
|
|
280 267 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $TextFile: Column label containing the word Formula doesn't exist\n"</span><span class="sc">;</span>
|
|
|
281 268 <span class="s">}</span>
|
|
|
282 269 <span class="i">$TextFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
|
|
|
283 270 <span class="s">}</span>
|
|
|
284 271 <span class="s">}</span>
|
|
|
285 272 <span class="s">}</span>
|
|
|
286 273 <span class="s">}</span>
|
|
|
287 274
|
|
|
288 275 <span class="c"># Setup starting column number for adding calculated values and</span>
|
|
|
289 276 <span class="c"># column lables to use for these values...</span>
|
|
|
290 <a name="RetrieveStartColumnsAndValueLabelsInfo-"></a> 277 <span class="k">sub </span><span class="m">RetrieveStartColumnsAndValueLabelsInfo</span> <span class="s">{</span>
|
|
|
291 278 <span class="k">my</span><span class="s">(</span><span class="i">$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>
|
|
|
292 279
|
|
|
293 280 <span class="c"># Start column number for inserting new values...</span>
|
|
|
294 281 <span class="i">$SpecifiedStartColNum</span> = <span class="q">"last"</span><span class="sc">;</span>
|
|
|
295 282 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">StartCol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
296 283 <span class="k">if</span> <span class="s">(</span><span class="k">length</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">StartCol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
297 284 <span class="i">$SpecifiedStartColNum</span> = <span class="i">$OptionsInfo</span>{<span class="w">StartCol</span>}
|
|
|
298 285 <span class="s">}</span>
|
|
|
299 286 <span class="s">}</span>
|
|
|
300 287
|
|
|
301 288 <span class="c"># Column labels for for new calculated values...</span>
|
|
|
302 289 <span class="k">my</span><span class="s">(</span><span class="i">%NewValueLabels</span><span class="s">)</span> = <span class="s">(</span><span class="w">ElementalAnalysis</span> <span class="cm">=></span> <span class="q">'ElementalAnalysis'</span><span class="cm">,</span> <span class="w">MolecularWeight</span> <span class="cm">=></span> <span class="q">'MolecularWeight'</span><span class="cm">,</span> <span class="w">ExactMass</span> <span class="cm">=></span> <span class="q">'ExactMass'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
303 290 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedValueLabels</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
304 291 <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>
|
|
|
305 292 <span class="i">$Value</span> = <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedValueLabels</span>}[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
306 293 <span class="i">$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>
|
|
|
307 294 <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>
|
|
|
308 295 <span class="i">$NewValueLabels</span>{<span class="i">$Value</span>} = <span class="i">$Label</span><span class="sc">;</span>
|
|
|
309 296 <span class="s">}</span>
|
|
|
310 297 <span class="s">}</span>
|
|
|
311 298 <span class="s">}</span>
|
|
|
312 299
|
|
|
313 300 <span class="i">@</span>{<span class="i">$TextFilesInfo</span>{<span class="w">ColNumsBeforeNew</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
314 301 <span class="i">@</span>{<span class="i">$TextFilesInfo</span>{<span class="w">ColNumsAfterNew</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
315 302 <span class="i">@</span>{<span class="i">$TextFilesInfo</span>{<span class="w">ValueLabelsMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
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316 303
|
|
|
317 304 <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>
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|
|
318 305 <span class="i">$TextFile</span> = <span class="i">$TextFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
319 306
|
|
|
320 307 <span class="i">@</span>{<span class="i">$TextFilesInfo</span>{<span class="w">ColNumsBeforeNew</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
321 308 <span class="i">@</span>{<span class="i">$TextFilesInfo</span>{<span class="w">ColNumsAfterNew</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
322 309 <span class="i">%</span>{<span class="i">$TextFilesInfo</span>{<span class="w">ValueLabelsMap</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
323 310
|
|
|
324 311 <span class="k">if</span> <span class="s">(</span>!<span class="i">$TextFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>]<span class="s">)</span> <span class="s">{</span>
|
|
|
325 312 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
|
|
|
326 313 <span class="s">}</span>
|
|
|
327 314
|
|
|
328 315 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedStartColNum</span> !~ <span class="q">/^last$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
329 316 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">ColMode</span>} =~ <span class="q">/^collabel$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
330 317 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$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>
|
|
|
331 318 <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>
|
|
|
332 319 <span class="s">}</span>
|
|
|
333 320 <span class="k">else</span> <span class="s">{</span>
|
|
|
334 321 <span class="k">die</span> <span class="q">"Error: Invalid value $SpecifiedStartColNum specified using \"-s --startcol\" option: column name doesn't exist in $TextFile \n"</span><span class="sc">;</span>
|
|
|
335 322 <span class="s">}</span>
|
|
|
336 323 <span class="s">}</span>
|
|
|
337 324 <span class="k">else</span> <span class="s">{</span>
|
|
|
338 325 <span class="k">if</span> <span class="s">(</span><span class="i">$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">$Index</span>]<span class="s">)</span> <span class="s">{</span>
|
|
|
339 326 <span class="i">$StartColNum</span> -= <span class="n">1</span><span class="sc">;</span>
|
|
|
340 327 <span class="s">}</span>
|
|
|
341 328 <span class="k">else</span> <span class="s">{</span>
|
|
|
342 329 <span class="k">die</span> <span class="q">"Error: Invalid value $SpecifiedStartColNum specified using \"-s --startcol\" option: column number doesn't exist in $TextFile \n"</span><span class="sc">;</span>
|
|
|
343 330 <span class="s">}</span>
|
|
|
344 331 <span class="s">}</span>
|
|
|
345 332 <span class="s">}</span>
|
|
|
346 333 <span class="k">else</span> <span class="s">{</span>
|
|
|
347 334 <span class="i">$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>
|
|
|
348 335 <span class="s">}</span>
|
|
|
349 336 <span class="c"># Set up columns lists for before and after the addition of calculated column values</span>
|
|
|
350 337 <span class="c"># for each text file...</span>
|
|
|
351 338 <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">$Part2EndColNum</span><span class="cm">,</span> <span class="i">@Part1ColNums</span><span class="cm">,</span> <span class="i">@Part2ColNums</span><span class="s">)</span><span class="sc">;</span>
|
|
|
352 339
|
|
|
353 340 <span class="i">$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">$Index</span>] - <span class="n">1</span><span class="sc">;</span>
|
|
|
354 341
|
|
|
355 342 <span class="i">$BeforeStartColNum</span> = <span class="i">$StartColNum</span> - <span class="n">1</span><span class="sc">;</span>
|
|
|
356 343 <span class="i">$AfterStartColNum</span> = <span class="i">$StartColNum</span> + <span class="n">1</span><span class="sc">;</span>
|
|
|
357 344
|
|
|
358 345 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">StartColMode</span>} =~ <span class="q">/^after$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
359 346 <span class="i">$Part1StartColNum</span> = <span class="i">$FirstColNum</span><span class="sc">;</span> <span class="i">$Part1EndColNum</span> = <span class="i">$StartColNum</span><span class="sc">;</span>
|
|
|
360 347 <span class="i">$Part2StartColNum</span> = <span class="i">$AfterStartColNum</span><span class="sc">;</span> <span class="i">$Part2EndColNum</span> = <span class="i">$LastColNum</span><span class="sc">;</span>
|
|
|
361 348 <span class="s">}</span>
|
|
|
362 349 <span class="k">else</span> <span class="s">{</span>
|
|
|
363 350 <span class="i">$Part1StartColNum</span> = <span class="i">$FirstColNum</span><span class="sc">;</span> <span class="i">$Part1EndColNum</span> = <span class="i">$BeforeStartColNum</span><span class="sc">;</span>
|
|
|
364 351 <span class="i">$Part2StartColNum</span> = <span class="i">$StartColNum</span><span class="sc">;</span> <span class="i">$Part2EndColNum</span> = <span class="i">$LastColNum</span><span class="sc">;</span>
|
|
|
365 352 <span class="s">}</span>
|
|
|
366 353 <span class="i">@Part1ColNums</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@Part2ColNums</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
367 354 <span class="k">for</span> <span class="i">$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>
|
|
|
368 355 <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>
|
|
|
369 356 <span class="k">push</span> <span class="i">@Part1ColNums</span><span class="cm">,</span> <span class="i">$ColNum</span><span class="sc">;</span>
|
|
|
370 357 <span class="s">}</span>
|
|
|
371 358 <span class="s">}</span>
|
|
|
372 359 <span class="k">for</span> <span class="i">$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>
|
|
|
373 360 <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>
|
|
|
374 361 <span class="k">push</span> <span class="i">@Part2ColNums</span><span class="cm">,</span> <span class="i">$ColNum</span><span class="sc">;</span>
|
|
|
375 362 <span class="s">}</span>
|
|
|
376 363 <span class="s">}</span>
|
|
|
377 364 <span class="k">push</span> <span class="i">@</span>{<span class="i">$TextFilesInfo</span>{<span class="w">ColNumsBeforeNew</span>}[<span class="i">$Index</span>]}<span class="cm">,</span> <span class="i">@Part1ColNums</span><span class="sc">;</span>
|
|
|
378 365 <span class="k">push</span> <span class="i">@</span>{<span class="i">$TextFilesInfo</span>{<span class="w">ColNumsAfterNew</span>}[<span class="i">$Index</span>]}<span class="cm">,</span> <span class="i">@Part2ColNums</span><span class="sc">;</span>
|
|
|
379 366
|
|
|
380 367 <span class="c"># Setup column labels for calculated values...</span>
|
|
|
381 368 <span class="k">for</span> <span class="i">$Value</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%NewValueLabels</span><span class="s">)</span> <span class="s">{</span>
|
|
|
382 369 <span class="i">$Label</span> = <span class="i">$NewValueLabels</span>{<span class="i">$Value</span>}<span class="sc">;</span>
|
|
|
383 370
|
|
|
384 371 <span class="c"># Make sure it doesn't already exists...</span>
|
|
|
385 372 <span class="i">$Count</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
386 373 <span class="i">$NewLabel</span> = <span class="i">$Label</span><span class="sc">;</span>
|
|
|
387 374 <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">$NewLabel</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
388 375 <span class="i">$Count</span>++<span class="sc">;</span>
|
|
|
389 376 <span class="i">$NewLabel</span> = <span class="i">$Label</span> . <span class="i">$Count</span><span class="sc">;</span>
|
|
|
390 377 <span class="s">}</span>
|
|
|
391 378 <span class="i">$TextFilesInfo</span>{<span class="w">ValueLabelsMap</span>}[<span class="i">$Index</span>]{<span class="i">$Value</span>} = <span class="i">$NewLabel</span><span class="sc">;</span>
|
|
|
392 379 <span class="s">}</span>
|
|
|
393 380 <span class="s">}</span>
|
|
|
394 381 <span class="s">}</span>
|
|
|
395 382
|
|
|
396 383 <span class="c"># Retrieve information about input text files...</span>
|
|
|
397 <a name="RetrieveTextFilesInfo-"></a> 384 <span class="k">sub </span><span class="m">RetrieveTextFilesInfo</span> <span class="s">{</span>
|
|
|
398 385 <span class="k">my</span><span class="s">(</span><span class="i">$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>
|
|
|
399 386
|
|
|
400 387 <span class="i">%TextFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
401 388
|
|
|
402 389 <span class="i">@</span>{<span class="i">$TextFilesInfo</span>{<span class="w">FileOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
403 390 <span class="i">@</span>{<span class="i">$TextFilesInfo</span>{<span class="w">ColCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
404 391 <span class="i">@</span>{<span class="i">$TextFilesInfo</span>{<span class="w">ColLabels</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
405 392 <span class="i">@</span>{<span class="i">$TextFilesInfo</span>{<span class="w">ColLabelToNumMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
406 393 <span class="i">@</span>{<span class="i">$TextFilesInfo</span>{<span class="w">InDelim</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
407 394 <span class="i">@</span>{<span class="i">$TextFilesInfo</span>{<span class="w">OutFile</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
408 395
|
|
|
409 396 <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>
|
|
|
410 397 <span class="i">$TextFile</span> = <span class="i">$TextFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
411 398
|
|
|
412 399 <span class="i">$TextFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
|
|
|
413 400 <span class="i">$TextFilesInfo</span>{<span class="w">ColCount</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
|
|
|
414 401 <span class="i">$TextFilesInfo</span>{<span class="w">InDelim</span>}[<span class="i">$Index</span>] = <span class="q">""</span><span class="sc">;</span>
|
|
|
415 402 <span class="i">$TextFilesInfo</span>{<span class="w">OutFile</span>}[<span class="i">$Index</span>] = <span class="q">""</span><span class="sc">;</span>
|
|
|
416 403
|
|
|
417 404 <span class="i">@</span>{<span class="i">$TextFilesInfo</span>{<span class="w">ColLabels</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
418 405 <span class="i">%</span>{<span class="i">$TextFilesInfo</span>{<span class="w">ColLabelToNumMap</span>}[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
419 406
|
|
|
420 407 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">-e</span> <span class="i">$TextFile</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
421 408 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $TextFile: It doesn't exist\n"</span><span class="sc">;</span>
|
|
|
422 409 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
|
|
|
423 410 <span class="s">}</span>
|
|
|
424 411 <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckFileType</span><span class="s">(</span><span class="i">$TextFile</span><span class="cm">,</span> <span class="q">"csv tsv"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
425 412 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $TextFile: It's not a csv or tsv file\n"</span><span class="sc">;</span>
|
|
|
426 413 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
|
|
|
427 414 <span class="s">}</span>
|
|
|
428 415 <span class="s">(</span><span class="i">$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">$TextFile</span><span class="s">)</span><span class="sc">;</span>
|
|
|
429 416 <span class="k">if</span> <span class="s">(</span><span class="i">$FileExt</span> =~ <span class="q">/^tsv$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
430 417 <span class="i">$InDelim</span> = <span class="q">"\t"</span><span class="sc">;</span>
|
|
|
431 418 <span class="s">}</span>
|
|
|
432 419 <span class="k">else</span> <span class="s">{</span>
|
|
|
433 420 <span class="i">$InDelim</span> = <span class="q">"\,"</span><span class="sc">;</span>
|
|
|
434 421 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">indelim</span>} !~ <span class="q">/^(comma|semicolon)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
435 422 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $TextFile: The value specified, $Options{indelim}, for option \"--indelim\" is not valid for csv files\n"</span><span class="sc">;</span>
|
|
|
436 423 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
|
|
|
437 424 <span class="s">}</span>
|
|
|
438 425 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">indelim</span>} =~ <span class="q">/^semicolon$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
439 426 <span class="i">$InDelim</span> = <span class="q">"\;"</span><span class="sc">;</span>
|
|
|
440 427 <span class="s">}</span>
|
|
|
441 428 <span class="s">}</span>
|
|
|
442 429
|
|
|
443 430 <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>
|
|
|
444 431 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $TextFile: Couldn't open it: $! \n"</span><span class="sc">;</span>
|
|
|
445 432 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
|
|
|
446 433 <span class="s">}</span>
|
|
|
447 434
|
|
|
448 435 <span class="i">$Line</span> = <span class="i">GetTextLine</span><span class="s">(</span>\<span class="i">*TEXTFILE</span><span class="s">)</span><span class="sc">;</span>
|
|
|
449 436 <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>
|
|
|
450 437 <span class="k">close</span> <span class="w">TEXTFILE</span><span class="sc">;</span>
|
|
|
451 438
|
|
|
452 439 <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">$FileExt</span> = <span class="q">""</span><span class="sc">;</span>
|
|
|
453 440 <span class="s">(</span><span class="i">$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">$TextFile</span><span class="s">)</span><span class="sc">;</span>
|
|
|
454 441 <span class="i">$FileExt</span> = <span class="q">"csv"</span><span class="sc">;</span>
|
|
|
455 442 <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>
|
|
|
456 443 <span class="i">$FileExt</span> = <span class="q">"tsv"</span><span class="sc">;</span>
|
|
|
457 444 <span class="s">}</span>
|
|
|
458 445 <span class="k">if</span> <span class="s">(</span><span class="i">$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>
|
|
|
459 446 <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>
|
|
|
460 447 <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>
|
|
|
461 448 <span class="i">$FileName</span> = <span class="i">$RootFileName</span><span class="sc">;</span>
|
|
|
462 449 <span class="s">}</span>
|
|
|
463 450 <span class="k">else</span> <span class="s">{</span>
|
|
|
464 451 <span class="i">$FileName</span> = <span class="i">$Options</span>{<span class="w">root</span>}<span class="sc">;</span>
|
|
|
465 452 <span class="s">}</span>
|
|
|
466 453 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span>
|
|
|
467 454 <span class="s">}</span>
|
|
|
468 455 <span class="k">else</span> <span class="s">{</span>
|
|
|
469 456 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span> . <span class="q">"ElementalAnalysis"</span><span class="sc">;</span>
|
|
|
470 457 <span class="s">}</span>
|
|
|
471 458
|
|
|
472 459 <span class="i">$OutFile</span> = <span class="i">$OutFileRoot</span> . <span class="q">".$FileExt"</span><span class="sc">;</span>
|
|
|
473 460 <span class="k">if</span> <span class="s">(</span><span class="k">lc</span><span class="s">(</span><span class="i">$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>
|
|
|
474 461 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $TextFile:Output file name, $OutFile, is same as input text file name, $TextFile\n"</span><span class="sc">;</span>
|
|
|
475 462 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
|
|
|
476 463 <span class="s">}</span>
|
|
|
477 464 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">overwrite</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
478 465 <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>
|
|
|
479 466 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $TextFile: The file $OutFile already exists\n"</span><span class="sc">;</span>
|
|
|
480 467 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
|
|
|
481 468 <span class="s">}</span>
|
|
|
482 469 <span class="s">}</span>
|
|
|
483 470
|
|
|
484 471 <span class="i">$TextFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span>
|
|
|
485 472 <span class="i">$TextFilesInfo</span>{<span class="w">InDelim</span>}[<span class="i">$Index</span>] = <span class="i">$InDelim</span><span class="sc">;</span>
|
|
|
486 473 <span class="i">$TextFilesInfo</span>{<span class="w">OutFile</span>}[<span class="i">$Index</span>] = <span class="q">"$OutFile"</span><span class="sc">;</span>
|
|
|
487 474
|
|
|
488 475 <span class="i">$TextFilesInfo</span>{<span class="w">ColCount</span>}[<span class="i">$Index</span>] = <span class="i">@ColLabels</span><span class="sc">;</span>
|
|
|
489 476 <span class="k">push</span> <span class="i">@</span>{<span class="i">$TextFilesInfo</span>{<span class="w">ColLabels</span>}[<span class="i">$Index</span>]}<span class="cm">,</span> <span class="i">@ColLabels</span><span class="sc">;</span>
|
|
|
490 477 <span class="k">for</span> <span class="i">$ColNum</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#ColLabels</span><span class="s">)</span> <span class="s">{</span>
|
|
|
491 478 <span class="i">$ColLabel</span> = <span class="i">$ColLabels</span>[<span class="i">$ColNum</span>]<span class="sc">;</span>
|
|
|
492 479 <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>
|
|
|
493 480 <span class="s">}</span>
|
|
|
494 481 <span class="s">}</span>
|
|
|
495 482
|
|
|
496 483 <span class="s">}</span>
|
|
|
497 484
|
|
|
498 485 <span class="c"># Process option values...</span>
|
|
|
499 <a name="ProcessOptions-"></a> 486 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span>
|
|
|
500 487 <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
501 488
|
|
|
502 489 <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span>
|
|
|
503 490
|
|
|
504 491 <span class="i">$OptionsInfo</span>{<span class="w">ColMode</span>} = <span class="i">$Options</span>{<span class="w">colmode</span>}<span class="sc">;</span>
|
|
|
505 492 <span class="i">$OptionsInfo</span>{<span class="w">StartColMode</span>} = <span class="i">$Options</span>{<span class="w">startcolmode</span>}<span class="sc">;</span>
|
|
|
506 493
|
|
|
507 494 <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">$Options</span>{<span class="w">fast</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
508 495
|
|
|
509 496 <span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} = <span class="i">$Options</span>{<span class="w">detail</span>}<span class="sc">;</span>
|
|
|
510 497 <span class="i">$OptionsInfo</span>{<span class="w">CheckFormula</span>} = <span class="i">$Options</span>{<span class="w">fast</span>} ? <span class="n">0</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
511 498 <span class="i">$OptionsInfo</span>{<span class="w">Precision</span>} = <span class="i">$Options</span>{<span class="w">precision</span>}<span class="sc">;</span>
|
|
|
512 499
|
|
|
513 500 <span class="i">$OptionsInfo</span>{<span class="w">InDelim</span>} = <span class="i">$Options</span>{<span class="w">indelim</span>}<span class="sc">;</span>
|
|
|
514 501
|
|
|
515 502 <span class="i">$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>
|
|
|
516 503 <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$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
517 504
|
|
|
518 505 <span class="i">$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>
|
|
|
519 506 <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">$Options</span>{<span class="w">root</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
520 507
|
|
|
521 508 <span class="i">$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>
|
|
|
522 509
|
|
|
523 510 <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">$Options</span>{<span class="w">formulacol</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
524 511 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedFormulaCol</span>} = <span class="q">""</span><span class="sc">;</span>
|
|
|
525 512
|
|
|
526 513 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$Options</span>{<span class="w">formulacol</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
527 514 <span class="i">$OptionsInfo</span>{<span class="w">SpecifiedFormulaCol</span>} = <span class="i">$Options</span>{<span class="w">formulacol</span>}<span class="sc">;</span>
|
|
|
528 515 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">colmode</span>} =~ <span class="q">/^colnum$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
529 516 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SpecifiedFormulaCol</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
530 517 <span class="k">die</span> <span class="q">"Error: Invalid value $Options{formulacol} specified using \"-f -formulacol\" option: Allowed values: > 0\n"</span><span class="sc">;</span>
|
|
|
531 518 <span class="s">}</span>
|
|
|
532 519 <span class="s">}</span>
|
|
|
533 520 <span class="s">}</span>
|
|
|
534 521
|
|
|
535 522 <span class="c"># Setup what to calculate...</span>
|
|
|
536 523 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedCalculations</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
537 524 <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>
|
|
|
538 525 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedCalculations</span>}} = <span class="q">qw(ElementalAnalysis MolecularWeight ExactMass)</span><span class="sc">;</span>
|
|
|
539 526 <span class="s">}</span>
|
|
|
540 527 <span class="k">else</span> <span class="s">{</span>
|
|
|
541 528 <span class="k">my</span><span class="s">(</span><span class="i">$Mode</span><span class="cm">,</span> <span class="i">$ModeValue</span><span class="cm">,</span> <span class="i">@SpecifiedModeValues</span><span class="s">)</span><span class="sc">;</span>
|
|
|
542 529 <span class="i">$Mode</span> = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span>
|
|
|
543 530 <span class="i">$Mode</span> =~ <span class="q">s/ //g</span><span class="sc">;</span>
|
|
|
544 531 <span class="i">@SpecifiedModeValues</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Mode</span><span class="sc">;</span>
|
|
|
545 532 <span class="k">for</span> <span class="i">$ModeValue</span> <span class="s">(</span><span class="i">@SpecifiedModeValues</span><span class="s">)</span> <span class="s">{</span>
|
|
|
546 533 <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>
|
|
|
547 534 <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>
|
|
|
548 535 <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>
|
|
|
549 536 <span class="s">}</span>
|
|
|
550 537 <span class="k">else</span> <span class="s">{</span>
|
|
|
551 538 <span class="k">die</span> <span class="q">"Error: The value specified, $ModeValue, for option \"-m --mode\" is not valid. Allowed values: ElementalAnalysis, MolecularWeight, or ExactMass\n"</span><span class="sc">;</span>
|
|
|
552 539 <span class="s">}</span>
|
|
|
553 540 <span class="s">}</span>
|
|
|
554 541 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedCalculations</span>}}<span class="cm">,</span> <span class="i">$ModeValue</span><span class="sc">;</span>
|
|
|
555 542 <span class="s">}</span>
|
|
|
556 543 <span class="s">}</span>
|
|
|
557 544
|
|
|
558 545 <span class="i">$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>
|
|
|
559 546 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedValueLabels</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
560 547
|
|
|
561 548 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">valuecollabels</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
562 549 <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>
|
|
|
563 550 <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>
|
|
|
564 551 <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>
|
|
|
565 552 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{valuecollabels}, for option \"-v --valuecollabels\" is not valid: It must contain even number of comma delimited values\n"</span><span class="sc">;</span>
|
|
|
566 553 <span class="s">}</span>
|
|
|
567 554 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="s">)</span><span class="sc">;</span>
|
|
|
568 555 <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">$Index</span> +=<span class="n">2</span><span class="s">)</span> <span class="s">{</span>
|
|
|
569 556 <span class="i">$Value</span> = <span class="i">$ValueLabels</span>[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
570 557 <span class="i">$Value</span> =~ <span class="q">s/ //g</span><span class="sc">;</span>
|
|
|
571 558 <span class="i">$Label</span> = <span class="i">$ValueLabels</span>[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span>
|
|
|
572 559 <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>
|
|
|
573 560 <span class="k">die</span> <span class="q">"Error: The value specified, $Value, using option \"-v --valuecollabels\" is not valid. Allowed values: ElementalAnalysis, MolecularWeight, or ExactMass\n"</span><span class="sc">;</span>
|
|
|
574 561 <span class="s">}</span>
|
|
|
575 562 <span class="k">push</span> <span class="i">@</span>{<span class="i">$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>
|
|
|
576 563 <span class="s">}</span>
|
|
|
577 564 <span class="s">}</span>
|
|
|
578 565 <span class="s">}</span>
|
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579 566
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580 567 <span class="c"># Setup script usage and retrieve command line arguments specified using various options...</span>
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581 <a name="SetupScriptUsage-"></a> 568 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span>
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582 569
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583 570 <span class="c"># Retrieve all the options...</span>
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584 571 <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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585 572 <span class="i">$Options</span>{<span class="w">colmode</span>} = <span class="q">"colnum"</span><span class="sc">;</span>
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586 573 <span class="i">$Options</span>{<span class="w">detail</span>} = <span class="n">1</span><span class="sc">;</span>
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587 574 <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">"All"</span><span class="sc">;</span>
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588 575 <span class="i">$Options</span>{<span class="w">indelim</span>} = <span class="q">"comma"</span><span class="sc">;</span>
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589 576 <span class="i">$Options</span>{<span class="w">outdelim</span>} = <span class="q">"comma"</span><span class="sc">;</span>
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590 577 <span class="i">$Options</span>{<span class="w">precision</span>} = <span class="n">2</span><span class="sc">;</span>
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591 578 <span class="i">$Options</span>{<span class="w">quote</span>} = <span class="q">"yes"</span><span class="sc">;</span>
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592 579 <span class="i">$Options</span>{<span class="w">startcolmode</span>} = <span class="q">"after"</span><span class="sc">;</span>
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593 580
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594 581 <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>
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595 582 <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 $ScriptName -h\" command and try again...\n"</span><span class="sc">;</span>
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596 583 <span class="s">}</span>
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597 584 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
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598 585 <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>
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599 586 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"</span><span class="sc">;</span>
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600 587 <span class="s">}</span>
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601 588 <span class="k">chdir</span> <span class="i">$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}: $! \n"</span><span class="sc">;</span>
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602 589 <span class="s">}</span>
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603 590 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">colmode</span>} !~ <span class="q">/^(colnum|collabel)$/i</span><span class="s">)</span> <span class="s">{</span>
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604 591 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{colmode}, for option \"-c --colmode\" is not valid. Allowed values: colnum or collabel\n"</span><span class="sc">;</span>
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605 592 <span class="s">}</span>
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606 593 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">indelim</span>} !~ <span class="q">/^(comma|semicolon)$/i</span><span class="s">)</span> <span class="s">{</span>
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607 594 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{indelim}, for option \"--indelim\" is not valid. Allowed values: comma or semicolon\n"</span><span class="sc">;</span>
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608 595 <span class="s">}</span>
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609 596 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} !~ <span class="q">/^(comma|semicolon|tab)$/i</span><span class="s">)</span> <span class="s">{</span>
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610 597 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n"</span><span class="sc">;</span>
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611 598 <span class="s">}</span>
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612 599 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">precision</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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613 600 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{precision}, for option \"-p --precision\" is not valid. Allowed values: > 0 \n"</span><span class="sc">;</span>
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614 601 <span class="s">}</span>
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615 602 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">quote</span>} !~ <span class="q">/^(yes|no)$/i</span><span class="s">)</span> <span class="s">{</span>
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616 603 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: yes or no\n"</span><span class="sc">;</span>
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617 604 <span class="s">}</span>
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618 605 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">startcolmode</span>} !~ <span class="q">/^(before|after)$/i</span><span class="s">)</span> <span class="s">{</span>
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619 606 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{quote}, for option \"--startcolmode\" is not valid. Allowed values: before or after\n"</span><span class="sc">;</span>
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620 607 <span class="s">}</span>
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621 608 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">detail</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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622 609 <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>
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623 610 <span class="s">}</span>
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624 611 <span class="s">}</span>
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625 612
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626 <a name="EOF-"></a></pre>
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627 <p> </p>
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628 <br />
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629 <center>
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630 <img src="../../../images/h2o2.png">
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631 </center>
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632 </body>
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633 </html>
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