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3 <title>MayaChemTools:Code:ElementalAnalysisTextFiles.pl</title>
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14 1 #!/usr/bin/perl -w
15 2 <span class="c">#</span>
16 3 <span class="c"># $RCSfile: ElementalAnalysisTextFiles.pl,v $</span>
17 4 <span class="c"># $Date: 2015/02/28 20:46:19 $</span>
18 5 <span class="c"># $Revision: 1.28 $</span>
19 6 <span class="c">#</span>
20 7 <span class="c"># Author: Manish Sud &lt;msud@san.rr.com&gt;</span>
21 8 <span class="c">#</span>
22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
23 10 <span class="c">#</span>
24 11 <span class="c"># This file is part of MayaChemTools.</span>
25 12 <span class="c">#</span>
26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
29 16 <span class="c"># later version.</span>
30 17 <span class="c">#</span>
31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span>
34 21 <span class="c"># details.</span>
35 22 <span class="c">#</span>
36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
37 24 <span class="c"># along with MayaChemTools; if not, see &lt;http://www.gnu.org/licenses/&gt; or</span>
38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
40 27 <span class="c">#</span>
41 28
42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
43 30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">&quot;$FindBin::Bin/../lib&quot;</span><span class="sc">;</span>
44 31 <span class="k">use</span> <span class="w">Getopt::Long</span><span class="sc">;</span>
45 32 <span class="k">use</span> <span class="w">File::Basename</span><span class="sc">;</span>
46 33 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span>
47 34 <span class="k">use</span> <span class="w">Benchmark</span><span class="sc">;</span>
48 35 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span>
49 36 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span>
50 37 <span class="k">use</span> <span class="w">MolecularFormula</span><span class="sc">;</span>
51 38
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>
53 40
54 41 <span class="c"># Autoflush STDOUT</span>
55 42 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span>
56 43
57 44 <span class="c"># Starting message...</span>
58 45 <span class="i">$ScriptName</span> = <span class="i">basename</span><span class="s">(</span><span class="i">$0</span><span class="s">)</span><span class="sc">;</span>
59 46 <span class="k">print</span> <span class="q">&quot;\n$ScriptName: Starting...\n\n&quot;</span><span class="sc">;</span>
60 47 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
61 48
62 49 <span class="c"># Get the options and setup script...</span>
63 50 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
64 51 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">help</span>} || <span class="i">@ARGV</span> &lt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
65 52 <span class="k">die</span> <span class="i">GetUsageFromPod</span><span class="s">(</span><span class="q">&quot;$FindBin::Bin/$ScriptName&quot;</span><span class="s">)</span><span class="sc">;</span>
66 53 <span class="s">}</span>
67 54
68 55 <span class="k">my</span><span class="s">(</span><span class="i">@TextFilesList</span><span class="s">)</span><span class="sc">;</span>
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">&quot;csv tsv&quot;</span><span class="s">)</span><span class="sc">;</span>
70 57
71 58 <span class="c"># Process options...</span>
72 59 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span>
73 60 <span class="k">print</span> <span class="q">&quot;Processing options...\n&quot;</span><span class="sc">;</span>
74 61 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
75 62
76 63 <span class="k">print</span> <span class="q">&quot;Checking input text file(s)...\n&quot;</span><span class="sc">;</span>
77 64 <span class="k">my</span><span class="s">(</span><span class="i">%TextFilesInfo</span><span class="s">)</span><span class="sc">;</span>
78 65 <span class="i">RetrieveTextFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
79 66 <span class="i">RetrieveColumnsAndLabelsInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
80 67
81 68 <span class="c"># Generate output files...</span>
82 69 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
83 70 <span class="k">if</span> <span class="s">(</span><span class="i">@TextFilesList</span> &gt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
84 71 <span class="k">print</span> <span class="q">&quot;\nProcessing text files...\n&quot;</span><span class="sc">;</span>
85 72 <span class="s">}</span>
86 73 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#TextFilesList</span><span class="s">)</span> <span class="s">{</span>
87 74 <span class="k">if</span> <span class="s">(</span><span class="i">$TextFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span>
88 75 <span class="k">print</span> <span class="q">&quot;\nProcessing file $TextFilesList[$FileIndex]...\n&quot;</span><span class="sc">;</span>
89 76 <span class="i">PerformElementalAnalysis</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
90 77 <span class="s">}</span>
91 78 <span class="s">}</span>
92 79 <span class="k">print</span> <span class="q">&quot;\n$ScriptName:Done...\n\n&quot;</span><span class="sc">;</span>
93 80
94 81 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
95 82 <span class="i">$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>
96 83 <span class="k">print</span> <span class="q">&quot;Total time: &quot;</span><span class="cm">,</span> <span class="i">timestr</span><span class="s">(</span><span class="i">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
97 84
98 85 <span class="c">###############################################################################</span>
99 86
100 87 <span class="c"># Perform elemental analysis...</span>
101 <a name="PerformElementalAnalysis-"></a> 88 <span class="k">sub </span><span class="m">PerformElementalAnalysis</span> <span class="s">{</span>
102 89 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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">$ErrorMsg</span><span class="cm">,</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">@ColNumsBeforeNew</span><span class="cm">,</span> <span class="i">@ColNumsAfterNew</span><span class="s">)</span><span class="sc">;</span>
104 91
105 92 <span class="i">$TextFile</span> = <span class="i">$TextFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
106 93 <span class="i">$InDelim</span> = <span class="i">$TextFilesInfo</span>{<span class="w">InDelim</span>}[<span class="i">$Index</span>]<span class="sc">;</span>
107 94 <span class="i">$NewTextFile</span> = <span class="i">$TextFilesInfo</span>{<span class="w">OutFile</span>}[<span class="i">$Index</span>]<span class="sc">;</span>
108 95 <span class="i">$FormulaCol</span> = <span class="i">$TextFilesInfo</span>{<span class="w">FormulaColNum</span>}[<span class="i">$Index</span>]<span class="sc">;</span>
109 96
110 97 <span class="i">@ColNumsBeforeNew</span> = <span class="i">@</span>{<span class="i">$TextFilesInfo</span>{<span class="w">ColNumsBeforeNew</span>}[<span class="i">$Index</span>]}<span class="sc">;</span>
111 98 <span class="i">@ColNumsAfterNew</span> = <span class="i">@</span>{<span class="i">$TextFilesInfo</span>{<span class="w">ColNumsAfterNew</span>}[<span class="i">$Index</span>]}<span class="sc">;</span>
112 99
113 100 <span class="k">print</span> <span class="q">&quot;Generating new Text file $NewTextFile...\n&quot;</span><span class="sc">;</span>
114 101 <span class="k">open</span> <span class="w">NEWTEXTFILE</span><span class="cm">,</span> <span class="q">&quot;&gt;$NewTextFile&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Couldn&#39;t open $NewTextFile: $! \n&quot;</span><span class="sc">;</span>
115 102 <span class="k">open</span> <span class="w">TEXTFILE</span><span class="cm">,</span> <span class="q">&quot;$TextFile&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Can&#39;t open $TextFile: $! \n&quot;</span><span class="sc">;</span>
116 103
117 104 <span class="c"># Skip over column labels from old file...</span>
118 105 <span class="i">$Line</span> = <span class="i">GetTextLine</span><span class="s">(</span>\<span class="i">*TEXTFILE</span><span class="s">)</span><span class="sc">;</span>
119 106
120 107 <span class="c"># Add column lablels in new file...</span>
121 108 <span class="i">@ColLabels</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
122 109 <span class="k">for</span> <span class="i">$ColNum</span> <span class="s">(</span><span class="i">@ColNumsBeforeNew</span><span class="s">)</span> <span class="s">{</span>
123 110 <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">$TextFilesInfo</span>{<span class="w">ColLabels</span>}[<span class="i">$Index</span>][<span class="i">$ColNum</span>]<span class="sc">;</span>
124 111 <span class="s">}</span>
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>
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">$Value</span>}<span class="sc">;</span>
127 114 <span class="s">}</span>
128 115 <span class="k">for</span> <span class="i">$ColNum</span> <span class="s">(</span><span class="i">@ColNumsAfterNew</span><span class="s">)</span> <span class="s">{</span>
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">$ColNum</span>]<span class="sc">;</span>
130 117 <span class="s">}</span>
131 118 <span class="i">$NewLine</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
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">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span>
133 120 <span class="k">print</span> <span class="i">NEWTEXTFILE</span> <span class="q">&quot;$NewLine\n&quot;</span><span class="sc">;</span>
134 121
135 122 <span class="c"># Go over all rows...</span>
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">$CalculatedValue</span><span class="cm">,</span> <span class="i">@CalculatedValues</span><span class="s">)</span><span class="sc">;</span>
137 124
138 125 <span class="i">$LineCount</span> = <span class="n">1</span><span class="sc">;</span>
139 126 <span class="j">TEXTLINE:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$Line</span> = <span class="i">GetTextLine</span><span class="s">(</span>\<span class="i">*TEXTFILE</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
140 127 <span class="i">@LineWords</span> = <span class="i">quotewords</span><span class="s">(</span><span class="i">$InDelim</span><span class="cm">,</span> <span class="n">0</span><span class="cm">,</span> <span class="i">$Line</span><span class="s">)</span><span class="sc">;</span>
141 128 <span class="i">$LineCount</span>++<span class="sc">;</span>
142 129
143 130 <span class="i">@CalculatedValues</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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>
145 132 <span class="k">push</span> <span class="i">@CalculatedValues</span><span class="cm">,</span> <span class="q">&#39;&#39;</span><span class="sc">;</span>
146 133 <span class="s">}</span>
147 134 <span class="k">if</span> <span class="s">(</span><span class="i">$FormulaCol</span> &gt; <span class="i">@LineWords</span><span class="s">)</span> <span class="s">{</span>
148 135 <span class="i">$ErrorMsg</span> = <span class="q">&quot;Ignoring line $LineCount: Formula column $ColLabels[$FormulaCol] not found&quot;</span><span class="sc">;</span>
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>
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>
151 138 <span class="k">next</span> <span class="j">TEXTLINE</span><span class="sc">;</span>
152 139 <span class="s">}</span>
153 140
154 141 <span class="c"># Make sure it&#39;s a valid molecular formula...</span>
155 142 <span class="i">$FormulaColValue</span> = <span class="i">$LineWords</span>[<span class="i">$FormulaCol</span>]<span class="sc">;</span>
156 143 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CheckFormula</span>}<span class="s">)</span> <span class="s">{</span>
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">$FormulaColValue</span><span class="s">)</span><span class="sc">;</span>
158 145 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Status</span><span class="s">)</span> <span class="s">{</span>
159 146 <span class="i">$ErrorMsg</span> = <span class="q">&quot;Ignoring line $LineCount: Formula column $ColLabels[$FormulaCol] value is not valid: $ErrorMsg&quot;</span><span class="sc">;</span>
160 147 <span class="i">PrintErrorMsg</span><span class="s">(</span><span class="i">$Line</span><span class="cm">,</span> <span class="i">$ErrorMsg</span><span class="s">)</span><span class="sc">;</span>
161 148 <span class="i">ComposeAndWriteNewLine</span><span class="s">(</span>\<span class="i">*NEWTEXTFILE</span><span class="cm">,</span> \<span class="i">@LineWords</span><span class="cm">,</span> \<span class="i">@ColNumsBeforeNew</span><span class="cm">,</span> \<span class="i">@ColNumsAfterNew</span><span class="cm">,</span> \<span class="i">@CalculatedValues</span><span class="s">)</span><span class="sc">;</span>
162 149 <span class="k">next</span> <span class="j">TEXTLINE</span><span class="sc">;</span>
163 150 <span class="s">}</span>
164 151 <span class="s">}</span>
165 152
166 153 <span class="c"># Calculate appropriate values and write &#39;em out...</span>
167 154 <span class="i">@CalculatedValues</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
168 155 <span class="k">for</span> <span class="i">$CalculationType</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedCalculations</span>}}<span class="s">)</span> <span class="s">{</span>
169 156 <span class="k">if</span> <span class="s">(</span><span class="i">$CalculationType</span> =~ <span class="q">/^ElementalAnalysis$/i</span><span class="s">)</span> <span class="s">{</span>
170 157 <span class="s">(</span><span class="i">$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> &amp;&amp; <span class="k">defined</span><span class="s">(</span><span class="i">$ElementCompositionRef</span><span class="s">)</span><span class="s">)</span> ? <span class="i">MolecularFormula::FormatCompositionInfomation</span><span class="s">(</span><span class="i">$ElementsRef</span><span class="cm">,</span> <span class="i">$ElementCompositionRef</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">Precision</span>}<span class="s">)</span> <span class="co">:</span> <span class="q">&#39;&#39;</span><span class="sc">;</span>
172 159 <span class="s">}</span>
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>
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>
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> &amp;&amp; <span class="k">length</span><span class="s">(</span><span class="i">$CalculatedValue</span><span class="s">)</span><span class="s">)</span> ? <span class="s">(</span><span class="k">sprintf</span><span class="s">(</span><span class="q">&quot;%.$OptionsInfo{Precision}f&quot;</span><span class="cm">,</span> <span class="i">$CalculatedValue</span><span class="s">)</span><span class="s">)</span> <span class="co">:</span> <span class="q">&quot;&quot;</span><span class="sc">;</span>
176 163 <span class="s">}</span>
177 164 <span class="k">elsif</span> <span class="s">(</span><span class="i">$CalculationType</span> =~ <span class="q">/^ExactMass$/i</span><span class="s">)</span> <span class="s">{</span>
178 165 <span class="i">$CalculatedValue</span> = <span class="i">MolecularFormula::CalculateExactMass</span><span class="s">(</span><span class="i">$FormulaColValue</span><span class="s">)</span><span class="sc">;</span>
179 166 <span class="i">$CalculatedValue</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$CalculatedValue</span><span class="s">)</span> &amp;&amp; <span class="k">length</span><span class="s">(</span><span class="i">$CalculatedValue</span><span class="s">)</span><span class="s">)</span> ? <span class="s">(</span><span class="k">sprintf</span><span class="s">(</span><span class="q">&quot;%.$OptionsInfo{Precision}f&quot;</span><span class="cm">,</span> <span class="i">$CalculatedValue</span><span class="s">)</span><span class="s">)</span> <span class="co">:</span> <span class="q">&quot;&quot;</span><span class="sc">;</span>
180 167 <span class="s">}</span>
181 168 <span class="k">else</span> <span class="s">{</span>
182 169 <span class="i">$CalculatedValue</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
183 170 <span class="s">}</span>
184 171 <span class="k">push</span> <span class="i">@CalculatedValues</span><span class="cm">,</span> <span class="i">$CalculatedValue</span><span class="sc">;</span>
185 172 <span class="s">}</span>
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>
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">$OldLineWordsRef</span>-&gt;[<span class="i">$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>-&gt;[<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">$NewTextFileRef</span> <span class="q">&quot;$NewLine\n&quot;</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">$OptionsInfo</span>{<span class="w">DetailLevel</span>} &gt;= <span class="n">2</span> <span class="s">)</span> <span class="s">{</span>
218 205 <span class="k">print</span> <span class="q">&quot;$ErrorMsg: $Line\n&quot;</span><span class="sc">;</span>
219 206 <span class="s">}</span>
220 207 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetailLevel</span>} &gt;= <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
221 208 <span class="k">print</span> <span class="q">&quot;$ErrorMsg\n&quot;</span><span class="sc">;</span>
222 209 <span class="s">}</span>
223 210 <span class="s">}</span>
224 211
225 212 <span class="c"># Process formula columns and other information...</span>
226 <a name="RetrieveColumnsAndLabelsInfo-"></a> 213 <span class="k">sub </span><span class="m">RetrieveColumnsAndLabelsInfo</span> <span class="s">{</span>
227 214 <span class="i">RetrieveFormulaColumnsInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
228 215 <span class="i">RetrieveStartColumnsAndValueLabelsInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
229 216 <span class="s">}</span>
230 217
231 218 <span class="c"># Make sure specified formula column are okay...</span>
232 <a name="RetrieveFormulaColumnsInfo-"></a> 219 <span class="k">sub </span><span class="m">RetrieveFormulaColumnsInfo</span> <span class="s">{</span>
233 220 <span class="k">my</span><span class="s">(</span><span class="i">$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">$OptionsInfo</span>{<span class="w">SpecifiedFormulaCol</span>} &lt;= <span class="i">$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">&quot;Warning: Ignoring file $TextFile: Formula column specified, $OptionsInfo{SpecifiedFormulaCol}, using \&quot;f --formulacol\&quot; option doesn&#39;t exist\n&quot;</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">&quot;Warning: Ignoring file $TextFile: Column label containing the word Formula doesn&#39;t exist\n&quot;</span><span class="sc">;</span>
281 268 <span class="s">}</span>
282 269 <span class="i">$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">$SpecifiedStartColNum</span> = <span class="q">&quot;last&quot;</span><span class="sc">;</span>
295 282 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$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">$OptionsInfo</span>{<span class="w">StartCol</span>}
298 285 <span class="s">}</span>
299 286 <span class="s">}</span>
300 287
301 288 <span class="c"># Column labels for for new calculated values...</span>
302 289 <span class="k">my</span><span class="s">(</span><span class="i">%NewValueLabels</span><span class="s">)</span> = <span class="s">(</span><span class="w">ElementalAnalysis</span> <span class="cm">=&gt;</span> <span class="q">&#39;ElementalAnalysis&#39;</span><span class="cm">,</span> <span class="w">MolecularWeight</span> <span class="cm">=&gt;</span> <span class="q">&#39;MolecularWeight&#39;</span><span class="cm">,</span> <span class="w">ExactMass</span> <span class="cm">=&gt;</span> <span class="q">&#39;ExactMass&#39;</span><span class="s">)</span><span class="sc">;</span>
303 290 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$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> &lt; <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedValueLabels</span>}}<span class="sc">;</span> <span class="i">$Index</span> +=<span class="n">2</span><span class="s">)</span> <span class="s">{</span>
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>
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>
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">&quot;Error: Invalid value $SpecifiedStartColNum specified using \&quot;-s --startcol\&quot; option: column name doesn&#39;t exist in $TextFile \n&quot;</span><span class="sc">;</span>
335 322 <span class="s">}</span>
336 323 <span class="s">}</span>
337 324 <span class="k">else</span> <span class="s">{</span>
338 325 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedStartColNum</span> &gt; <span class="n">0</span> &amp;&amp; <span class="i">$SpecifiedStartColNum</span> &lt;= <span class="i">$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">&quot;Error: Invalid value $SpecifiedStartColNum specified using \&quot;-s --startcol\&quot; option: column number doesn&#39;t exist in $TextFile \n&quot;</span><span class="sc">;</span>
343 330 <span class="s">}</span>
344 331 <span class="s">}</span>
345 332 <span class="s">}</span>
346 333 <span class="k">else</span> <span class="s">{</span>
347 334 <span class="i">$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">$ColNum</span> &gt;= <span class="i">$Part1StartColNum</span> &amp;&amp; <span class="i">$ColNum</span> &lt;= <span class="i">$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">$ColNum</span> &gt;= <span class="i">$Part2StartColNum</span> &amp;&amp; <span class="i">$ColNum</span> &lt;= <span class="i">$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">$Value</span>}<span class="sc">;</span>
383 370
384 371 <span class="c"># Make sure it doesn&#39;t already exists...</span>
385 372 <span class="i">$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">$Index</span>] = <span class="q">&quot;&quot;</span><span class="sc">;</span>
415 402 <span class="i">$TextFilesInfo</span>{<span class="w">OutFile</span>}[<span class="i">$Index</span>] = <span class="q">&quot;&quot;</span><span class="sc">;</span>
416 403
417 404 <span class="i">@</span>{<span class="i">$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">&quot;Warning: Ignoring file $TextFile: It doesn&#39;t exist\n&quot;</span><span class="sc">;</span>
422 409 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
423 410 <span class="s">}</span>
424 411 <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckFileType</span><span class="s">(</span><span class="i">$TextFile</span><span class="cm">,</span> <span class="q">&quot;csv tsv&quot;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
425 412 <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $TextFile: It&#39;s not a csv or tsv file\n&quot;</span><span class="sc">;</span>
426 413 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
427 414 <span class="s">}</span>
428 415 <span class="s">(</span><span class="i">$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">&quot;\t&quot;</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">$InDelim</span> = <span class="q">&quot;\,&quot;</span><span class="sc">;</span>
434 421 <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;Warning: Ignoring file $TextFile: The value specified, $Options{indelim}, for option \&quot;--indelim\&quot; is not valid for csv files\n&quot;</span><span class="sc">;</span>
436 423 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
437 424 <span class="s">}</span>
438 425 <span class="k">if</span> <span class="s">(</span><span class="i">$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">&quot;\;&quot;</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">&quot;$TextFile&quot;</span><span class="s">)</span> <span class="s">{</span>
444 431 <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $TextFile: Couldn&#39;t open it: $! \n&quot;</span><span class="sc">;</span>
445 432 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
446 433 <span class="s">}</span>
447 434
448 435 <span class="i">$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">$FileDir</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span> <span class="i">$FileName</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span> <span class="i">$FileExt</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span>
453 440 <span class="s">(</span><span class="i">$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">&quot;csv&quot;</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">$FileExt</span> = <span class="q">&quot;tsv&quot;</span><span class="sc">;</span>
457 444 <span class="s">}</span>
458 445 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">root</span>} &amp;&amp; <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">$RootFileName</span> &amp;&amp; <span class="i">$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">&quot;ElementalAnalysis&quot;</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">&quot;.$FileExt&quot;</span><span class="sc">;</span>
473 460 <span class="k">if</span> <span class="s">(</span><span class="k">lc</span><span class="s">(</span><span class="i">$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">&quot;Warning: Ignoring file $TextFile:Output file name, $OutFile, is same as input text file name, $TextFile\n&quot;</span><span class="sc">;</span>
475 462 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
476 463 <span class="s">}</span>
477 464 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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">&quot;Warning: Ignoring file $TextFile: The file $OutFile already exists\n&quot;</span><span class="sc">;</span>
480 467 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
481 468 <span class="s">}</span>
482 469 <span class="s">}</span>
483 470
484 471 <span class="i">$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">&quot;$OutFile&quot;</span><span class="sc">;</span>
487 474
488 475 <span class="i">$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">&quot;\t&quot;</span> <span class="co">:</span> <span class="s">(</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/^semicolon$/i</span><span class="s">)</span> ? <span class="q">&quot;\;&quot;</span> <span class="co">:</span> <span class="q">&quot;\,&quot;</span><span class="s">)</span><span class="sc">;</span>
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">&quot;&quot;</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">&quot;Error: Invalid value $Options{formulacol} specified using \&quot;-f -formulacol\&quot; option: Allowed values: &gt; 0\n&quot;</span><span class="sc">;</span>
531 518 <span class="s">}</span>
532 519 <span class="s">}</span>
533 520 <span class="s">}</span>
534 521
535 522 <span class="c"># Setup what to calculate...</span>
536 523 <span class="i">@</span>{<span class="i">$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">&quot;Error: All value for option \&quot;-m --mode\&quot; is not allowed with other valid values.\n&quot;</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">&quot;Error: The value specified, $ModeValue, for option \&quot;-m --mode\&quot; is not valid. Allowed values: ElementalAnalysis, MolecularWeight, or ExactMass\n&quot;</span><span class="sc">;</span>
552 539 <span class="s">}</span>
553 540 <span class="s">}</span>
554 541 <span class="k">push</span> <span class="i">@</span>{<span class="i">$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">&quot;Error: The value specified, $Options{valuecollabels}, for option \&quot;-v --valuecollabels\&quot; is not valid: It must contain even number of comma delimited values\n&quot;</span><span class="sc">;</span>
566 553 <span class="s">}</span>
567 554 <span class="k">my</span><span class="s">(</span><span class="i">$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> &lt; <span class="i">@ValueLabels</span><span class="sc">;</span> <span class="i">$Index</span> +=<span class="n">2</span><span class="s">)</span> <span class="s">{</span>
569 556 <span class="i">$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">&quot;Error: The value specified, $Value, using option \&quot;-v --valuecollabels\&quot; is not valid. Allowed values: ElementalAnalysis, MolecularWeight, or ExactMass\n&quot;</span><span class="sc">;</span>
574 561 <span class="s">}</span>
575 562 <span class="k">push</span> <span class="i">@</span>{<span class="i">$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>
579 566
580 567 <span class="c"># Setup script usage and retrieve command line arguments specified using various options...</span>
581 <a name="SetupScriptUsage-"></a> 568 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span>
582 569
583 570 <span class="c"># Retrieve all the options...</span>
584 571 <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
585 572 <span class="i">$Options</span>{<span class="w">colmode</span>} = <span class="q">&quot;colnum&quot;</span><span class="sc">;</span>
586 573 <span class="i">$Options</span>{<span class="w">detail</span>} = <span class="n">1</span><span class="sc">;</span>
587 574 <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">&quot;All&quot;</span><span class="sc">;</span>
588 575 <span class="i">$Options</span>{<span class="w">indelim</span>} = <span class="q">&quot;comma&quot;</span><span class="sc">;</span>
589 576 <span class="i">$Options</span>{<span class="w">outdelim</span>} = <span class="q">&quot;comma&quot;</span><span class="sc">;</span>
590 577 <span class="i">$Options</span>{<span class="w">precision</span>} = <span class="n">2</span><span class="sc">;</span>
591 578 <span class="i">$Options</span>{<span class="w">quote</span>} = <span class="q">&quot;yes&quot;</span><span class="sc">;</span>
592 579 <span class="i">$Options</span>{<span class="w">startcolmode</span>} = <span class="q">&quot;after&quot;</span><span class="sc">;</span>
593 580
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">&quot;colmode|c=s&quot;</span><span class="cm">,</span> <span class="q">&quot;detail|d=i&quot;</span><span class="cm">,</span> <span class="q">&quot;fast&quot;</span><span class="cm">,</span> <span class="q">&quot;formulacol|f=s&quot;</span><span class="cm">,</span> <span class="q">&quot;help|h&quot;</span><span class="cm">,</span> <span class="q">&quot;indelim=s&quot;</span><span class="cm">,</span> <span class="q">&quot;mode|m=s&quot;</span><span class="cm">,</span> <span class="q">&quot;outdelim=s&quot;</span><span class="cm">,</span> <span class="q">&quot;overwrite|o&quot;</span><span class="cm">,</span> <span class="q">&quot;precision|p=i&quot;</span><span class="cm">,</span> <span class="q">&quot;quote|q=s&quot;</span><span class="cm">,</span> <span class="q">&quot;root|r=s&quot;</span><span class="cm">,</span> <span class="q">&quot;startcol|s=s&quot;</span><span class="cm">,</span> <span class="q">&quot;startcolmode=s&quot;</span><span class="cm">,</span> <span class="q">&quot;valuecollabels|v=s&quot;</span><span class="cm">,</span> <span class="q">&quot;workingdir|w=s&quot;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
595 582 <span class="k">die</span> <span class="q">&quot;\nTo get a list of valid options and their values, use \&quot;$ScriptName -h\&quot; or\n\&quot;perl -S $ScriptName -h\&quot; command and try again...\n&quot;</span><span class="sc">;</span>
596 583 <span class="s">}</span>
597 584 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
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>
599 586 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{workingdir}, for option \&quot;-w --workingdir\&quot; is not a directory name.\n&quot;</span><span class="sc">;</span>
600 587 <span class="s">}</span>
601 588 <span class="k">chdir</span> <span class="i">$Options</span>{<span class="w">workingdir</span>} <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Couldn&#39;t chdir $Options{workingdir}: $! \n&quot;</span><span class="sc">;</span>
602 589 <span class="s">}</span>
603 590 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">colmode</span>} !~ <span class="q">/^(colnum|collabel)$/i</span><span class="s">)</span> <span class="s">{</span>
604 591 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{colmode}, for option \&quot;-c --colmode\&quot; is not valid. Allowed values: colnum or collabel\n&quot;</span><span class="sc">;</span>
605 592 <span class="s">}</span>
606 593 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">indelim</span>} !~ <span class="q">/^(comma|semicolon)$/i</span><span class="s">)</span> <span class="s">{</span>
607 594 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{indelim}, for option \&quot;--indelim\&quot; is not valid. Allowed values: comma or semicolon\n&quot;</span><span class="sc">;</span>
608 595 <span class="s">}</span>
609 596 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} !~ <span class="q">/^(comma|semicolon|tab)$/i</span><span class="s">)</span> <span class="s">{</span>
610 597 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{outdelim}, for option \&quot;--outdelim\&quot; is not valid. Allowed values: comma, tab, or semicolon\n&quot;</span><span class="sc">;</span>
611 598 <span class="s">}</span>
612 599 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">precision</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
613 600 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{precision}, for option \&quot;-p --precision\&quot; is not valid. Allowed values: &gt; 0 \n&quot;</span><span class="sc">;</span>
614 601 <span class="s">}</span>
615 602 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">quote</span>} !~ <span class="q">/^(yes|no)$/i</span><span class="s">)</span> <span class="s">{</span>
616 603 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{quote}, for option \&quot;-q --quote\&quot; is not valid. Allowed values: yes or no\n&quot;</span><span class="sc">;</span>
617 604 <span class="s">}</span>
618 605 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">startcolmode</span>} !~ <span class="q">/^(before|after)$/i</span><span class="s">)</span> <span class="s">{</span>
619 606 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{quote}, for option \&quot;--startcolmode\&quot; is not valid. Allowed values: before or after\n&quot;</span><span class="sc">;</span>
620 607 <span class="s">}</span>
621 608 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">detail</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
622 609 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{detail}, for option \&quot;-d --detail\&quot; is not valid. Allowed values: &gt; 0\n&quot;</span><span class="sc">;</span>
623 610 <span class="s">}</span>
624 611 <span class="s">}</span>
625 612
626 <a name="EOF-"></a></pre>
627 <p>&nbsp;</p>
628 <br />
629 <center>
630 <img src="../../../images/h2o2.png">
631 </center>
632 </body>
633 </html>