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+++ b/docs/scripts/html/code/InfoAminoAcids.html	Wed Jan 20 09:23:18 2016 -0500
@@ -0,0 +1,436 @@
+<html>
+<head>
+<title>MayaChemTools:Code:InfoAminoAcids.pl</title>
+<meta http-equiv="content-type" content="text/html;charset=utf-8">
+<link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css">
+</head>
+<body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10">
+<br/>
+<center>
+<a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a>
+</center>
+<br/>
+<pre>
+   1 #!/usr/bin/perl -w
+   2 <span class="c">#</span>
+   3 <span class="c"># $RCSfile: InfoAminoAcids.pl,v $</span>
+   4 <span class="c"># $Date: 2015/02/28 20:46:20 $</span>
+   5 <span class="c"># $Revision: 1.26 $</span>
+   6 <span class="c">#</span>
+   7 <span class="c"># Author: Manish Sud &lt;msud@san.rr.com&gt;</span>
+   8 <span class="c">#</span>
+   9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
+  10 <span class="c">#</span>
+  11 <span class="c"># This file is part of MayaChemTools.</span>
+  12 <span class="c">#</span>
+  13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
+  14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
+  15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
+  16 <span class="c"># later version.</span>
+  17 <span class="c">#</span>
+  18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
+  19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
+  20 <span class="c"># for a particular purpose.  See the GNU Lesser General Public License for more</span>
+  21 <span class="c"># details.</span>
+  22 <span class="c">#</span>
+  23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
+  24 <span class="c"># along with MayaChemTools; if not, see &lt;http://www.gnu.org/licenses/&gt; or</span>
+  25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
+  26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
+  27 <span class="c">#</span>
+  28 
+  29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
+  30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">&quot;$FindBin::Bin/../lib&quot;</span><span class="sc">;</span>
+  31 <span class="k">use</span> <span class="w">Getopt::Long</span><span class="sc">;</span>
+  32 <span class="k">use</span> <span class="w">File::Basename</span><span class="sc">;</span>
+  33 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span>
+  34 <span class="k">use</span> <span class="w">Benchmark</span><span class="sc">;</span>
+  35 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span>
+  36 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span>
+  37 <span class="k">use</span> <span class="w">AminoAcids</span><span class="sc">;</span>
+  38 
+  39 <span class="k">my</span><span class="s">(</span><span class="i">$ScriptName</span><span class="cm">,</span> <span class="i">%Options</span><span class="cm">,</span> <span class="i">$StartTime</span><span class="cm">,</span> <span class="i">$EndTime</span><span class="cm">,</span> <span class="i">$TotalTime</span><span class="s">)</span><span class="sc">;</span>
+  40 
+  41 <span class="c"># Autoflush STDOUT</span>
+  42 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span>
+  43 
+  44 <span class="c"># Starting message...</span>
+  45 <span class="i">$ScriptName</span> = <span class="i">basename</span><span class="s">(</span><span class="i">$0</span><span class="s">)</span><span class="sc">;</span>
+  46 <span class="k">print</span> <span class="q">&quot;\n$ScriptName: Starting...\n\n&quot;</span><span class="sc">;</span>
+  47 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
+  48 
+  49 <span class="c"># Get the options and setup script...</span>
+  50 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  51 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">help</span>}<span class="s">)</span> <span class="s">{</span>
+  52   <span class="k">die</span> <span class="i">GetUsageFromPod</span><span class="s">(</span><span class="q">&quot;$FindBin::Bin/$ScriptName&quot;</span><span class="s">)</span><span class="sc">;</span>
+  53 <span class="s">}</span>
+  54 
+  55 <span class="k">print</span> <span class="q">&quot;Processing options...\n&quot;</span><span class="sc">;</span>
+  56 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span>
+  57 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  58 
+  59 <span class="i">ListAminoAcidProperties</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  60 <span class="k">print</span> <span class="q">&quot;\n$ScriptName:Done...\n\n&quot;</span><span class="sc">;</span>
+  61 
+  62 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
+  63 <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">$StartTime</span><span class="s">)</span><span class="sc">;</span>
+  64 <span class="k">print</span> <span class="q">&quot;Total time: &quot;</span><span class="cm">,</span> <span class="i">timestr</span><span class="s">(</span><span class="i">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+  65 
+  66 <span class="c">###############################################################################</span>
+  67 
+  68 <span class="c"># List data for an amino acid...</span>
+<a name="ListAminoAcidData-"></a>  69 <span class="k">sub </span><span class="m">ListAminoAcidData</span> <span class="s">{</span>
+  70   <span class="k">my</span><span class="s">(</span><span class="i">$DataLabelRef</span><span class="cm">,</span> <span class="i">$DataValueRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+  71   <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$Line</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
+  72 
+  73   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">AminoAcidRowsOutput</span>}<span class="s">)</span> <span class="s">{</span>
+  74     <span class="i">$Line</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+  75     <span class="c"># Format data...</span>
+  76     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>} || <span class="i">$Options</span>{<span class="w">outdelim</span>} !~ <span class="q">/^comma$/i</span><span class="s">)</span> <span class="s">{</span>
+  77       <span class="i">$Line</span> = <span class="i">JoinWords</span><span class="s">(</span><span class="i">$DataValueRef</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>}<span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span>
+  78     <span class="s">}</span>
+  79     <span class="k">else</span> <span class="s">{</span>
+  80       <span class="c"># Always quote values containing commas...</span>
+  81       <span class="i">$Line</span> = <span class="s">(</span><span class="i">$DataValueRef</span>-&gt;[<span class="n">0</span>] =~ <span class="q">/\,/</span><span class="s">)</span> ? <span class="q">qq(&quot;$DataValueRef-&gt;[0]&quot;)</span> <span class="co">:</span> <span class="i">$DataValueRef</span>-&gt;[<span class="n">0</span>]<span class="sc">;</span>
+  82       <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">1</span> .. <span class="i">$#</span>{<span class="i">$DataValueRef</span>} <span class="s">)</span> <span class="s">{</span>
+  83         <span class="i">$Value</span> = <span class="i">$DataValueRef</span>-&gt;[<span class="i">$Index</span>]<span class="sc">;</span>
+  84         <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> =~ <span class="q">/\,/</span><span class="s">)</span> <span class="s">{</span>
+  85           <span class="i">$Value</span> = <span class="q">qq(&quot;$Value&quot;)</span><span class="sc">;</span>
+  86         <span class="s">}</span>
+  87         <span class="i">$Line</span> .= <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>} . <span class="i">$Value</span><span class="sc">;</span>
+  88       <span class="s">}</span>
+  89     <span class="s">}</span>
+  90     <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FileOutput</span>}<span class="s">)</span> <span class="s">{</span>
+  91       <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$Line\n&quot;</span><span class="sc">;</span>
+  92     <span class="s">}</span>
+  93     <span class="k">else</span> <span class="s">{</span>
+  94       <span class="k">print</span> <span class="q">&quot;$Line\n&quot;</span><span class="sc">;</span>
+  95     <span class="s">}</span>
+  96   <span class="s">}</span>
+  97   <span class="k">else</span> <span class="s">{</span>
+  98     <span class="c"># Format and list data...</span>
+  99     <span class="i">$Line</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+ 100     <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$DataLabelRef</span>} <span class="s">)</span> <span class="s">{</span>
+ 101       <span class="i">$Line</span> = <span class="i">$DataLabelRef</span>-&gt;[<span class="i">$Index</span>] . <span class="q">&#39; &#39;</span> . <span class="i">$DataValueRef</span>-&gt;[<span class="i">$Index</span>]<span class="sc">;</span>
+ 102       <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FileOutput</span>}<span class="s">)</span> <span class="s">{</span>
+ 103         <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$Line\n&quot;</span><span class="sc">;</span>
+ 104       <span class="s">}</span>
+ 105       <span class="k">else</span> <span class="s">{</span>
+ 106         <span class="k">print</span> <span class="q">&quot;$Line\n&quot;</span><span class="sc">;</span>
+ 107       <span class="s">}</span>
+ 108     <span class="s">}</span>
+ 109   <span class="s">}</span>
+ 110 <span class="s">}</span>
+ 111 
+ 112 <span class="c"># List data for an amino acid...</span>
+<a name="ListHeaderRowData-"></a> 113 <span class="k">sub </span><span class="m">ListHeaderRowData</span> <span class="s">{</span>
+ 114   <span class="k">my</span><span class="s">(</span><span class="i">$DataLabelRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 115   <span class="k">my</span><span class="s">(</span><span class="i">$Line</span><span class="s">)</span><span class="sc">;</span>
+ 116 
+ 117   <span class="c"># Format data...</span>
+ 118   <span class="i">$Line</span> = <span class="i">JoinWords</span><span class="s">(</span><span class="i">$DataLabelRef</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>}<span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span>
+ 119   <span class="i">$Line</span> =~ <span class="q">s/\://g</span><span class="sc">;</span>
+ 120   <span class="c"># List data...</span>
+ 121   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FileOutput</span>}<span class="s">)</span> <span class="s">{</span>
+ 122     <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;$Line\n&quot;</span><span class="sc">;</span>
+ 123   <span class="s">}</span>
+ 124   <span class="k">else</span> <span class="s">{</span>
+ 125     <span class="k">print</span> <span class="q">&quot;$Line\n&quot;</span><span class="sc">;</span>
+ 126   <span class="s">}</span>
+ 127 <span class="s">}</span>
+ 128 
+ 129 <span class="c"># List properties for amino acids...</span>
+<a name="ListAminoAcidProperties-"></a> 130 <span class="k">sub </span><span class="m">ListAminoAcidProperties</span> <span class="s">{</span>
+ 131   <span class="k">my</span><span class="s">(</span><span class="i">$AminoAcidID</span><span class="cm">,</span> <span class="i">$AminoAcidDataRef</span><span class="cm">,</span> <span class="i">$PropertyName</span><span class="cm">,</span> <span class="i">$PropertyValue</span><span class="cm">,</span> <span class="i">@PropertyLabels</span><span class="cm">,</span> <span class="i">@PropertyValues</span><span class="s">)</span><span class="sc">;</span>
+ 132 
+ 133   <span class="k">print</span> <span class="q">&quot;Listing information for amino acid(s)...\n&quot;</span><span class="sc">;</span>
+ 134 
+ 135   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FileOutput</span>}<span class="s">)</span> <span class="s">{</span>
+ 136     <span class="k">print</span> <span class="q">&quot;Generating file $OptionsInfo{OutFileName}...\n&quot;</span><span class="sc">;</span>
+ 137     <span class="k">open</span> <span class="w">OUTFILE</span><span class="cm">,</span> <span class="q">&quot;&gt;$OptionsInfo{OutFileName}&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Couldn&#39;t open $OptionsInfo{OutFileName}: $!\n&quot;</span><span class="sc">;</span>
+ 138   <span class="s">}</span>
+ 139 
+ 140   <span class="c"># Setup property labels...</span>
+ 141   <span class="i">@PropertyLabels</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 142   <span class="k">for</span> <span class="i">$PropertyName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}}<span class="s">)</span> <span class="s">{</span>
+ 143     <span class="k">push</span> <span class="i">@PropertyLabels</span><span class="cm">,</span> <span class="s">(</span><span class="q">&quot;$PropertyName:&quot;</span><span class="s">)</span><span class="sc">;</span>
+ 144   <span class="s">}</span>
+ 145 
+ 146   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">AminoAcidRowsOutput</span>}<span class="s">)</span> <span class="s">{</span>
+ 147     <span class="i">ListHeaderRowData</span><span class="s">(</span>\<span class="i">@PropertyLabels</span><span class="s">)</span><span class="sc">;</span>
+ 148   <span class="s">}</span>
+ 149 
+ 150   <span class="c"># Go over specified properties...</span>
+ 151   <span class="k">for</span> <span class="i">$AminoAcidID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAminoAcidIDs</span>}}<span class="s">)</span> <span class="s">{</span>
+ 152     <span class="i">$AminoAcidDataRef</span> = <span class="i">AminoAcids::GetAminoAcidPropertiesData</span><span class="s">(</span><span class="i">$AminoAcidID</span><span class="s">)</span><span class="sc">;</span>
+ 153 
+ 154     <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">AminoAcidRowsOutput</span>}<span class="s">)</span> <span class="s">{</span>
+ 155       <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FileOutput</span>}<span class="s">)</span> <span class="s">{</span>
+ 156         <span class="k">print</span> <span class="i">OUTFILE</span> <span class="q">&quot;\nListing properties for amino acid $AminoAcidID...\n\n&quot;</span><span class="sc">;</span>
+ 157       <span class="s">}</span>
+ 158       <span class="k">else</span> <span class="s">{</span>
+ 159         <span class="k">print</span> <span class="q">&quot;\nListing properties for amino acid $AminoAcidID...\n\n&quot;</span><span class="sc">;</span>
+ 160       <span class="s">}</span>
+ 161     <span class="s">}</span>
+ 162 
+ 163     <span class="c"># Collect data..</span>
+ 164     <span class="i">@PropertyValues</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 165     <span class="k">for</span> <span class="i">$PropertyName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}}<span class="s">)</span> <span class="s">{</span>
+ 166       <span class="i">$PropertyValue</span> = <span class="i">$AminoAcidDataRef</span>-&gt;{<span class="i">$PropertyName</span>}<span class="sc">;</span>
+ 167       <span class="k">if</span> <span class="s">(</span><span class="i">IsFloat</span><span class="s">(</span><span class="i">$PropertyValue</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 168         <span class="i">$PropertyValue</span> = <span class="k">sprintf</span><span class="s">(</span><span class="q">&quot;%.$OptionsInfo{Precision}f&quot;</span><span class="cm">,</span> <span class="i">$PropertyValue</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span>
+ 169       <span class="s">}</span>
+ 170       <span class="k">push</span> <span class="i">@PropertyValues</span><span class="cm">,</span> <span class="i">$PropertyValue</span><span class="sc">;</span>
+ 171     <span class="s">}</span>
+ 172     <span class="c"># List data...</span>
+ 173     <span class="i">ListAminoAcidData</span><span class="s">(</span>\<span class="i">@PropertyLabels</span><span class="cm">,</span> \<span class="i">@PropertyValues</span><span class="s">)</span><span class="sc">;</span>
+ 174   <span class="s">}</span>
+ 175   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FileOutput</span>}<span class="s">)</span> <span class="s">{</span>
+ 176     <span class="k">close</span> <span class="w">OUTFILE</span><span class="sc">;</span>
+ 177   <span class="s">}</span>
+ 178   <span class="k">print</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
+ 179 <span class="s">}</span>
+ 180 
+ 181 <span class="c"># Get propery names from categories...</span>
+<a name="GetPropertyNamesFromCategories-"></a> 182 <span class="k">sub </span><span class="m">GetPropertyNamesFromCategories</span> <span class="s">{</span>
+ 183   <span class="k">my</span><span class="s">(</span><span class="i">$CategoryName</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 184   <span class="k">my</span><span class="s">(</span><span class="i">@PropertyNames</span><span class="s">)</span><span class="sc">;</span>
+ 185 
+ 186   <span class="i">@PropertyNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 187   <span class="k">if</span> <span class="s">(</span><span class="i">$CategoryName</span> =~ <span class="q">/^Basic$/i</span><span class="s">)</span> <span class="s">{</span>
+ 188     <span class="i">@PropertyNames</span> = <span class="s">(</span><span class="q">&#39;ThreeLetterCode&#39;</span><span class="cm">,</span> <span class="q">&#39;OneLetterCode&#39;</span><span class="cm">,</span> <span class="q">&#39;AminoAcid&#39;</span><span class="cm">,</span> <span class="q">&#39;DNACodons&#39;</span><span class="cm">,</span> <span class="q">&#39;RNACodons&#39;</span><span class="cm">,</span> <span class="q">&#39;ChemicalFormula&#39;</span><span class="cm">,</span><span class="q">&#39;MolecularWeight&#39;</span><span class="cm">,</span> <span class="q">&#39;LinearStructure&#39;</span><span class="cm">,</span> <span class="q">&#39;LinearStructureAtpH7.4&#39;</span><span class="s">)</span><span class="sc">;</span>
+ 189   <span class="s">}</span> <span class="k">elsif</span> <span class="s">(</span><span class="i">$CategoryName</span> =~ <span class="q">/^BasicPlus$/i</span><span class="s">)</span> <span class="s">{</span>
+ 190     <span class="i">@PropertyNames</span> = <span class="s">(</span><span class="q">&#39;ThreeLetterCode&#39;</span><span class="cm">,</span> <span class="q">&#39;OneLetterCode&#39;</span><span class="cm">,</span> <span class="q">&#39;AminoAcid&#39;</span><span class="cm">,</span> <span class="q">&#39;DNACodons&#39;</span><span class="cm">,</span> <span class="q">&#39;RNACodons&#39;</span><span class="cm">,</span> <span class="q">&#39;AcidicBasic&#39;</span><span class="cm">,</span> <span class="q">&#39;PolarNonpolar&#39;</span><span class="cm">,</span> <span class="q">&#39;Charged&#39;</span><span class="cm">,</span> <span class="q">&#39;Aromatic&#39;</span><span class="cm">,</span> <span class="q">&#39;HydrophobicHydophilic&#39;</span><span class="cm">,</span> <span class="q">&#39;IsoelectricPoint&#39;</span><span class="cm">,</span> <span class="q">&#39;pKCOOH&#39;</span><span class="cm">,</span> <span class="q">&#39;pKNH3+&#39;</span><span class="cm">,</span> <span class="q">&#39;ChemicalFormula&#39;</span><span class="cm">,</span> <span class="q">&#39;MolecularWeight&#39;</span><span class="cm">,</span> <span class="q">&#39;ExactMass&#39;</span><span class="cm">,</span> <span class="q">&#39;ChemicalFormulaMinusH2O&#39;</span><span class="cm">,</span> <span class="q">&#39;MolecularWeightMinusH2O(18.01524)&#39;</span><span class="cm">,</span> <span class="q">&#39;ExactMassMinusH2O(18.01056)&#39;</span><span class="cm">,</span><span class="q">&#39;LinearStructure&#39;</span><span class="cm">,</span> <span class="q">&#39;LinearStructureAtpH7.4&#39;</span><span class="s">)</span><span class="sc">;</span>
+ 191   <span class="s">}</span> <span class="k">elsif</span> <span class="s">(</span><span class="i">$CategoryName</span> =~ <span class="q">/^BasicAndHydrophobicity$/i</span><span class="s">)</span> <span class="s">{</span>
+ 192     <span class="i">@PropertyNames</span> = <span class="s">(</span><span class="q">&#39;ThreeLetterCode&#39;</span><span class="cm">,</span> <span class="q">&#39;OneLetterCode&#39;</span><span class="cm">,</span> <span class="q">&#39;AminoAcid&#39;</span><span class="cm">,</span> <span class="q">&#39;DNACodons&#39;</span><span class="cm">,</span> <span class="q">&#39;RNACodons&#39;</span><span class="cm">,</span> <span class="q">&#39;ChemicalFormula&#39;</span><span class="cm">,</span> <span class="q">&#39;MolecularWeight&#39;</span><span class="cm">,</span> <span class="q">&#39;LinearStructure&#39;</span><span class="cm">,</span> <span class="q">&#39;LinearStructureAtpH7.4&#39;</span><span class="cm">,</span> <span class="q">&#39;HydrophobicityEisenbergAndOthers&#39;</span><span class="cm">,</span> <span class="q">&#39;HydrophobicityHoppAndWoods&#39;</span><span class="cm">,</span> <span class="q">&#39;HydrophobicityJanin&#39;</span><span class="cm">,</span> <span class="q">&#39;HydrophobicityKyteAndDoolittle&#39;</span><span class="cm">,</span> <span class="q">&#39;HydrophobicityRoseAndOthers&#39;</span><span class="cm">,</span> <span class="q">&#39;HydrophobicityWolfendenAndOthers&#39;</span><span class="s">)</span><span class="sc">;</span>
+ 193   <span class="s">}</span> <span class="k">elsif</span> <span class="s">(</span><span class="i">$CategoryName</span> =~ <span class="q">/^BasicAndHydrophobicityPlus$/i</span><span class="s">)</span> <span class="s">{</span>
+ 194     <span class="i">@PropertyNames</span> = <span class="s">(</span><span class="q">&#39;ThreeLetterCode&#39;</span><span class="cm">,</span> <span class="q">&#39;OneLetterCode&#39;</span><span class="cm">,</span> <span class="q">&#39;AminoAcid&#39;</span><span class="cm">,</span> <span class="q">&#39;DNACodons&#39;</span><span class="cm">,</span> <span class="q">&#39;RNACodons&#39;</span><span class="cm">,</span> <span class="q">&#39;ChemicalFormula&#39;</span><span class="cm">,</span> <span class="q">&#39;MolecularWeight&#39;</span><span class="cm">,</span> <span class="q">&#39;LinearStructure&#39;</span><span class="cm">,</span> <span class="q">&#39;LinearStructureAtpH7.4&#39;</span><span class="cm">,</span> <span class="q">&#39;HydrophobicityAbrahamAndLeo&#39;</span><span class="cm">,</span> <span class="q">&#39;HydrophobicityBlack&#39;</span><span class="cm">,</span> <span class="q">&#39;HydrophobicityBullAndBreese&#39;</span><span class="cm">,</span> <span class="q">&#39;HydrophobicityChothia&#39;</span><span class="cm">,</span> <span class="q">&#39;HydrophobicityEisenbergAndOthers&#39;</span><span class="cm">,</span> <span class="q">&#39;HydrophobicityFauchereAndOthers&#39;</span><span class="cm">,</span> <span class="q">&#39;HydrophobicityGuy&#39;</span><span class="cm">,</span> <span class="q">&#39;HydrophobicityHPLCAtpH3.4Cowan&#39;</span><span class="cm">,</span> <span class="q">&#39;HydrophobicityHPLCAtpH7.5Cowan&#39;</span><span class="cm">,</span> <span class="q">&#39;HydrophobicityHPLCParkerAndOthers&#39;</span><span class="cm">,</span> <span class="q">&#39;HydrophobicityHPLCWilsonAndOthers&#39;</span><span class="cm">,</span> <span class="q">&#39;HydrophobicityHoppAndWoods&#39;</span><span class="cm">,</span> <span class="q">&#39;HydrophobicityJanin&#39;</span><span class="cm">,</span> <span class="q">&#39;HydrophobicityKyteAndDoolittle&#39;</span><span class="cm">,</span> <span class="q">&#39;HydrophobicityManavalanAndOthers&#39;</span><span class="cm">,</span> <span class="q">&#39;HydrophobicityMiyazawaAndOthers&#39;</span><span class="cm">,</span> <span class="q">&#39;HydrophobicityOMHSweetAndOthers&#39;</span><span class="cm">,</span> <span class="q">&#39;HydrophobicityRaoAndArgos&#39;</span><span class="cm">,</span> <span class="q">&#39;HydrophobicityRfMobility&#39;</span><span class="cm">,</span> <span class="q">&#39;HydrophobicityRoseAndOthers&#39;</span><span class="cm">,</span> <span class="q">&#39;HydrophobicityRoseman&#39;</span><span class="cm">,</span> <span class="q">&#39;HydrophobicityWellingAndOthers&#39;</span><span class="cm">,</span> <span class="q">&#39;HydrophobicityWolfendenAndOthers&#39;</span><span class="s">)</span><span class="sc">;</span>
+ 195   <span class="s">}</span>
+ 196 
+ 197   <span class="k">return</span> <span class="i">@PropertyNames</span><span class="sc">;</span>
+ 198 <span class="s">}</span>
+ 199 
+ 200 <span class="c"># Process option values...</span>
+<a name="ProcessOptions-"></a> 201 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span>
+ 202   <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 203 
+ 204   <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>
+ 205   <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$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+ 206 
+ 207   <span class="i">$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>
+ 208   <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">$Options</span>{<span class="w">root</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
+ 209 
+ 210   <span class="i">$OptionsInfo</span>{<span class="w">OutputStyle</span>} = <span class="i">$Options</span>{<span class="w">outputstyle</span>}<span class="sc">;</span>
+ 211 
+ 212   <span class="i">$OptionsInfo</span>{<span class="w">AminoAcidRowsOutput</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">outputstyle</span>} =~ <span class="q">/^AminoAcidRows$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+ 213   <span class="i">$OptionsInfo</span>{<span class="w">FileOutput</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">output</span>} =~ <span class="q">/^File$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+ 214 
+ 215   <span class="i">$OptionsInfo</span>{<span class="w">Precision</span>} = <span class="i">$Options</span>{<span class="w">precision</span>}<span class="sc">;</span>
+ 216 
+ 217   <span class="k">my</span><span class="s">(</span><span class="i">$AminoAcidID</span><span class="cm">,</span> <span class="i">@AminoAcidIDs</span><span class="s">)</span><span class="sc">;</span>
+ 218 
+ 219   <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAminoAcidIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 220 
+ 221   <span class="c"># Set up Amino Acids IDs except for All mode...</span>
+ 222   <span class="i">@AminoAcidIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 223 
+ 224   <span class="k">if</span> <span class="s">(</span><span class="i">@ARGV</span> &gt;= <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
+ 225     <span class="k">push</span> <span class="i">@AminoAcidIDs</span><span class="cm">,</span> <span class="i">@ARGV</span><span class="sc">;</span>
+ 226   <span class="s">}</span>
+ 227   <span class="k">else</span> <span class="s">{</span>
+ 228     <span class="c"># Setup mode specified default values...</span>
+ 229     <span class="k">push</span> <span class="i">@AminoAcidIDs</span><span class="cm">,</span> <span class="q">&#39;Ala&#39;</span><span class="sc">;</span>
+ 230   <span class="s">}</span>
+ 231 
+ 232   <span class="c"># Generate list of amino acids...</span>
+ 233   <span class="k">if</span> <span class="s">(</span><span class="i">@ARGV</span> == <span class="n">1</span> &amp;&amp; <span class="i">$ARGV</span>[<span class="n">0</span>] =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span>
+ 234     <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAminoAcidIDs</span>}}<span class="cm">,</span> <span class="i">AminoAcids::GetAminoAcids</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 235   <span class="s">}</span>
+ 236   <span class="k">else</span> <span class="s">{</span>
+ 237     <span class="j">ID:</span> <span class="k">for</span> <span class="i">$AminoAcidID</span> <span class="s">(</span><span class="i">@AminoAcidIDs</span><span class="s">)</span> <span class="s">{</span>
+ 238       <span class="k">if</span> <span class="s">(</span><span class="i">AminoAcids::IsAminoAcid</span><span class="s">(</span><span class="i">$AminoAcidID</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 239         <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedAminoAcidIDs</span>}}<span class="cm">,</span> <span class="i">$AminoAcidID</span><span class="sc">;</span>
+ 240       <span class="s">}</span>
+ 241       <span class="k">else</span> <span class="s">{</span>
+ 242         <span class="k">warn</span> <span class="q">&quot;Ignoring amino acid ID, $AminoAcidID, specified using command line parameter option: Unknown amino acid ID...\n&quot;</span><span class="sc">;</span>
+ 243         <span class="k">next</span> <span class="j">ID</span><span class="sc">;</span>
+ 244       <span class="s">}</span>
+ 245     <span class="s">}</span>
+ 246   <span class="s">}</span>
+ 247   <span class="i">SetupSpecifiedProperties</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 248 
+ 249   <span class="c"># Setup output file name...</span>
+ 250   <span class="i">$OptionsInfo</span>{<span class="w">OutFileName</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+ 251   <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FileOutput</span>}<span class="s">)</span> <span class="s">{</span>
+ 252     <span class="k">my</span><span class="s">(</span><span class="i">$OutFileRoot</span><span class="cm">,</span> <span class="i">$OutFileExt</span><span class="s">)</span><span class="sc">;</span>
+ 253 
+ 254     <span class="i">$OutFileRoot</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+ 255     <span class="i">$OutFileExt</span> = <span class="q">&quot;csv&quot;</span><span class="sc">;</span>
+ 256     <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/^tab$/i</span><span class="s">)</span> <span class="s">{</span>
+ 257       <span class="i">$OutFileExt</span> = <span class="q">&quot;tsv&quot;</span><span class="sc">;</span>
+ 258     <span class="s">}</span>
+ 259     <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">root</span>}<span class="s">)</span> <span class="s">{</span>
+ 260       <span class="k">my</span> <span class="s">(</span><span class="i">$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">$Options</span>{<span class="w">root</span>}<span class="s">)</span><span class="sc">;</span>
+ 261       <span class="k">if</span> <span class="s">(</span><span class="i">$RootFileName</span> &amp;&amp; <span class="i">$RootFileExt</span><span class="s">)</span> <span class="s">{</span>
+ 262         <span class="i">$OutFileRoot</span> = <span class="i">$RootFileName</span><span class="sc">;</span>
+ 263       <span class="s">}</span>
+ 264       <span class="k">else</span> <span class="s">{</span>
+ 265         <span class="i">$OutFileRoot</span> = <span class="i">$Options</span>{<span class="w">root</span>}<span class="sc">;</span>
+ 266       <span class="s">}</span>
+ 267     <span class="s">}</span>
+ 268     <span class="k">else</span> <span class="s">{</span>
+ 269       <span class="i">$OutFileRoot</span> = <span class="q">&#39;AminoAcidsInfo&#39;</span><span class="sc">;</span>
+ 270     <span class="s">}</span>
+ 271     <span class="i">$OptionsInfo</span>{<span class="w">OutFileName</span>} = <span class="i">$OutFileRoot</span> . <span class="q">&#39;.&#39;</span> . <span class="i">$OutFileExt</span><span class="sc">;</span>
+ 272     <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">overwrite</span>}<span class="s">)</span> <span class="s">{</span>
+ 273       <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="i">$OptionsInfo</span>{<span class="w">OutFileName</span>}<span class="s">)</span> <span class="s">{</span>
+ 274         <span class="k">die</span> <span class="q">&quot;Error: Output file, $OptionsInfo{OutFileName}, already exists.\nUse \-o --overwrite\ option or specify a different name using \&quot;-r --root\&quot; option.\n&quot;</span><span class="sc">;</span>
+ 275       <span class="s">}</span>
+ 276     <span class="s">}</span>
+ 277   <span class="s">}</span>
+ 278 <span class="s">}</span>
+ 279 
+ 280 <span class="c"># Setup properties to list...</span>
+<a name="SetupSpecifiedProperties-"></a> 281 <span class="k">sub </span><span class="m">SetupSpecifiedProperties</span> <span class="s">{</span>
+ 282 
+ 283   <span class="i">$OptionsInfo</span>{<span class="w">Properties</span>} = <span class="k">defined</span> <span class="i">$Options</span>{<span class="w">properties</span>} ? <span class="i">$Options</span>{<span class="w">properties</span>} <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
+ 284 
+ 285   <span class="i">$OptionsInfo</span>{<span class="w">PropertiesMode</span>} = <span class="i">$Options</span>{<span class="w">propertiesmode</span>}<span class="sc">;</span>
+ 286   <span class="i">$OptionsInfo</span>{<span class="w">PropertiesListing</span>} = <span class="i">$Options</span>{<span class="w">propertieslisting</span>}<span class="sc">;</span>
+ 287 
+ 288   <span class="c"># Make sure appropriate properties/category names are specified...</span>
+ 289   <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 290   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">properties</span>} &amp;&amp; <span class="s">(</span><span class="i">$Options</span>{<span class="w">propertiesmode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span>
+ 291     <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring values specifed by \&quot;-p --properties\&quot; option: Not valid for All value of \&quot;--propertiesmode\&quot; option...\n&quot;</span><span class="sc">;</span>
+ 292   <span class="s">}</span>
+ 293   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">propertiesmode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span>
+ 294     <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">propertieslisting</span>} =~ <span class="q">/^Alphabetical$/i</span><span class="s">)</span> <span class="s">{</span>
+ 295       <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}}<span class="cm">,</span> <span class="i">AminoAcids::GetAminoAcidPropertiesNames</span><span class="s">(</span><span class="q">&#39;Alphabetical&#39;</span><span class="s">)</span><span class="sc">;</span>
+ 296     <span class="s">}</span>
+ 297     <span class="k">else</span> <span class="s">{</span>
+ 298       <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}}<span class="cm">,</span> <span class="i">AminoAcids::GetAminoAcidPropertiesNames</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 299     <span class="s">}</span>
+ 300   <span class="s">}</span>
+ 301   <span class="k">else</span> <span class="s">{</span>
+ 302     <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">properties</span>}<span class="s">)</span> <span class="s">{</span>
+ 303       <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">propertiesmode</span>} =~ <span class="q">/^Categories$/i</span><span class="s">)</span> <span class="s">{</span>
+ 304         <span class="c"># Check category name...</span>
+ 305         <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">properties</span>} !~ <span class="q">/^(Basic|BasicPlus|BasicAndHydrophobicity|BasicAndHydrophobicityPlus)$/i</span><span class="s">)</span> <span class="s">{</span>
+ 306           <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{properties}, for option \&quot;-p --properties\&quot; in conjunction with \&quot;Categories\&quot; value for option \&quot;--propertiesmode\&quot; is not valid. Allowed values: Basic, BasicPlus, BasicAndHydrophobicity, and BasicAndHydrophobicityPlus\n&quot;</span><span class="sc">;</span>
+ 307         <span class="s">}</span>
+ 308         <span class="c"># Set propertynames...</span>
+ 309         <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}}<span class="cm">,</span> <span class="i">GetPropertyNamesFromCategories</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">properties</span>}<span class="s">)</span><span class="sc">;</span>
+ 310       <span class="s">}</span>
+ 311       <span class="k">else</span> <span class="s">{</span>
+ 312         <span class="c"># Check property names..</span>
+ 313         <span class="k">my</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$PropertyName</span><span class="cm">,</span> <span class="i">@Names</span><span class="s">)</span><span class="sc">;</span>
+ 314         <span class="i">@Names</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">properties</span>}<span class="sc">;</span>
+ 315         <span class="j">NAME:</span> <span class="k">for</span> <span class="i">$Name</span> <span class="s">(</span><span class="i">@Names</span><span class="s">)</span> <span class="s">{</span>
+ 316           <span class="i">$PropertyName</span> = <span class="i">RemoveLeadingAndTrailingWhiteSpaces</span><span class="s">(</span><span class="i">$Name</span><span class="s">)</span><span class="sc">;</span>
+ 317           <span class="k">if</span> <span class="s">(</span><span class="i">AminoAcids::IsAminoAcidProperty</span><span class="s">(</span><span class="i">$PropertyName</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 318             <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}}<span class="cm">,</span> <span class="i">$PropertyName</span><span class="sc">;</span>
+ 319           <span class="s">}</span>
+ 320           <span class="k">else</span> <span class="s">{</span>
+ 321             <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring value, $Name, specifed by \&quot;-p --properties\&quot; option: Unknown property name...\n&quot;</span><span class="sc">;</span>
+ 322           <span class="s">}</span>
+ 323         <span class="s">}</span>
+ 324         <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">propertieslisting</span>} =~ <span class="q">/^Alphabetical$/i</span><span class="s">)</span> <span class="s">{</span>
+ 325           <span class="c"># ThreeLetterCode, OneLetterCode and AminoAcid are always listed first...</span>
+ 326           <span class="c"># NaturalIsotopeData in the end...</span>
+ 327           <span class="k">my</span><span class="s">(</span><span class="i">$OneLetterCodePresent</span><span class="cm">,</span> <span class="i">$ThreeLetterCodePresent</span><span class="cm">,</span> <span class="i">$AminoAcidPresent</span><span class="cm">,</span>  <span class="i">@AlphabeticalProperties</span><span class="cm">,</span> <span class="i">%PropertiesMap</span><span class="s">)</span><span class="sc">;</span>
+ 328           <span class="i">%PropertiesMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 329           <span class="i">@AlphabeticalProperties</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 330           <span class="i">$OneLetterCodePresent</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$ThreeLetterCodePresent</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$AminoAcidPresent</span> = <span class="n">0</span><span class="sc">;</span>
+ 331           <span class="j">NAME:</span> <span class="k">for</span> <span class="i">$Name</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}}<span class="s">)</span> <span class="s">{</span>
+ 332             <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^OneLetterCode$/i</span><span class="s">)</span> <span class="s">{</span>
+ 333               <span class="i">$OneLetterCodePresent</span> = <span class="n">1</span><span class="sc">;</span>
+ 334               <span class="k">next</span> <span class="j">NAME</span><span class="sc">;</span>
+ 335             <span class="s">}</span>
+ 336             <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^ThreeLetterCode$/i</span><span class="s">)</span> <span class="s">{</span>
+ 337               <span class="i">$ThreeLetterCodePresent</span> = <span class="n">1</span><span class="sc">;</span>
+ 338               <span class="k">next</span> <span class="j">NAME</span><span class="sc">;</span>
+ 339             <span class="s">}</span>
+ 340             <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^AminoAcid$/i</span><span class="s">)</span> <span class="s">{</span>
+ 341               <span class="i">$AminoAcidPresent</span> = <span class="n">1</span><span class="sc">;</span>
+ 342               <span class="k">next</span> <span class="j">NAME</span><span class="sc">;</span>
+ 343             <span class="s">}</span>
+ 344             <span class="i">$PropertiesMap</span>{<span class="i">$Name</span>} = <span class="i">$Name</span><span class="sc">;</span>
+ 345           <span class="s">}</span>
+ 346           <span class="c"># Setup the alphabetical list...</span>
+ 347           <span class="k">if</span> <span class="s">(</span><span class="i">$ThreeLetterCodePresent</span><span class="s">)</span> <span class="s">{</span>
+ 348             <span class="k">push</span> <span class="i">@AlphabeticalProperties</span><span class="cm">,</span> <span class="q">&#39;ThreeLetterCode&#39;</span><span class="sc">;</span>
+ 349           <span class="s">}</span>
+ 350           <span class="k">if</span> <span class="s">(</span><span class="i">$OneLetterCodePresent</span><span class="s">)</span> <span class="s">{</span>
+ 351             <span class="k">push</span> <span class="i">@AlphabeticalProperties</span><span class="cm">,</span> <span class="q">&#39;OneLetterCode&#39;</span><span class="sc">;</span>
+ 352           <span class="s">}</span>
+ 353           <span class="k">if</span> <span class="s">(</span><span class="i">$AminoAcidPresent</span><span class="s">)</span> <span class="s">{</span>
+ 354             <span class="k">push</span> <span class="i">@AlphabeticalProperties</span><span class="cm">,</span> <span class="q">&#39;AminoAcid&#39;</span><span class="sc">;</span>
+ 355           <span class="s">}</span>
+ 356           <span class="k">for</span> <span class="i">$Name</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%PropertiesMap</span><span class="s">)</span> <span class="s">{</span>
+ 357             <span class="k">push</span> <span class="i">@AlphabeticalProperties</span><span class="cm">,</span> <span class="i">$Name</span><span class="sc">;</span>
+ 358           <span class="s">}</span>
+ 359           <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 360           <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}}<span class="cm">,</span> <span class="i">@AlphabeticalProperties</span><span class="sc">;</span>
+ 361         <span class="s">}</span>
+ 362       <span class="s">}</span>
+ 363     <span class="s">}</span>
+ 364     <span class="k">else</span> <span class="s">{</span>
+ 365       <span class="c"># Set default value...</span>
+ 366       <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedProperies</span>}}<span class="cm">,</span> <span class="i">GetPropertyNamesFromCategories</span><span class="s">(</span><span class="q">&#39;Basic&#39;</span><span class="s">)</span><span class="sc">;</span>
+ 367     <span class="s">}</span>
+ 368   <span class="s">}</span>
+ 369 <span class="s">}</span>
+ 370 
+ 371 <span class="c"># Setup script usage  and retrieve command line arguments specified using various options...</span>
+<a name="SetupScriptUsage-"></a> 372 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span>
+ 373 
+ 374   <span class="c"># Retrieve all the options...</span>
+ 375   <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 376   <span class="i">$Options</span>{<span class="w">outdelim</span>} = <span class="q">&quot;comma&quot;</span><span class="sc">;</span>
+ 377   <span class="i">$Options</span>{<span class="w">output</span>} = <span class="q">&quot;STDOUT&quot;</span><span class="sc">;</span>
+ 378   <span class="i">$Options</span>{<span class="w">outputstyle</span>} = <span class="q">&quot;AminoAcidBlock&quot;</span><span class="sc">;</span>
+ 379   <span class="i">$Options</span>{<span class="w">precision</span>} = <span class="n">4</span><span class="sc">;</span>
+ 380   <span class="i">$Options</span>{<span class="w">propertiesmode</span>} = <span class="q">&quot;Categories&quot;</span><span class="sc">;</span>
+ 381   <span class="i">$Options</span>{<span class="w">propertieslisting</span>} = <span class="q">&quot;ByGroup&quot;</span><span class="sc">;</span>
+ 382   <span class="i">$Options</span>{<span class="w">quote</span>} = <span class="q">&quot;yes&quot;</span><span class="sc">;</span>
+ 383 
+ 384   <span class="k">if</span> <span class="s">(</span>!<span class="i">GetOptions</span><span class="s">(</span>\<span class="i">%Options</span><span class="cm">,</span> <span class="q">&quot;help|h&quot;</span><span class="cm">,</span> <span class="q">&quot;outdelim=s&quot;</span><span class="cm">,</span> <span class="q">&quot;output=s&quot;</span><span class="cm">,</span> <span class="q">&quot;outputstyle=s&quot;</span><span class="cm">,</span> <span class="q">&quot;overwrite|o&quot;</span><span class="cm">,</span> <span class="q">&quot;precision=i&quot;</span><span class="cm">,</span> <span class="q">&quot;properties|p=s&quot;</span><span class="cm">,</span> <span class="q">&quot;propertieslisting=s&quot;</span><span class="cm">,</span> <span class="q">&quot;propertiesmode=s&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;workingdir|w=s&quot;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 385     <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 $ScriptName -h\&quot; command and try again...\n&quot;</span><span class="sc">;</span>
+ 386   <span class="s">}</span>
+ 387   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
+ 388     <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>
+ 389       <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{workingdir}, for option \&quot;-w --workingdir\&quot; is not a directory name.\n&quot;</span><span class="sc">;</span>
+ 390     <span class="s">}</span>
+ 391     <span class="k">chdir</span> <span class="i">$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}: $! \n&quot;</span><span class="sc">;</span>
+ 392   <span class="s">}</span>
+ 393   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} !~ <span class="q">/^(comma|semicolon|tab)$/i</span><span class="s">)</span> <span class="s">{</span>
+ 394     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{outdelim}, for option \&quot;--outdelim\&quot; is not valid. Allowed values: comma, tab, or semicolon\n&quot;</span><span class="sc">;</span>
+ 395   <span class="s">}</span>
+ 396   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">output</span>} !~ <span class="q">/^(STDOUT|File)$/i</span><span class="s">)</span> <span class="s">{</span>
+ 397     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{output}, for option \&quot;--output\&quot; is not valid. Allowed values: STDOUT or File\n&quot;</span><span class="sc">;</span>
+ 398   <span class="s">}</span>
+ 399   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outputstyle</span>} !~ <span class="q">/^(AminoAcidBlock|AminoAcidRows)$/i</span><span class="s">)</span> <span class="s">{</span>
+ 400     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{outputstyle}, for option \&quot;--outputstyle\&quot; is not valid. Allowed values: AminoAcidBlock or AminoAcidRows\n&quot;</span><span class="sc">;</span>
+ 401   <span class="s">}</span>
+ 402   <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">precision</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 403     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{precision}, for option \&quot;-p --precision\&quot; is not valid. Allowed values: &gt; 0 \n&quot;</span><span class="sc">;</span>
+ 404   <span class="s">}</span>
+ 405   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">propertiesmode</span>} !~ <span class="q">/^(Categories|Names|All)$/i</span><span class="s">)</span> <span class="s">{</span>
+ 406     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{propertiesmode}, for option \&quot;--propertiesmode\&quot; is not valid. Allowed values: Categories, Names, or All\n&quot;</span><span class="sc">;</span>
+ 407   <span class="s">}</span>
+ 408   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">propertieslisting</span>} !~ <span class="q">/^(ByGroup|Alphabetical)$/i</span><span class="s">)</span> <span class="s">{</span>
+ 409     <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{propertieslisting}, for option \&quot;--propertieslisting\&quot; is not valid. Allowed values: ByGroup, or Alphabetical\n&quot;</span><span class="sc">;</span>
+ 410   <span class="s">}</span>
+ 411   <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">quote</span>} !~ <span class="q">/^(yes|no)$/i</span><span class="s">)</span> <span class="s">{</span>
+ 412     <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>
+ 413   <span class="s">}</span>
+ 414 <span class="s">}</span>
+ 415 
+<a name="EOF-"></a></pre>
+<p>&nbsp;</p>
+<br />
+<center>
+<img src="../../../images/h2o2.png">
+</center>
+</body>
+</html>