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1 <html>
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2 <head>
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3 <title>MayaChemTools:Code:NucleicAcids.pm</title>
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4 <meta http-equiv="content-type" content="text/html;charset=utf-8">
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5 <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css">
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6 </head>
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7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10">
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8 <br/>
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9 <center>
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10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a>
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11 </center>
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12 <br/>
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13 <pre>
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14 <a name="package-NucleicAcids-"></a> 1 <span class="k">package </span><span class="i">NucleicAcids</span><span class="sc">;</span>
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15 2 <span class="c">#</span>
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16 3 <span class="c"># $RCSfile: NucleicAcids.pm,v $</span>
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17 4 <span class="c"># $Date: 2015/02/28 20:47:18 $</span>
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18 5 <span class="c"># $Revision: 1.25 $</span>
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19 6 <span class="c">#</span>
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20 7 <span class="c"># Author: Manish Sud &lt;msud@san.rr.com&gt;</span>
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21 8 <span class="c">#</span>
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22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
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23 10 <span class="c">#</span>
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24 11 <span class="c"># This file is part of MayaChemTools.</span>
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25 12 <span class="c">#</span>
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26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
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27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
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28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
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29 16 <span class="c"># later version.</span>
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30 17 <span class="c">#</span>
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31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
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32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
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33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span>
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34 21 <span class="c"># details.</span>
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35 22 <span class="c">#</span>
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36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
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37 24 <span class="c"># along with MayaChemTools; if not, see &lt;http://www.gnu.org/licenses/&gt; or</span>
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38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
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39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
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40 27 <span class="c">#</span>
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41 28
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42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
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43 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span>
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44 31 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span>
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45 32 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span>
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46 33 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span>
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47 34
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48 35 <span class="k">use</span> <span class="w">vars</span> <span class="q">qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS)</span><span class="sc">;</span>
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49 36
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50 37 <span class="i">@ISA</span> = <span class="q">qw(Exporter)</span><span class="sc">;</span>
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51 38 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span>
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52 39 <span class="i">@EXPORT_OK</span> = <span class="q">qw(GetNucleicAcids GetNucleicAcidsByType GetNucleicAcidPropertiesData GetNucleicAcidPropertiesNames IsNucleicAcid IsNucleicAcidProperty IsNucleicAcidType)</span><span class="sc">;</span>
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53 40
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54 41 <span class="i">%EXPORT_TAGS</span> = <span class="s">(</span><span class="w">all</span> <span class="cm">=&gt;</span> <span class="s">[</span><span class="i">@EXPORT</span><span class="cm">,</span> <span class="i">@EXPORT_OK</span><span class="s">]</span><span class="s">)</span><span class="sc">;</span>
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55 42
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56 43 <span class="c">#</span>
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57 44 <span class="c"># Load nucleic acids data...</span>
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58 45 <span class="c">#</span>
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59 46 <span class="k">my</span><span class="s">(</span><span class="i">%NucleicAcidDataMap</span><span class="cm">,</span> <span class="i">%NucleicAcidCodeMap</span><span class="cm">,</span> <span class="i">%NucleicAcidOtherCodeMap</span><span class="cm">,</span> <span class="i">%NucleicAcidNameMap</span><span class="cm">,</span> <span class="i">@NucleicAcidCodes</span><span class="cm">,</span> <span class="i">@NucleicAcidPropertyNames</span><span class="cm">,</span> <span class="i">%NucleicAcidPropertyNamesMap</span><span class="cm">,</span> <span class="i">%NucleicAcidTypesMap</span><span class="s">)</span><span class="sc">;</span>
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60 47 <span class="i">_LoadNucleicAcidsData</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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61 48
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62 49 <span class="c">#</span>
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63 50 <span class="c"># Get a list of all known nucleic acids as one of these values:</span>
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64 51 <span class="c"># code or nucleic acid name...</span>
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65 52 <span class="c">#</span>
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66 <a name="GetNucleicAcids-"></a> 53 <span class="k">sub </span><span class="m">GetNucleicAcids</span> <span class="s">{</span>
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67 54 <span class="k">my</span><span class="s">(</span><span class="i">$NameType</span><span class="cm">,</span> <span class="i">$Code</span><span class="cm">,</span> <span class="i">$Name</span><span class="cm">,</span> <span class="i">@NucleicAcidNames</span><span class="s">)</span><span class="sc">;</span>
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68 55
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69 56 <span class="i">$NameType</span> = <span class="q">&#39;Code&#39;</span><span class="sc">;</span>
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70 57 <span class="k">if</span> <span class="s">(</span><span class="i">@_</span> &gt;= <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
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71 58 <span class="s">(</span><span class="i">$NameType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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72 59 <span class="s">}</span>
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73 60
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74 61 <span class="c"># Collect names...</span>
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75 62 <span class="i">@NucleicAcidNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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76 63 <span class="k">for</span> <span class="i">$Code</span> <span class="s">(</span><span class="i">@NucleicAcidCodes</span><span class="s">)</span> <span class="s">{</span>
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77 64 <span class="j">NAME :</span> <span class="s">{</span>
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78 65 <span class="k">if</span> <span class="s">(</span><span class="i">$NameType</span> =~ <span class="q">/^Name$/i</span><span class="s">)</span> <span class="s">{</span><span class="i">$Name</span> = <span class="i">$NucleicAcidDataMap</span>{<span class="i">$Code</span>}{<span class="w">Name</span>}<span class="sc">;</span> <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span> <span class="s">}</span>
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79 66 <span class="i">$Name</span> = <span class="i">$Code</span><span class="sc">;</span>
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80 67 <span class="s">}</span>
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81 68 <span class="k">push</span> <span class="i">@NucleicAcidNames</span><span class="cm">,</span> <span class="i">$Name</span><span class="sc">;</span>
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82 69 <span class="s">}</span>
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83 70
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84 71 <span class="k">return</span> <span class="s">(</span><span class="k">wantarray</span> ? <span class="i">@NucleicAcidNames</span> <span class="co">:</span> \<span class="i">@NucleicAcidNames</span><span class="s">)</span><span class="sc">;</span>
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85 72 <span class="s">}</span>
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86 73
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87 74 <span class="c">#</span>
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88 75 <span class="c"># Get a list of all known nucleic acids by one of these specified types:</span>
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89 76 <span class="c"># Nucleobase, Nucleoside, Deoxynucleoside, Nucleotide, Deoxynucleotide. Default: Nucleoside</span>
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90 77 <span class="c">#</span>
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91 <a name="GetNucleicAcidsByType-"></a> 78 <span class="k">sub </span><span class="m">GetNucleicAcidsByType</span> <span class="s">{</span>
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92 79 <span class="k">my</span><span class="s">(</span><span class="i">$NameType</span><span class="cm">,</span> <span class="i">$Type</span><span class="cm">,</span> <span class="i">$Code</span><span class="cm">,</span> <span class="i">$Name</span><span class="cm">,</span> <span class="i">@NucleicAcidNames</span><span class="s">)</span><span class="sc">;</span>
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93 80
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94 81 <span class="i">$Type</span> = <span class="q">&#39;Nucleoside&#39;</span><span class="sc">;</span>
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95 82 <span class="i">$NameType</span> = <span class="q">&#39;Code&#39;</span><span class="sc">;</span>
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96 83 <span class="k">if</span> <span class="s">(</span><span class="i">@_</span> == <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
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97 84 <span class="s">(</span><span class="i">$Type</span><span class="cm">,</span> <span class="i">$NameType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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98 85 <span class="s">}</span>
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99 86 <span class="k">elsif</span> <span class="s">(</span><span class="i">@_</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
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100 87 <span class="s">(</span><span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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101 88 <span class="s">}</span>
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102 89
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103 90 <span class="c"># Collect names...</span>
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104 91 <span class="i">@NucleicAcidNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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105 92 <span class="j">CODE:</span> <span class="k">for</span> <span class="i">$Code</span> <span class="s">(</span><span class="i">@NucleicAcidCodes</span><span class="s">)</span> <span class="s">{</span>
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106 93 <span class="k">if</span> <span class="s">(</span><span class="i">$NucleicAcidDataMap</span>{<span class="i">$Code</span>}{<span class="w">Type</span>} !~ <span class="q">/^$Type$/i</span> <span class="s">)</span> <span class="s">{</span>
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107 94 <span class="k">next</span> <span class="j">CODE</span><span class="sc">;</span>
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108 95 <span class="s">}</span>
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109 96 <span class="j">NAME :</span> <span class="s">{</span>
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110 97 <span class="k">if</span> <span class="s">(</span><span class="i">$NameType</span> =~ <span class="q">/^Name$/i</span><span class="s">)</span> <span class="s">{</span><span class="i">$Name</span> = <span class="i">$NucleicAcidDataMap</span>{<span class="i">$Code</span>}{<span class="w">Name</span>}<span class="sc">;</span> <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span> <span class="s">}</span>
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111 98 <span class="i">$Name</span> = <span class="i">$Code</span><span class="sc">;</span>
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112 99 <span class="s">}</span>
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113 100 <span class="k">push</span> <span class="i">@NucleicAcidNames</span><span class="cm">,</span> <span class="i">$Name</span><span class="sc">;</span>
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114 101 <span class="s">}</span>
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115 102
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116 103 <span class="k">return</span> <span class="s">(</span><span class="k">wantarray</span> ? <span class="i">@NucleicAcidNames</span> <span class="co">:</span> \<span class="i">@NucleicAcidNames</span><span class="s">)</span><span class="sc">;</span>
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117 104 <span class="s">}</span>
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118 105
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119 106 <span class="c">#</span>
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120 107 <span class="c"># Get all available properties data for an nucleic acid using any of these symbols:</span>
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121 108 <span class="c"># code, other code or name.</span>
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122 109 <span class="c">#</span>
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123 110 <span class="c"># A reference to a hash array is returned with keys and values representing property</span>
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124 111 <span class="c"># name and its values respectively.</span>
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125 112 <span class="c">#</span>
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126 <a name="GetNucleicAcidPropertiesData-"></a> 113 <span class="k">sub </span><span class="m">GetNucleicAcidPropertiesData</span> <span class="s">{</span>
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127 114 <span class="k">my</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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128 115 <span class="k">my</span><span class="s">(</span><span class="i">$Code</span><span class="s">)</span><span class="sc">;</span>
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129 116
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130 117 <span class="k">if</span> <span class="s">(</span><span class="i">$Code</span> = <span class="i">_ValidateNucleicAcidID</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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131 118 <span class="k">return</span> \<span class="i">%</span>{<span class="i">$NucleicAcidDataMap</span>{<span class="i">$Code</span>}}<span class="sc">;</span>
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132 119 <span class="s">}</span>
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133 120 <span class="k">else</span> <span class="s">{</span>
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134 121 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
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135 122 <span class="s">}</span>
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136 123 <span class="s">}</span>
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137 124
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138 125 <span class="c">#</span>
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139 126 <span class="c"># Get names of all available nucleic acid properties. A reference to an array containing</span>
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140 127 <span class="c"># names of all available properties is returned.</span>
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141 128 <span class="c">#</span>
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142 <a name="GetNucleicAcidPropertiesNames-"></a> 129 <span class="k">sub </span><span class="m">GetNucleicAcidPropertiesNames</span> <span class="s">{</span>
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143 130 <span class="k">my</span><span class="s">(</span><span class="i">$Mode</span><span class="s">)</span><span class="sc">;</span>
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144 131 <span class="k">my</span><span class="s">(</span><span class="i">$PropertyName</span><span class="cm">,</span> <span class="i">@PropertyNames</span><span class="s">)</span><span class="sc">;</span>
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145 132
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146 133 <span class="i">$Mode</span> = <span class="q">&#39;ByGroup&#39;</span><span class="sc">;</span>
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147 134 <span class="k">if</span> <span class="s">(</span><span class="i">@_</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
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148 135 <span class="s">(</span><span class="i">$Mode</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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149 136 <span class="s">}</span>
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150 137
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151 138 <span class="i">@PropertyNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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152 139 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^Alphabetical$/i</span><span class="s">)</span> <span class="s">{</span>
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153 140 <span class="k">my</span><span class="s">(</span><span class="i">$PropertyName</span><span class="s">)</span><span class="sc">;</span>
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154 141 <span class="c"># Code, OtherCodes and Name are always listed first...</span>
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155 142 <span class="k">push</span> <span class="i">@PropertyNames</span><span class="cm">,</span> <span class="q">qw(Code OtherCodes Name)</span><span class="sc">;</span>
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156 143 <span class="k">for</span> <span class="i">$PropertyName</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%NucleicAcidPropertyNamesMap</span><span class="s">)</span> <span class="s">{</span>
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157 144 <span class="k">if</span> <span class="s">(</span><span class="i">$PropertyName</span> !~ <span class="q">/^(Code|OtherCodes|Name)$/</span><span class="s">)</span> <span class="s">{</span>
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158 145 <span class="k">push</span> <span class="i">@PropertyNames</span><span class="cm">,</span> <span class="i">$PropertyName</span><span class="sc">;</span>
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159 146 <span class="s">}</span>
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160 147 <span class="s">}</span>
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161 148 <span class="s">}</span>
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162 149 <span class="k">else</span> <span class="s">{</span>
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163 150 <span class="k">push</span> <span class="i">@PropertyNames</span><span class="cm">,</span> <span class="i">@NucleicAcidPropertyNames</span><span class="sc">;</span>
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164 151 <span class="s">}</span>
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165 152 <span class="k">return</span> <span class="s">(</span><span class="k">wantarray</span> ? <span class="i">@PropertyNames</span> <span class="co">:</span> \<span class="i">@PropertyNames</span><span class="s">)</span><span class="sc">;</span>
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166 153 <span class="s">}</span>
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167 154
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168 155 <span class="c">#</span>
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169 156 <span class="c"># Is it a known nucleic acid? Input is either a code or a name</span>
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170 157 <span class="c">#</span>
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171 <a name="IsNucleicAcid-"></a> 158 <span class="k">sub </span><span class="m">IsNucleicAcid</span> <span class="s">{</span>
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172 159 <span class="k">my</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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173 160 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="s">)</span><span class="sc">;</span>
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174 161
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175 162 <span class="i">$Status</span> = <span class="s">(</span><span class="i">_ValidateNucleicAcidID</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
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176 163
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177 164 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span>
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178 165 <span class="s">}</span>
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179 166
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180 167 <span class="c">#</span>
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181 168 <span class="c"># Is it an available nucleic acid property?</span>
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182 169 <span class="c">#</span>
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183 <a name="IsNucleicAcidProperty-"></a> 170 <span class="k">sub </span><span class="m">IsNucleicAcidProperty</span> <span class="s">{</span>
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184 171 <span class="k">my</span><span class="s">(</span><span class="i">$PropertyName</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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185 172 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="s">)</span><span class="sc">;</span>
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186 173
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187 174 <span class="i">$Status</span> = <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$NucleicAcidPropertyNamesMap</span>{<span class="i">$PropertyName</span>}<span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
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188 175
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189 176 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span>
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190 177 <span class="s">}</span>
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191 178
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192 179 <span class="c">#</span>
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193 180 <span class="c"># Is it an available nucleic acid type?</span>
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194 181 <span class="c">#</span>
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195 <a name="IsNucleicAcidType-"></a> 182 <span class="k">sub </span><span class="m">IsNucleicAcidType</span> <span class="s">{</span>
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196 183 <span class="k">my</span><span class="s">(</span><span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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197 184 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="s">)</span><span class="sc">;</span>
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198 185
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199 186 <span class="i">$Status</span> = <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$NucleicAcidTypesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$Type</span><span class="s">)</span>}<span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
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200 187
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201 188 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span>
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202 189 <span class="s">}</span>
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203 190
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204 191 <span class="c">#</span>
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205 192 <span class="c"># Implents GetNucleicAcid&lt;PropertyName&gt; for a valid proprty name.</span>
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206 193 <span class="c">#</span>
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207 <a name="AUTOLOAD-"></a> 194 <span class="k">sub </span><span class="m">AUTOLOAD</span> <span class="s">{</span>
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208 195 <span class="k">my</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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209 196 <span class="k">my</span><span class="s">(</span><span class="i">$FunctionName</span><span class="cm">,</span> <span class="i">$PropertyName</span><span class="cm">,</span> <span class="i">$PropertyValue</span><span class="cm">,</span> <span class="i">$Code</span><span class="s">)</span><span class="sc">;</span>
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210 197
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211 198 <span class="i">$PropertyValue</span> = <span class="k">undef</span><span class="sc">;</span>
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212 199
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213 200 <span class="k">use</span> <span class="w">vars</span> <span class="q">qw($AUTOLOAD)</span><span class="sc">;</span>
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214 201 <span class="i">$FunctionName</span> = <span class="i">$AUTOLOAD</span><span class="sc">;</span>
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215 202 <span class="i">$FunctionName</span> =~ <span class="q">s/.*:://</span><span class="sc">;</span>
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216 203
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217 204 <span class="c"># Only Get&lt;PropertyName&gt; functions are supported...</span>
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218 205 <span class="k">if</span> <span class="s">(</span><span class="i">$FunctionName</span> !~ <span class="q">/^Get/</span><span class="s">)</span> <span class="s">{</span>
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219 206 <span class="w">croak</span> <span class="q">&quot;Error: Function, NucleicAcid::$FunctionName, is not supported by AUTOLOAD in NucleicAcid module: Only Get&lt;PropertyName&gt; functions are implemented...&quot;</span><span class="sc">;</span>
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220 207 <span class="s">}</span>
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221 208
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222 209 <span class="i">$PropertyName</span> = <span class="i">$FunctionName</span><span class="sc">;</span>
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223 210 <span class="i">$PropertyName</span> =~ <span class="q">s/^GetNucleicAcid//</span><span class="sc">;</span>
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224 211 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NucleicAcidPropertyNamesMap</span>{<span class="i">$PropertyName</span>}<span class="s">)</span> <span class="s">{</span>
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225 212 <span class="w">croak</span> <span class="q">&quot;Error: Function, NucleicAcid::$FunctionName, is not supported by AUTOLOAD in NucleicAcid module: Unknown nucleic acid property name, $PropertyName, specified...&quot;</span><span class="sc">;</span>
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226 213 <span class="s">}</span>
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227 214
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228 215 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$Code</span> = <span class="i">_ValidateNucleicAcidID</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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229 216 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
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230 217 <span class="s">}</span>
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231 218 <span class="i">$PropertyValue</span> = <span class="i">$NucleicAcidDataMap</span>{<span class="i">$Code</span>}{<span class="i">$PropertyName</span>}<span class="sc">;</span>
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232 219 <span class="k">return</span> <span class="i">$PropertyValue</span><span class="sc">;</span>
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233 220 <span class="s">}</span>
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234 221
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235 222 <span class="c">#</span>
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236 223 <span class="c"># Load NucleicAcidsData.csv files from &lt;MayaChemTools&gt;/lib directory...</span>
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237 224 <span class="c">#</span>
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238 <a name="_LoadNucleicAcidsData-"></a> 225 <span class="k">sub </span><span class="m">_LoadNucleicAcidsData</span> <span class="s">{</span>
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239 226 <span class="k">my</span><span class="s">(</span><span class="i">$NucleicAcidsDataFile</span><span class="cm">,</span> <span class="i">$MayaChemToolsLibDir</span><span class="s">)</span><span class="sc">;</span>
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240 227
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241 228 <span class="i">$MayaChemToolsLibDir</span> = <span class="i">GetMayaChemToolsLibDirName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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242 229
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243 230 <span class="i">$NucleicAcidsDataFile</span> = <span class="q">&quot;$MayaChemToolsLibDir&quot;</span> . <span class="q">&quot;/data/NucleicAcidsData.csv&quot;</span><span class="sc">;</span>
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244 231
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245 232 <span class="k">if</span> <span class="s">(</span>! <span class="k">-e</span> <span class="q">&quot;$NucleicAcidsDataFile&quot;</span><span class="s">)</span> <span class="s">{</span>
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246 233 <span class="w">croak</span> <span class="q">&quot;Error: MayaChemTools package file, $NucleicAcidsDataFile, is missing: Possible installation problems...&quot;</span><span class="sc">;</span>
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247 234 <span class="s">}</span>
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248 235
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249 236 <span class="i">_LoadData</span><span class="s">(</span><span class="i">$NucleicAcidsDataFile</span><span class="s">)</span><span class="sc">;</span>
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250 237 <span class="s">}</span>
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251 238
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252 239 <span class="c">#</span>
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253 240 <span class="c"># Load NucleicAcidsData.csv file from &lt;MayaChemTools&gt;/lib directory...</span>
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254 241 <span class="c">#</span>
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255 <a name="_LoadData-"></a> 242 <span class="k">sub </span><span class="m">_LoadData</span> <span class="s">{</span>
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256 243 <span class="k">my</span><span class="s">(</span><span class="i">$NucleicAcidsDataFile</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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257 244
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258 245 <span class="i">%NucleicAcidDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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259 246 <span class="i">@NucleicAcidCodes</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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260 247 <span class="i">@NucleicAcidPropertyNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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261 248 <span class="i">%NucleicAcidPropertyNamesMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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262 249 <span class="i">%NucleicAcidCodeMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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263 250 <span class="i">%NucleicAcidOtherCodeMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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264 251 <span class="i">%NucleicAcidNameMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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265 252 <span class="i">%NucleicAcidTypesMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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266 253
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267 254 <span class="c"># Load property data for all nucleic acids...</span>
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268 255 <span class="c">#</span>
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269 256 <span class="c"># File Format:</span>
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270 257 <span class="c"># &quot;Code&quot;,&quot;OtherCodes&quot;,&quot;BasePair&quot;,&quot;Name&quot;,&quot;Type&quot;,&quot;ChemicalFormula&quot;,&quot;ChemicalFormulaAtpH7.5&quot;,&quot;MolecularWeight&quot;,&quot;ExactMass&quot;,&quot;ElementalComposition&quot;</span>
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271 258 <span class="c">#</span>
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272 259 <span class="k">my</span><span class="s">(</span><span class="i">$Code</span><span class="cm">,</span> <span class="i">$OtherCodes</span><span class="cm">,</span> <span class="i">$NucleicAcidName</span><span class="cm">,</span> <span class="i">$Line</span><span class="cm">,</span> <span class="i">$NumOfCols</span><span class="cm">,</span> <span class="i">$InDelim</span><span class="cm">,</span> <span class="i">$Index</span><span class="cm">,</span> <span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">$Units</span><span class="cm">,</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">@ColLabels</span><span class="s">)</span><span class="sc">;</span>
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273 260
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274 261 <span class="i">$InDelim</span> = <span class="q">&quot;\,&quot;</span><span class="sc">;</span>
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275 262 <span class="k">open</span> <span class="w">NUCLEICACIDSDATAFILE</span><span class="cm">,</span> <span class="q">&quot;$NucleicAcidsDataFile&quot;</span> <span class="k">or</span> <span class="w">croak</span> <span class="q">&quot;Couldn&#39;t open $NucleicAcidsDataFile: $! ...&quot;</span><span class="sc">;</span>
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276 263
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277 264 <span class="c"># Skip lines up to column labels...</span>
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278 265 <span class="j">LINE:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$Line</span> = <span class="i">GetTextLine</span><span class="s">(</span>\<span class="i">*NUCLEICACIDSDATAFILE</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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279 266 <span class="k">if</span> <span class="s">(</span><span class="i">$Line</span> !~ <span class="q">/^#/</span><span class="s">)</span> <span class="s">{</span>
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280 267 <span class="k">last</span> <span class="j">LINE</span><span class="sc">;</span>
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281 268 <span class="s">}</span>
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282 269 <span class="s">}</span>
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283 270 <span class="i">@ColLabels</span>= <span class="i">quotewords</span><span class="s">(</span><span class="i">$InDelim</span><span class="cm">,</span> <span class="n">0</span><span class="cm">,</span> <span class="i">$Line</span><span class="s">)</span><span class="sc">;</span>
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284 271 <span class="i">$NumOfCols</span> = <span class="i">@ColLabels</span><span class="sc">;</span>
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285 272
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286 273 <span class="c"># Extract property names from column labels...</span>
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287 274 <span class="i">@NucleicAcidPropertyNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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288 275 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#ColLabels</span><span class="s">)</span> <span class="s">{</span>
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289 276 <span class="i">$Name</span> = <span class="i">$ColLabels</span>[<span class="i">$Index</span>]<span class="sc">;</span>
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290 277 <span class="k">push</span> <span class="i">@NucleicAcidPropertyNames</span><span class="cm">,</span> <span class="i">$Name</span><span class="sc">;</span>
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291 278
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292 279 <span class="c"># Store property names...</span>
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293 280 <span class="i">$NucleicAcidPropertyNamesMap</span>{<span class="i">$Name</span>} = <span class="i">$Name</span><span class="sc">;</span>
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294 281 <span class="s">}</span>
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295 282
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296 283 <span class="c"># Process nucleic acid data...</span>
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297 284 <span class="j">LINE:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$Line</span> = <span class="i">GetTextLine</span><span class="s">(</span>\<span class="i">*NUCLEICACIDSDATAFILE</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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298 285 <span class="k">if</span> <span class="s">(</span><span class="i">$Line</span> =~ <span class="q">/^#/</span><span class="s">)</span> <span class="s">{</span>
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299 286 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span>
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300 287 <span class="s">}</span>
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301 288 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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302 289 <span class="i">@LineWords</span> = <span class="i">quotewords</span><span class="s">(</span><span class="i">$InDelim</span><span class="cm">,</span> <span class="n">0</span><span class="cm">,</span> <span class="i">$Line</span><span class="s">)</span><span class="sc">;</span>
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303 290 <span class="k">if</span> <span class="s">(</span><span class="i">@LineWords</span> != <span class="i">$NumOfCols</span><span class="s">)</span> <span class="s">{</span>
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304 291 <span class="w">croak</span> <span class="q">&quot;Error: The number of data fields, @LineWords, in $NucleicAcidsDataFile must be $NumOfCols.\nLine: $Line...&quot;</span><span class="sc">;</span>
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305 292 <span class="s">}</span>
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306 293 <span class="i">$Code</span> = <span class="i">$LineWords</span>[<span class="n">0</span>]<span class="sc">;</span> <span class="i">$OtherCodes</span> = <span class="i">$LineWords</span>[<span class="n">1</span>]<span class="sc">;</span> <span class="i">$NucleicAcidName</span> = <span class="i">$LineWords</span>[<span class="n">3</span>]<span class="sc">;</span>
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307 294 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$NucleicAcidDataMap</span>{<span class="i">$Code</span>}<span class="s">)</span> <span class="s">{</span>
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308 295 <span class="w">carp</span> <span class="q">&quot;Warning: Ignoring data for nucleic acid $Code: It has already been loaded.\nLine: $Line....&quot;</span><span class="sc">;</span>
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309 296 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span>
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310 297 <span class="s">}</span>
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311 298
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312 299 <span class="c"># Store all the values...</span>
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313 300 <span class="k">push</span> <span class="i">@NucleicAcidCodes</span><span class="cm">,</span> <span class="i">$Code</span><span class="sc">;</span>
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314 301 <span class="i">%</span>{<span class="i">$NucleicAcidDataMap</span>{<span class="i">$Code</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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315 302 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#LineWords</span><span class="s">)</span> <span class="s">{</span>
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316 303 <span class="i">$Name</span> = <span class="i">$NucleicAcidPropertyNames</span>[<span class="i">$Index</span>]<span class="sc">;</span>
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317 304 <span class="i">$Value</span> = <span class="i">$LineWords</span>[<span class="i">$Index</span>]<span class="sc">;</span>
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318 305 <span class="i">$NucleicAcidDataMap</span>{<span class="i">$Code</span>}{<span class="i">$Name</span>} = <span class="i">$Value</span><span class="sc">;</span>
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319 306 <span class="s">}</span>
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320 307 <span class="s">}</span>
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321 308 <span class="k">close</span> <span class="w">NUCLEICACIDSDATAFILE</span><span class="sc">;</span>
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322 309
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323 310 <span class="c"># Setup one letter and nucleic acid name maps...</span>
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324 311 <span class="i">_SetupNucleicAcidIDMap</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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325 312 <span class="s">}</span>
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326 313
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327 314 <span class="c">#</span>
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328 315 <span class="c"># Setup lowercase other codes and name maps pointing</span>
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329 316 <span class="c"># to code as show in data file.</span>
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330 317 <span class="c">#</span>
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331 <a name="_SetupNucleicAcidIDMap-"></a> 318 <span class="k">sub </span><span class="m">_SetupNucleicAcidIDMap</span> <span class="s">{</span>
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332 319 <span class="k">my</span><span class="s">(</span><span class="i">$Code</span><span class="cm">,</span> <span class="i">@OtherCodes</span><span class="cm">,</span> <span class="i">$OtherCode</span><span class="cm">,</span> <span class="i">$NucleicAcidName</span><span class="cm">,</span> <span class="i">$NucleicAcidType</span><span class="s">)</span><span class="sc">;</span>
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333 320
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334 321 <span class="i">%NucleicAcidCodeMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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335 322 <span class="i">%NucleicAcidOtherCodeMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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336 323 <span class="i">%NucleicAcidNameMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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337 324 <span class="i">%NucleicAcidTypesMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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338 325
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339 326 <span class="k">for</span> <span class="i">$Code</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%NucleicAcidDataMap</span><span class="s">)</span> <span class="s">{</span>
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340 327 <span class="i">$NucleicAcidCodeMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$Code</span><span class="s">)</span>} = <span class="i">$Code</span><span class="sc">;</span>
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341 328
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342 329 <span class="i">$NucleicAcidName</span> = <span class="i">$NucleicAcidDataMap</span>{<span class="i">$Code</span>}{<span class="w">Name</span>}<span class="sc">;</span>
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343 330 <span class="i">$NucleicAcidNameMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$NucleicAcidName</span><span class="s">)</span>} = <span class="i">$Code</span><span class="sc">;</span>
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344 331
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345 332 <span class="i">$NucleicAcidType</span> = <span class="i">$NucleicAcidDataMap</span>{<span class="i">$Code</span>}{<span class="w">Type</span>}<span class="sc">;</span>
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346 333 <span class="k">if</span> <span class="s">(</span>! <span class="k">exists</span> <span class="i">$NucleicAcidTypesMap</span>{<span class="i">$NucleicAcidType</span>}<span class="s">)</span> <span class="s">{</span>
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347 334 <span class="i">$NucleicAcidTypesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$NucleicAcidType</span><span class="s">)</span>} = <span class="i">$NucleicAcidType</span><span class="sc">;</span>
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348 335 <span class="s">}</span>
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349 336
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350 337 <span class="i">@OtherCodes</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$NucleicAcidDataMap</span>{<span class="i">$Code</span>}{<span class="w">OtherCodes</span>}<span class="sc">;</span>
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351 338 <span class="j">OTHERCODE:</span> <span class="k">for</span> <span class="i">$OtherCode</span> <span class="s">(</span><span class="i">@OtherCodes</span><span class="s">)</span> <span class="s">{</span>
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352 339 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OtherCode</span><span class="s">)</span> <span class="s">{</span>
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353 340 <span class="k">next</span> <span class="j">OTHERCODE</span><span class="sc">;</span>
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354 341 <span class="s">}</span>
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355 342 <span class="i">$OtherCode</span> = <span class="i">RemoveLeadingAndTrailingWhiteSpaces</span><span class="s">(</span><span class="i">$OtherCode</span><span class="s">)</span><span class="sc">;</span>
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356 343 <span class="i">$NucleicAcidOtherCodeMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$OtherCode</span><span class="s">)</span>} = <span class="i">$Code</span><span class="sc">;</span>
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357 344 <span class="s">}</span>
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358 345 <span class="s">}</span>
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359 346 <span class="s">}</span>
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360 347
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361 348 <span class="c"># Validate Nucleic acid ID...</span>
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362 <a name="_ValidateNucleicAcidID-"></a> 349 <span class="k">sub </span><span class="m">_ValidateNucleicAcidID</span> <span class="s">{</span>
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363 350 <span class="k">my</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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364 351 <span class="k">my</span><span class="s">(</span><span class="i">$Code</span><span class="s">)</span> = <span class="k">undef</span><span class="sc">;</span>
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365 352
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366 353 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$NucleicAcidCodeMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span>
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367 354 <span class="i">$Code</span> = <span class="i">$NucleicAcidCodeMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span>}<span class="sc">;</span>
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368 355 <span class="s">}</span>
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369 356 <span class="k">elsif</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$NucleicAcidOtherCodeMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span>
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370 357 <span class="i">$Code</span> = <span class="i">$NucleicAcidOtherCodeMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span>}<span class="sc">;</span>
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371 358 <span class="s">}</span>
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372 359 <span class="k">elsif</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$NucleicAcidNameMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span>
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373 360 <span class="i">$Code</span> = <span class="i">$NucleicAcidNameMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span>}<span class="sc">;</span>
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374 361 <span class="s">}</span>
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375 362 <span class="k">return</span> <span class="i">$Code</span><span class="sc">;</span>
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376 363 <span class="s">}</span>
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377 364
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