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14 <a name="package-Fingerprints::FingerprintsFileUtil-"></a> 1 <span class="k">package </span><span class="i">Fingerprints::FingerprintsFileUtil</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: FingerprintsFileUtil.pm,v $</span>
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17 4 <span class="c"># $Date: 2015/02/28 20:48:54 $</span>
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18 5 <span class="c"># $Revision: 1.14 $</span>
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19 6 <span class="c">#</span>
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20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span>
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21 8 <span class="c">#</span>
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22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
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23 10 <span class="c">#</span>
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24 11 <span class="c"># This file is part of MayaChemTools.</span>
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25 12 <span class="c">#</span>
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26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
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27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
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28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
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29 16 <span class="c"># later version.</span>
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30 17 <span class="c">#</span>
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31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
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32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
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33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span>
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34 21 <span class="c"># details.</span>
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35 22 <span class="c">#</span>
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36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
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37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span>
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38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
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39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
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40 27 <span class="c">#</span>
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41 28
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42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
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43 30 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span>
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44 31 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span>
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45 32 <span class="k">use</span> <span class="w">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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46 33 <span class="k">use</span> <span class="w">FileUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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47 34 <span class="k">use</span> <span class="w">FileIO::FingerprintsSDFileIO</span><span class="sc">;</span>
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48 35 <span class="k">use</span> <span class="w">FileIO::FingerprintsTextFileIO</span><span class="sc">;</span>
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49 36 <span class="k">use</span> <span class="w">FileIO::FingerprintsFPFileIO</span><span class="sc">;</span>
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50 37
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51 38 <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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52 39
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53 40 <span class="i">@ISA</span> = <span class="q">qw(Exporter)</span><span class="sc">;</span>
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54 41 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span>
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55 42 <span class="i">@EXPORT_OK</span> = <span class="q">qw(GetFingerprintsFileType ReadAndProcessFingerpritsData NewFingerprintsFileIO)</span><span class="sc">;</span>
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56 43
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57 44 <span class="i">%EXPORT_TAGS</span> = <span class="s">(</span><span class="w">all</span> <span class="cm">=></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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58 45
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59 46 <span class="c"># Generate new FingerprintsFileIO object for a SD, FP or Text fingerprints file specified using file name</span>
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60 47 <span class="c"># along other appropriate parameters...</span>
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61 48 <span class="c">#</span>
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62 <a name="NewFingerprintsFileIO-"></a> 49 <span class="k">sub </span><span class="m">NewFingerprintsFileIO</span> <span class="s">{</span>
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63 50 <span class="k">my</span><span class="s">(</span><span class="i">%FingerprintsFileIOParams</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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64 51 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsFileIO</span><span class="cm">,</span> <span class="i">$FileType</span><span class="s">)</span><span class="sc">;</span>
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65 52
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66 53 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$FingerprintsFileIOParams</span>{<span class="w">Name</span>}<span class="s">)</span> && <span class="i">TextUtil::IsNotEmpty</span><span class="s">(</span><span class="i">$FingerprintsFileIOParams</span>{<span class="w">Name</span>}<span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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67 54 <span class="w">carp</span> <span class="q">"Warning: Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO: Can't create new FingerprintsFileIO object: File name is not specified...\n"</span><span class="sc">;</span>
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68 55 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
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69 56 <span class="s">}</span>
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70 57
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71 58 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$FingerprintsFileIOParams</span>{<span class="w">Mode</span>}<span class="s">)</span> && <span class="i">TextUtil::IsNotEmpty</span><span class="s">(</span><span class="i">$FingerprintsFileIOParams</span>{<span class="w">Mode</span>}<span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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72 59 <span class="w">carp</span> <span class="q">"Warning: Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO: Can't create new FingerprintsFileIO object: File mode is not specified...\n"</span><span class="sc">;</span>
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73 60 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
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74 61 <span class="s">}</span>
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75 62
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76 63 <span class="i">$FileType</span> = <span class="i">GetFingerprintsFileType</span><span class="s">(</span><span class="i">$FingerprintsFileIOParams</span>{<span class="w">Name</span>}<span class="s">)</span><span class="sc">;</span>
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77 64 <span class="k">if</span> <span class="s">(</span><span class="i">TextUtil::IsEmpty</span><span class="s">(</span><span class="i">$FileType</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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78 65 <span class="w">carp</span> <span class="q">"Warning: Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO: Can't create new FingerprintsFileIO object: File type is not specified...\n"</span><span class="sc">;</span>
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79 66 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
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80 67 <span class="s">}</span>
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81 68
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82 69 <span class="c"># Generate fingerprints IO object...</span>
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83 70 <span class="j">FILETYPE:</span> <span class="s">{</span>
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84 71 <span class="k">if</span> <span class="s">(</span><span class="i">$FileType</span> =~ <span class="q">/^SD$/i</span><span class="s">)</span> <span class="s">{</span>
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85 72 <span class="i">$FingerprintsFileIO</span> = <span class="w">new</span> <span class="i">FileIO::FingerprintsSDFileIO</span><span class="s">(</span><span class="i">%FingerprintsFileIOParams</span><span class="s">)</span><span class="sc">;</span>
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86 73 <span class="k">last</span> <span class="j">FILETYPE</span><span class="sc">;</span>
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87 74 <span class="s">}</span>
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88 75 <span class="k">if</span> <span class="s">(</span><span class="i">$FileType</span> =~ <span class="q">/^FP$/i</span><span class="s">)</span> <span class="s">{</span>
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89 76 <span class="i">$FingerprintsFileIO</span> = <span class="w">new</span> <span class="i">FileIO::FingerprintsFPFileIO</span><span class="s">(</span><span class="i">%FingerprintsFileIOParams</span><span class="s">)</span><span class="sc">;</span>
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90 77 <span class="k">last</span> <span class="j">FILETYPE</span><span class="sc">;</span>
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91 78 <span class="s">}</span>
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92 79 <span class="k">if</span> <span class="s">(</span><span class="i">$FileType</span> =~ <span class="q">/^Text$/i</span><span class="s">)</span> <span class="s">{</span>
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93 80 <span class="i">$FingerprintsFileIO</span> = <span class="w">new</span> <span class="i">FileIO::FingerprintsTextFileIO</span><span class="s">(</span><span class="i">%FingerprintsFileIOParams</span><span class="s">)</span><span class="sc">;</span>
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94 81 <span class="k">last</span> <span class="j">FILETYPE</span><span class="sc">;</span>
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95 82 <span class="s">}</span>
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96 83 <span class="i">$FingerprintsFileIO</span> = <span class="k">undef</span><span class="sc">;</span>
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97 84 <span class="w">carp</span> <span class="q">"Warning: Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO: Fingerprints file type, $FileType, is not valid. Supported file types: SD, FP or Text\n"</span><span class="sc">;</span>
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98 85 <span class="s">}</span>
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99 86
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100 87 <span class="k">return</span> <span class="i">$FingerprintsFileIO</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"># Get fingerpritns file type from fingerprints file name...</span>
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104 91 <span class="c">#</span>
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105 <a name="GetFingerprintsFileType-"></a> 92 <span class="k">sub </span><span class="m">GetFingerprintsFileType</span> <span class="s">{</span>
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106 93 <span class="k">my</span><span class="s">(</span><span class="i">$FileName</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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107 94 <span class="k">my</span><span class="s">(</span><span class="i">$FileType</span><span class="s">)</span><span class="sc">;</span>
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108 95
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109 96 <span class="i">$FileType</span> = <span class="q">''</span><span class="sc">;</span>
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110 97 <span class="j">FILETYPE:</span> <span class="s">{</span>
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111 98 <span class="k">if</span> <span class="s">(</span><span class="i">FileUtil::CheckFileType</span><span class="s">(</span><span class="i">$FileName</span><span class="cm">,</span> <span class="q">"sdf sd"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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112 99 <span class="i">$FileType</span> = <span class="q">'SD'</span><span class="sc">;</span>
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113 100 <span class="k">last</span> <span class="j">FILETYPE</span><span class="sc">;</span>
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114 101 <span class="s">}</span>
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115 102 <span class="k">if</span> <span class="s">(</span><span class="i">FileUtil::CheckFileType</span><span class="s">(</span><span class="i">$FileName</span><span class="cm">,</span> <span class="q">"fpf fp"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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116 103 <span class="i">$FileType</span> = <span class="q">'FP'</span><span class="sc">;</span>
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117 104 <span class="k">last</span> <span class="j">FILETYPE</span><span class="sc">;</span>
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118 105 <span class="s">}</span>
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119 106 <span class="k">if</span> <span class="s">(</span><span class="i">FileUtil::CheckFileType</span><span class="s">(</span><span class="i">$FileName</span><span class="cm">,</span> <span class="q">"csv tsv"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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120 107 <span class="i">$FileType</span> = <span class="q">'Text'</span><span class="sc">;</span>
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121 108 <span class="k">last</span> <span class="j">FILETYPE</span><span class="sc">;</span>
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122 109 <span class="s">}</span>
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123 110 <span class="i">$FileType</span> = <span class="q">''</span><span class="sc">;</span>
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124 111 <span class="w">carp</span> <span class="q">"Warning: Fingerprints::FingerprintsFileUtil::GetFingerprintsFileType: Can't determine fingerprints file type for $FileName: It's not a fingerprints file...\n"</span><span class="sc">;</span>
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125 112 <span class="s">}</span>
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126 113
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127 114 <span class="k">return</span> <span class="i">$FileType</span><span class="sc">;</span>
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128 115 <span class="s">}</span>
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129 116
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130 117
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131 118 <span class="c"># Process fingerprints bit-vector and vector string data in a file using FingerprintsFileIO</span>
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132 119 <span class="c"># object and return a references to arrays of CompoundIDs and FingerprintsObjects...</span>
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133 120 <span class="c">#</span>
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134 121 <span class="c"># Note:</span>
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135 122 <span class="c"># . The file open and close is automatically performed during processing.</span>
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136 123 <span class="c">#</span>
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137 <a name="ReadAndProcessFingerpritsData-"></a> 124 <span class="k">sub </span><span class="m">ReadAndProcessFingerpritsData</span> <span class="s">{</span>
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138 125 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsFileIO</span><span class="cm">,</span> <span class="i">$CheckCompoundIDs</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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139 126 <span class="k">my</span><span class="s">(</span><span class="i">$CompoundID</span><span class="cm">,</span> <span class="i">$FingerprintsCount</span><span class="cm">,</span> <span class="i">$IgnoredFingerprintsCount</span><span class="cm">,</span> <span class="i">@CompundIDs</span><span class="cm">,</span> <span class="i">@FingerprintsObjects</span><span class="cm">,</span> <span class="i">%UniqueCompoundIDs</span><span class="s">)</span><span class="sc">;</span>
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140 127
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141 128 <span class="k">if</span> <span class="s">(</span>!<span class="i">$FingerprintsFileIO</span><span class="s">)</span> <span class="s">{</span>
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142 129 <span class="k">return</span> <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span>
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143 130 <span class="s">}</span>
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144 131 <span class="i">$CheckCompoundIDs</span> = <span class="k">defined</span> <span class="i">$CheckCompoundIDs</span> ? <span class="i">$CheckCompoundIDs</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
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145 132
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146 133 <span class="k">print</span> <span class="q">"\nReading and processing fingerprints data...\n"</span><span class="sc">;</span>
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147 134
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148 135 <span class="s">(</span><span class="i">$FingerprintsCount</span><span class="cm">,</span> <span class="i">$IgnoredFingerprintsCount</span><span class="s">)</span> = <span class="s">(</span><span class="n">0</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span>
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149 136
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150 137 <span class="i">@CompundIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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151 138 <span class="i">@FingerprintsObjects</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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152 139
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153 140 <span class="i">%UniqueCompoundIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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154 141
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155 142 <span class="c"># Check and open file for reading...</span>
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156 143 <span class="k">if</span> <span class="s">(</span>!<span class="i">$FingerprintsFileIO</span><span class="i">->GetStatus</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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157 144 <span class="i">$FingerprintsFileIO</span><span class="i">->Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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158 145 <span class="s">}</span>
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159 146
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160 147 <span class="j">FINGERPRINTS:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$FingerprintsFileIO</span><span class="i">->Read</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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161 148 <span class="i">$FingerprintsCount</span>++<span class="sc">;</span>
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162 149
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163 150 <span class="k">if</span> <span class="s">(</span>!<span class="i">$FingerprintsFileIO</span><span class="i">->IsFingerprintsDataValid</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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164 151 <span class="i">$IgnoredFingerprintsCount</span>++<span class="sc">;</span>
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165 152 <span class="k">next</span> <span class="j">FINGERPRINTS</span><span class="sc">;</span>
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166 153 <span class="s">}</span>
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167 154
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168 155 <span class="k">if</span> <span class="s">(</span><span class="i">$CheckCompoundIDs</span><span class="s">)</span> <span class="s">{</span>
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169 156 <span class="i">$CompoundID</span> = <span class="i">$FingerprintsFileIO</span><span class="i">->GetCompoundID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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170 157 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$UniqueCompoundIDs</span>{<span class="i">$CompoundID</span>}<span class="s">)</span> <span class="s">{</span>
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171 158 <span class="k">warn</span> <span class="q">"Warning: Ignoring fingerprints data for compound ID $CompoundID: Multiple entries for compound ID in fingerprints file.\n"</span><span class="sc">;</span>
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172 159 <span class="i">$IgnoredFingerprintsCount</span>++<span class="sc">;</span>
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173 160 <span class="k">next</span> <span class="j">FINGERPRINTS</span><span class="sc">;</span>
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174 161 <span class="s">}</span>
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175 162 <span class="i">$UniqueCompoundIDs</span>{<span class="i">$CompoundID</span>} = <span class="i">$CompoundID</span><span class="sc">;</span>
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176 163 <span class="s">}</span>
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177 164
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178 165 <span class="k">push</span> <span class="i">@FingerprintsObjects</span><span class="cm">,</span> <span class="i">$FingerprintsFileIO</span><span class="i">->GetFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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179 166 <span class="k">push</span> <span class="i">@CompundIDs</span><span class="cm">,</span> <span class="i">$FingerprintsFileIO</span><span class="i">->GetCompoundID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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180 167 <span class="s">}</span>
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181 168 <span class="i">$FingerprintsFileIO</span><span class="i">->Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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182 169
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183 170 <span class="k">print</span> <span class="q">"Number of fingerprints data entries: $FingerprintsCount\n"</span><span class="sc">;</span>
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184 171 <span class="k">print</span> <span class="q">"Number of fingerprints date entries processed successfully: "</span><span class="cm">,</span> <span class="s">(</span><span class="i">$FingerprintsCount</span> - <span class="i">$IgnoredFingerprintsCount</span><span class="s">)</span> <span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
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185 172 <span class="k">print</span> <span class="q">"Number of fingerprints data entries ignored due to missing/invalid data: $IgnoredFingerprintsCount\n\n"</span><span class="sc">;</span>
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186 173
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187 174 <span class="k">return</span> <span class="s">(</span>\<span class="i">@CompundIDs</span><span class="cm">,</span> \<span class="i">@FingerprintsObjects</span><span class="s">)</span><span class="sc">;</span>
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188 175 <span class="s">}</span>
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189 176
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190 177
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191 <a name="EOF-"></a></pre>
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192 <p> </p>
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193 <br />
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194 <center>
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195 <img src="../../../images/h2o2.png">
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196 </center>
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197 </body>
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198 </html>
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