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13 <pre>
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14 <a name="package-FileIO::FingerprintsTextFileIO-"></a> 1 <span class="k">package </span><span class="i">FileIO::FingerprintsTextFileIO</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: FingerprintsTextFileIO.pm,v $</span>
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17 4 <span class="c"># $Date: 2015/02/28 20:48:43 $</span>
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18 5 <span class="c"># $Revision: 1.19 $</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">Carp</span><span class="sc">;</span>
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44 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span>
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45 32 <span class="k">use</span> <span class="w">Scalar::Util</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">TextUtil</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">FileUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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48 35 <span class="k">use</span> <span class="w">Fingerprints::FingerprintsStringUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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49 36 <span class="k">use</span> <span class="w">FileIO::FileIO</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(FileIO::FileIO 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(IsFingerprintsTextFile)</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"># Setup class variables...</span>
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60 47 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="sc">;</span>
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61 48 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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62 49
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63 50 <span class="c"># Class constructor...</span>
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64 <a name="new-"></a> 51 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span>
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65 52 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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66 53
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67 54 <span class="c"># Initialize object...</span>
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68 55 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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69 56 <span class="k">bless</span> <span class="i">$This</span><span class="cm">,</span> <span class="k">ref</span><span class="s">(</span><span class="i">$Class</span><span class="s">)</span> || <span class="i">$Class</span><span class="sc">;</span>
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70 57 <span class="i">$This</span><span class="i">->_InitializeFingerprintsTextFileIO</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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71 58
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72 59 <span class="i">$This</span><span class="i">->_InitializeFingerprintsTextFileIOProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span>
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73 60
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74 61 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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75 62 <span class="s">}</span>
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76 63
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77 64 <span class="c"># Initialize object data...</span>
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78 65 <span class="c">#</span>
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79 <a name="_InitializeFingerprintsTextFileIO-"></a> 66 <span class="k">sub </span><span class="m">_InitializeFingerprintsTextFileIO</span> <span class="s">{</span>
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80 67 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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81 68
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82 69 <span class="c"># Fingerprints string data format during read/write...</span>
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83 70 <span class="c">#</span>
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84 71 <span class="c"># For file read:</span>
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85 72 <span class="c">#</span>
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86 73 <span class="c"># AutoDetect - automatically detect format of fingerprints string</span>
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87 74 <span class="c"># FingerprintsBitVectorString - Bit vector fingerprints string format</span>
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88 75 <span class="c"># FingerprintsVectorString - Vector fingerprints string format</span>
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89 76 <span class="c">#</span>
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90 77 <span class="c"># Default value: AutoDetect</span>
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91 78 <span class="c">#</span>
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92 79 <span class="c"># For file write:</span>
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93 80 <span class="c">#</span>
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94 81 <span class="c"># FingerprintsBitVectorString - Bit vector fingerprints string format</span>
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95 82 <span class="c"># FingerprintsVectorString - Vector fingerprints string format</span>
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96 83 <span class="c">#</span>
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97 84 <span class="c"># Default value: undef</span>
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98 85 <span class="c">#</span>
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99 86 <span class="i">$This</span>->{<span class="w">FingerprintsStringMode</span>} = <span class="k">undef</span><span class="sc">;</span>
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100 87
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101 88 <span class="c"># For file read:</span>
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102 89 <span class="c">#</span>
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103 90 <span class="c"># o Fingerprints bit-vector and vector object for current fingerprints string</span>
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104 91 <span class="c">#</span>
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105 92 <span class="c"># For file write:</span>
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106 93 <span class="c">#</span>
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107 94 <span class="c"># o Fingerprints bit-vector and vector object for current fingerprints string</span>
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108 95 <span class="c"># o Any supported fingerprints object: PathLengthFingerprints, ExtendedConnectivity, and so on.</span>
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109 96 <span class="c">#</span>
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110 97 <span class="i">$This</span>->{<span class="w">FingerprintsObject</span>} = <span class="k">undef</span><span class="sc">;</span>
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111 98
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112 99 <span class="c"># Fingepritns string for current line during read/write...</span>
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113 100 <span class="i">$This</span>->{<span class="w">FingerprintsString</span>} = <span class="k">undef</span><span class="sc">;</span>
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114 101
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115 102 <span class="c"># First data line read/write...</span>
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116 103 <span class="i">$This</span>->{<span class="w">FirstDataLineIO</span>} = <span class="n">1</span><span class="sc">;</span>
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117 104
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118 105 <span class="c"># Current fingerprints string data line number during read/write...</span>
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119 106 <span class="i">$This</span>->{<span class="w">LineNum</span>} = <span class="n">0</span><span class="sc">;</span>
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120 107
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121 108 <span class="c"># Text line data during read/write...</span>
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122 109 <span class="i">$This</span>->{<span class="w">DataLine</span>} = <span class="k">undef</span><span class="sc">;</span>
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123 110 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DataLineWords</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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124 111
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125 112 <span class="c"># Text file column data during read/write...</span>
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126 113 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DataColLabels</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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127 114
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128 115 <span class="c"># Text file delimiter during read/write...</span>
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129 116 <span class="i">$This</span>->{<span class="w">Delim</span>} = <span class="q">''</span><span class="sc">;</span>
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130 117
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131 118 <span class="c"># Initialize parameters for read...</span>
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132 119 <span class="i">$This</span><span class="i">->_InitializeFingerprintsTextFileIORead</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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133 120
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134 121 <span class="c"># Initialize parameters for write...</span>
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135 122 <span class="i">$This</span><span class="i">->_InitializeFingerprintsTextFileIOWrite</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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136 123
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137 124 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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138 125 <span class="s">}</span>
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139 126
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140 127 <span class="c"># Initialize class ...</span>
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141 <a name="_InitializeClass-"></a> 128 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span>
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142 129 <span class="c">#Class name...</span>
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143 130 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span>
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144 131
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145 132 <span class="s">}</span>
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146 133
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147 134 <span class="c"># Initialize object data for reading fingerprints text file...</span>
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148 135 <span class="c">#</span>
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149 <a name="_InitializeFingerprintsTextFileIORead-"></a> 136 <span class="k">sub </span><span class="m">_InitializeFingerprintsTextFileIORead</span> <span class="s">{</span>
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150 137 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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151 138
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152 139 <span class="c"># Column ID specification for identification of comound ID or fingerints string</span>
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153 140 <span class="c"># data column...</span>
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154 141 <span class="c">#</span>
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155 142 <span class="c"># ColNum - A valid column number</span>
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156 143 <span class="c"># ColLabel - A valid column name</span>
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157 144 <span class="c">#</span>
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158 145 <span class="i">$This</span>->{<span class="w">ColMode</span>} = <span class="q">'ColNum'</span><span class="sc">;</span>
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159 146
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160 147 <span class="c"># Fingerprints column to use for retrieving fingerprints string data...</span>
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161 148 <span class="c">#</span>
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162 149 <span class="c"># Value of AutoDetect implies use first column containing the word Fingerprints in its</span>
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163 150 <span class="c"># column label to retrieve fingerprints string data. Othwewise, a valid column number</span>
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164 151 <span class="c"># or column name must be specified based on the value of ColMode.</span>
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165 152 <span class="c">#</span>
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166 153 <span class="i">$This</span>->{<span class="w">FingerprintsCol</span>} = <span class="q">'AutoDetect'</span><span class="sc">;</span>
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167 154
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168 155 <span class="c"># Compound ID column to use for retrieving compound IDs for fingerprints...</span>
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169 156 <span class="c">#</span>
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170 157 <span class="c"># Value of AutoDetect implies use first column containing the word CompoundID in its column</span>
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171 158 <span class="c"># label to retrieve compound IDs or assign seqyentially generated compound IDs. Othwewise,</span>
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172 159 <span class="c"># a valid column number or column name must be specified based on the value of ColMode.</span>
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173 160 <span class="c">#</span>
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174 161 <span class="i">$This</span>->{<span class="w">CompoundIDCol</span>} = <span class="q">'AutoDetect'</span><span class="sc">;</span>
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175 162
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176 163 <span class="c"># A prefix string used for generating compound IDs like LabelPrefixString<Number> during</span>
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177 164 <span class="c"># sequential generation of compound IDs. Default value, Cmpd, generates compound IDs</span>
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178 165 <span class="c"># which look like like Cmpd<Number>.</span>
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179 166 <span class="c">#</span>
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180 167 <span class="i">$This</span>->{<span class="w">CompoundIDPrefix</span>} = <span class="q">'Cmpd'</span><span class="sc">;</span>
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181 168
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182 169 <span class="c"># Input delimiter for fingerprints CSV text file. Possible values: comma, semicolon or tab. This</span>
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183 170 <span class="c"># option is ignored for TSV text file and tab is used as the delimiter.</span>
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184 171 <span class="c">#</span>
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185 172 <span class="i">$This</span>->{<span class="w">InDelim</span>} = <span class="q">'comma'</span><span class="sc">;</span>
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186 173
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187 174 <span class="c"># By default, the fingerprints data corresponding to FingerprintsCol is assumed to</span>
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188 175 <span class="c"># be valid and no validation is performed before generating fingerprints objects...</span>
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189 176 <span class="c">#</span>
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190 177 <span class="i">$This</span>->{<span class="w">ValidateData</span>} = <span class="n">1</span><span class="sc">;</span>
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191 178
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192 179 <span class="c"># Level of detail to print during validation of data for invalid or missing data...</span>
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193 180 <span class="i">$This</span>->{<span class="w">DetailLevel</span>} = <span class="n">1</span><span class="sc">;</span>
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194 181
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195 182 <span class="c"># Number of missing and invalid fingerprints string data lines...</span>
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196 183 <span class="i">$This</span>->{<span class="w">NumOfLinesWithMissingData</span>} = <span class="n">0</span><span class="sc">;</span>
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197 184 <span class="i">$This</span>->{<span class="w">NumOfLinesWithInvalidData</span>} = <span class="n">0</span><span class="sc">;</span>
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198 185
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199 186 <span class="c"># Compound ID for current fingerprints string...</span>
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200 187 <span class="i">$This</span>->{<span class="w">CompoundID</span>} = <span class="k">undef</span><span class="sc">;</span>
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201 188
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202 189 <span class="c"># Status of data in fingerprints text file...</span>
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203 190 <span class="i">$This</span>->{<span class="w">ValidFileData</span>} = <span class="n">0</span><span class="sc">;</span>
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204 191
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205 192 <span class="i">$This</span>->{<span class="w">ValidCompoundIDCol</span>} = <span class="n">0</span><span class="sc">;</span>
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206 193 <span class="i">$This</span>->{<span class="w">ValidFingerprintsCol</span>} = <span class="n">0</span><span class="sc">;</span>
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207 194
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208 195 <span class="i">$This</span>->{<span class="w">ValidFingerprintsStringMode</span>} = <span class="n">0</span><span class="sc">;</span>
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209 196
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210 197 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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211 198 <span class="s">}</span>
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212 199
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213 200 <span class="c"># Initialize object data for writing fingerprints text file...</span>
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214 201 <span class="c">#</span>
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215 <a name="_InitializeFingerprintsTextFileIOWrite-"></a> 202 <span class="k">sub </span><span class="m">_InitializeFingerprintsTextFileIOWrite</span> <span class="s">{</span>
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216 203 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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217 204
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218 205 <span class="c"># Fingerprints bit vector string format...</span>
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219 206 <span class="c">#</span>
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220 207 <span class="c"># Possible values: BinaryString or HexadecimalString [Default]</span>
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221 208 <span class="c">#</span>
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222 209 <span class="c"># Default BitStringFormat is set during first write using Fingerprints::FingerprintsStringUtil::GetDefaultBitStringFormat.</span>
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223 210 <span class="c">#</span>
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224 211 <span class="i">$This</span>->{<span class="w">BitStringFormat</span>} = <span class="k">undef</span><span class="sc">;</span>
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225 212
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226 213 <span class="c"># Bits order in fingerprints bit vector string...</span>
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227 214 <span class="c">#</span>
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228 215 <span class="c"># Ascending - First bit in each byte as the lowest bit [Default]</span>
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229 216 <span class="c"># Descending - First bit in each byte as the highest bit</span>
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230 217 <span class="c">#</span>
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231 218 <span class="c"># Default BitsOrder is set during first write using Fingerprints::FingerprintsStringUtil::GetDefaultBitsOrder.</span>
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232 219 <span class="c">#</span>
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233 220 <span class="i">$This</span>->{<span class="w">BitsOrder</span>} = <span class="k">undef</span><span class="sc">;</span>
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234 221
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235 222 <span class="c"># Fingerprints vector string format...</span>
|
|
|
236 223 <span class="c">#</span>
|
|
|
237 224 <span class="c"># Possible values: IDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString, ValuesAndIDsPairsString, ValuesString</span>
|
|
|
238 225 <span class="c">#</span>
|
|
|
239 226 <span class="c"># Default VectorStringFormat is set during first write using Fingerprints::FingerprintsStringUtil::GetDefaultVectorStringFormat.</span>
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|
|
240 227 <span class="c"># For fingerprints vector object containing vector NumericalValues, it corresponds to IDsAndValuesString; othwerwise,</span>
|
|
|
241 228 <span class="c"># it's set to ValuesString.</span>
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|
|
242 229 <span class="c">#</span>
|
|
|
243 230 <span class="i">$This</span>->{<span class="w">VectorStringFormat</span>} = <span class="k">undef</span><span class="sc">;</span>
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244 231
|
|
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245 232 <span class="c"># Delimiter for output fingerprints CSV/TSV file. Possible values: comma, tab, semicolon. This</span>
|
|
|
246 233 <span class="c"># option is ignored for TSV text file and tab is used as the delimiter.</span>
|
|
|
247 234 <span class="c">#</span>
|
|
|
248 235 <span class="i">$This</span>->{<span class="w">OutDelim</span>} = <span class="q">'comma'</span><span class="sc">;</span>
|
|
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249 236
|
|
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250 237 <span class="c"># Quotes around column values for output fingerprints CSV/TSV text file...</span>
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|
|
251 238 <span class="i">$This</span>->{<span class="w">OutQuote</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
252 239
|
|
|
253 240 <span class="c"># Overwriting existing file...</span>
|
|
|
254 241 <span class="i">$This</span>->{<span class="w">Overwrite</span>} = <span class="n">0</span><span class="sc">;</span>
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|
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255 242
|
|
|
256 243 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
257 244 <span class="s">}</span>
|
|
|
258 245
|
|
|
259 246 <span class="c"># Initialize object values...</span>
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260 <a name="_InitializeFingerprintsTextFileIOProperties-"></a> 247 <span class="k">sub </span><span class="m">_InitializeFingerprintsTextFileIOProperties</span> <span class="s">{</span>
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261 248 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
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|
262 249
|
|
|
263 250 <span class="c"># All other property names and values along with all Set/Get<PropertyName> methods</span>
|
|
|
264 251 <span class="c"># are implemented on-demand using ObjectProperty class.</span>
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|
|
265 252
|
|
|
266 253 <span class="k">my</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">$MethodName</span><span class="s">)</span><span class="sc">;</span>
|
|
|
267 254 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span>
|
|
|
268 255 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span>
|
|
|
269 256 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
|
|
|
270 257 <span class="s">}</span>
|
|
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271 258
|
|
|
272 259 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">Name</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
273 260 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying file name..."</span><span class="sc">;</span>
|
|
|
274 261 <span class="s">}</span>
|
|
|
275 262
|
|
|
276 263 <span class="c"># Make sure it's a fingerprints file...</span>
|
|
|
277 264 <span class="i">$Name</span> = <span class="i">$NamesAndValues</span>{<span class="w">Name</span>}<span class="sc">;</span>
|
|
|
278 265 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->IsFingerprintsTextFile</span><span class="s">(</span><span class="i">$Name</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
279 266 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated: File, $Name, doesn't appear to be fingerprints format..."</span><span class="sc">;</span>
|
|
|
280 267 <span class="s">}</span>
|
|
|
281 268
|
|
|
282 269 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetMode</span><span class="s">(</span><span class="s">)</span> =~ <span class="q">/^Read$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
283 270 <span class="i">$This</span><span class="i">->_InitializeFingerprintsTextFileIOReadProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span>
|
|
|
284 271 <span class="s">}</span>
|
|
|
285 272 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetMode</span><span class="s">(</span><span class="s">)</span> =~ <span class="q">/^(Write|Append)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
286 273 <span class="i">$This</span><span class="i">->_InitializeFingerprintsTextFileIOWriteProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span>
|
|
|
287 274 <span class="s">}</span>
|
|
|
288 275
|
|
|
289 276 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
290 277 <span class="s">}</span>
|
|
|
291 278
|
|
|
292 279 <span class="c"># Initialize object properties for reading fingerprints text file...</span>
|
|
|
293 280 <span class="c">#</span>
|
|
|
294 <a name="_InitializeFingerprintsTextFileIOReadProperties-"></a> 281 <span class="k">sub </span><span class="m">_InitializeFingerprintsTextFileIOReadProperties</span> <span class="s">{</span>
|
|
|
295 282 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
296 283
|
|
|
297 284 <span class="c"># Set default value for FingerprintsStringMode...</span>
|
|
|
298 285 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">FingerprintsStringMode</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
299 286 <span class="i">$This</span>->{<span class="w">FingerprintsStringMode</span>} = <span class="q">'AutoDetect'</span><span class="sc">;</span>
|
|
|
300 287 <span class="s">}</span>
|
|
|
301 288
|
|
|
302 289 <span class="i">$This</span><span class="i">->_PrepareForReadingFingerprintsTextFileData</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
303 290
|
|
|
304 291 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
305 292 <span class="s">}</span>
|
|
|
306 293
|
|
|
307 294 <span class="c"># Initialize object properties for writing fingerprints text file...</span>
|
|
|
308 295 <span class="c">#</span>
|
|
|
309 <a name="_InitializeFingerprintsTextFileIOWriteProperties-"></a> 296 <span class="k">sub </span><span class="m">_InitializeFingerprintsTextFileIOWriteProperties</span> <span class="s">{</span>
|
|
|
310 297 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
311 298
|
|
|
312 299 <span class="c"># Check FingerprintsStringMode value...</span>
|
|
|
313 300 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">FingerprintsStringMode</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
314 301 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying FingerprintsStringMode..."</span><span class="sc">;</span>
|
|
|
315 302 <span class="s">}</span>
|
|
|
316 303
|
|
|
317 304 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FingerprintsStringMode</span>} !~ <span class="q">/^(FingerprintsBitVectorString|FingerprintsVectorString)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
318 305 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->: Object can't be instantiated: FingerprintsStringMode value, $This->{FingerprintsStringMode}, is not valid; Supported values for write/append: FingerprintsBitVectorString or FingerprintsVectorString..."</span><span class="sc">;</span>
|
|
|
319 306 <span class="s">}</span>
|
|
|
320 307
|
|
|
321 308 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">DataColLabels</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
322 309 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying DataColLabels..."</span><span class="sc">;</span>
|
|
|
323 310 <span class="s">}</span>
|
|
|
324 311
|
|
|
325 312 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">OutDelim</span>} =~ <span class="q">/semicolon/i</span> && !<span class="i">$This</span>->{<span class="w">OutQuote</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
326 313 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->: Object can't be instantiated: The value specified, $This->{OutQuote}, using \"OutQuote\" is not allowed with semicolon value of \"OutDelim\": Fingerprints string use semicolon as delimiter for various data fields and must be quoted.\n"</span><span class="sc">;</span>
|
|
|
327 314 <span class="s">}</span>
|
|
|
328 315
|
|
|
329 316 <span class="i">$This</span><span class="i">->_PrepareForWritingFingerprintsTextFileData</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
330 317
|
|
|
331 318 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
332 319 <span class="s">}</span>
|
|
|
333 320
|
|
|
334 321 <span class="c"># Set FingerprintsStringMode...</span>
|
|
|
335 322 <span class="c">#</span>
|
|
|
336 <a name="SetFingerprintsStringMode-"></a> 323 <span class="k">sub </span><span class="m">SetFingerprintsStringMode</span> <span class="s">{</span>
|
|
|
337 324 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
338 325
|
|
|
339 326 <span class="c"># AutoDetect - automatically detect format of fingerprints string</span>
|
|
|
340 327 <span class="c"># FingerprintsBitVectorString - Bit vector fingerprints string format</span>
|
|
|
341 328 <span class="c"># FingerprintsVectorString - Vector fingerprints string format</span>
|
|
|
342 329
|
|
|
343 330 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(AutoDetect|FingerprintsBitVectorString|FingerprintsVectorString)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
344 331 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFingerprintsStringMode: FingerprintsStringMode value, $Value, is not valid; Supported values: AutoDetect, FingerprintsBitVectorString or FingerprintsVectorString..."</span><span class="sc">;</span>
|
|
|
345 332 <span class="s">}</span>
|
|
|
346 333
|
|
|
347 334 <span class="i">$This</span>->{<span class="w">FingerprintsStringMode</span>} = <span class="i">$Value</span><span class="sc">;</span>
|
|
|
348 335
|
|
|
349 336 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
350 337 <span class="s">}</span>
|
|
|
351 338
|
|
|
352 339 <span class="c"># Set ColMode...</span>
|
|
|
353 340 <span class="c">#</span>
|
|
|
354 <a name="SetColMode-"></a> 341 <span class="k">sub </span><span class="m">SetColMode</span> <span class="s">{</span>
|
|
|
355 342 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
356 343
|
|
|
357 344 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(ColNum|ColLabel)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
358 345 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetColMode: ColMode value, $Value, is not valid; Supported values: ColNum or ColLabel..."</span><span class="sc">;</span>
|
|
|
359 346 <span class="s">}</span>
|
|
|
360 347
|
|
|
361 348 <span class="i">$This</span>->{<span class="w">ColMode</span>} = <span class="i">$Value</span><span class="sc">;</span>
|
|
|
362 349
|
|
|
363 350 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
364 351 <span class="s">}</span>
|
|
|
365 352
|
|
|
366 353 <span class="c"># Set InDelim...</span>
|
|
|
367 354 <span class="c">#</span>
|
|
|
368 <a name="SetInDelim-"></a> 355 <span class="k">sub </span><span class="m">SetInDelim</span> <span class="s">{</span>
|
|
|
369 356 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
370 357
|
|
|
371 358 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(comma|semicolon|tab)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
372 359 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetInDelim: InDelim value, $Value, is not valid; Supported values: comma, semicolon, or tab..."</span><span class="sc">;</span>
|
|
|
373 360 <span class="s">}</span>
|
|
|
374 361
|
|
|
375 362 <span class="i">$This</span>->{<span class="w">InDelim</span>} = <span class="i">$Value</span><span class="sc">;</span>
|
|
|
376 363
|
|
|
377 364 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
378 365 <span class="s">}</span>
|
|
|
379 366
|
|
|
380 367 <span class="c"># Set DetailLevel...</span>
|
|
|
381 368 <span class="c">#</span>
|
|
|
382 <a name="SetDetailLevel-"></a> 369 <span class="k">sub </span><span class="m">SetDetailLevel</span> <span class="s">{</span>
|
|
|
383 370 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
384 371
|
|
|
385 372 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
386 373 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetDetailLevel: DetailLevel value, $Value, is not valid; Supported values: > 0..."</span><span class="sc">;</span>
|
|
|
387 374 <span class="s">}</span>
|
|
|
388 375
|
|
|
389 376 <span class="i">$This</span>->{<span class="w">DetailLevel</span>} = <span class="i">$Value</span><span class="sc">;</span>
|
|
|
390 377
|
|
|
391 378 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
392 379 <span class="s">}</span>
|
|
|
393 380
|
|
|
394 381 <span class="c"># Set BitStringFormat...</span>
|
|
|
395 382 <span class="c">#</span>
|
|
|
396 <a name="SetBitStringFormat-"></a> 383 <span class="k">sub </span><span class="m">SetBitStringFormat</span> <span class="s">{</span>
|
|
|
397 384 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
398 385
|
|
|
399 386 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(BinaryString|HexadecimalString)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
400 387 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetBitStringFormat: BitStringFormat value, $Value, is not valid; Supported values: BinaryString or HexadecimalString..."</span><span class="sc">;</span>
|
|
|
401 388 <span class="s">}</span>
|
|
|
402 389
|
|
|
403 390 <span class="i">$This</span>->{<span class="w">BitStringFormat</span>} = <span class="i">$Value</span><span class="sc">;</span>
|
|
|
404 391
|
|
|
405 392 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
406 393 <span class="s">}</span>
|
|
|
407 394
|
|
|
408 395 <span class="c"># Set BitsOrder...</span>
|
|
|
409 396 <span class="c">#</span>
|
|
|
410 <a name="SetBitsOrder-"></a> 397 <span class="k">sub </span><span class="m">SetBitsOrder</span> <span class="s">{</span>
|
|
|
411 398 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
412 399
|
|
|
413 400 <span class="c"># Ascending - First bit in each byte as the lowest bit</span>
|
|
|
414 401 <span class="c"># Descending - First bit in each byte as the highest bit</span>
|
|
|
415 402 <span class="c">#</span>
|
|
|
416 403 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(Ascending|Descending)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
417 404 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetBitsOrder: FingerprintsStringMode value, $Value, is not valid; Supported values: Ascending or Descending..."</span><span class="sc">;</span>
|
|
|
418 405 <span class="s">}</span>
|
|
|
419 406
|
|
|
420 407 <span class="i">$This</span>->{<span class="w">BitsOrder</span>} = <span class="i">$Value</span><span class="sc">;</span>
|
|
|
421 408
|
|
|
422 409 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
423 410 <span class="s">}</span>
|
|
|
424 411
|
|
|
425 412 <span class="c"># Set VectorStringFormat...</span>
|
|
|
426 413 <span class="c">#</span>
|
|
|
427 <a name="SetVectorStringFormat-"></a> 414 <span class="k">sub </span><span class="m">SetVectorStringFormat</span> <span class="s">{</span>
|
|
|
428 415 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
429 416
|
|
|
430 417 <span class="c"># Possible values: IDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString, ValuesAndIDsPairsString, ValuesString</span>
|
|
|
431 418
|
|
|
432 419 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(IDsAndValuesString|IDsAndValuesPairsString|ValuesAndIDsString|ValuesAndIDsPairsString|ValuesString)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
433 420 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetVectorStringFormat: FingerprintsStringMode value, $Value, is not valid; Supported values: IDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString, ValuesAndIDsPairsString, or ValuesString..."</span><span class="sc">;</span>
|
|
|
434 421 <span class="s">}</span>
|
|
|
435 422
|
|
|
436 423 <span class="i">$This</span>->{<span class="w">VectorStringFormat</span>} = <span class="i">$Value</span><span class="sc">;</span>
|
|
|
437 424
|
|
|
438 425 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
439 426 <span class="s">}</span>
|
|
|
440 427
|
|
|
441 428 <span class="c"># Set FingerprintsStringMode...</span>
|
|
|
442 429 <span class="c">#</span>
|
|
|
443 <a name="SetOutDelim-"></a> 430 <span class="k">sub </span><span class="m">SetOutDelim</span> <span class="s">{</span>
|
|
|
444 431 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
445 432
|
|
|
446 433 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(comma|tab|semicolon)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
447 434 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetOutDelim: OutDelim value, $Value, is not valid; Supported values: comma, tab or semicolon..."</span><span class="sc">;</span>
|
|
|
448 435 <span class="s">}</span>
|
|
|
449 436
|
|
|
450 437 <span class="i">$This</span>->{<span class="w">OutDelim</span>} = <span class="i">$Value</span><span class="sc">;</span>
|
|
|
451 438
|
|
|
452 439 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
453 440 <span class="s">}</span>
|
|
|
454 441
|
|
|
455 442 <span class="c"># Set DataColLabels...</span>
|
|
|
456 443 <span class="c">#</span>
|
|
|
457 444 <span class="c"># Set output data column labels using:</span>
|
|
|
458 445 <span class="c"># o List of column labels</span>
|
|
|
459 446 <span class="c"># o Reference to an list of column labels</span>
|
|
|
460 447 <span class="c">#</span>
|
|
|
461 <a name="SetDataColLabels-"></a> 448 <span class="k">sub </span><span class="m">SetDataColLabels</span> <span class="s">{</span>
|
|
|
462 449 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
463 450 <span class="k">my</span><span class="s">(</span><span class="i">$FirstValue</span><span class="cm">,</span> <span class="i">$TypeOfFirstValue</span><span class="s">)</span><span class="sc">;</span>
|
|
|
464 451
|
|
|
465 452 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span>
|
|
|
466 453 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_SetDataColLabels: No data column labels specified..."</span><span class="sc">;</span>
|
|
|
467 454 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
468 455 <span class="s">}</span>
|
|
|
469 456
|
|
|
470 457 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DataColLabels</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
471 458
|
|
|
472 459 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span>
|
|
|
473 460 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span>
|
|
|
474 461
|
|
|
475 462 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
476 463 <span class="c"># Initialize using array refernce...</span>
|
|
|
477 464 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DataColLabels</span>}}<span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span>
|
|
|
478 465 <span class="s">}</span>
|
|
|
479 466 <span class="k">else</span> <span class="s">{</span>
|
|
|
480 467 <span class="c"># It's a list of values...</span>
|
|
|
481 468 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DataColLabels</span>}}<span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span>
|
|
|
482 469 <span class="s">}</span>
|
|
|
483 470
|
|
|
484 471 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
485 472 <span class="s">}</span>
|
|
|
486 473
|
|
|
487 474 <span class="c"># Get column labels or number of column labels in first text line...</span>
|
|
|
488 475 <span class="c">#</span>
|
|
|
489 <a name="GetDataColLabels-"></a> 476 <span class="k">sub </span><span class="m">GetDataColLabels</span> <span class="s">{</span>
|
|
|
490 477 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
491 478
|
|
|
492 479 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DataColLabels</span>}} <span class="co">:</span> <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DataColLabels</span>}}<span class="sc">;</span>
|
|
|
493 480 <span class="s">}</span>
|
|
|
494 481
|
|
|
495 482 <span class="c"># Get words or number of words in current data line...</span>
|
|
|
496 483 <span class="c">#</span>
|
|
|
497 <a name="GetDataLineWords-"></a> 484 <span class="k">sub </span><span class="m">GetDataLineWords</span> <span class="s">{</span>
|
|
|
498 485 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
499 486
|
|
|
500 487 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DataLineWords</span>}} <span class="co">:</span> <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DataLineWords</span>}}<span class="sc">;</span>
|
|
|
501 488 <span class="s">}</span>
|
|
|
502 489
|
|
|
503 490 <span class="c"># Set DataLineWords...</span>
|
|
|
504 491 <span class="c">#</span>
|
|
|
505 492 <span class="c"># Set data line words using:</span>
|
|
|
506 493 <span class="c"># o List of line words</span>
|
|
|
507 494 <span class="c"># o Reference to an list of line words</span>
|
|
|
508 495 <span class="c">#</span>
|
|
|
509 <a name="SetDataLineWords-"></a> 496 <span class="k">sub </span><span class="m">SetDataLineWords</span> <span class="s">{</span>
|
|
|
510 497 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
511 498 <span class="k">my</span><span class="s">(</span><span class="i">$FirstValue</span><span class="cm">,</span> <span class="i">$TypeOfFirstValue</span><span class="s">)</span><span class="sc">;</span>
|
|
|
512 499
|
|
|
513 500 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span>
|
|
|
514 501 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetDataLineWords: No line words specified..."</span><span class="sc">;</span>
|
|
|
515 502 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
516 503 <span class="s">}</span>
|
|
|
517 504
|
|
|
518 505 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DataLineWords</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
519 506
|
|
|
520 507 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span>
|
|
|
521 508 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span>
|
|
|
522 509
|
|
|
523 510 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
524 511 <span class="c"># Initialize using array refernce...</span>
|
|
|
525 512 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DataLineWords</span>}}<span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span>
|
|
|
526 513 <span class="s">}</span>
|
|
|
527 514 <span class="k">else</span> <span class="s">{</span>
|
|
|
528 515 <span class="c"># It's a list of values...</span>
|
|
|
529 516 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DataLineWords</span>}}<span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span>
|
|
|
530 517 <span class="s">}</span>
|
|
|
531 518
|
|
|
532 519 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
533 520 <span class="s">}</span>
|
|
|
534 521
|
|
|
535 522 <span class="c"># Get fingerprints object for current data line using fingerprints, fingerprints bit-vector</span>
|
|
|
536 523 <span class="c"># fingerprints vector object. Fingerprints object correspond to any of supported fingerprints</span>
|
|
|
537 524 <span class="c"># objects such as PathLengthFingerprints, ExtendedConnectivity, and so on.</span>
|
|
|
538 525 <span class="c">#</span>
|
|
|
539 <a name="GetFingerprints-"></a> 526 <span class="k">sub </span><span class="m">GetFingerprints</span> <span class="s">{</span>
|
|
|
540 527 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
541 528
|
|
|
542 529 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">FingerprintsObject</span>}<span class="sc">;</span>
|
|
|
543 530 <span class="s">}</span>
|
|
|
544 531
|
|
|
545 532 <span class="c"># Set fingerprints object for current data line...</span>
|
|
|
546 533 <span class="c">#</span>
|
|
|
547 <a name="SetFingerprints-"></a> 534 <span class="k">sub </span><span class="m">SetFingerprints</span> <span class="s">{</span>
|
|
|
548 535 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsObject</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
549 536
|
|
|
550 537 <span class="i">$This</span>->{<span class="w">FingerprintsObject</span>} = <span class="i">$FingerprintsObject</span><span class="sc">;</span>
|
|
|
551 538
|
|
|
552 539 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
553 540 <span class="s">}</span>
|
|
|
554 541
|
|
|
555 542 <span class="c"># Get fingerprints string for current data line...</span>
|
|
|
556 543 <span class="c">#</span>
|
|
|
557 <a name="GetFingerprintsString-"></a> 544 <span class="k">sub </span><span class="m">GetFingerprintsString</span> <span class="s">{</span>
|
|
|
558 545 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
559 546
|
|
|
560 547 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">FingerprintsString</span>} ? <span class="i">$This</span>->{<span class="w">FingerprintsString</span>} <span class="co">:</span> <span class="q">'None'</span><span class="sc">;</span>
|
|
|
561 548 <span class="s">}</span>
|
|
|
562 549
|
|
|
563 550 <span class="c"># Set fingerprints string for current data line...</span>
|
|
|
564 551 <span class="c">#</span>
|
|
|
565 <a name="SetFingerprintsString-"></a> 552 <span class="k">sub </span><span class="m">SetFingerprintsString</span> <span class="s">{</span>
|
|
|
566 553 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsString</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
567 554
|
|
|
568 555 <span class="i">$This</span>->{<span class="w">FingerprintsString</span>} = <span class="i">$FingerprintsString</span><span class="sc">;</span>
|
|
|
569 556
|
|
|
570 557 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
571 558 <span class="s">}</span>
|
|
|
572 559
|
|
|
573 560 <span class="c"># Does fingerprints text file contain valid data?</span>
|
|
|
574 561 <span class="c">#</span>
|
|
|
575 <a name="IsFingerprintsFileDataValid-"></a> 562 <span class="k">sub </span><span class="m">IsFingerprintsFileDataValid</span> <span class="s">{</span>
|
|
|
576 563 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
577 564
|
|
|
578 565 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">ValidFileData</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
579 566 <span class="s">}</span>
|
|
|
580 567
|
|
|
581 568 <span class="c"># Does current data line contains valid fingerprints object data?</span>
|
|
|
582 569 <span class="c">#</span>
|
|
|
583 <a name="IsFingerprintsDataValid-"></a> 570 <span class="k">sub </span><span class="m">IsFingerprintsDataValid</span> <span class="s">{</span>
|
|
|
584 571 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
585 572
|
|
|
586 573 <span class="k">return</span> <span class="k">defined</span> <span class="i">$This</span>->{<span class="w">FingerprintsObject</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
587 574 <span class="s">}</span>
|
|
|
588 575
|
|
|
589 576 <span class="c"># Read next available fingerprints line, process it and generate appropriate fingerprints</span>
|
|
|
590 577 <span class="c"># objects...</span>
|
|
|
591 578 <span class="c">#</span>
|
|
|
592 <a name="Read-"></a> 579 <span class="k">sub </span><span class="m">Read</span> <span class="s">{</span>
|
|
|
593 580 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
594 581
|
|
|
595 582 <span class="c"># Read data line...</span>
|
|
|
596 583 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_ReadDataLine</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
597 584 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
598 585 <span class="s">}</span>
|
|
|
599 586
|
|
|
600 587 <span class="c"># No need to process invalid text file with invalid data...</span>
|
|
|
601 588 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">ValidFileData</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
602 589 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">ValidateData</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
603 590 <span class="i">$This</span>->{<span class="w">NumOfLinesWithMissingData</span>} += <span class="n">1</span><span class="sc">;</span>
|
|
|
604 591 <span class="s">}</span>
|
|
|
605 592 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
606 593 <span class="s">}</span>
|
|
|
607 594
|
|
|
608 595 <span class="c"># Perform data validation...</span>
|
|
|
609 596 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">ValidateData</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
610 597 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_ValidateReadDataLine</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
611 598 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
612 599 <span class="s">}</span>
|
|
|
613 600 <span class="s">}</span>
|
|
|
614 601
|
|
|
615 602 <span class="c"># Setup fingerprints string after checking again to handle problematic data for</span>
|
|
|
616 603 <span class="c"># non-validated data lines...</span>
|
|
|
617 604 <span class="c">#</span>
|
|
|
618 605 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FingerprintsColNum</span>} <= <span class="i">$#</span>{<span class="i">$This</span>->{<span class="w">DataLineWords</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
619 606 <span class="i">$This</span>->{<span class="w">FingerprintsString</span>} = <span class="i">$This</span>->{<span class="w">DataLineWords</span>}[<span class="i">$This</span>->{<span class="w">FingerprintsColNum</span>}]<span class="sc">;</span>
|
|
|
620 607 <span class="s">}</span>
|
|
|
621 608
|
|
|
622 609 <span class="c"># Generate fingeprints object...</span>
|
|
|
623 610 <span class="i">$This</span><span class="i">->_GenerateFingerprintsObject</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
624 611
|
|
|
625 612 <span class="c"># Setup fingerprints compound ID for fingerprints string...</span>
|
|
|
626 613 <span class="i">$This</span><span class="i">->_GenerateCompoundID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
627 614
|
|
|
628 615 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
629 616 <span class="s">}</span>
|
|
|
630 617
|
|
|
631 618 <span class="c"># Read next available fingerprints line, process it and generate appropriate fingerprints</span>
|
|
|
632 619 <span class="c"># objects...</span>
|
|
|
633 620 <span class="c">#</span>
|
|
|
634 <a name="Next-"></a> 621 <span class="k">sub </span><span class="m">Next</span> <span class="s">{</span>
|
|
|
635 622 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
636 623
|
|
|
637 624 <span class="k">return</span> <span class="i">$This</span><span class="i">->Read</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
638 625 <span class="s">}</span>
|
|
|
639 626
|
|
|
640 627 <span class="c"># Read fingerprints data line line...</span>
|
|
|
641 628 <span class="c">#</span>
|
|
|
642 <a name="_ReadDataLine-"></a> 629 <span class="k">sub </span><span class="m">_ReadDataLine</span> <span class="s">{</span>
|
|
|
643 630 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
644 631
|
|
|
645 632 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FirstDataLineIO</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
646 633 <span class="i">$This</span><span class="i">->_ProcessFirstDataLineRead</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
647 634 <span class="s">}</span>
|
|
|
648 635
|
|
|
649 636 <span class="c"># Initialize data for current line...</span>
|
|
|
650 637 <span class="i">$This</span><span class="i">->_InitializeReadDataLine</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
651 638
|
|
|
652 639 <span class="c"># Get next data line...</span>
|
|
|
653 640 <span class="i">$This</span>->{<span class="w">DataLine</span>} = <span class="i">TextUtil::GetTextLine</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">FileHandle</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
654 641 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">DataLine</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
655 642 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
656 643 <span class="s">}</span>
|
|
|
657 644
|
|
|
658 645 <span class="c"># Get line words...</span>
|
|
|
659 646 <span class="i">$This</span>->{<span class="w">LineNum</span>} += <span class="n">1</span><span class="sc">;</span>
|
|
|
660 647 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DataLineWords</span>}} = <span class="i">TextUtil::SplitWords</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">DataLine</span>}<span class="cm">,</span> <span class="i">$This</span>->{<span class="w">Delim</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
661 648
|
|
|
662 649 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
663 650 <span class="s">}</span>
|
|
|
664 651
|
|
|
665 652 <span class="c"># Initialize data line for reading...</span>
|
|
|
666 653 <span class="c">#</span>
|
|
|
667 <a name="_InitializeReadDataLine-"></a> 654 <span class="k">sub </span><span class="m">_InitializeReadDataLine</span> <span class="s">{</span>
|
|
|
668 655 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
669 656
|
|
|
670 657 <span class="i">$This</span>->{<span class="w">CompoundID</span>} = <span class="k">undef</span><span class="sc">;</span>
|
|
|
671 658
|
|
|
672 659 <span class="i">$This</span>->{<span class="w">DataLine</span>} = <span class="k">undef</span><span class="sc">;</span>
|
|
|
673 660 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DataLineWords</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
674 661
|
|
|
675 662 <span class="i">$This</span>->{<span class="w">FingerprintsObject</span>} = <span class="k">undef</span><span class="sc">;</span>
|
|
|
676 663 <span class="i">$This</span>->{<span class="w">FingerprintsString</span>} = <span class="k">undef</span><span class="sc">;</span>
|
|
|
677 664
|
|
|
678 665 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
679 666 <span class="s">}</span>
|
|
|
680 667
|
|
|
681 668 <span class="c"># Validate fingerprints string data line...</span>
|
|
|
682 669 <span class="c">#</span>
|
|
|
683 <a name="_ValidateReadDataLine-"></a> 670 <span class="k">sub </span><span class="m">_ValidateReadDataLine</span> <span class="s">{</span>
|
|
|
684 671 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
685 672
|
|
|
686 673 <span class="c"># Check for missing data...</span>
|
|
|
687 674 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FingerprintsColNum</span>} > <span class="i">$#</span>{<span class="i">$This</span>->{<span class="w">DataLineWords</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
688 675 <span class="c"># Missing data...</span>
|
|
|
689 676 <span class="i">$This</span>->{<span class="w">NumOfLinesWithMissingData</span>} += <span class="n">1</span><span class="sc">;</span>
|
|
|
690 677 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">DetailLevel</span>} >= <span class="n">3</span><span class="s">)</span> <span class="s">{</span>
|
|
|
691 678 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ValidateReadDataLine: Data line number $This->{LineNum} contains no fingerprints data: $This->{DataLine}..."</span><span class="sc">;</span>
|
|
|
692 679 <span class="s">}</span>
|
|
|
693 680 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">DetailLevel</span>} >= <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
|
|
|
694 681 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ValidateReadDataLine: Data line number $This->{LineNum} contains no fingerprints data..."</span><span class="sc">;</span>
|
|
|
695 682 <span class="s">}</span>
|
|
|
696 683 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
697 684 <span class="s">}</span>
|
|
|
698 685
|
|
|
699 686 <span class="c"># Check for invalid data...</span>
|
|
|
700 687 <span class="k">my</span><span class="s">(</span><span class="i">$InvalidFingerprintsData</span><span class="cm">,</span> <span class="i">$FingerprintsColNum</span><span class="cm">,</span> <span class="i">$FingerprintsType</span><span class="cm">,</span> <span class="i">$FingerprintsDescription</span><span class="s">)</span><span class="sc">;</span>
|
|
|
701 688
|
|
|
702 689 <span class="i">$InvalidFingerprintsData</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
703 690 <span class="i">$FingerprintsColNum</span> = <span class="i">$This</span>->{<span class="w">FingerprintsColNum</span>}<span class="sc">;</span>
|
|
|
704 691
|
|
|
705 692 <span class="k">if</span> <span class="s">(</span><span class="i">Fingerprints::FingerprintsStringUtil::AreFingerprintsStringValuesValid</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">DataLineWords</span>}[<span class="i">$FingerprintsColNum</span>]<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
706 693 <span class="s">(</span><span class="i">$FingerprintsType</span><span class="cm">,</span> <span class="i">$FingerprintsDescription</span><span class="s">)</span> = <span class="i">Fingerprints::FingerprintsStringUtil::GetFingerprintsStringTypeAndDescription</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">DataLineWords</span>}[<span class="i">$FingerprintsColNum</span>]<span class="s">)</span><span class="sc">;</span>
|
|
|
707 694 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FirstFingerprintsStringType</span>} !~ <span class="q">/^$FingerprintsType$/i</span> || <span class="i">$This</span>->{<span class="w">FirstFingerprintsStringDescription</span>} !~ <span class="q">/^$FingerprintsDescription$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
708 695 <span class="i">$InvalidFingerprintsData</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
709 696 <span class="s">}</span>
|
|
|
710 697 <span class="s">}</span>
|
|
|
711 698 <span class="k">else</span> <span class="s">{</span>
|
|
|
712 699 <span class="i">$InvalidFingerprintsData</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
713 700 <span class="s">}</span>
|
|
|
714 701
|
|
|
715 702 <span class="k">if</span> <span class="s">(</span><span class="i">$InvalidFingerprintsData</span><span class="s">)</span> <span class="s">{</span>
|
|
|
716 703 <span class="i">$This</span>->{<span class="w">NumOfLinesWithInvalidData</span>} += <span class="n">1</span><span class="sc">;</span>
|
|
|
717 704 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">DetailLevel</span>} >= <span class="n">3</span><span class="s">)</span> <span class="s">{</span>
|
|
|
718 705 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ValidateReadDataLine: Data line number $This->{LineNum} contains invalid fingerprints data: $This->{DataLine}..."</span><span class="sc">;</span>
|
|
|
719 706 <span class="s">}</span>
|
|
|
720 707 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">DetailLevel</span>} >= <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
|
|
|
721 708 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ValidateReadDataLine: Data line number $This->{LineNum} contains invalid fingerprints data..."</span><span class="sc">;</span>
|
|
|
722 709 <span class="s">}</span>
|
|
|
723 710 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
724 711 <span class="s">}</span>
|
|
|
725 712
|
|
|
726 713 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
727 714 <span class="s">}</span>
|
|
|
728 715
|
|
|
729 716 <span class="c"># Setup fingerprints compound ID for fingerprints string...</span>
|
|
|
730 <a name="_GenerateCompoundID-"></a> 717 <span class="k">sub </span><span class="m">_GenerateCompoundID</span> <span class="s">{</span>
|
|
|
731 718 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
732 719 <span class="k">my</span><span class="s">(</span><span class="i">$CompoundID</span><span class="s">)</span><span class="sc">;</span>
|
|
|
733 720
|
|
|
734 721 <span class="i">$CompoundID</span> = <span class="q">''</span><span class="sc">;</span>
|
|
|
735 722
|
|
|
736 723 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">UseSequentialCompoundIDs</span>} || <span class="s">(</span><span class="i">$This</span>->{<span class="w">CompoundIDColNum</span>} > <span class="i">$#</span>{<span class="i">$This</span>->{<span class="w">DataLineWords</span>}}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
737 724 <span class="k">my</span><span class="s">(</span><span class="i">$CompoundNum</span><span class="s">)</span><span class="sc">;</span>
|
|
|
738 725
|
|
|
739 726 <span class="i">$CompoundNum</span> = <span class="i">$This</span>->{<span class="w">LineNum</span>} - <span class="n">1</span><span class="sc">;</span>
|
|
|
740 727 <span class="i">$CompoundID</span> = <span class="q">"$This->{CompoundIDPrefix}${CompoundNum}"</span><span class="sc">;</span>
|
|
|
741 728 <span class="s">}</span>
|
|
|
742 729 <span class="k">else</span> <span class="s">{</span>
|
|
|
743 730 <span class="i">$CompoundID</span> = <span class="i">$This</span>->{<span class="w">DataLineWords</span>}[<span class="i">$This</span>->{<span class="w">CompoundIDColNum</span>}]<span class="sc">;</span>
|
|
|
744 731 <span class="s">}</span>
|
|
|
745 732
|
|
|
746 733 <span class="i">$This</span>->{<span class="w">CompoundID</span>} = <span class="i">$CompoundID</span><span class="sc">;</span>
|
|
|
747 734
|
|
|
748 735 <span class="c"># Set fingerprints ID...</span>
|
|
|
749 736 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FingerprintsObject</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
750 737 <span class="i">$This</span>->{<span class="w">FingerprintsObject</span>}<span class="i">->SetID</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">CompoundID</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
751 738 <span class="s">}</span>
|
|
|
752 739
|
|
|
753 740 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
754 741 <span class="s">}</span>
|
|
|
755 742
|
|
|
756 743 <span class="c"># Process first read...</span>
|
|
|
757 744 <span class="c">#</span>
|
|
|
758 <a name="_ProcessFirstDataLineRead-"></a> 745 <span class="k">sub </span><span class="m">_ProcessFirstDataLineRead</span> <span class="s">{</span>
|
|
|
759 746 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
760 747
|
|
|
761 748 <span class="c"># Skip column label line...</span>
|
|
|
762 749 <span class="i">$This</span>->{<span class="w">LineNum</span>} += <span class="n">1</span><span class="sc">;</span>
|
|
|
763 750 <span class="i">TextUtil::GetTextLine</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">FileHandle</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
764 751
|
|
|
765 752 <span class="i">$This</span>->{<span class="w">FirstDataLineIO</span>} = <span class="n">0</span><span class="sc">;</span>
|
|
|
766 753
|
|
|
767 754 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
768 755 <span class="s">}</span>
|
|
|
769 756
|
|
|
770 757 <span class="c"># Get ready for reading fingerprints text file...</span>
|
|
|
771 758 <span class="c">#</span>
|
|
|
772 <a name="_PrepareForReadingFingerprintsTextFileData-"></a> 759 <span class="k">sub </span><span class="m">_PrepareForReadingFingerprintsTextFileData</span> <span class="s">{</span>
|
|
|
773 760 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
774 761
|
|
|
775 762 <span class="c"># Retrieve text file columns information....</span>
|
|
|
776 763 <span class="i">$This</span><span class="i">->_RetrieveTextFileColData</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
777 764
|
|
|
778 765 <span class="c"># Validate columns information...</span>
|
|
|
779 766 <span class="i">$This</span><span class="i">->_ValidateReadCompoundIDCol</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
780 767 <span class="i">$This</span><span class="i">->_ValidateReadFingerprintsCol</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
781 768
|
|
|
782 769 <span class="c"># Validate fingeprints string mode information...</span>
|
|
|
783 770 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">ValidFingerprintsCol</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
784 771 <span class="i">$This</span><span class="i">->_ValidateReadFingerprintsStringMode</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
785 772 <span class="s">}</span>
|
|
|
786 773
|
|
|
787 774 <span class="c"># Set status of text file data...</span>
|
|
|
788 775 <span class="i">$This</span>->{<span class="w">ValidFileData</span>} = <span class="s">(</span><span class="i">$This</span>->{<span class="w">ValidCompoundIDCol</span>} && <span class="i">$This</span>->{<span class="w">ValidFingerprintsCol</span>} && <span class="i">$This</span>->{<span class="w">ValidFingerprintsStringMode</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
789 776
|
|
|
790 777 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
791 778 <span class="s">}</span>
|
|
|
792 779
|
|
|
793 780 <span class="c"># Retrieve information about columns and fingerprints string...</span>
|
|
|
794 781 <span class="c">#</span>
|
|
|
795 <a name="_RetrieveTextFileColData-"></a> 782 <span class="k">sub </span><span class="m">_RetrieveTextFileColData</span> <span class="s">{</span>
|
|
|
796 783 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
797 784 <span class="k">my</span><span class="s">(</span><span class="i">$TextFile</span><span class="cm">,</span> <span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="cm">,</span> <span class="i">$InDelim</span><span class="cm">,</span> <span class="i">$Line</span><span class="cm">,</span> <span class="i">$ColLabel</span><span class="cm">,</span> <span class="i">$ColNum</span><span class="cm">,</span> <span class="i">@ColLabels</span><span class="s">)</span><span class="sc">;</span>
|
|
|
798 785
|
|
|
799 786 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DataColLabels</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
800 787 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">DataColLabelToNumMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
801 788
|
|
|
802 789 <span class="i">$TextFile</span> = <span class="i">$This</span>->{<span class="w">Name</span>}<span class="sc">;</span>
|
|
|
803 790
|
|
|
804 791 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">-e</span> <span class="i">$TextFile</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
805 792 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated: File, $TextFile, doesn't exist..."</span><span class="sc">;</span>
|
|
|
806 793 <span class="s">}</span>
|
|
|
807 794
|
|
|
808 795 <span class="i">$FileDir</span> = <span class="q">""</span><span class="sc">;</span> <span class="i">$FileName</span> = <span class="q">""</span><span class="sc">;</span> <span class="i">$FileExt</span> = <span class="q">""</span><span class="sc">;</span>
|
|
|
809 796 <span class="s">(</span><span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="s">)</span> = <span class="i">FileUtil::ParseFileName</span><span class="s">(</span><span class="i">$TextFile</span><span class="s">)</span><span class="sc">;</span>
|
|
|
810 797
|
|
|
811 798 <span class="i">$InDelim</span> = <span class="s">(</span><span class="i">$FileExt</span> =~ <span class="q">/^tsv$/i</span><span class="s">)</span> ? <span class="q">"\t"</span> <span class="co">:</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">InDelim</span>} =~ <span class="q">/semicolon/i</span> ? <span class="q">"\;"</span> <span class="co">:</span> <span class="q">"\,"</span><span class="s">)</span><span class="sc">;</span>
|
|
|
812 799 <span class="i">$This</span>->{<span class="w">Delim</span>} = <span class="i">$InDelim</span><span class="sc">;</span>
|
|
|
813 800
|
|
|
814 801 <span class="k">if</span> <span class="s">(</span>!<span class="k">open</span> <span class="w">TEXTFILE</span><span class="cm">,</span> <span class="q">"$TextFile"</span><span class="s">)</span> <span class="s">{</span>
|
|
|
815 802 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated: Couldn't open input text file $TextFile: $! ..."</span><span class="sc">;</span>
|
|
|
816 803 <span class="s">}</span>
|
|
|
817 804
|
|
|
818 805 <span class="c"># Get column label line...</span>
|
|
|
819 806 <span class="i">$Line</span> = <span class="i">TextUtil::GetTextLine</span><span class="s">(</span>\<span class="i">*TEXTFILE</span><span class="s">)</span><span class="sc">;</span>
|
|
|
820 807
|
|
|
821 808 <span class="k">close</span> <span class="w">TEXTFILE</span><span class="sc">;</span>
|
|
|
822 809
|
|
|
823 810 <span class="i">@ColLabels</span> = <span class="i">TextUtil::SplitWords</span><span class="s">(</span><span class="i">$Line</span><span class="cm">,</span> <span class="i">$InDelim</span><span class="s">)</span><span class="sc">;</span>
|
|
|
824 811
|
|
|
825 812 <span class="c"># Set text file columns info....</span>
|
|
|
826 813 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DataColLabels</span>}}<span class="cm">,</span> <span class="i">@ColLabels</span><span class="sc">;</span>
|
|
|
827 814
|
|
|
828 815 <span class="k">for</span> <span class="i">$ColNum</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#ColLabels</span><span class="s">)</span> <span class="s">{</span>
|
|
|
829 816 <span class="i">$ColLabel</span> = <span class="i">$ColLabels</span>[<span class="i">$ColNum</span>]<span class="sc">;</span>
|
|
|
830 817 <span class="i">$This</span>->{<span class="w">DataColLabelToNumMap</span>}{<span class="i">$ColLabel</span>} = <span class="i">$ColNum</span><span class="sc">;</span>
|
|
|
831 818 <span class="s">}</span>
|
|
|
832 819
|
|
|
833 820 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
834 821 <span class="s">}</span>
|
|
|
835 822
|
|
|
836 823 <span class="c"># Validate compound ID column information...</span>
|
|
|
837 824 <span class="c">#</span>
|
|
|
838 <a name="_ValidateReadCompoundIDCol-"></a> 825 <span class="k">sub </span><span class="m">_ValidateReadCompoundIDCol</span> <span class="s">{</span>
|
|
|
839 826 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
840 827 <span class="k">my</span><span class="s">(</span><span class="i">$CompoundIDCol</span><span class="cm">,</span> <span class="i">$CompoundIDColNum</span><span class="cm">,</span> <span class="i">$UseSequentialCompoundIDs</span><span class="cm">,</span> <span class="i">$ColFound</span><span class="cm">,</span> <span class="i">$ColLabel</span><span class="cm">,</span> <span class="i">$ColNum</span><span class="s">)</span><span class="sc">;</span>
|
|
|
841 828
|
|
|
842 829 <span class="i">$This</span>->{<span class="w">ValidCompoundIDCol</span>} = <span class="n">0</span><span class="sc">;</span>
|
|
|
843 830 <span class="i">$This</span>->{<span class="w">CompoundIDColNum</span>} = <span class="k">undef</span><span class="sc">;</span>
|
|
|
844 831 <span class="i">$This</span>->{<span class="w">UseSequentialCompoundIDs</span>} = <span class="n">0</span><span class="sc">;</span>
|
|
|
845 832
|
|
|
846 833 <span class="i">$CompoundIDCol</span> = <span class="i">$This</span>->{<span class="w">CompoundIDCol</span>}<span class="sc">;</span>
|
|
|
847 834
|
|
|
848 835 <span class="i">$UseSequentialCompoundIDs</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
849 836 <span class="i">$CompoundIDColNum</span> = <span class="q">''</span><span class="sc">;</span>
|
|
|
850 837
|
|
|
851 838 <span class="k">if</span> <span class="s">(</span><span class="i">$CompoundIDCol</span> =~ <span class="q">/^AutoDetect$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
852 839 <span class="c"># First column containing the word CompoundID in its label or sequential generation...</span>
|
|
|
853 840
|
|
|
854 841 <span class="i">$ColFound</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
855 842 <span class="j">COLLABEL:</span> <span class="k">for</span> <span class="i">$ColLabel</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DataColLabels</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
856 843 <span class="k">if</span> <span class="s">(</span><span class="i">$ColLabel</span> =~ <span class="q">/CompoundID/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
857 844 <span class="i">$ColFound</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
858 845 <span class="i">$ColNum</span> = <span class="i">$This</span>->{<span class="w">DataColLabelToNumMap</span>}{<span class="i">$ColLabel</span>}<span class="sc">;</span>
|
|
|
859 846 <span class="k">last</span> <span class="j">COLLABEL</span><span class="sc">;</span>
|
|
|
860 847 <span class="s">}</span>
|
|
|
861 848 <span class="s">}</span>
|
|
|
862 849 <span class="k">if</span> <span class="s">(</span><span class="i">$ColFound</span><span class="s">)</span> <span class="s">{</span>
|
|
|
863 850 <span class="i">$CompoundIDColNum</span> = <span class="i">$ColNum</span><span class="sc">;</span>
|
|
|
864 851 <span class="s">}</span>
|
|
|
865 852 <span class="k">else</span> <span class="s">{</span>
|
|
|
866 853 <span class="i">$UseSequentialCompoundIDs</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
867 854 <span class="s">}</span>
|
|
|
868 855 <span class="s">}</span>
|
|
|
869 856 <span class="k">else</span> <span class="s">{</span>
|
|
|
870 857 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">ColMode</span>} =~ <span class="q">/^ColNum$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
871 858 <span class="c"># Is it a valid column number?</span>
|
|
|
872 859 <span class="k">if</span> <span class="s">(</span><span class="i">$CompoundIDCol</span> > <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DataColLabels</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
873 860 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ValidateReadCompoundIDCol: Column number, $CompoundIDCol, specified using CompoundIDCol doesn't exist..."</span><span class="sc">;</span>
|
|
|
874 861 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
875 862 <span class="s">}</span>
|
|
|
876 863 <span class="i">$CompoundIDColNum</span> = <span class="i">$CompoundIDCol</span> - <span class="n">1</span><span class="sc">;</span>
|
|
|
877 864 <span class="s">}</span>
|
|
|
878 865 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">ColMode</span>} =~ <span class="q">/^ColLabel$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
879 866 <span class="c"># Does this column exists?</span>
|
|
|
880 867 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$This</span>->{<span class="w">DataColLabelToNumMap</span>}{<span class="i">$CompoundIDCol</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
881 868 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ValidateReadCompoundIDCol: Column name, $CompoundIDCol, specified using CompoundIDCol doesn't exist..."</span><span class="sc">;</span>
|
|
|
882 869 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
883 870 <span class="s">}</span>
|
|
|
884 871 <span class="i">$CompoundIDColNum</span> = <span class="i">$This</span>->{<span class="w">DataColLabelToNumMap</span>}{<span class="i">$CompoundIDCol</span>}<span class="sc">;</span>
|
|
|
885 872 <span class="s">}</span>
|
|
|
886 873 <span class="s">}</span>
|
|
|
887 874
|
|
|
888 875 <span class="i">$This</span>->{<span class="w">ValidCompoundIDCol</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
889 876 <span class="i">$This</span>->{<span class="w">CompoundIDColNum</span>} = <span class="i">$CompoundIDColNum</span><span class="sc">;</span>
|
|
|
890 877 <span class="i">$This</span>->{<span class="w">UseSequentialCompoundIDs</span>} = <span class="i">$UseSequentialCompoundIDs</span><span class="sc">;</span>
|
|
|
891 878
|
|
|
892 879 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
893 880 <span class="s">}</span>
|
|
|
894 881
|
|
|
895 882 <span class="c"># Validate fingerprints string column information...</span>
|
|
|
896 883 <span class="c">#</span>
|
|
|
897 <a name="_ValidateReadFingerprintsCol-"></a> 884 <span class="k">sub </span><span class="m">_ValidateReadFingerprintsCol</span> <span class="s">{</span>
|
|
|
898 885 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
899 886 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsColNum</span><span class="cm">,</span> <span class="i">$FingerprintsCol</span><span class="cm">,</span> <span class="i">$ColFound</span><span class="cm">,</span> <span class="i">$ColLabel</span><span class="cm">,</span> <span class="i">$ColNum</span><span class="s">)</span><span class="sc">;</span>
|
|
|
900 887
|
|
|
901 888 <span class="i">$This</span>->{<span class="w">ValidFingerprintsCol</span>} = <span class="n">0</span><span class="sc">;</span>
|
|
|
902 889 <span class="i">$This</span>->{<span class="w">FingerprintsColNum</span>} = <span class="k">undef</span><span class="sc">;</span>
|
|
|
903 890
|
|
|
904 891 <span class="i">$FingerprintsColNum</span> = <span class="k">undef</span><span class="sc">;</span>
|
|
|
905 892 <span class="i">$FingerprintsCol</span> = <span class="i">$This</span>->{<span class="w">FingerprintsCol</span>}<span class="sc">;</span>
|
|
|
906 893
|
|
|
907 894 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsCol</span> =~ <span class="q">/^AutoDetect$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
908 895 <span class="c"># First column containing the word Fingerprints in its label...</span>
|
|
|
909 896
|
|
|
910 897 <span class="i">$ColFound</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
911 898 <span class="j">COLLABEL:</span> <span class="k">for</span> <span class="i">$ColLabel</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DataColLabels</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
912 899 <span class="k">if</span> <span class="s">(</span><span class="i">$ColLabel</span> =~ <span class="q">/Fingerprints/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
913 900 <span class="i">$ColFound</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
914 901 <span class="i">$ColNum</span> = <span class="i">$This</span>->{<span class="w">DataColLabelToNumMap</span>}{<span class="i">$ColLabel</span>}<span class="sc">;</span>
|
|
|
915 902 <span class="k">last</span> <span class="j">COLLABEL</span><span class="sc">;</span>
|
|
|
916 903 <span class="s">}</span>
|
|
|
917 904 <span class="s">}</span>
|
|
|
918 905 <span class="k">if</span> <span class="s">(</span>!<span class="i">$ColFound</span><span class="s">)</span> <span class="s">{</span>
|
|
|
919 906 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ValidateReadFingerprintsCol: Column label containing \"Fingerprints\" string in its name doesn't exist..."</span><span class="sc">;</span>
|
|
|
920 907 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
921 908 <span class="s">}</span>
|
|
|
922 909 <span class="i">$FingerprintsColNum</span> = <span class="i">$ColNum</span><span class="sc">;</span>
|
|
|
923 910 <span class="s">}</span>
|
|
|
924 911 <span class="k">else</span> <span class="s">{</span>
|
|
|
925 912 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">ColMode</span>} =~ <span class="q">/^ColNum$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
926 913 <span class="c"># Is it a valid column number?</span>
|
|
|
927 914 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsCol</span> > <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DataColLabels</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
928 915 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ValidateReadFingerprintsCol: Column number, $FingerprintsCol, specified using FingerprintsCol doesn't exist..."</span><span class="sc">;</span>
|
|
|
929 916 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
930 917 <span class="s">}</span>
|
|
|
931 918 <span class="i">$FingerprintsColNum</span> = <span class="i">$FingerprintsCol</span> - <span class="n">1</span><span class="sc">;</span>
|
|
|
932 919 <span class="s">}</span>
|
|
|
933 920 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">ColMode</span>} =~ <span class="q">/^ColLabel$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
934 921 <span class="c"># Does this column exists?</span>
|
|
|
935 922 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$This</span>->{<span class="w">DataColLabelToNumMap</span>}{<span class="i">$FingerprintsCol</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
936 923 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ValidateReadFingerprintsCol: Column label, $FingerprintsCol, specified using FingerprintsCol doesn't exist..."</span><span class="sc">;</span>
|
|
|
937 924 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
938 925 <span class="s">}</span>
|
|
|
939 926 <span class="i">$FingerprintsColNum</span> = <span class="i">$This</span>->{<span class="w">DataColLabelToNumMap</span>}{<span class="i">$FingerprintsCol</span>}<span class="sc">;</span>
|
|
|
940 927 <span class="s">}</span>
|
|
|
941 928 <span class="s">}</span>
|
|
|
942 929
|
|
|
943 930 <span class="i">$This</span>->{<span class="w">ValidFingerprintsCol</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
944 931 <span class="i">$This</span>->{<span class="w">FingerprintsColNum</span>} = <span class="i">$FingerprintsColNum</span><span class="sc">;</span>
|
|
|
945 932
|
|
|
946 933 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
947 934 <span class="s">}</span>
|
|
|
948 935
|
|
|
949 936 <span class="c"># Validate fingerprints string mode information...</span>
|
|
|
950 937 <span class="c">#</span>
|
|
|
951 <a name="_ValidateReadFingerprintsStringMode-"></a> 938 <span class="k">sub </span><span class="m">_ValidateReadFingerprintsStringMode</span> <span class="s">{</span>
|
|
|
952 939 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
953 940 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsBitVectorStringMode</span><span class="cm">,</span> <span class="i">$FingerprintsVectorStringMode</span><span class="cm">,</span> <span class="i">$FirstFingerprintsStringType</span><span class="cm">,</span> <span class="i">$FirstFingerprintsStringDescription</span><span class="cm">,</span> <span class="i">$TextFile</span><span class="cm">,</span> <span class="i">$Line</span><span class="cm">,</span> <span class="i">$FingerprintsColNum</span><span class="cm">,</span> <span class="i">$InDelim</span><span class="cm">,</span> <span class="i">$FingerprintsType</span><span class="cm">,</span> <span class="i">$FingerprintsDescription</span><span class="cm">,</span> <span class="i">@LineWords</span><span class="s">)</span><span class="sc">;</span>
|
|
|
954 941
|
|
|
955 942 <span class="i">$This</span>->{<span class="w">ValidFingerprintsStringMode</span>} = <span class="n">0</span><span class="sc">;</span>
|
|
|
956 943
|
|
|
957 944 <span class="i">$This</span>->{<span class="w">FingerprintsBitVectorStringMode</span>} = <span class="n">0</span><span class="sc">;</span>
|
|
|
958 945 <span class="i">$This</span>->{<span class="w">FingerprintsVectorStringMode</span>} = <span class="n">0</span><span class="sc">;</span>
|
|
|
959 946
|
|
|
960 947 <span class="i">$This</span>->{<span class="w">FirstFingerprintsStringType</span>} = <span class="q">''</span><span class="sc">;</span>
|
|
|
961 948 <span class="i">$This</span>->{<span class="w">FirstFingerprintsStringDescription</span>} = <span class="q">''</span><span class="sc">;</span>
|
|
|
962 949
|
|
|
963 950 <span class="i">$FingerprintsBitVectorStringMode</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
964 951 <span class="i">$FingerprintsVectorStringMode</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
965 952
|
|
|
966 953 <span class="i">$FirstFingerprintsStringType</span> = <span class="q">''</span><span class="sc">;</span>
|
|
|
967 954 <span class="i">$FirstFingerprintsStringDescription</span> = <span class="q">''</span><span class="sc">;</span>
|
|
|
968 955
|
|
|
969 956 <span class="i">$TextFile</span> = <span class="i">$This</span>->{<span class="w">Name</span>}<span class="sc">;</span>
|
|
|
970 957
|
|
|
971 958 <span class="k">if</span> <span class="s">(</span>!<span class="k">open</span> <span class="w">TEXTFILE</span><span class="cm">,</span> <span class="q">"$TextFile"</span><span class="s">)</span> <span class="s">{</span>
|
|
|
972 959 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated: Couldn't open input text file $TextFile: $! ..."</span><span class="sc">;</span>
|
|
|
973 960 <span class="s">}</span>
|
|
|
974 961
|
|
|
975 962 <span class="c"># Skip column label line...</span>
|
|
|
976 963 <span class="i">$Line</span> = <span class="i">TextUtil::GetTextLine</span><span class="s">(</span>\<span class="i">*TEXTFILE</span><span class="s">)</span><span class="sc">;</span>
|
|
|
977 964
|
|
|
978 965 <span class="c"># First first fingerprints data line...</span>
|
|
|
979 966 <span class="i">$Line</span> = <span class="i">TextUtil::GetTextLine</span><span class="s">(</span>\<span class="i">*TEXTFILE</span><span class="s">)</span><span class="sc">;</span>
|
|
|
980 967
|
|
|
981 968 <span class="k">close</span> <span class="w">TEXTFILE</span><span class="sc">;</span>
|
|
|
982 969
|
|
|
983 970 <span class="c"># Get first fingerprints type and description...</span>
|
|
|
984 971 <span class="i">$InDelim</span> = <span class="i">$This</span>->{<span class="w">Delim</span>}<span class="sc">;</span>
|
|
|
985 972 <span class="i">@LineWords</span> = <span class="i">TextUtil::SplitWords</span><span class="s">(</span><span class="i">$Line</span><span class="cm">,</span> <span class="i">$InDelim</span><span class="s">)</span><span class="sc">;</span>
|
|
|
986 973
|
|
|
987 974 <span class="i">$FingerprintsColNum</span> = <span class="i">$This</span>->{<span class="w">FingerprintsColNum</span>}<span class="sc">;</span>
|
|
|
988 975
|
|
|
989 976 <span class="s">(</span><span class="i">$FingerprintsType</span><span class="cm">,</span> <span class="i">$FingerprintsDescription</span><span class="s">)</span> = <span class="i">Fingerprints::FingerprintsStringUtil::GetFingerprintsStringTypeAndDescription</span><span class="s">(</span><span class="i">$LineWords</span>[<span class="i">$FingerprintsColNum</span>]<span class="s">)</span><span class="sc">;</span>
|
|
|
990 977
|
|
|
991 978 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FingerprintsStringMode</span>} =~ <span class="q">/^FingerprintsBitVectorString$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
992 979 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsType</span> !~ <span class="q">/^FingerprintsBitVector$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
993 980 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ValidateReadFingerprintsStringMode: First fingerprint string data type, $FingerprintsType, doesn't match value, FingerprintsBitVectorString, specified using \"FingerprintsStringMode\"..."</span><span class="sc">;</span>
|
|
|
994 981 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
995 982 <span class="s">}</span>
|
|
|
996 983 <span class="i">$FingerprintsBitVectorStringMode</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
997 984 <span class="i">$FirstFingerprintsStringType</span> = <span class="q">'FingerprintsBitVector'</span><span class="sc">;</span>
|
|
|
998 985 <span class="i">$FirstFingerprintsStringDescription</span> = <span class="i">$FingerprintsDescription</span><span class="sc">;</span>
|
|
|
999 986 <span class="s">}</span>
|
|
|
1000 987 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FingerprintsStringMode</span>} =~ <span class="q">/^FingerprintsVectorString$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1001 988 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsType</span> !~ <span class="q">/^FingerprintsVector$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1002 989 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ValidateReadFingerprintsStringMode: First fingerprint string data type, $FingerprintsType, doesn't match value, FingerprintsVectorString, specified using \"FingerprintsStringMode\"..."</span><span class="sc">;</span>
|
|
|
1003 990 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1004 991 <span class="s">}</span>
|
|
|
1005 992 <span class="i">$FingerprintsVectorStringMode</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
1006 993 <span class="i">$FirstFingerprintsStringType</span> = <span class="q">'FingerprintsVector'</span><span class="sc">;</span>
|
|
|
1007 994 <span class="i">$FirstFingerprintsStringDescription</span> = <span class="i">$FingerprintsDescription</span><span class="sc">;</span>
|
|
|
1008 995 <span class="s">}</span>
|
|
|
1009 996 <span class="k">else</span> <span class="s">{</span>
|
|
|
1010 997 <span class="c"># AutoDetect mode...</span>
|
|
|
1011 998 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsType</span> =~ <span class="q">/^FingerprintsBitVector$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1012 999 <span class="i">$FingerprintsBitVectorStringMode</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
1013 1000 <span class="s">}</span>
|
|
|
1014 1001 <span class="k">elsif</span> <span class="s">(</span><span class="i">$FingerprintsType</span> =~ <span class="q">/^FingerprintsVector$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1015 1002 <span class="i">$FingerprintsVectorStringMode</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
1016 1003 <span class="s">}</span>
|
|
|
1017 1004 <span class="k">else</span> <span class="s">{</span>
|
|
|
1018 1005 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ValidateReadFingerprintsStringMode: First fingerprint string data type, $FingerprintsType, identified during, AutoDetect, value of \"FingerprintsStringMode\" is not valid; Supported fingerprints types: FingerprintBitVector or FingerprintsVector..."</span><span class="sc">;</span>
|
|
|
1019 1006 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1020 1007 <span class="s">}</span>
|
|
|
1021 1008 <span class="i">$FirstFingerprintsStringType</span> = <span class="i">$FingerprintsType</span><span class="sc">;</span>
|
|
|
1022 1009 <span class="i">$FirstFingerprintsStringDescription</span> = <span class="i">$FingerprintsDescription</span><span class="sc">;</span>
|
|
|
1023 1010 <span class="s">}</span>
|
|
|
1024 1011
|
|
|
1025 1012 <span class="i">$This</span>->{<span class="w">ValidFingerprintsStringMode</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
1026 1013
|
|
|
1027 1014 <span class="i">$This</span>->{<span class="w">FingerprintsBitVectorStringMode</span>} = <span class="i">$FingerprintsBitVectorStringMode</span><span class="sc">;</span>
|
|
|
1028 1015 <span class="i">$This</span>->{<span class="w">FingerprintsVectorStringMode</span>} = <span class="i">$FingerprintsVectorStringMode</span><span class="sc">;</span>
|
|
|
1029 1016
|
|
|
1030 1017 <span class="i">$This</span>->{<span class="w">FirstFingerprintsStringType</span>} = <span class="i">$FirstFingerprintsStringType</span><span class="sc">;</span>
|
|
|
1031 1018 <span class="i">$This</span>->{<span class="w">FirstFingerprintsStringDescription</span>} = <span class="i">$FirstFingerprintsStringDescription</span><span class="sc">;</span>
|
|
|
1032 1019
|
|
|
1033 1020 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
1034 1021 <span class="s">}</span>
|
|
|
1035 1022
|
|
|
1036 1023 <span class="c"># Write fingerprints string generated from specified fingerprints, fingerprints-bit vector, or</span>
|
|
|
1037 1024 <span class="c"># fingerprints vector object and other data to text file...</span>
|
|
|
1038 1025 <span class="c">#</span>
|
|
|
1039 <a name="WriteFingerprints-"></a>1026 <span class="k">sub </span><span class="m">WriteFingerprints</span> <span class="s">{</span>
|
|
|
1040 1027 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsObject</span><span class="cm">,</span> <span class="i">@DataColValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1041 1028
|
|
|
1042 1029 <span class="c"># Initialize data for current line...</span>
|
|
|
1043 1030 <span class="i">$This</span><span class="i">->_InitializeWriteDataLine</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1044 1031
|
|
|
1045 1032 <span class="c"># Set fingerprints object...</span>
|
|
|
1046 1033 <span class="i">$This</span>->{<span class="w">FingerprintsObject</span>} = <span class="i">$FingerprintsObject</span><span class="sc">;</span>
|
|
|
1047 1034
|
|
|
1048 1035 <span class="c"># Generate fingerprints string...</span>
|
|
|
1049 1036 <span class="i">$This</span><span class="i">->_GenerateFingerprintsString</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1050 1037
|
|
|
1051 1038 <span class="c"># Set data line words...</span>
|
|
|
1052 1039 <span class="i">$This</span><span class="i">->SetDataLineWords</span><span class="s">(</span><span class="i">@DataColValues</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1053 1040 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DataLineWords</span>}}<span class="cm">,</span> <span class="i">$This</span>->{<span class="w">FingerprintsString</span>}<span class="sc">;</span>
|
|
|
1054 1041
|
|
|
1055 1042 <span class="c"># Write data line..</span>
|
|
|
1056 1043 <span class="i">$This</span><span class="i">->_WriteDataLine</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1057 1044
|
|
|
1058 1045 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
1059 1046 <span class="s">}</span>
|
|
|
1060 1047
|
|
|
1061 1048 <span class="c"># Write fingerprints string and other data to text file...</span>
|
|
|
1062 1049 <span class="c">#</span>
|
|
|
1063 1050 <span class="c"># Note:</span>
|
|
|
1064 1051 <span class="c"># o FingerprintsStringMode, BitStringFormat, BitsOrder, VectorStringFormat values</span>
|
|
|
1065 1052 <span class="c"># are ignored during writing of fingerprints and it's written to the file as it is.</span>
|
|
|
1066 1053 <span class="c">#</span>
|
|
|
1067 1054 <span class="c">#</span>
|
|
|
1068 <a name="WriteFingerprintsString-"></a>1055 <span class="k">sub </span><span class="m">WriteFingerprintsString</span> <span class="s">{</span>
|
|
|
1069 1056 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsString</span><span class="cm">,</span> <span class="i">@DataColValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1070 1057
|
|
|
1071 1058 <span class="c"># Initialize data for current line...</span>
|
|
|
1072 1059 <span class="i">$This</span><span class="i">->_InitializeWriteDataLine</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1073 1060
|
|
|
1074 1061 <span class="c"># Set fingerprints string...</span>
|
|
|
1075 1062 <span class="i">$This</span>->{<span class="w">FingerprintsString</span>} = <span class="i">$FingerprintsString</span><span class="sc">;</span>
|
|
|
1076 1063
|
|
|
1077 1064 <span class="c"># Generate fingerprints object...</span>
|
|
|
1078 1065 <span class="i">$This</span><span class="i">->_GenerateFingerprintsObject</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1079 1066
|
|
|
1080 1067 <span class="c"># Set data line words...</span>
|
|
|
1081 1068 <span class="i">$This</span><span class="i">->SetDataLineWords</span><span class="s">(</span><span class="i">@DataColValues</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1082 1069 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DataLineWords</span>}}<span class="cm">,</span> <span class="i">$FingerprintsString</span><span class="sc">;</span>
|
|
|
1083 1070
|
|
|
1084 1071 <span class="c"># Write data line..</span>
|
|
|
1085 1072 <span class="i">$This</span><span class="i">->_WriteDataLine</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1086 1073
|
|
|
1087 1074 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
1088 1075 <span class="s">}</span>
|
|
|
1089 1076
|
|
|
1090 1077 <span class="c"># Initialize data line for reading...</span>
|
|
|
1091 1078 <span class="c">#</span>
|
|
|
1092 <a name="_InitializeWriteDataLine-"></a>1079 <span class="k">sub </span><span class="m">_InitializeWriteDataLine</span> <span class="s">{</span>
|
|
|
1093 1080 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1094 1081
|
|
|
1095 1082 <span class="i">$This</span>->{<span class="w">DataLine</span>} = <span class="k">undef</span><span class="sc">;</span>
|
|
|
1096 1083 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DataLineWords</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1097 1084
|
|
|
1098 1085 <span class="i">$This</span>->{<span class="w">FingerprintsObject</span>} = <span class="k">undef</span><span class="sc">;</span>
|
|
|
1099 1086 <span class="i">$This</span>->{<span class="w">FingerprintsString</span>} = <span class="k">undef</span><span class="sc">;</span>
|
|
|
1100 1087
|
|
|
1101 1088 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
1102 1089 <span class="s">}</span>
|
|
|
1103 1090
|
|
|
1104 1091 <span class="c"># Write fingerprints data line line...</span>
|
|
|
1105 1092 <span class="c">#</span>
|
|
|
1106 <a name="_WriteDataLine-"></a>1093 <span class="k">sub </span><span class="m">_WriteDataLine</span> <span class="s">{</span>
|
|
|
1107 1094 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1108 1095 <span class="k">my</span><span class="s">(</span><span class="i">$FileHandle</span><span class="cm">,</span> <span class="i">$Line</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1109 1096
|
|
|
1110 1097 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FirstDataLineIO</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1111 1098 <span class="i">$This</span><span class="i">->_ProcessFirstDataLineWrite</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1112 1099 <span class="s">}</span>
|
|
|
1113 1100
|
|
|
1114 1101 <span class="c"># Write out line words...</span>
|
|
|
1115 1102 <span class="i">$Line</span> = <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DataLineWords</span>}}<span class="cm">,</span> <span class="i">$This</span>->{<span class="w">Delim</span>}<span class="cm">,</span> <span class="i">$This</span>->{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
1116 1103
|
|
|
1117 1104 <span class="i">$This</span>->{<span class="w">LineNum</span>} += <span class="n">1</span><span class="sc">;</span>
|
|
|
1118 1105 <span class="i">$FileHandle</span> = <span class="i">$This</span>->{<span class="w">FileHandle</span>}<span class="sc">;</span>
|
|
|
1119 1106 <span class="k">print</span> <span class="i">$FileHandle</span> <span class="q">"$Line\n"</span><span class="sc">;</span>
|
|
|
1120 1107
|
|
|
1121 1108 <span class="i">$This</span>->{<span class="w">DataLine</span>} = <span class="i">$Line</span><span class="sc">;</span>
|
|
|
1122 1109
|
|
|
1123 1110 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
1124 1111 <span class="s">}</span>
|
|
|
1125 1112
|
|
|
1126 1113 <span class="c"># Process first write...</span>
|
|
|
1127 1114 <span class="c">#</span>
|
|
|
1128 <a name="_ProcessFirstDataLineWrite-"></a>1115 <span class="k">sub </span><span class="m">_ProcessFirstDataLineWrite</span> <span class="s">{</span>
|
|
|
1129 1116 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1130 1117 <span class="k">my</span><span class="s">(</span><span class="i">$Line</span><span class="cm">,</span> <span class="i">$FileHandle</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1131 1118
|
|
|
1132 1119 <span class="i">$This</span>->{<span class="w">FirstDataLineIO</span>} = <span class="n">0</span><span class="sc">;</span>
|
|
|
1133 1120
|
|
|
1134 1121 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetMode</span><span class="s">(</span><span class="s">)</span> =~ <span class="q">/^Write$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1135 1122 <span class="c"># Write out column label line...</span>
|
|
|
1136 1123 <span class="i">$Line</span> = <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DataColLabels</span>}}<span class="cm">,</span> <span class="i">$This</span>->{<span class="w">Delim</span>}<span class="cm">,</span> <span class="i">$This</span>->{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
1137 1124
|
|
|
1138 1125 <span class="i">$This</span>->{<span class="w">LineNum</span>} += <span class="n">1</span><span class="sc">;</span>
|
|
|
1139 1126 <span class="i">$FileHandle</span> = <span class="i">$This</span>->{<span class="w">FileHandle</span>}<span class="sc">;</span>
|
|
|
1140 1127 <span class="k">print</span> <span class="i">$FileHandle</span> <span class="q">"$Line\n"</span><span class="sc">;</span>
|
|
|
1141 1128 <span class="s">}</span>
|
|
|
1142 1129
|
|
|
1143 1130 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
1144 1131 <span class="s">}</span>
|
|
|
1145 1132
|
|
|
1146 1133 <span class="c"># Get ready for writing fingerprints text file...</span>
|
|
|
1147 1134 <span class="c">#</span>
|
|
|
1148 <a name="_PrepareForWritingFingerprintsTextFileData-"></a>1135 <span class="k">sub </span><span class="m">_PrepareForWritingFingerprintsTextFileData</span> <span class="s">{</span>
|
|
|
1149 1136 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1150 1137 <span class="k">my</span><span class="s">(</span><span class="i">$TextFile</span><span class="cm">,</span> <span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="cm">,</span> <span class="i">$OutDelim</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1151 1138
|
|
|
1152 1139 <span class="i">$TextFile</span> = <span class="i">$This</span>->{<span class="w">Name</span>}<span class="sc">;</span>
|
|
|
1153 1140 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">Overwrite</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1154 1141 <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="i">$TextFile</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1155 1142 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated: File, $TextFile, already exist. Use overwrite option..."</span><span class="sc">;</span>
|
|
|
1156 1143 <span class="s">}</span>
|
|
|
1157 1144 <span class="s">}</span>
|
|
|
1158 1145
|
|
|
1159 1146 <span class="c"># Set up delimiter for writing file...</span>
|
|
|
1160 1147
|
|
|
1161 1148 <span class="i">$FileDir</span> = <span class="q">""</span><span class="sc">;</span> <span class="i">$FileName</span> = <span class="q">""</span><span class="sc">;</span> <span class="i">$FileExt</span> = <span class="q">""</span><span class="sc">;</span>
|
|
|
1162 1149 <span class="s">(</span><span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="s">)</span> = <span class="i">FileUtil::ParseFileName</span><span class="s">(</span><span class="i">$TextFile</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1163 1150
|
|
|
1164 1151 <span class="i">$OutDelim</span> = <span class="s">(</span><span class="i">$FileExt</span> =~ <span class="q">/^tsv$/i</span><span class="s">)</span> ? <span class="q">"\t"</span> <span class="co">:</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">OutDelim</span>} =~ <span class="q">/semicolon/i</span> ? <span class="q">"\;"</span> <span class="co">:</span> <span class="q">"\,"</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1165 1152 <span class="i">$This</span>->{<span class="w">Delim</span>} = <span class="i">$OutDelim</span><span class="sc">;</span>
|
|
|
1166 1153
|
|
|
1167 1154 <span class="c"># Setup FingerprintsStringMode status...</span>
|
|
|
1168 1155
|
|
|
1169 1156 <span class="i">$This</span>->{<span class="w">FingerprintsBitVectorStringMode</span>} = <span class="n">0</span><span class="sc">;</span>
|
|
|
1170 1157 <span class="i">$This</span>->{<span class="w">FingerprintsVectorStringMode</span>} = <span class="n">0</span><span class="sc">;</span>
|
|
|
1171 1158 <span class="i">$This</span>->{<span class="w">ValidFingerprintsStringMode</span>} = <span class="n">0</span><span class="sc">;</span>
|
|
|
1172 1159
|
|
|
1173 1160 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FingerprintsStringMode</span>} =~ <span class="q">/^FingerprintsBitVectorString$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1174 1161 <span class="i">$This</span>->{<span class="w">FingerprintsBitVectorStringMode</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
1175 1162 <span class="s">}</span>
|
|
|
1176 1163 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FingerprintsStringMode</span>} =~ <span class="q">/^FingerprintsVectorString$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1177 1164 <span class="i">$This</span>->{<span class="w">FingerprintsVectorStringMode</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
1178 1165 <span class="s">}</span>
|
|
|
1179 1166
|
|
|
1180 1167 <span class="i">$This</span>->{<span class="w">ValidFingerprintsStringMode</span>} = <span class="s">(</span><span class="i">$This</span>->{<span class="w">FingerprintsBitVectorStringMode</span>} || <span class="i">$This</span>->{<span class="w">FingerprintsVectorStringMode</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1181 1168
|
|
|
1182 1169 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FingerprintsBitVectorStringMode</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1183 1170 <span class="i">$This</span><span class="i">->_SetDefaultBitStringFormat</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1184 1171 <span class="i">$This</span><span class="i">->_SetDefaultBitsOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1185 1172 <span class="s">}</span>
|
|
|
1186 1173 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FingerprintsVectorStringMode</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1187 1174 <span class="i">$This</span><span class="i">->_SetDefaultVectorStringFormat</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1188 1175 <span class="s">}</span>
|
|
|
1189 1176
|
|
|
1190 1177 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
1191 1178 <span class="s">}</span>
|
|
|
1192 1179
|
|
|
1193 1180 <span class="c"># Set default value for bit string format...</span>
|
|
|
1194 1181 <span class="c">#</span>
|
|
|
1195 <a name="_SetDefaultBitStringFormat-"></a>1182 <span class="k">sub </span><span class="m">_SetDefaultBitStringFormat</span> <span class="s">{</span>
|
|
|
1196 1183 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1197 1184
|
|
|
1198 1185 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">BitStringFormat</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1199 1186 <span class="i">$This</span>->{<span class="w">BitStringFormat</span>} = <span class="i">Fingerprints::FingerprintsStringUtil::GetDefaultBitStringFormat</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1200 1187 <span class="s">}</span>
|
|
|
1201 1188
|
|
|
1202 1189 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
1203 1190 <span class="s">}</span>
|
|
|
1204 1191
|
|
|
1205 1192 <span class="c"># Set default value for bit string format...</span>
|
|
|
1206 1193 <span class="c">#</span>
|
|
|
1207 <a name="_SetDefaultBitsOrder-"></a>1194 <span class="k">sub </span><span class="m">_SetDefaultBitsOrder</span> <span class="s">{</span>
|
|
|
1208 1195 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1209 1196
|
|
|
1210 1197 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">BitsOrder</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1211 1198 <span class="i">$This</span>->{<span class="w">BitsOrder</span>} = <span class="i">Fingerprints::FingerprintsStringUtil::GetDefaultBitsOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1212 1199 <span class="s">}</span>
|
|
|
1213 1200
|
|
|
1214 1201 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
1215 1202 <span class="s">}</span>
|
|
|
1216 1203
|
|
|
1217 1204 <span class="c"># Set default value for vector string format...</span>
|
|
|
1218 1205 <span class="c">#</span>
|
|
|
1219 <a name="_SetDefaultVectorStringFormat-"></a>1206 <span class="k">sub </span><span class="m">_SetDefaultVectorStringFormat</span> <span class="s">{</span>
|
|
|
1220 1207 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1221 1208
|
|
|
1222 1209 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">VectorStringFormat</span>} && <span class="i">$This</span>->{<span class="w">FingerprintsObject</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1223 1210 <span class="i">$This</span>->{<span class="w">VectorStringFormat</span>} = <span class="i">Fingerprints::FingerprintsStringUtil::GetDefaultVectorStringFormat</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">FingerprintsObject</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
1224 1211 <span class="s">}</span>
|
|
|
1225 1212
|
|
|
1226 1213 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
1227 1214 <span class="s">}</span>
|
|
|
1228 1215
|
|
|
1229 1216 <span class="c"># Generate fingerprints object using current fingerprints string...</span>
|
|
|
1230 1217 <span class="c">#</span>
|
|
|
1231 <a name="_GenerateFingerprintsObject-"></a>1218 <span class="k">sub </span><span class="m">_GenerateFingerprintsObject</span> <span class="s">{</span>
|
|
|
1232 1219 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1233 1220
|
|
|
1234 1221 <span class="i">$This</span>->{<span class="w">FingerprintsObject</span>} = <span class="k">undef</span><span class="sc">;</span>
|
|
|
1235 1222
|
|
|
1236 1223 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">FingerprintsString</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1237 1224 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
1238 1225 <span class="s">}</span>
|
|
|
1239 1226
|
|
|
1240 1227 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FingerprintsBitVectorStringMode</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1241 1228 <span class="i">$This</span>->{<span class="w">FingerprintsObject</span>} = <span class="i">Fingerprints::FingerprintsStringUtil::ParseFingerprintsBitVectorString</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">FingerprintsString</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
1242 1229 <span class="s">}</span>
|
|
|
1243 1230 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FingerprintsVectorStringMode</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1244 1231 <span class="i">$This</span>->{<span class="w">FingerprintsObject</span>} = <span class="i">Fingerprints::FingerprintsStringUtil::ParseFingerprintsVectorString</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">FingerprintsString</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
1245 1232 <span class="s">}</span>
|
|
|
1246 1233 <span class="k">else</span> <span class="s">{</span>
|
|
|
1247 1234 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
1248 1235 <span class="s">}</span>
|
|
|
1249 1236
|
|
|
1250 1237 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
1251 1238 <span class="s">}</span>
|
|
|
1252 1239
|
|
|
1253 1240 <span class="c"># Generate fingerprints string using current fingerprints object...</span>
|
|
|
1254 1241 <span class="c">#</span>
|
|
|
1255 <a name="_GenerateFingerprintsString-"></a>1242 <span class="k">sub </span><span class="m">_GenerateFingerprintsString</span> <span class="s">{</span>
|
|
|
1256 1243 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1257 1244
|
|
|
1258 1245 <span class="i">$This</span>->{<span class="w">FingerprintsString</span>} = <span class="q">''</span><span class="sc">;</span>
|
|
|
1259 1246
|
|
|
1260 1247 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">FingerprintsObject</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1261 1248 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
1262 1249 <span class="s">}</span>
|
|
|
1263 1250
|
|
|
1264 1251 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FingerprintsBitVectorStringMode</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1265 1252 <span class="i">$This</span>->{<span class="w">FingerprintsString</span>} = <span class="i">Fingerprints::FingerprintsStringUtil::GenerateFingerprintsString</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">FingerprintsObject</span>}<span class="cm">,</span> <span class="i">$This</span>->{<span class="w">BitStringFormat</span>}<span class="cm">,</span> <span class="i">$This</span>->{<span class="w">BitsOrder</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
1266 1253 <span class="s">}</span>
|
|
|
1267 1254 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FingerprintsVectorStringMode</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1268 1255 <span class="i">$This</span>->{<span class="w">FingerprintsString</span>} = <span class="i">Fingerprints::FingerprintsStringUtil::GenerateFingerprintsString</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">FingerprintsObject</span>}<span class="cm">,</span> <span class="i">$This</span>->{<span class="w">VectorStringFormat</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
1269 1256 <span class="s">}</span>
|
|
|
1270 1257
|
|
|
1271 1258 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
1272 1259 <span class="s">}</span>
|
|
|
1273 1260
|
|
|
1274 1261 <span class="c"># Is it a fingerprints file?</span>
|
|
|
1275 <a name="IsFingerprintsTextFile-"></a>1262 <span class="k">sub </span><span class="m">IsFingerprintsTextFile ($;$)</span> <span class="s">{</span>
|
|
|
1276 1263 <span class="k">my</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1277 1264 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$Status</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1278 1265
|
|
|
1279 1266 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">@_</span> == <span class="n">2</span><span class="s">)</span> && <span class="s">(</span><span class="i">_IsFingerprintsTextFileIO</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1280 1267 <span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FileName</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1281 1268 <span class="s">}</span>
|
|
|
1282 1269 <span class="k">else</span> <span class="s">{</span>
|
|
|
1283 1270 <span class="i">$FileName</span> = <span class="i">$FirstParameter</span><span class="sc">;</span>
|
|
|
1284 1271 <span class="s">}</span>
|
|
|
1285 1272
|
|
|
1286 1273 <span class="c"># Check file extension...</span>
|
|
|
1287 1274 <span class="i">$Status</span> = <span class="i">FileUtil::CheckFileType</span><span class="s">(</span><span class="i">$FileName</span><span class="cm">,</span> <span class="q">"csv tsv"</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1288 1275
|
|
|
1289 1276 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span>
|
|
|
1290 1277 <span class="s">}</span>
|
|
|
1291 1278
|
|
|
1292 1279 <span class="c"># Is it a FingerprintsTextFileIO object?</span>
|
|
|
1293 <a name="_IsFingerprintsTextFileIO-"></a>1280 <span class="k">sub </span><span class="m">_IsFingerprintsTextFileIO</span> <span class="s">{</span>
|
|
|
1294 1281 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1295 1282
|
|
|
1296 1283 <span class="k">return</span> <span class="s">(</span><span class="i">Scalar::Util::blessed</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> && <span class="i">$Object</span><span class="i">->isa</span><span class="s">(</span><span class="i">$ClassName</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>
|
|
|
1297 1284 <span class="s">}</span>
|
|
|
1298 1285
|
|
|
1299 <a name="EOF-"></a></pre>
|
|
|
1300 <p> </p>
|
|
|
1301 <br />
|
|
|
1302 <center>
|
|
|
1303 <img src="../../../images/h2o2.png">
|
|
|
1304 </center>
|
|
|
1305 </body>
|
|
|
1306 </html>
|
