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comparison mayachemtools/docs/modules/html/code/FingerprintsTextFileIO.html @ 0:73ae111cf86f draft
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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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| 1 <html> | |
| 2 <head> | |
| 3 <title>MayaChemTools:Code:FileIO::FingerprintsTextFileIO.pm</title> | |
| 4 <meta http-equiv="content-type" content="text/html;charset=utf-8"> | |
| 5 <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> | |
| 6 </head> | |
| 7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> | |
| 8 <br/> | |
| 9 <center> | |
| 10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> | |
| 11 </center> | |
| 12 <br/> | |
| 13 <pre> | |
| 14 <a name="package-FileIO::FingerprintsTextFileIO-"></a> 1 <span class="k">package </span><span class="i">FileIO::FingerprintsTextFileIO</span><span class="sc">;</span> | |
| 15 2 <span class="c">#</span> | |
| 16 3 <span class="c"># $RCSfile: FingerprintsTextFileIO.pm,v $</span> | |
| 17 4 <span class="c"># $Date: 2015/02/28 20:48:43 $</span> | |
| 18 5 <span class="c"># $Revision: 1.19 $</span> | |
| 19 6 <span class="c">#</span> | |
| 20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> | |
| 21 8 <span class="c">#</span> | |
| 22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> | |
| 23 10 <span class="c">#</span> | |
| 24 11 <span class="c"># This file is part of MayaChemTools.</span> | |
| 25 12 <span class="c">#</span> | |
| 26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> | |
| 27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> | |
| 28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> | |
| 29 16 <span class="c"># later version.</span> | |
| 30 17 <span class="c">#</span> | |
| 31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> | |
| 32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> | |
| 33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> | |
| 34 21 <span class="c"># details.</span> | |
| 35 22 <span class="c">#</span> | |
| 36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> | |
| 37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> | |
| 38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> | |
| 39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> | |
| 40 27 <span class="c">#</span> | |
| 41 28 | |
| 42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> | |
| 43 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span> | |
| 44 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span> | |
| 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> | |
| 46 33 <span class="k">use</span> <span class="w">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 47 34 <span class="k">use</span> <span class="w">FileUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 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> | |
| 49 36 <span class="k">use</span> <span class="w">FileIO::FileIO</span><span class="sc">;</span> | |
| 50 37 | |
| 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> | |
| 52 39 | |
| 53 40 <span class="i">@ISA</span> = <span class="q">qw(FileIO::FileIO Exporter)</span><span class="sc">;</span> | |
| 54 41 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> | |
| 55 42 <span class="i">@EXPORT_OK</span> = <span class="q">qw(IsFingerprintsTextFile)</span><span class="sc">;</span> | |
| 56 43 | |
| 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> | |
| 58 45 | |
| 59 46 <span class="c"># Setup class variables...</span> | |
| 60 47 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="sc">;</span> | |
| 61 48 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 62 49 | |
| 63 50 <span class="c"># Class constructor...</span> | |
| 64 <a name="new-"></a> 51 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> | |
| 65 52 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 66 53 | |
| 67 54 <span class="c"># Initialize object...</span> | |
| 68 55 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 69 56 <span class="k">bless</span> <span class="i">$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> | |
| 70 57 <span class="i">$This</span><span class="i">->_InitializeFingerprintsTextFileIO</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 71 58 | |
| 72 59 <span class="i">$This</span><span class="i">->_InitializeFingerprintsTextFileIOProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> | |
| 73 60 | |
| 74 61 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 75 62 <span class="s">}</span> | |
| 76 63 | |
| 77 64 <span class="c"># Initialize object data...</span> | |
| 78 65 <span class="c">#</span> | |
| 79 <a name="_InitializeFingerprintsTextFileIO-"></a> 66 <span class="k">sub </span><span class="m">_InitializeFingerprintsTextFileIO</span> <span class="s">{</span> | |
| 80 67 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 81 68 | |
| 82 69 <span class="c"># Fingerprints string data format during read/write...</span> | |
| 83 70 <span class="c">#</span> | |
| 84 71 <span class="c"># For file read:</span> | |
| 85 72 <span class="c">#</span> | |
| 86 73 <span class="c"># AutoDetect - automatically detect format of fingerprints string</span> | |
| 87 74 <span class="c"># FingerprintsBitVectorString - Bit vector fingerprints string format</span> | |
| 88 75 <span class="c"># FingerprintsVectorString - Vector fingerprints string format</span> | |
| 89 76 <span class="c">#</span> | |
| 90 77 <span class="c"># Default value: AutoDetect</span> | |
| 91 78 <span class="c">#</span> | |
| 92 79 <span class="c"># For file write:</span> | |
| 93 80 <span class="c">#</span> | |
| 94 81 <span class="c"># FingerprintsBitVectorString - Bit vector fingerprints string format</span> | |
| 95 82 <span class="c"># FingerprintsVectorString - Vector fingerprints string format</span> | |
| 96 83 <span class="c">#</span> | |
| 97 84 <span class="c"># Default value: undef</span> | |
| 98 85 <span class="c">#</span> | |
| 99 86 <span class="i">$This</span>->{<span class="w">FingerprintsStringMode</span>} = <span class="k">undef</span><span class="sc">;</span> | |
| 100 87 | |
| 101 88 <span class="c"># For file read:</span> | |
| 102 89 <span class="c">#</span> | |
| 103 90 <span class="c"># o Fingerprints bit-vector and vector object for current fingerprints string</span> | |
| 104 91 <span class="c">#</span> | |
| 105 92 <span class="c"># For file write:</span> | |
| 106 93 <span class="c">#</span> | |
| 107 94 <span class="c"># o Fingerprints bit-vector and vector object for current fingerprints string</span> | |
| 108 95 <span class="c"># o Any supported fingerprints object: PathLengthFingerprints, ExtendedConnectivity, and so on.</span> | |
| 109 96 <span class="c">#</span> | |
| 110 97 <span class="i">$This</span>->{<span class="w">FingerprintsObject</span>} = <span class="k">undef</span><span class="sc">;</span> | |
| 111 98 | |
| 112 99 <span class="c"># Fingepritns string for current line during read/write...</span> | |
| 113 100 <span class="i">$This</span>->{<span class="w">FingerprintsString</span>} = <span class="k">undef</span><span class="sc">;</span> | |
| 114 101 | |
| 115 102 <span class="c"># First data line read/write...</span> | |
| 116 103 <span class="i">$This</span>->{<span class="w">FirstDataLineIO</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 117 104 | |
| 118 105 <span class="c"># Current fingerprints string data line number during read/write...</span> | |
| 119 106 <span class="i">$This</span>->{<span class="w">LineNum</span>} = <span class="n">0</span><span class="sc">;</span> | |
| 120 107 | |
| 121 108 <span class="c"># Text line data during read/write...</span> | |
| 122 109 <span class="i">$This</span>->{<span class="w">DataLine</span>} = <span class="k">undef</span><span class="sc">;</span> | |
| 123 110 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DataLineWords</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 124 111 | |
| 125 112 <span class="c"># Text file column data during read/write...</span> | |
| 126 113 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DataColLabels</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 127 114 | |
| 128 115 <span class="c"># Text file delimiter during read/write...</span> | |
| 129 116 <span class="i">$This</span>->{<span class="w">Delim</span>} = <span class="q">''</span><span class="sc">;</span> | |
| 130 117 | |
| 131 118 <span class="c"># Initialize parameters for read...</span> | |
| 132 119 <span class="i">$This</span><span class="i">->_InitializeFingerprintsTextFileIORead</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 133 120 | |
| 134 121 <span class="c"># Initialize parameters for write...</span> | |
| 135 122 <span class="i">$This</span><span class="i">->_InitializeFingerprintsTextFileIOWrite</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 136 123 | |
| 137 124 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 138 125 <span class="s">}</span> | |
| 139 126 | |
| 140 127 <span class="c"># Initialize class ...</span> | |
| 141 <a name="_InitializeClass-"></a> 128 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> | |
| 142 129 <span class="c">#Class name...</span> | |
| 143 130 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> | |
| 144 131 | |
| 145 132 <span class="s">}</span> | |
| 146 133 | |
| 147 134 <span class="c"># Initialize object data for reading fingerprints text file...</span> | |
| 148 135 <span class="c">#</span> | |
| 149 <a name="_InitializeFingerprintsTextFileIORead-"></a> 136 <span class="k">sub </span><span class="m">_InitializeFingerprintsTextFileIORead</span> <span class="s">{</span> | |
| 150 137 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 151 138 | |
| 152 139 <span class="c"># Column ID specification for identification of comound ID or fingerints string</span> | |
| 153 140 <span class="c"># data column...</span> | |
| 154 141 <span class="c">#</span> | |
| 155 142 <span class="c"># ColNum - A valid column number</span> | |
| 156 143 <span class="c"># ColLabel - A valid column name</span> | |
| 157 144 <span class="c">#</span> | |
| 158 145 <span class="i">$This</span>->{<span class="w">ColMode</span>} = <span class="q">'ColNum'</span><span class="sc">;</span> | |
| 159 146 | |
| 160 147 <span class="c"># Fingerprints column to use for retrieving fingerprints string data...</span> | |
| 161 148 <span class="c">#</span> | |
| 162 149 <span class="c"># Value of AutoDetect implies use first column containing the word Fingerprints in its</span> | |
| 163 150 <span class="c"># column label to retrieve fingerprints string data. Othwewise, a valid column number</span> | |
| 164 151 <span class="c"># or column name must be specified based on the value of ColMode.</span> | |
| 165 152 <span class="c">#</span> | |
| 166 153 <span class="i">$This</span>->{<span class="w">FingerprintsCol</span>} = <span class="q">'AutoDetect'</span><span class="sc">;</span> | |
| 167 154 | |
| 168 155 <span class="c"># Compound ID column to use for retrieving compound IDs for fingerprints...</span> | |
| 169 156 <span class="c">#</span> | |
| 170 157 <span class="c"># Value of AutoDetect implies use first column containing the word CompoundID in its column</span> | |
| 171 158 <span class="c"># label to retrieve compound IDs or assign seqyentially generated compound IDs. Othwewise,</span> | |
| 172 159 <span class="c"># a valid column number or column name must be specified based on the value of ColMode.</span> | |
| 173 160 <span class="c">#</span> | |
| 174 161 <span class="i">$This</span>->{<span class="w">CompoundIDCol</span>} = <span class="q">'AutoDetect'</span><span class="sc">;</span> | |
| 175 162 | |
| 176 163 <span class="c"># A prefix string used for generating compound IDs like LabelPrefixString<Number> during</span> | |
| 177 164 <span class="c"># sequential generation of compound IDs. Default value, Cmpd, generates compound IDs</span> | |
| 178 165 <span class="c"># which look like like Cmpd<Number>.</span> | |
| 179 166 <span class="c">#</span> | |
| 180 167 <span class="i">$This</span>->{<span class="w">CompoundIDPrefix</span>} = <span class="q">'Cmpd'</span><span class="sc">;</span> | |
| 181 168 | |
| 182 169 <span class="c"># Input delimiter for fingerprints CSV text file. Possible values: comma, semicolon or tab. This</span> | |
| 183 170 <span class="c"># option is ignored for TSV text file and tab is used as the delimiter.</span> | |
| 184 171 <span class="c">#</span> | |
| 185 172 <span class="i">$This</span>->{<span class="w">InDelim</span>} = <span class="q">'comma'</span><span class="sc">;</span> | |
| 186 173 | |
| 187 174 <span class="c"># By default, the fingerprints data corresponding to FingerprintsCol is assumed to</span> | |
| 188 175 <span class="c"># be valid and no validation is performed before generating fingerprints objects...</span> | |
| 189 176 <span class="c">#</span> | |
| 190 177 <span class="i">$This</span>->{<span class="w">ValidateData</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 191 178 | |
| 192 179 <span class="c"># Level of detail to print during validation of data for invalid or missing data...</span> | |
| 193 180 <span class="i">$This</span>->{<span class="w">DetailLevel</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 194 181 | |
| 195 182 <span class="c"># Number of missing and invalid fingerprints string data lines...</span> | |
| 196 183 <span class="i">$This</span>->{<span class="w">NumOfLinesWithMissingData</span>} = <span class="n">0</span><span class="sc">;</span> | |
| 197 184 <span class="i">$This</span>->{<span class="w">NumOfLinesWithInvalidData</span>} = <span class="n">0</span><span class="sc">;</span> | |
| 198 185 | |
| 199 186 <span class="c"># Compound ID for current fingerprints string...</span> | |
| 200 187 <span class="i">$This</span>->{<span class="w">CompoundID</span>} = <span class="k">undef</span><span class="sc">;</span> | |
| 201 188 | |
| 202 189 <span class="c"># Status of data in fingerprints text file...</span> | |
| 203 190 <span class="i">$This</span>->{<span class="w">ValidFileData</span>} = <span class="n">0</span><span class="sc">;</span> | |
| 204 191 | |
| 205 192 <span class="i">$This</span>->{<span class="w">ValidCompoundIDCol</span>} = <span class="n">0</span><span class="sc">;</span> | |
| 206 193 <span class="i">$This</span>->{<span class="w">ValidFingerprintsCol</span>} = <span class="n">0</span><span class="sc">;</span> | |
| 207 194 | |
| 208 195 <span class="i">$This</span>->{<span class="w">ValidFingerprintsStringMode</span>} = <span class="n">0</span><span class="sc">;</span> | |
| 209 196 | |
| 210 197 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 211 198 <span class="s">}</span> | |
| 212 199 | |
| 213 200 <span class="c"># Initialize object data for writing fingerprints text file...</span> | |
| 214 201 <span class="c">#</span> | |
| 215 <a name="_InitializeFingerprintsTextFileIOWrite-"></a> 202 <span class="k">sub </span><span class="m">_InitializeFingerprintsTextFileIOWrite</span> <span class="s">{</span> | |
| 216 203 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 217 204 | |
| 218 205 <span class="c"># Fingerprints bit vector string format...</span> | |
| 219 206 <span class="c">#</span> | |
| 220 207 <span class="c"># Possible values: BinaryString or HexadecimalString [Default]</span> | |
| 221 208 <span class="c">#</span> | |
| 222 209 <span class="c"># Default BitStringFormat is set during first write using Fingerprints::FingerprintsStringUtil::GetDefaultBitStringFormat.</span> | |
| 223 210 <span class="c">#</span> | |
| 224 211 <span class="i">$This</span>->{<span class="w">BitStringFormat</span>} = <span class="k">undef</span><span class="sc">;</span> | |
| 225 212 | |
| 226 213 <span class="c"># Bits order in fingerprints bit vector string...</span> | |
| 227 214 <span class="c">#</span> | |
| 228 215 <span class="c"># Ascending - First bit in each byte as the lowest bit [Default]</span> | |
| 229 216 <span class="c"># Descending - First bit in each byte as the highest bit</span> | |
| 230 217 <span class="c">#</span> | |
| 231 218 <span class="c"># Default BitsOrder is set during first write using Fingerprints::FingerprintsStringUtil::GetDefaultBitsOrder.</span> | |
| 232 219 <span class="c">#</span> | |
| 233 220 <span class="i">$This</span>->{<span class="w">BitsOrder</span>} = <span class="k">undef</span><span class="sc">;</span> | |
| 234 221 | |
| 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> | |
| 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> | |
| 242 229 <span class="c">#</span> | |
| 243 230 <span class="i">$This</span>->{<span class="w">VectorStringFormat</span>} = <span class="k">undef</span><span class="sc">;</span> | |
| 244 231 | |
| 245 232 <span class="c"># Delimiter for output fingerprints CSV/TSV file. Possible values: comma, tab, semicolon. This</span> | |
| 246 233 <span class="c"># option is ignored for TSV text file and tab is used as the delimiter.</span> | |
| 247 234 <span class="c">#</span> | |
| 248 235 <span class="i">$This</span>->{<span class="w">OutDelim</span>} = <span class="q">'comma'</span><span class="sc">;</span> | |
| 249 236 | |
| 250 237 <span class="c"># Quotes around column values for output fingerprints CSV/TSV text file...</span> | |
| 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> | |
| 255 242 | |
| 256 243 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 257 244 <span class="s">}</span> | |
| 258 245 | |
| 259 246 <span class="c"># Initialize object values...</span> | |
| 260 <a name="_InitializeFingerprintsTextFileIOProperties-"></a> 247 <span class="k">sub </span><span class="m">_InitializeFingerprintsTextFileIOProperties</span> <span class="s">{</span> | |
| 261 248 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 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> | |
| 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> | |
| 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> |