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| author | deepakjadmin |
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| date | Thu, 15 Dec 2016 14:18:03 -0500 |
| parents | 73ae111cf86f |
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<html> <head> <title>MayaChemTools:Code:FileIO::FingerprintsTextFileIO.pm</title> <meta http-equiv="content-type" content="text/html;charset=utf-8"> <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> </head> <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> <br/> <center> <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> </center> <br/> <pre> <a name="package-FileIO::FingerprintsTextFileIO-"></a> 1 <span class="k">package </span><span class="i">FileIO::FingerprintsTextFileIO</span><span class="sc">;</span> 2 <span class="c">#</span> 3 <span class="c"># $RCSfile: FingerprintsTextFileIO.pm,v $</span> 4 <span class="c"># $Date: 2015/02/28 20:48:43 $</span> 5 <span class="c"># $Revision: 1.19 $</span> 6 <span class="c">#</span> 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> 8 <span class="c">#</span> 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> 10 <span class="c">#</span> 11 <span class="c"># This file is part of MayaChemTools.</span> 12 <span class="c">#</span> 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> 16 <span class="c"># later version.</span> 17 <span class="c">#</span> 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> 21 <span class="c"># details.</span> 22 <span class="c">#</span> 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> 27 <span class="c">#</span> 28 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span> 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span> 32 <span class="k">use</span> <span class="w">Scalar::Util</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 33 <span class="k">use</span> <span class="w">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 34 <span class="k">use</span> <span class="w">FileUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 35 <span class="k">use</span> <span class="w">Fingerprints::FingerprintsStringUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 36 <span class="k">use</span> <span class="w">FileIO::FileIO</span><span class="sc">;</span> 37 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> 39 40 <span class="i">@ISA</span> = <span class="q">qw(FileIO::FileIO Exporter)</span><span class="sc">;</span> 41 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> 42 <span class="i">@EXPORT_OK</span> = <span class="q">qw(IsFingerprintsTextFile)</span><span class="sc">;</span> 43 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> 45 46 <span class="c"># Setup class variables...</span> 47 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="sc">;</span> 48 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 49 50 <span class="c"># Class constructor...</span> <a name="new-"></a> 51 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> 52 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 53 54 <span class="c"># Initialize object...</span> 55 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 56 <span class="k">bless</span> <span class="i">$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> 57 <span class="i">$This</span><span class="i">->_InitializeFingerprintsTextFileIO</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 58 59 <span class="i">$This</span><span class="i">->_InitializeFingerprintsTextFileIOProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> 60 61 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 62 <span class="s">}</span> 63 64 <span class="c"># Initialize object data...</span> 65 <span class="c">#</span> <a name="_InitializeFingerprintsTextFileIO-"></a> 66 <span class="k">sub </span><span class="m">_InitializeFingerprintsTextFileIO</span> <span class="s">{</span> 67 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 68 69 <span class="c"># Fingerprints string data format during read/write...</span> 70 <span class="c">#</span> 71 <span class="c"># For file read:</span> 72 <span class="c">#</span> 73 <span class="c"># AutoDetect - automatically detect format of fingerprints string</span> 74 <span class="c"># FingerprintsBitVectorString - Bit vector fingerprints string format</span> 75 <span class="c"># FingerprintsVectorString - Vector fingerprints string format</span> 76 <span class="c">#</span> 77 <span class="c"># Default value: AutoDetect</span> 78 <span class="c">#</span> 79 <span class="c"># For file write:</span> 80 <span class="c">#</span> 81 <span class="c"># FingerprintsBitVectorString - Bit vector fingerprints string format</span> 82 <span class="c"># FingerprintsVectorString - Vector fingerprints string format</span> 83 <span class="c">#</span> 84 <span class="c"># Default value: undef</span> 85 <span class="c">#</span> 86 <span class="i">$This</span>->{<span class="w">FingerprintsStringMode</span>} = <span class="k">undef</span><span class="sc">;</span> 87 88 <span class="c"># For file read:</span> 89 <span class="c">#</span> 90 <span class="c"># o Fingerprints bit-vector and vector object for current fingerprints string</span> 91 <span class="c">#</span> 92 <span class="c"># For file write:</span> 93 <span class="c">#</span> 94 <span class="c"># o Fingerprints bit-vector and vector object for current fingerprints string</span> 95 <span class="c"># o Any supported fingerprints object: PathLengthFingerprints, ExtendedConnectivity, and so on.</span> 96 <span class="c">#</span> 97 <span class="i">$This</span>->{<span class="w">FingerprintsObject</span>} = <span class="k">undef</span><span class="sc">;</span> 98 99 <span class="c"># Fingepritns string for current line during read/write...</span> 100 <span class="i">$This</span>->{<span class="w">FingerprintsString</span>} = <span class="k">undef</span><span class="sc">;</span> 101 102 <span class="c"># First data line read/write...</span> 103 <span class="i">$This</span>->{<span class="w">FirstDataLineIO</span>} = <span class="n">1</span><span class="sc">;</span> 104 105 <span class="c"># Current fingerprints string data line number during read/write...</span> 106 <span class="i">$This</span>->{<span class="w">LineNum</span>} = <span class="n">0</span><span class="sc">;</span> 107 108 <span class="c"># Text line data during read/write...</span> 109 <span class="i">$This</span>->{<span class="w">DataLine</span>} = <span class="k">undef</span><span class="sc">;</span> 110 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DataLineWords</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 111 112 <span class="c"># Text file column data during read/write...</span> 113 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DataColLabels</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 114 115 <span class="c"># Text file delimiter during read/write...</span> 116 <span class="i">$This</span>->{<span class="w">Delim</span>} = <span class="q">''</span><span class="sc">;</span> 117 118 <span class="c"># Initialize parameters for read...</span> 119 <span class="i">$This</span><span class="i">->_InitializeFingerprintsTextFileIORead</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 120 121 <span class="c"># Initialize parameters for write...</span> 122 <span class="i">$This</span><span class="i">->_InitializeFingerprintsTextFileIOWrite</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 123 124 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 125 <span class="s">}</span> 126 127 <span class="c"># Initialize class ...</span> <a name="_InitializeClass-"></a> 128 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> 129 <span class="c">#Class name...</span> 130 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> 131 132 <span class="s">}</span> 133 134 <span class="c"># Initialize object data for reading fingerprints text file...</span> 135 <span class="c">#</span> <a name="_InitializeFingerprintsTextFileIORead-"></a> 136 <span class="k">sub </span><span class="m">_InitializeFingerprintsTextFileIORead</span> <span class="s">{</span> 137 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 138 139 <span class="c"># Column ID specification for identification of comound ID or fingerints string</span> 140 <span class="c"># data column...</span> 141 <span class="c">#</span> 142 <span class="c"># ColNum - A valid column number</span> 143 <span class="c"># ColLabel - A valid column name</span> 144 <span class="c">#</span> 145 <span class="i">$This</span>->{<span class="w">ColMode</span>} = <span class="q">'ColNum'</span><span class="sc">;</span> 146 147 <span class="c"># Fingerprints column to use for retrieving fingerprints string data...</span> 148 <span class="c">#</span> 149 <span class="c"># Value of AutoDetect implies use first column containing the word Fingerprints in its</span> 150 <span class="c"># column label to retrieve fingerprints string data. Othwewise, a valid column number</span> 151 <span class="c"># or column name must be specified based on the value of ColMode.</span> 152 <span class="c">#</span> 153 <span class="i">$This</span>->{<span class="w">FingerprintsCol</span>} = <span class="q">'AutoDetect'</span><span class="sc">;</span> 154 155 <span class="c"># Compound ID column to use for retrieving compound IDs for fingerprints...</span> 156 <span class="c">#</span> 157 <span class="c"># Value of AutoDetect implies use first column containing the word CompoundID in its column</span> 158 <span class="c"># label to retrieve compound IDs or assign seqyentially generated compound IDs. Othwewise,</span> 159 <span class="c"># a valid column number or column name must be specified based on the value of ColMode.</span> 160 <span class="c">#</span> 161 <span class="i">$This</span>->{<span class="w">CompoundIDCol</span>} = <span class="q">'AutoDetect'</span><span class="sc">;</span> 162 163 <span class="c"># A prefix string used for generating compound IDs like LabelPrefixString<Number> during</span> 164 <span class="c"># sequential generation of compound IDs. Default value, Cmpd, generates compound IDs</span> 165 <span class="c"># which look like like Cmpd<Number>.</span> 166 <span class="c">#</span> 167 <span class="i">$This</span>->{<span class="w">CompoundIDPrefix</span>} = <span class="q">'Cmpd'</span><span class="sc">;</span> 168 169 <span class="c"># Input delimiter for fingerprints CSV text file. Possible values: comma, semicolon or tab. This</span> 170 <span class="c"># option is ignored for TSV text file and tab is used as the delimiter.</span> 171 <span class="c">#</span> 172 <span class="i">$This</span>->{<span class="w">InDelim</span>} = <span class="q">'comma'</span><span class="sc">;</span> 173 174 <span class="c"># By default, the fingerprints data corresponding to FingerprintsCol is assumed to</span> 175 <span class="c"># be valid and no validation is performed before generating fingerprints objects...</span> 176 <span class="c">#</span> 177 <span class="i">$This</span>->{<span class="w">ValidateData</span>} = <span class="n">1</span><span class="sc">;</span> 178 179 <span class="c"># Level of detail to print during validation of data for invalid or missing data...</span> 180 <span class="i">$This</span>->{<span class="w">DetailLevel</span>} = <span class="n">1</span><span class="sc">;</span> 181 182 <span class="c"># Number of missing and invalid fingerprints string data lines...</span> 183 <span class="i">$This</span>->{<span class="w">NumOfLinesWithMissingData</span>} = <span class="n">0</span><span class="sc">;</span> 184 <span class="i">$This</span>->{<span class="w">NumOfLinesWithInvalidData</span>} = <span class="n">0</span><span class="sc">;</span> 185 186 <span class="c"># Compound ID for current fingerprints string...</span> 187 <span class="i">$This</span>->{<span class="w">CompoundID</span>} = <span class="k">undef</span><span class="sc">;</span> 188 189 <span class="c"># Status of data in fingerprints text file...</span> 190 <span class="i">$This</span>->{<span class="w">ValidFileData</span>} = <span class="n">0</span><span class="sc">;</span> 191 192 <span class="i">$This</span>->{<span class="w">ValidCompoundIDCol</span>} = <span class="n">0</span><span class="sc">;</span> 193 <span class="i">$This</span>->{<span class="w">ValidFingerprintsCol</span>} = <span class="n">0</span><span class="sc">;</span> 194 195 <span class="i">$This</span>->{<span class="w">ValidFingerprintsStringMode</span>} = <span class="n">0</span><span class="sc">;</span> 196 197 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 198 <span class="s">}</span> 199 200 <span class="c"># Initialize object data for writing fingerprints text file...</span> 201 <span class="c">#</span> <a name="_InitializeFingerprintsTextFileIOWrite-"></a> 202 <span class="k">sub </span><span class="m">_InitializeFingerprintsTextFileIOWrite</span> <span class="s">{</span> 203 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 204 205 <span class="c"># Fingerprints bit vector string format...</span> 206 <span class="c">#</span> 207 <span class="c"># Possible values: BinaryString or HexadecimalString [Default]</span> 208 <span class="c">#</span> 209 <span class="c"># Default BitStringFormat is set during first write using Fingerprints::FingerprintsStringUtil::GetDefaultBitStringFormat.</span> 210 <span class="c">#</span> 211 <span class="i">$This</span>->{<span class="w">BitStringFormat</span>} = <span class="k">undef</span><span class="sc">;</span> 212 213 <span class="c"># Bits order in fingerprints bit vector string...</span> 214 <span class="c">#</span> 215 <span class="c"># Ascending - First bit in each byte as the lowest bit [Default]</span> 216 <span class="c"># Descending - First bit in each byte as the highest bit</span> 217 <span class="c">#</span> 218 <span class="c"># Default BitsOrder is set during first write using Fingerprints::FingerprintsStringUtil::GetDefaultBitsOrder.</span> 219 <span class="c">#</span> 220 <span class="i">$This</span>->{<span class="w">BitsOrder</span>} = <span class="k">undef</span><span class="sc">;</span> 221 222 <span class="c"># Fingerprints vector string format...</span> 223 <span class="c">#</span> 224 <span class="c"># Possible values: IDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString, ValuesAndIDsPairsString, ValuesString</span> 225 <span class="c">#</span> 226 <span class="c"># Default VectorStringFormat is set during first write using Fingerprints::FingerprintsStringUtil::GetDefaultVectorStringFormat.</span> 227 <span class="c"># For fingerprints vector object containing vector NumericalValues, it corresponds to IDsAndValuesString; othwerwise,</span> 228 <span class="c"># it's set to ValuesString.</span> 229 <span class="c">#</span> 230 <span class="i">$This</span>->{<span class="w">VectorStringFormat</span>} = <span class="k">undef</span><span class="sc">;</span> 231 232 <span class="c"># Delimiter for output fingerprints CSV/TSV file. Possible values: comma, tab, semicolon. This</span> 233 <span class="c"># option is ignored for TSV text file and tab is used as the delimiter.</span> 234 <span class="c">#</span> 235 <span class="i">$This</span>->{<span class="w">OutDelim</span>} = <span class="q">'comma'</span><span class="sc">;</span> 236 237 <span class="c"># Quotes around column values for output fingerprints CSV/TSV text file...</span> 238 <span class="i">$This</span>->{<span class="w">OutQuote</span>} = <span class="n">1</span><span class="sc">;</span> 239 240 <span class="c"># Overwriting existing file...</span> 241 <span class="i">$This</span>->{<span class="w">Overwrite</span>} = <span class="n">0</span><span class="sc">;</span> 242 243 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 244 <span class="s">}</span> 245 246 <span class="c"># Initialize object values...</span> <a name="_InitializeFingerprintsTextFileIOProperties-"></a> 247 <span class="k">sub </span><span class="m">_InitializeFingerprintsTextFileIOProperties</span> <span class="s">{</span> 248 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 249 250 <span class="c"># All other property names and values along with all Set/Get<PropertyName> methods</span> 251 <span class="c"># are implemented on-demand using ObjectProperty class.</span> 252 253 <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">$MethodName</span><span class="s">)</span><span class="sc">;</span> 254 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span> 255 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> 256 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> 257 <span class="s">}</span> 258 259 <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> 260 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying file name..."</span><span class="sc">;</span> 261 <span class="s">}</span> 262 263 <span class="c"># Make sure it's a fingerprints file...</span> 264 <span class="i">$Name</span> = <span class="i">$NamesAndValues</span>{<span class="w">Name</span>}<span class="sc">;</span> 265 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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> 266 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated: File, $Name, doesn't appear to be fingerprints format..."</span><span class="sc">;</span> 267 <span class="s">}</span> 268 269 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetMode</span><span class="s">(</span><span class="s">)</span> =~ <span class="q">/^Read$/i</span><span class="s">)</span> <span class="s">{</span> 270 <span class="i">$This</span><span class="i">->_InitializeFingerprintsTextFileIOReadProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> 271 <span class="s">}</span> 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> 273 <span class="i">$This</span><span class="i">->_InitializeFingerprintsTextFileIOWriteProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> 274 <span class="s">}</span> 275 276 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 277 <span class="s">}</span> 278 279 <span class="c"># Initialize object properties for reading fingerprints text file...</span> 280 <span class="c">#</span> <a name="_InitializeFingerprintsTextFileIOReadProperties-"></a> 281 <span class="k">sub </span><span class="m">_InitializeFingerprintsTextFileIOReadProperties</span> <span class="s">{</span> 282 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 283 284 <span class="c"># Set default value for FingerprintsStringMode...</span> 285 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">FingerprintsStringMode</span>}<span class="s">)</span> <span class="s">{</span> 286 <span class="i">$This</span>->{<span class="w">FingerprintsStringMode</span>} = <span class="q">'AutoDetect'</span><span class="sc">;</span> 287 <span class="s">}</span> 288 289 <span class="i">$This</span><span class="i">->_PrepareForReadingFingerprintsTextFileData</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 290 291 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 292 <span class="s">}</span> 293 294 <span class="c"># Initialize object properties for writing fingerprints text file...</span> 295 <span class="c">#</span> <a name="_InitializeFingerprintsTextFileIOWriteProperties-"></a> 296 <span class="k">sub </span><span class="m">_InitializeFingerprintsTextFileIOWriteProperties</span> <span class="s">{</span> 297 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 298 299 <span class="c"># Check FingerprintsStringMode value...</span> 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> 301 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying FingerprintsStringMode..."</span><span class="sc">;</span> 302 <span class="s">}</span> 303 304 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FingerprintsStringMode</span>} !~ <span class="q">/^(FingerprintsBitVectorString|FingerprintsVectorString)$/i</span><span class="s">)</span> <span class="s">{</span> 305 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->: Object can't be instantiated: FingerprintsStringMode value, $This->{FingerprintsStringMode}, is not valid; Supported values for write/append: FingerprintsBitVectorString or FingerprintsVectorString..."</span><span class="sc">;</span> 306 <span class="s">}</span> 307 308 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">DataColLabels</span>}<span class="s">)</span> <span class="s">{</span> 309 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying DataColLabels..."</span><span class="sc">;</span> 310 <span class="s">}</span> 311 312 <span class="k">if</span> <span class="s">(</span><span class="i">$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> 313 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->: Object can't be instantiated: The value specified, $This->{OutQuote}, using \"OutQuote\" is not allowed with semicolon value of \"OutDelim\": Fingerprints string use semicolon as delimiter for various data fields and must be quoted.\n"</span><span class="sc">;</span> 314 <span class="s">}</span> 315 316 <span class="i">$This</span><span class="i">->_PrepareForWritingFingerprintsTextFileData</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 317 318 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 319 <span class="s">}</span> 320 321 <span class="c"># Set FingerprintsStringMode...</span> 322 <span class="c">#</span> <a name="SetFingerprintsStringMode-"></a> 323 <span class="k">sub </span><span class="m">SetFingerprintsStringMode</span> <span class="s">{</span> 324 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 325 326 <span class="c"># AutoDetect - automatically detect format of fingerprints string</span> 327 <span class="c"># FingerprintsBitVectorString - Bit vector fingerprints string format</span> 328 <span class="c"># FingerprintsVectorString - Vector fingerprints string format</span> 329 330 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(AutoDetect|FingerprintsBitVectorString|FingerprintsVectorString)$/i</span><span class="s">)</span> <span class="s">{</span> 331 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFingerprintsStringMode: FingerprintsStringMode value, $Value, is not valid; Supported values: AutoDetect, FingerprintsBitVectorString or FingerprintsVectorString..."</span><span class="sc">;</span> 332 <span class="s">}</span> 333 334 <span class="i">$This</span>->{<span class="w">FingerprintsStringMode</span>} = <span class="i">$Value</span><span class="sc">;</span> 335 336 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 337 <span class="s">}</span> 338 339 <span class="c"># Set ColMode...</span> 340 <span class="c">#</span> <a name="SetColMode-"></a> 341 <span class="k">sub </span><span class="m">SetColMode</span> <span class="s">{</span> 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> 343 344 <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> 345 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetColMode: ColMode value, $Value, is not valid; Supported values: ColNum or ColLabel..."</span><span class="sc">;</span> 346 <span class="s">}</span> 347 348 <span class="i">$This</span>->{<span class="w">ColMode</span>} = <span class="i">$Value</span><span class="sc">;</span> 349 350 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 351 <span class="s">}</span> 352 353 <span class="c"># Set InDelim...</span> 354 <span class="c">#</span> <a name="SetInDelim-"></a> 355 <span class="k">sub </span><span class="m">SetInDelim</span> <span class="s">{</span> 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> 357 358 <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> 359 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetInDelim: InDelim value, $Value, is not valid; Supported values: comma, semicolon, or tab..."</span><span class="sc">;</span> 360 <span class="s">}</span> 361 362 <span class="i">$This</span>->{<span class="w">InDelim</span>} = <span class="i">$Value</span><span class="sc">;</span> 363 364 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 365 <span class="s">}</span> 366 367 <span class="c"># Set DetailLevel...</span> 368 <span class="c">#</span> <a name="SetDetailLevel-"></a> 369 <span class="k">sub </span><span class="m">SetDetailLevel</span> <span class="s">{</span> 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> 371 372 <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> 373 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetDetailLevel: DetailLevel value, $Value, is not valid; Supported values: > 0..."</span><span class="sc">;</span> 374 <span class="s">}</span> 375 376 <span class="i">$This</span>->{<span class="w">DetailLevel</span>} = <span class="i">$Value</span><span class="sc">;</span> 377 378 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 379 <span class="s">}</span> 380 381 <span class="c"># Set BitStringFormat...</span> 382 <span class="c">#</span> <a name="SetBitStringFormat-"></a> 383 <span class="k">sub </span><span class="m">SetBitStringFormat</span> <span class="s">{</span> 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> 385 386 <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> 387 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetBitStringFormat: BitStringFormat value, $Value, is not valid; Supported values: BinaryString or HexadecimalString..."</span><span class="sc">;</span> 388 <span class="s">}</span> 389 390 <span class="i">$This</span>->{<span class="w">BitStringFormat</span>} = <span class="i">$Value</span><span class="sc">;</span> 391 392 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 393 <span class="s">}</span> 394 395 <span class="c"># Set BitsOrder...</span> 396 <span class="c">#</span> <a name="SetBitsOrder-"></a> 397 <span class="k">sub </span><span class="m">SetBitsOrder</span> <span class="s">{</span> 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> 399 400 <span class="c"># Ascending - First bit in each byte as the lowest bit</span> 401 <span class="c"># Descending - First bit in each byte as the highest bit</span> 402 <span class="c">#</span> 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> 404 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetBitsOrder: FingerprintsStringMode value, $Value, is not valid; Supported values: Ascending or Descending..."</span><span class="sc">;</span> 405 <span class="s">}</span> 406 407 <span class="i">$This</span>->{<span class="w">BitsOrder</span>} = <span class="i">$Value</span><span class="sc">;</span> 408 409 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 410 <span class="s">}</span> 411 412 <span class="c"># Set VectorStringFormat...</span> 413 <span class="c">#</span> <a name="SetVectorStringFormat-"></a> 414 <span class="k">sub </span><span class="m">SetVectorStringFormat</span> <span class="s">{</span> 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> 416 417 <span class="c"># Possible values: IDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString, ValuesAndIDsPairsString, ValuesString</span> 418 419 <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> 420 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetVectorStringFormat: FingerprintsStringMode value, $Value, is not valid; Supported values: IDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString, ValuesAndIDsPairsString, or ValuesString..."</span><span class="sc">;</span> 421 <span class="s">}</span> 422 423 <span class="i">$This</span>->{<span class="w">VectorStringFormat</span>} = <span class="i">$Value</span><span class="sc">;</span> 424 425 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 426 <span class="s">}</span> 427 428 <span class="c"># Set FingerprintsStringMode...</span> 429 <span class="c">#</span> <a name="SetOutDelim-"></a> 430 <span class="k">sub </span><span class="m">SetOutDelim</span> <span class="s">{</span> 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> 432 433 <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> 434 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetOutDelim: OutDelim value, $Value, is not valid; Supported values: comma, tab or semicolon..."</span><span class="sc">;</span> 435 <span class="s">}</span> 436 437 <span class="i">$This</span>->{<span class="w">OutDelim</span>} = <span class="i">$Value</span><span class="sc">;</span> 438 439 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 440 <span class="s">}</span> 441 442 <span class="c"># Set DataColLabels...</span> 443 <span class="c">#</span> 444 <span class="c"># Set output data column labels using:</span> 445 <span class="c"># o List of column labels</span> 446 <span class="c"># o Reference to an list of column labels</span> 447 <span class="c">#</span> <a name="SetDataColLabels-"></a> 448 <span class="k">sub </span><span class="m">SetDataColLabels</span> <span class="s">{</span> 449 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 450 <span class="k">my</span><span class="s">(</span><span class="i">$FirstValue</span><span class="cm">,</span> <span class="i">$TypeOfFirstValue</span><span class="s">)</span><span class="sc">;</span> 451 452 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span> 453 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_SetDataColLabels: No data column labels specified..."</span><span class="sc">;</span> 454 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 455 <span class="s">}</span> 456 457 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DataColLabels</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 458 459 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span> 460 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span> 461 462 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span> 463 <span class="c"># Initialize using array refernce...</span> 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> 465 <span class="s">}</span> 466 <span class="k">else</span> <span class="s">{</span> 467 <span class="c"># It's a list of values...</span> 468 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DataColLabels</span>}}<span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span> 469 <span class="s">}</span> 470 471 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 472 <span class="s">}</span> 473 474 <span class="c"># Get column labels or number of column labels in first text line...</span> 475 <span class="c">#</span> <a name="GetDataColLabels-"></a> 476 <span class="k">sub </span><span class="m">GetDataColLabels</span> <span class="s">{</span> 477 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 478 479 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DataColLabels</span>}} <span class="co">:</span> <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DataColLabels</span>}}<span class="sc">;</span> 480 <span class="s">}</span> 481 482 <span class="c"># Get words or number of words in current data line...</span> 483 <span class="c">#</span> <a name="GetDataLineWords-"></a> 484 <span class="k">sub </span><span class="m">GetDataLineWords</span> <span class="s">{</span> 485 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 486 487 <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> 488 <span class="s">}</span> 489 490 <span class="c"># Set DataLineWords...</span> 491 <span class="c">#</span> 492 <span class="c"># Set data line words using:</span> 493 <span class="c"># o List of line words</span> 494 <span class="c"># o Reference to an list of line words</span> 495 <span class="c">#</span> <a name="SetDataLineWords-"></a> 496 <span class="k">sub </span><span class="m">SetDataLineWords</span> <span class="s">{</span> 497 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 498 <span class="k">my</span><span class="s">(</span><span class="i">$FirstValue</span><span class="cm">,</span> <span class="i">$TypeOfFirstValue</span><span class="s">)</span><span class="sc">;</span> 499 500 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span> 501 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetDataLineWords: No line words specified..."</span><span class="sc">;</span> 502 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 503 <span class="s">}</span> 504 505 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DataLineWords</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 506 507 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span> 508 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span> 509 510 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span> 511 <span class="c"># Initialize using array refernce...</span> 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> 513 <span class="s">}</span> 514 <span class="k">else</span> <span class="s">{</span> 515 <span class="c"># It's a list of values...</span> 516 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DataLineWords</span>}}<span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span> 517 <span class="s">}</span> 518 519 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 520 <span class="s">}</span> 521 522 <span class="c"># Get fingerprints object for current data line using fingerprints, fingerprints bit-vector</span> 523 <span class="c"># fingerprints vector object. Fingerprints object correspond to any of supported fingerprints</span> 524 <span class="c"># objects such as PathLengthFingerprints, ExtendedConnectivity, and so on.</span> 525 <span class="c">#</span> <a name="GetFingerprints-"></a> 526 <span class="k">sub </span><span class="m">GetFingerprints</span> <span class="s">{</span> 527 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 528 529 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">FingerprintsObject</span>}<span class="sc">;</span> 530 <span class="s">}</span> 531 532 <span class="c"># Set fingerprints object for current data line...</span> 533 <span class="c">#</span> <a name="SetFingerprints-"></a> 534 <span class="k">sub </span><span class="m">SetFingerprints</span> <span class="s">{</span> 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> 536 537 <span class="i">$This</span>->{<span class="w">FingerprintsObject</span>} = <span class="i">$FingerprintsObject</span><span class="sc">;</span> 538 539 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 540 <span class="s">}</span> 541 542 <span class="c"># Get fingerprints string for current data line...</span> 543 <span class="c">#</span> <a name="GetFingerprintsString-"></a> 544 <span class="k">sub </span><span class="m">GetFingerprintsString</span> <span class="s">{</span> 545 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 546 547 <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> 548 <span class="s">}</span> 549 550 <span class="c"># Set fingerprints string for current data line...</span> 551 <span class="c">#</span> <a name="SetFingerprintsString-"></a> 552 <span class="k">sub </span><span class="m">SetFingerprintsString</span> <span class="s">{</span> 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> 554 555 <span class="i">$This</span>->{<span class="w">FingerprintsString</span>} = <span class="i">$FingerprintsString</span><span class="sc">;</span> 556 557 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 558 <span class="s">}</span> 559 560 <span class="c"># Does fingerprints text file contain valid data?</span> 561 <span class="c">#</span> <a name="IsFingerprintsFileDataValid-"></a> 562 <span class="k">sub </span><span class="m">IsFingerprintsFileDataValid</span> <span class="s">{</span> 563 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 564 565 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">ValidFileData</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 566 <span class="s">}</span> 567 568 <span class="c"># Does current data line contains valid fingerprints object data?</span> 569 <span class="c">#</span> <a name="IsFingerprintsDataValid-"></a> 570 <span class="k">sub </span><span class="m">IsFingerprintsDataValid</span> <span class="s">{</span> 571 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 572 573 <span class="k">return</span> <span class="k">defined</span> <span class="i">$This</span>->{<span class="w">FingerprintsObject</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 574 <span class="s">}</span> 575 576 <span class="c"># Read next available fingerprints line, process it and generate appropriate fingerprints</span> 577 <span class="c"># objects...</span> 578 <span class="c">#</span> <a name="Read-"></a> 579 <span class="k">sub </span><span class="m">Read</span> <span class="s">{</span> 580 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 581 582 <span class="c"># Read data line...</span> 583 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_ReadDataLine</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 584 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 585 <span class="s">}</span> 586 587 <span class="c"># No need to process invalid text file with invalid data...</span> 588 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">ValidFileData</span>}<span class="s">)</span> <span class="s">{</span> 589 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">ValidateData</span>}<span class="s">)</span> <span class="s">{</span> 590 <span class="i">$This</span>->{<span class="w">NumOfLinesWithMissingData</span>} += <span class="n">1</span><span class="sc">;</span> 591 <span class="s">}</span> 592 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 593 <span class="s">}</span> 594 595 <span class="c"># Perform data validation...</span> 596 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">ValidateData</span>}<span class="s">)</span> <span class="s">{</span> 597 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_ValidateReadDataLine</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 598 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 599 <span class="s">}</span> 600 <span class="s">}</span> 601 602 <span class="c"># Setup fingerprints string after checking again to handle problematic data for</span> 603 <span class="c"># non-validated data lines...</span> 604 <span class="c">#</span> 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">$This</span>->{<span class="w">DataLineWords</span>}}<span class="s">)</span> <span class="s">{</span> 606 <span class="i">$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> 607 <span class="s">}</span> 608 609 <span class="c"># Generate fingeprints object...</span> 610 <span class="i">$This</span><span class="i">->_GenerateFingerprintsObject</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 611 612 <span class="c"># Setup fingerprints compound ID for fingerprints string...</span> 613 <span class="i">$This</span><span class="i">->_GenerateCompoundID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 614 615 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 616 <span class="s">}</span> 617 618 <span class="c"># Read next available fingerprints line, process it and generate appropriate fingerprints</span> 619 <span class="c"># objects...</span> 620 <span class="c">#</span> <a name="Next-"></a> 621 <span class="k">sub </span><span class="m">Next</span> <span class="s">{</span> 622 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 623 624 <span class="k">return</span> <span class="i">$This</span><span class="i">->Read</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 625 <span class="s">}</span> 626 627 <span class="c"># Read fingerprints data line line...</span> 628 <span class="c">#</span> <a name="_ReadDataLine-"></a> 629 <span class="k">sub </span><span class="m">_ReadDataLine</span> <span class="s">{</span> 630 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 631 632 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FirstDataLineIO</span>}<span class="s">)</span> <span class="s">{</span> 633 <span class="i">$This</span><span class="i">->_ProcessFirstDataLineRead</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 634 <span class="s">}</span> 635 636 <span class="c"># Initialize data for current line...</span> 637 <span class="i">$This</span><span class="i">->_InitializeReadDataLine</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 638 639 <span class="c"># Get next data line...</span> 640 <span class="i">$This</span>->{<span class="w">DataLine</span>} = <span class="i">TextUtil::GetTextLine</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">FileHandle</span>}<span class="s">)</span><span class="sc">;</span> 641 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">DataLine</span>}<span class="s">)</span> <span class="s">{</span> 642 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 643 <span class="s">}</span> 644 645 <span class="c"># Get line words...</span> 646 <span class="i">$This</span>->{<span class="w">LineNum</span>} += <span class="n">1</span><span class="sc">;</span> 647 <span class="i">@</span>{<span class="i">$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> 648 649 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 650 <span class="s">}</span> 651 652 <span class="c"># Initialize data line for reading...</span> 653 <span class="c">#</span> <a name="_InitializeReadDataLine-"></a> 654 <span class="k">sub </span><span class="m">_InitializeReadDataLine</span> <span class="s">{</span> 655 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 656 657 <span class="i">$This</span>->{<span class="w">CompoundID</span>} = <span class="k">undef</span><span class="sc">;</span> 658 659 <span class="i">$This</span>->{<span class="w">DataLine</span>} = <span class="k">undef</span><span class="sc">;</span> 660 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DataLineWords</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 661 662 <span class="i">$This</span>->{<span class="w">FingerprintsObject</span>} = <span class="k">undef</span><span class="sc">;</span> 663 <span class="i">$This</span>->{<span class="w">FingerprintsString</span>} = <span class="k">undef</span><span class="sc">;</span> 664 665 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 666 <span class="s">}</span> 667 668 <span class="c"># Validate fingerprints string data line...</span> 669 <span class="c">#</span> <a name="_ValidateReadDataLine-"></a> 670 <span class="k">sub </span><span class="m">_ValidateReadDataLine</span> <span class="s">{</span> 671 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 672 673 <span class="c"># Check for missing data...</span> 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">$This</span>->{<span class="w">DataLineWords</span>}}<span class="s">)</span> <span class="s">{</span> 675 <span class="c"># Missing data...</span> 676 <span class="i">$This</span>->{<span class="w">NumOfLinesWithMissingData</span>} += <span class="n">1</span><span class="sc">;</span> 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> 678 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ValidateReadDataLine: Data line number $This->{LineNum} contains no fingerprints data: $This->{DataLine}..."</span><span class="sc">;</span> 679 <span class="s">}</span> 680 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">DetailLevel</span>} >= <span class="n">2</span><span class="s">)</span> <span class="s">{</span> 681 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ValidateReadDataLine: Data line number $This->{LineNum} contains no fingerprints data..."</span><span class="sc">;</span> 682 <span class="s">}</span> 683 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 684 <span class="s">}</span> 685 686 <span class="c"># Check for invalid data...</span> 687 <span class="k">my</span><span class="s">(</span><span class="i">$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">$FingerprintsDescription</span><span class="s">)</span><span class="sc">;</span> 688 689 <span class="i">$InvalidFingerprintsData</span> = <span class="n">0</span><span class="sc">;</span> 690 <span class="i">$FingerprintsColNum</span> = <span class="i">$This</span>->{<span class="w">FingerprintsColNum</span>}<span class="sc">;</span> 691 692 <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> 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> 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> 695 <span class="i">$InvalidFingerprintsData</span> = <span class="n">1</span><span class="sc">;</span> 696 <span class="s">}</span> 697 <span class="s">}</span> 698 <span class="k">else</span> <span class="s">{</span> 699 <span class="i">$InvalidFingerprintsData</span> = <span class="n">1</span><span class="sc">;</span> 700 <span class="s">}</span> 701 702 <span class="k">if</span> <span class="s">(</span><span class="i">$InvalidFingerprintsData</span><span class="s">)</span> <span class="s">{</span> 703 <span class="i">$This</span>->{<span class="w">NumOfLinesWithInvalidData</span>} += <span class="n">1</span><span class="sc">;</span> 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> 705 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ValidateReadDataLine: Data line number $This->{LineNum} contains invalid fingerprints data: $This->{DataLine}..."</span><span class="sc">;</span> 706 <span class="s">}</span> 707 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">DetailLevel</span>} >= <span class="n">2</span><span class="s">)</span> <span class="s">{</span> 708 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ValidateReadDataLine: Data line number $This->{LineNum} contains invalid fingerprints data..."</span><span class="sc">;</span> 709 <span class="s">}</span> 710 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 711 <span class="s">}</span> 712 713 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 714 <span class="s">}</span> 715 716 <span class="c"># Setup fingerprints compound ID for fingerprints string...</span> <a name="_GenerateCompoundID-"></a> 717 <span class="k">sub </span><span class="m">_GenerateCompoundID</span> <span class="s">{</span> 718 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 719 <span class="k">my</span><span class="s">(</span><span class="i">$CompoundID</span><span class="s">)</span><span class="sc">;</span> 720 721 <span class="i">$CompoundID</span> = <span class="q">''</span><span class="sc">;</span> 722 723 <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> 724 <span class="k">my</span><span class="s">(</span><span class="i">$CompoundNum</span><span class="s">)</span><span class="sc">;</span> 725 726 <span class="i">$CompoundNum</span> = <span class="i">$This</span>->{<span class="w">LineNum</span>} - <span class="n">1</span><span class="sc">;</span> 727 <span class="i">$CompoundID</span> = <span class="q">"$This->{CompoundIDPrefix}${CompoundNum}"</span><span class="sc">;</span> 728 <span class="s">}</span> 729 <span class="k">else</span> <span class="s">{</span> 730 <span class="i">$CompoundID</span> = <span class="i">$This</span>->{<span class="w">DataLineWords</span>}[<span class="i">$This</span>->{<span class="w">CompoundIDColNum</span>}]<span class="sc">;</span> 731 <span class="s">}</span> 732 733 <span class="i">$This</span>->{<span class="w">CompoundID</span>} = <span class="i">$CompoundID</span><span class="sc">;</span> 734 735 <span class="c"># Set fingerprints ID...</span> 736 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FingerprintsObject</span>}<span class="s">)</span> <span class="s">{</span> 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> 738 <span class="s">}</span> 739 740 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 741 <span class="s">}</span> 742 743 <span class="c"># Process first read...</span> 744 <span class="c">#</span> <a name="_ProcessFirstDataLineRead-"></a> 745 <span class="k">sub </span><span class="m">_ProcessFirstDataLineRead</span> <span class="s">{</span> 746 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 747 748 <span class="c"># Skip column label line...</span> 749 <span class="i">$This</span>->{<span class="w">LineNum</span>} += <span class="n">1</span><span class="sc">;</span> 750 <span class="i">TextUtil::GetTextLine</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">FileHandle</span>}<span class="s">)</span><span class="sc">;</span> 751 752 <span class="i">$This</span>->{<span class="w">FirstDataLineIO</span>} = <span class="n">0</span><span class="sc">;</span> 753 754 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 755 <span class="s">}</span> 756 757 <span class="c"># Get ready for reading fingerprints text file...</span> 758 <span class="c">#</span> <a name="_PrepareForReadingFingerprintsTextFileData-"></a> 759 <span class="k">sub </span><span class="m">_PrepareForReadingFingerprintsTextFileData</span> <span class="s">{</span> 760 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 761 762 <span class="c"># Retrieve text file columns information....</span> 763 <span class="i">$This</span><span class="i">->_RetrieveTextFileColData</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 764 765 <span class="c"># Validate columns information...</span> 766 <span class="i">$This</span><span class="i">->_ValidateReadCompoundIDCol</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 767 <span class="i">$This</span><span class="i">->_ValidateReadFingerprintsCol</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 768 769 <span class="c"># Validate fingeprints string mode information...</span> 770 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">ValidFingerprintsCol</span>}<span class="s">)</span> <span class="s">{</span> 771 <span class="i">$This</span><span class="i">->_ValidateReadFingerprintsStringMode</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 772 <span class="s">}</span> 773 774 <span class="c"># Set status of text file data...</span> 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> 776 777 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 778 <span class="s">}</span> 779 780 <span class="c"># Retrieve information about columns and fingerprints string...</span> 781 <span class="c">#</span> <a name="_RetrieveTextFileColData-"></a> 782 <span class="k">sub </span><span class="m">_RetrieveTextFileColData</span> <span class="s">{</span> 783 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 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> 785 786 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DataColLabels</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 787 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">DataColLabelToNumMap</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 788 789 <span class="i">$TextFile</span> = <span class="i">$This</span>->{<span class="w">Name</span>}<span class="sc">;</span> 790 791 <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> 792 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated: File, $TextFile, doesn't exist..."</span><span class="sc">;</span> 793 <span class="s">}</span> 794 795 <span class="i">$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> 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> 797 798 <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> 799 <span class="i">$This</span>->{<span class="w">Delim</span>} = <span class="i">$InDelim</span><span class="sc">;</span> 800 801 <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> 802 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated: Couldn't open input text file $TextFile: $! ..."</span><span class="sc">;</span> 803 <span class="s">}</span> 804 805 <span class="c"># Get column label line...</span> 806 <span class="i">$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> 807 808 <span class="k">close</span> <span class="w">TEXTFILE</span><span class="sc">;</span> 809 810 <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> 811 812 <span class="c"># Set text file columns info....</span> 813 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DataColLabels</span>}}<span class="cm">,</span> <span class="i">@ColLabels</span><span class="sc">;</span> 814 815 <span class="k">for</span> <span class="i">$ColNum</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#ColLabels</span><span class="s">)</span> <span class="s">{</span> 816 <span class="i">$ColLabel</span> = <span class="i">$ColLabels</span>[<span class="i">$ColNum</span>]<span class="sc">;</span> 817 <span class="i">$This</span>->{<span class="w">DataColLabelToNumMap</span>}{<span class="i">$ColLabel</span>} = <span class="i">$ColNum</span><span class="sc">;</span> 818 <span class="s">}</span> 819 820 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 821 <span class="s">}</span> 822 823 <span class="c"># Validate compound ID column information...</span> 824 <span class="c">#</span> <a name="_ValidateReadCompoundIDCol-"></a> 825 <span class="k">sub </span><span class="m">_ValidateReadCompoundIDCol</span> <span class="s">{</span> 826 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 827 <span class="k">my</span><span class="s">(</span><span class="i">$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">$ColNum</span><span class="s">)</span><span class="sc">;</span> 828 829 <span class="i">$This</span>->{<span class="w">ValidCompoundIDCol</span>} = <span class="n">0</span><span class="sc">;</span> 830 <span class="i">$This</span>->{<span class="w">CompoundIDColNum</span>} = <span class="k">undef</span><span class="sc">;</span> 831 <span class="i">$This</span>->{<span class="w">UseSequentialCompoundIDs</span>} = <span class="n">0</span><span class="sc">;</span> 832 833 <span class="i">$CompoundIDCol</span> = <span class="i">$This</span>->{<span class="w">CompoundIDCol</span>}<span class="sc">;</span> 834 835 <span class="i">$UseSequentialCompoundIDs</span> = <span class="n">0</span><span class="sc">;</span> 836 <span class="i">$CompoundIDColNum</span> = <span class="q">''</span><span class="sc">;</span> 837 838 <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> 839 <span class="c"># First column containing the word CompoundID in its label or sequential generation...</span> 840 841 <span class="i">$ColFound</span> = <span class="n">0</span><span class="sc">;</span> 842 <span class="j">COLLABEL:</span> <span class="k">for</span> <span class="i">$ColLabel</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DataColLabels</span>}}<span class="s">)</span> <span class="s">{</span> 843 <span class="k">if</span> <span class="s">(</span><span class="i">$ColLabel</span> =~ <span class="q">/CompoundID/i</span><span class="s">)</span> <span class="s">{</span> 844 <span class="i">$ColFound</span> = <span class="n">1</span><span class="sc">;</span> 845 <span class="i">$ColNum</span> = <span class="i">$This</span>->{<span class="w">DataColLabelToNumMap</span>}{<span class="i">$ColLabel</span>}<span class="sc">;</span> 846 <span class="k">last</span> <span class="j">COLLABEL</span><span class="sc">;</span> 847 <span class="s">}</span> 848 <span class="s">}</span> 849 <span class="k">if</span> <span class="s">(</span><span class="i">$ColFound</span><span class="s">)</span> <span class="s">{</span> 850 <span class="i">$CompoundIDColNum</span> = <span class="i">$ColNum</span><span class="sc">;</span> 851 <span class="s">}</span> 852 <span class="k">else</span> <span class="s">{</span> 853 <span class="i">$UseSequentialCompoundIDs</span> = <span class="n">1</span><span class="sc">;</span> 854 <span class="s">}</span> 855 <span class="s">}</span> 856 <span class="k">else</span> <span class="s">{</span> 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> 858 <span class="c"># Is it a valid column number?</span> 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> 860 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ValidateReadCompoundIDCol: Column number, $CompoundIDCol, specified using CompoundIDCol doesn't exist..."</span><span class="sc">;</span> 861 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 862 <span class="s">}</span> 863 <span class="i">$CompoundIDColNum</span> = <span class="i">$CompoundIDCol</span> - <span class="n">1</span><span class="sc">;</span> 864 <span class="s">}</span> 865 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">ColMode</span>} =~ <span class="q">/^ColLabel$/i</span><span class="s">)</span> <span class="s">{</span> 866 <span class="c"># Does this column exists?</span> 867 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$This</span>->{<span class="w">DataColLabelToNumMap</span>}{<span class="i">$CompoundIDCol</span>}<span class="s">)</span> <span class="s">{</span> 868 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ValidateReadCompoundIDCol: Column name, $CompoundIDCol, specified using CompoundIDCol doesn't exist..."</span><span class="sc">;</span> 869 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 870 <span class="s">}</span> 871 <span class="i">$CompoundIDColNum</span> = <span class="i">$This</span>->{<span class="w">DataColLabelToNumMap</span>}{<span class="i">$CompoundIDCol</span>}<span class="sc">;</span> 872 <span class="s">}</span> 873 <span class="s">}</span> 874 875 <span class="i">$This</span>->{<span class="w">ValidCompoundIDCol</span>} = <span class="n">1</span><span class="sc">;</span> 876 <span class="i">$This</span>->{<span class="w">CompoundIDColNum</span>} = <span class="i">$CompoundIDColNum</span><span class="sc">;</span> 877 <span class="i">$This</span>->{<span class="w">UseSequentialCompoundIDs</span>} = <span class="i">$UseSequentialCompoundIDs</span><span class="sc">;</span> 878 879 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 880 <span class="s">}</span> 881 882 <span class="c"># Validate fingerprints string column information...</span> 883 <span class="c">#</span> <a name="_ValidateReadFingerprintsCol-"></a> 884 <span class="k">sub </span><span class="m">_ValidateReadFingerprintsCol</span> <span class="s">{</span> 885 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 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">$ColNum</span><span class="s">)</span><span class="sc">;</span> 887 888 <span class="i">$This</span>->{<span class="w">ValidFingerprintsCol</span>} = <span class="n">0</span><span class="sc">;</span> 889 <span class="i">$This</span>->{<span class="w">FingerprintsColNum</span>} = <span class="k">undef</span><span class="sc">;</span> 890 891 <span class="i">$FingerprintsColNum</span> = <span class="k">undef</span><span class="sc">;</span> 892 <span class="i">$FingerprintsCol</span> = <span class="i">$This</span>->{<span class="w">FingerprintsCol</span>}<span class="sc">;</span> 893 894 <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> 895 <span class="c"># First column containing the word Fingerprints in its label...</span> 896 897 <span class="i">$ColFound</span> = <span class="n">0</span><span class="sc">;</span> 898 <span class="j">COLLABEL:</span> <span class="k">for</span> <span class="i">$ColLabel</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DataColLabels</span>}}<span class="s">)</span> <span class="s">{</span> 899 <span class="k">if</span> <span class="s">(</span><span class="i">$ColLabel</span> =~ <span class="q">/Fingerprints/i</span><span class="s">)</span> <span class="s">{</span> 900 <span class="i">$ColFound</span> = <span class="n">1</span><span class="sc">;</span> 901 <span class="i">$ColNum</span> = <span class="i">$This</span>->{<span class="w">DataColLabelToNumMap</span>}{<span class="i">$ColLabel</span>}<span class="sc">;</span> 902 <span class="k">last</span> <span class="j">COLLABEL</span><span class="sc">;</span> 903 <span class="s">}</span> 904 <span class="s">}</span> 905 <span class="k">if</span> <span class="s">(</span>!<span class="i">$ColFound</span><span class="s">)</span> <span class="s">{</span> 906 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ValidateReadFingerprintsCol: Column label containing \"Fingerprints\" string in its name doesn't exist..."</span><span class="sc">;</span> 907 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 908 <span class="s">}</span> 909 <span class="i">$FingerprintsColNum</span> = <span class="i">$ColNum</span><span class="sc">;</span> 910 <span class="s">}</span> 911 <span class="k">else</span> <span class="s">{</span> 912 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">ColMode</span>} =~ <span class="q">/^ColNum$/i</span><span class="s">)</span> <span class="s">{</span> 913 <span class="c"># Is it a valid column number?</span> 914 <span class="k">if</span> <span class="s">(</span><span class="i">$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> 915 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ValidateReadFingerprintsCol: Column number, $FingerprintsCol, specified using FingerprintsCol doesn't exist..."</span><span class="sc">;</span> 916 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 917 <span class="s">}</span> 918 <span class="i">$FingerprintsColNum</span> = <span class="i">$FingerprintsCol</span> - <span class="n">1</span><span class="sc">;</span> 919 <span class="s">}</span> 920 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">ColMode</span>} =~ <span class="q">/^ColLabel$/i</span><span class="s">)</span> <span class="s">{</span> 921 <span class="c"># Does this column exists?</span> 922 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$This</span>->{<span class="w">DataColLabelToNumMap</span>}{<span class="i">$FingerprintsCol</span>}<span class="s">)</span> <span class="s">{</span> 923 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ValidateReadFingerprintsCol: Column label, $FingerprintsCol, specified using FingerprintsCol doesn't exist..."</span><span class="sc">;</span> 924 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 925 <span class="s">}</span> 926 <span class="i">$FingerprintsColNum</span> = <span class="i">$This</span>->{<span class="w">DataColLabelToNumMap</span>}{<span class="i">$FingerprintsCol</span>}<span class="sc">;</span> 927 <span class="s">}</span> 928 <span class="s">}</span> 929 930 <span class="i">$This</span>->{<span class="w">ValidFingerprintsCol</span>} = <span class="n">1</span><span class="sc">;</span> 931 <span class="i">$This</span>->{<span class="w">FingerprintsColNum</span>} = <span class="i">$FingerprintsColNum</span><span class="sc">;</span> 932 933 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 934 <span class="s">}</span> 935 936 <span class="c"># Validate fingerprints string mode information...</span> 937 <span class="c">#</span> <a name="_ValidateReadFingerprintsStringMode-"></a> 938 <span class="k">sub </span><span class="m">_ValidateReadFingerprintsStringMode</span> <span class="s">{</span> 939 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 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> 941 942 <span class="i">$This</span>->{<span class="w">ValidFingerprintsStringMode</span>} = <span class="n">0</span><span class="sc">;</span> 943 944 <span class="i">$This</span>->{<span class="w">FingerprintsBitVectorStringMode</span>} = <span class="n">0</span><span class="sc">;</span> 945 <span class="i">$This</span>->{<span class="w">FingerprintsVectorStringMode</span>} = <span class="n">0</span><span class="sc">;</span> 946 947 <span class="i">$This</span>->{<span class="w">FirstFingerprintsStringType</span>} = <span class="q">''</span><span class="sc">;</span> 948 <span class="i">$This</span>->{<span class="w">FirstFingerprintsStringDescription</span>} = <span class="q">''</span><span class="sc">;</span> 949 950 <span class="i">$FingerprintsBitVectorStringMode</span> = <span class="n">0</span><span class="sc">;</span> 951 <span class="i">$FingerprintsVectorStringMode</span> = <span class="n">0</span><span class="sc">;</span> 952 953 <span class="i">$FirstFingerprintsStringType</span> = <span class="q">''</span><span class="sc">;</span> 954 <span class="i">$FirstFingerprintsStringDescription</span> = <span class="q">''</span><span class="sc">;</span> 955 956 <span class="i">$TextFile</span> = <span class="i">$This</span>->{<span class="w">Name</span>}<span class="sc">;</span> 957 958 <span class="k">if</span> <span class="s">(</span>!<span class="k">open</span> <span class="w">TEXTFILE</span><span class="cm">,</span> <span class="q">"$TextFile"</span><span class="s">)</span> <span class="s">{</span> 959 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated: Couldn't open input text file $TextFile: $! ..."</span><span class="sc">;</span> 960 <span class="s">}</span> 961 962 <span class="c"># Skip column label line...</span> 963 <span class="i">$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> 964 965 <span class="c"># First first fingerprints data line...</span> 966 <span class="i">$Line</span> = <span class="i">TextUtil::GetTextLine</span><span class="s">(</span>\<span class="i">*TEXTFILE</span><span class="s">)</span><span class="sc">;</span> 967 968 <span class="k">close</span> <span class="w">TEXTFILE</span><span class="sc">;</span> 969 970 <span class="c"># Get first fingerprints type and description...</span> 971 <span class="i">$InDelim</span> = <span class="i">$This</span>->{<span class="w">Delim</span>}<span class="sc">;</span> 972 <span class="i">@LineWords</span> = <span class="i">TextUtil::SplitWords</span><span class="s">(</span><span class="i">$Line</span><span class="cm">,</span> <span class="i">$InDelim</span><span class="s">)</span><span class="sc">;</span> 973 974 <span class="i">$FingerprintsColNum</span> = <span class="i">$This</span>->{<span class="w">FingerprintsColNum</span>}<span class="sc">;</span> 975 976 <span class="s">(</span><span class="i">$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">$FingerprintsColNum</span>]<span class="s">)</span><span class="sc">;</span> 977 978 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FingerprintsStringMode</span>} =~ <span class="q">/^FingerprintsBitVectorString$/i</span><span class="s">)</span> <span class="s">{</span> 979 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsType</span> !~ <span class="q">/^FingerprintsBitVector$/i</span><span class="s">)</span> <span class="s">{</span> 980 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ValidateReadFingerprintsStringMode: First fingerprint string data type, $FingerprintsType, doesn't match value, FingerprintsBitVectorString, specified using \"FingerprintsStringMode\"..."</span><span class="sc">;</span> 981 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 982 <span class="s">}</span> 983 <span class="i">$FingerprintsBitVectorStringMode</span> = <span class="n">1</span><span class="sc">;</span> 984 <span class="i">$FirstFingerprintsStringType</span> = <span class="q">'FingerprintsBitVector'</span><span class="sc">;</span> 985 <span class="i">$FirstFingerprintsStringDescription</span> = <span class="i">$FingerprintsDescription</span><span class="sc">;</span> 986 <span class="s">}</span> 987 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FingerprintsStringMode</span>} =~ <span class="q">/^FingerprintsVectorString$/i</span><span class="s">)</span> <span class="s">{</span> 988 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsType</span> !~ <span class="q">/^FingerprintsVector$/i</span><span class="s">)</span> <span class="s">{</span> 989 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ValidateReadFingerprintsStringMode: First fingerprint string data type, $FingerprintsType, doesn't match value, FingerprintsVectorString, specified using \"FingerprintsStringMode\"..."</span><span class="sc">;</span> 990 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 991 <span class="s">}</span> 992 <span class="i">$FingerprintsVectorStringMode</span> = <span class="n">1</span><span class="sc">;</span> 993 <span class="i">$FirstFingerprintsStringType</span> = <span class="q">'FingerprintsVector'</span><span class="sc">;</span> 994 <span class="i">$FirstFingerprintsStringDescription</span> = <span class="i">$FingerprintsDescription</span><span class="sc">;</span> 995 <span class="s">}</span> 996 <span class="k">else</span> <span class="s">{</span> 997 <span class="c"># AutoDetect mode...</span> 998 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsType</span> =~ <span class="q">/^FingerprintsBitVector$/i</span><span class="s">)</span> <span class="s">{</span> 999 <span class="i">$FingerprintsBitVectorStringMode</span> = <span class="n">1</span><span class="sc">;</span> 1000 <span class="s">}</span> 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> 1002 <span class="i">$FingerprintsVectorStringMode</span> = <span class="n">1</span><span class="sc">;</span> 1003 <span class="s">}</span> 1004 <span class="k">else</span> <span class="s">{</span> 1005 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ValidateReadFingerprintsStringMode: First fingerprint string data type, $FingerprintsType, identified during, AutoDetect, value of \"FingerprintsStringMode\" is not valid; Supported fingerprints types: FingerprintBitVector or FingerprintsVector..."</span><span class="sc">;</span> 1006 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 1007 <span class="s">}</span> 1008 <span class="i">$FirstFingerprintsStringType</span> = <span class="i">$FingerprintsType</span><span class="sc">;</span> 1009 <span class="i">$FirstFingerprintsStringDescription</span> = <span class="i">$FingerprintsDescription</span><span class="sc">;</span> 1010 <span class="s">}</span> 1011 1012 <span class="i">$This</span>->{<span class="w">ValidFingerprintsStringMode</span>} = <span class="n">1</span><span class="sc">;</span> 1013 1014 <span class="i">$This</span>->{<span class="w">FingerprintsBitVectorStringMode</span>} = <span class="i">$FingerprintsBitVectorStringMode</span><span class="sc">;</span> 1015 <span class="i">$This</span>->{<span class="w">FingerprintsVectorStringMode</span>} = <span class="i">$FingerprintsVectorStringMode</span><span class="sc">;</span> 1016 1017 <span class="i">$This</span>->{<span class="w">FirstFingerprintsStringType</span>} = <span class="i">$FirstFingerprintsStringType</span><span class="sc">;</span> 1018 <span class="i">$This</span>->{<span class="w">FirstFingerprintsStringDescription</span>} = <span class="i">$FirstFingerprintsStringDescription</span><span class="sc">;</span> 1019 1020 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 1021 <span class="s">}</span> 1022 1023 <span class="c"># Write fingerprints string generated from specified fingerprints, fingerprints-bit vector, or</span> 1024 <span class="c"># fingerprints vector object and other data to text file...</span> 1025 <span class="c">#</span> <a name="WriteFingerprints-"></a>1026 <span class="k">sub </span><span class="m">WriteFingerprints</span> <span class="s">{</span> 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> 1028 1029 <span class="c"># Initialize data for current line...</span> 1030 <span class="i">$This</span><span class="i">->_InitializeWriteDataLine</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1031 1032 <span class="c"># Set fingerprints object...</span> 1033 <span class="i">$This</span>->{<span class="w">FingerprintsObject</span>} = <span class="i">$FingerprintsObject</span><span class="sc">;</span> 1034 1035 <span class="c"># Generate fingerprints string...</span> 1036 <span class="i">$This</span><span class="i">->_GenerateFingerprintsString</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1037 1038 <span class="c"># Set data line words...</span> 1039 <span class="i">$This</span><span class="i">->SetDataLineWords</span><span class="s">(</span><span class="i">@DataColValues</span><span class="s">)</span><span class="sc">;</span> 1040 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DataLineWords</span>}}<span class="cm">,</span> <span class="i">$This</span>->{<span class="w">FingerprintsString</span>}<span class="sc">;</span> 1041 1042 <span class="c"># Write data line..</span> 1043 <span class="i">$This</span><span class="i">->_WriteDataLine</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1044 1045 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 1046 <span class="s">}</span> 1047 1048 <span class="c"># Write fingerprints string and other data to text file...</span> 1049 <span class="c">#</span> 1050 <span class="c"># Note:</span> 1051 <span class="c"># o FingerprintsStringMode, BitStringFormat, BitsOrder, VectorStringFormat values</span> 1052 <span class="c"># are ignored during writing of fingerprints and it's written to the file as it is.</span> 1053 <span class="c">#</span> 1054 <span class="c">#</span> <a name="WriteFingerprintsString-"></a>1055 <span class="k">sub </span><span class="m">WriteFingerprintsString</span> <span class="s">{</span> 1056 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsString</span><span class="cm">,</span> <span class="i">@DataColValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1057 1058 <span class="c"># Initialize data for current line...</span> 1059 <span class="i">$This</span><span class="i">->_InitializeWriteDataLine</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1060 1061 <span class="c"># Set fingerprints string...</span> 1062 <span class="i">$This</span>->{<span class="w">FingerprintsString</span>} = <span class="i">$FingerprintsString</span><span class="sc">;</span> 1063 1064 <span class="c"># Generate fingerprints object...</span> 1065 <span class="i">$This</span><span class="i">->_GenerateFingerprintsObject</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1066 1067 <span class="c"># Set data line words...</span> 1068 <span class="i">$This</span><span class="i">->SetDataLineWords</span><span class="s">(</span><span class="i">@DataColValues</span><span class="s">)</span><span class="sc">;</span> 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> 1070 1071 <span class="c"># Write data line..</span> 1072 <span class="i">$This</span><span class="i">->_WriteDataLine</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1073 1074 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 1075 <span class="s">}</span> 1076 1077 <span class="c"># Initialize data line for reading...</span> 1078 <span class="c">#</span> <a name="_InitializeWriteDataLine-"></a>1079 <span class="k">sub </span><span class="m">_InitializeWriteDataLine</span> <span class="s">{</span> 1080 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1081 1082 <span class="i">$This</span>->{<span class="w">DataLine</span>} = <span class="k">undef</span><span class="sc">;</span> 1083 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DataLineWords</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1084 1085 <span class="i">$This</span>->{<span class="w">FingerprintsObject</span>} = <span class="k">undef</span><span class="sc">;</span> 1086 <span class="i">$This</span>->{<span class="w">FingerprintsString</span>} = <span class="k">undef</span><span class="sc">;</span> 1087 1088 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 1089 <span class="s">}</span> 1090 1091 <span class="c"># Write fingerprints data line line...</span> 1092 <span class="c">#</span> <a name="_WriteDataLine-"></a>1093 <span class="k">sub </span><span class="m">_WriteDataLine</span> <span class="s">{</span> 1094 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1095 <span class="k">my</span><span class="s">(</span><span class="i">$FileHandle</span><span class="cm">,</span> <span class="i">$Line</span><span class="s">)</span><span class="sc">;</span> 1096 1097 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FirstDataLineIO</span>}<span class="s">)</span> <span class="s">{</span> 1098 <span class="i">$This</span><span class="i">->_ProcessFirstDataLineWrite</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1099 <span class="s">}</span> 1100 1101 <span class="c"># Write out line words...</span> 1102 <span class="i">$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">$This</span>->{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span> 1103 1104 <span class="i">$This</span>->{<span class="w">LineNum</span>} += <span class="n">1</span><span class="sc">;</span> 1105 <span class="i">$FileHandle</span> = <span class="i">$This</span>->{<span class="w">FileHandle</span>}<span class="sc">;</span> 1106 <span class="k">print</span> <span class="i">$FileHandle</span> <span class="q">"$Line\n"</span><span class="sc">;</span> 1107 1108 <span class="i">$This</span>->{<span class="w">DataLine</span>} = <span class="i">$Line</span><span class="sc">;</span> 1109 1110 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 1111 <span class="s">}</span> 1112 1113 <span class="c"># Process first write...</span> 1114 <span class="c">#</span> <a name="_ProcessFirstDataLineWrite-"></a>1115 <span class="k">sub </span><span class="m">_ProcessFirstDataLineWrite</span> <span class="s">{</span> 1116 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 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> 1118 1119 <span class="i">$This</span>->{<span class="w">FirstDataLineIO</span>} = <span class="n">0</span><span class="sc">;</span> 1120 1121 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetMode</span><span class="s">(</span><span class="s">)</span> =~ <span class="q">/^Write$/i</span><span class="s">)</span> <span class="s">{</span> 1122 <span class="c"># Write out column label line...</span> 1123 <span class="i">$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">$This</span>->{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span> 1124 1125 <span class="i">$This</span>->{<span class="w">LineNum</span>} += <span class="n">1</span><span class="sc">;</span> 1126 <span class="i">$FileHandle</span> = <span class="i">$This</span>->{<span class="w">FileHandle</span>}<span class="sc">;</span> 1127 <span class="k">print</span> <span class="i">$FileHandle</span> <span class="q">"$Line\n"</span><span class="sc">;</span> 1128 <span class="s">}</span> 1129 1130 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 1131 <span class="s">}</span> 1132 1133 <span class="c"># Get ready for writing fingerprints text file...</span> 1134 <span class="c">#</span> <a name="_PrepareForWritingFingerprintsTextFileData-"></a>1135 <span class="k">sub </span><span class="m">_PrepareForWritingFingerprintsTextFileData</span> <span class="s">{</span> 1136 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 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">$OutDelim</span><span class="s">)</span><span class="sc">;</span> 1138 1139 <span class="i">$TextFile</span> = <span class="i">$This</span>->{<span class="w">Name</span>}<span class="sc">;</span> 1140 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">Overwrite</span>}<span class="s">)</span> <span class="s">{</span> 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> 1142 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated: File, $TextFile, already exist. Use overwrite option..."</span><span class="sc">;</span> 1143 <span class="s">}</span> 1144 <span class="s">}</span> 1145 1146 <span class="c"># Set up delimiter for writing file...</span> 1147 1148 <span class="i">$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> 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> 1150 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> 1152 <span class="i">$This</span>->{<span class="w">Delim</span>} = <span class="i">$OutDelim</span><span class="sc">;</span> 1153 1154 <span class="c"># Setup FingerprintsStringMode status...</span> 1155 1156 <span class="i">$This</span>->{<span class="w">FingerprintsBitVectorStringMode</span>} = <span class="n">0</span><span class="sc">;</span> 1157 <span class="i">$This</span>->{<span class="w">FingerprintsVectorStringMode</span>} = <span class="n">0</span><span class="sc">;</span> 1158 <span class="i">$This</span>->{<span class="w">ValidFingerprintsStringMode</span>} = <span class="n">0</span><span class="sc">;</span> 1159 1160 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FingerprintsStringMode</span>} =~ <span class="q">/^FingerprintsBitVectorString$/i</span><span class="s">)</span> <span class="s">{</span> 1161 <span class="i">$This</span>->{<span class="w">FingerprintsBitVectorStringMode</span>} = <span class="n">1</span><span class="sc">;</span> 1162 <span class="s">}</span> 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> 1164 <span class="i">$This</span>->{<span class="w">FingerprintsVectorStringMode</span>} = <span class="n">1</span><span class="sc">;</span> 1165 <span class="s">}</span> 1166 1167 <span class="i">$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> 1168 1169 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FingerprintsBitVectorStringMode</span>}<span class="s">)</span> <span class="s">{</span> 1170 <span class="i">$This</span><span class="i">->_SetDefaultBitStringFormat</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1171 <span class="i">$This</span><span class="i">->_SetDefaultBitsOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1172 <span class="s">}</span> 1173 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FingerprintsVectorStringMode</span>}<span class="s">)</span> <span class="s">{</span> 1174 <span class="i">$This</span><span class="i">->_SetDefaultVectorStringFormat</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1175 <span class="s">}</span> 1176 1177 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 1178 <span class="s">}</span> 1179 1180 <span class="c"># Set default value for bit string format...</span> 1181 <span class="c">#</span> <a name="_SetDefaultBitStringFormat-"></a>1182 <span class="k">sub </span><span class="m">_SetDefaultBitStringFormat</span> <span class="s">{</span> 1183 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1184 1185 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">BitStringFormat</span>}<span class="s">)</span> <span class="s">{</span> 1186 <span class="i">$This</span>->{<span class="w">BitStringFormat</span>} = <span class="i">Fingerprints::FingerprintsStringUtil::GetDefaultBitStringFormat</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1187 <span class="s">}</span> 1188 1189 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 1190 <span class="s">}</span> 1191 1192 <span class="c"># Set default value for bit string format...</span> 1193 <span class="c">#</span> <a name="_SetDefaultBitsOrder-"></a>1194 <span class="k">sub </span><span class="m">_SetDefaultBitsOrder</span> <span class="s">{</span> 1195 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1196 1197 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">BitsOrder</span>}<span class="s">)</span> <span class="s">{</span> 1198 <span class="i">$This</span>->{<span class="w">BitsOrder</span>} = <span class="i">Fingerprints::FingerprintsStringUtil::GetDefaultBitsOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 1199 <span class="s">}</span> 1200 1201 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 1202 <span class="s">}</span> 1203 1204 <span class="c"># Set default value for vector string format...</span> 1205 <span class="c">#</span> <a name="_SetDefaultVectorStringFormat-"></a>1206 <span class="k">sub </span><span class="m">_SetDefaultVectorStringFormat</span> <span class="s">{</span> 1207 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1208 1209 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">VectorStringFormat</span>} && <span class="i">$This</span>->{<span class="w">FingerprintsObject</span>}<span class="s">)</span> <span class="s">{</span> 1210 <span class="i">$This</span>->{<span class="w">VectorStringFormat</span>} = <span class="i">Fingerprints::FingerprintsStringUtil::GetDefaultVectorStringFormat</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">FingerprintsObject</span>}<span class="s">)</span><span class="sc">;</span> 1211 <span class="s">}</span> 1212 1213 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 1214 <span class="s">}</span> 1215 1216 <span class="c"># Generate fingerprints object using current fingerprints string...</span> 1217 <span class="c">#</span> <a name="_GenerateFingerprintsObject-"></a>1218 <span class="k">sub </span><span class="m">_GenerateFingerprintsObject</span> <span class="s">{</span> 1219 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1220 1221 <span class="i">$This</span>->{<span class="w">FingerprintsObject</span>} = <span class="k">undef</span><span class="sc">;</span> 1222 1223 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">FingerprintsString</span>}<span class="s">)</span> <span class="s">{</span> 1224 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 1225 <span class="s">}</span> 1226 1227 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FingerprintsBitVectorStringMode</span>}<span class="s">)</span> <span class="s">{</span> 1228 <span class="i">$This</span>->{<span class="w">FingerprintsObject</span>} = <span class="i">Fingerprints::FingerprintsStringUtil::ParseFingerprintsBitVectorString</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">FingerprintsString</span>}<span class="s">)</span><span class="sc">;</span> 1229 <span class="s">}</span> 1230 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FingerprintsVectorStringMode</span>}<span class="s">)</span> <span class="s">{</span> 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> 1232 <span class="s">}</span> 1233 <span class="k">else</span> <span class="s">{</span> 1234 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 1235 <span class="s">}</span> 1236 1237 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 1238 <span class="s">}</span> 1239 1240 <span class="c"># Generate fingerprints string using current fingerprints object...</span> 1241 <span class="c">#</span> <a name="_GenerateFingerprintsString-"></a>1242 <span class="k">sub </span><span class="m">_GenerateFingerprintsString</span> <span class="s">{</span> 1243 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1244 1245 <span class="i">$This</span>->{<span class="w">FingerprintsString</span>} = <span class="q">''</span><span class="sc">;</span> 1246 1247 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">FingerprintsObject</span>}<span class="s">)</span> <span class="s">{</span> 1248 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 1249 <span class="s">}</span> 1250 1251 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FingerprintsBitVectorStringMode</span>}<span class="s">)</span> <span class="s">{</span> 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> 1253 <span class="s">}</span> 1254 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FingerprintsVectorStringMode</span>}<span class="s">)</span> <span class="s">{</span> 1255 <span class="i">$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> 1256 <span class="s">}</span> 1257 1258 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 1259 <span class="s">}</span> 1260 1261 <span class="c"># Is it a fingerprints file?</span> <a name="IsFingerprintsTextFile-"></a>1262 <span class="k">sub </span><span class="m">IsFingerprintsTextFile ($;$)</span> <span class="s">{</span> 1263 <span class="k">my</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1264 <span class="k">my</span><span class="s">(</span><span class="i">$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> 1265 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">$FirstParameter</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 1267 <span class="s">(</span><span class="i">$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">$SecondParameter</span><span class="s">)</span><span class="sc">;</span> 1268 <span class="s">}</span> 1269 <span class="k">else</span> <span class="s">{</span> 1270 <span class="i">$FileName</span> = <span class="i">$FirstParameter</span><span class="sc">;</span> 1271 <span class="s">}</span> 1272 1273 <span class="c"># Check file extension...</span> 1274 <span class="i">$Status</span> = <span class="i">FileUtil::CheckFileType</span><span class="s">(</span><span class="i">$FileName</span><span class="cm">,</span> <span class="q">"csv tsv"</span><span class="s">)</span><span class="sc">;</span> 1275 1276 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span> 1277 <span class="s">}</span> 1278 1279 <span class="c"># Is it a FingerprintsTextFileIO object?</span> <a name="_IsFingerprintsTextFileIO-"></a>1280 <span class="k">sub </span><span class="m">_IsFingerprintsTextFileIO</span> <span class="s">{</span> 1281 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 1282 1283 <span class="k">return</span> <span class="s">(</span><span class="i">Scalar::Util::blessed</span><span class="s">(</span><span class="i">$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> 1284 <span class="s">}</span> 1285 <a name="EOF-"></a></pre> <p> </p> <br /> <center> <img src="../../../images/h2o2.png"> </center> </body> </html>