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862 aurelien 1
<?php
2
 
3
/**
4
 * Taxamatch-Webservice PHP v1.0.0
5
 * @author Michael Giddens
6
 * @link http://www.silverbiology.com
7
 */
8
 
9
 /* Adapation par David Delon Decembre 2010 : gestion sous espece
10
 */
11
 
12
 
1318 aurelien 13
/**
14
 * Class NameParser
15
 * Used to convert a string to a standarized format.
16
 */
17
class NameParser {
18
 
862 aurelien 19
	/**
1318 aurelien 20
	 * Whether to debug or nor
21
	 * @var bool|integer
862 aurelien 22
	 */
1318 aurelien 23
	public $debug_flag;
862 aurelien 24
 
25
 
26
 
1318 aurelien 27
	/**
28
	 * Constructor
29
	 */
30
	public function __construct( ) {
31
	}
862 aurelien 32
 
1318 aurelien 33
	/**
34
	 * Sets value to the method property
35
	 * @param mixed $name class property name
36
	 * @param mixed $value class property value
37
	 */
38
	public function set($name,$value) {
39
		$this->$name = $value;
40
	}
862 aurelien 41
 
1318 aurelien 42
	/**
43
	 * Reduce Spaces
44
	 * This will reduce the string to only allow once space between characters
45
	 * @param string $str : string to reduce space
46
	 * @return string : string with only once space between characters
47
	 */
48
	private function reduce_spaces( $str ) {
49
 
50
		$str = preg_replace("/ {2,}/", ' ', $str );
51
		$str = trim( $str );
862 aurelien 52
 
1318 aurelien 53
		return( $str );
54
	}
862 aurelien 55
 
1318 aurelien 56
	/**
57
	 * Function: parse_auth
58
	 * Purpose: Produce a parsed version of authority of a taxon name
59
	 * @author Tony Rees (Tony.Rees@csiro.au)
60
	 * Date created: March 2008
61
	 * Inputs: authority string as str
62
	 * Remarks:
63
	 *  (1) Performs authority expension of known abbreviated authornames using
64
	 *   table "auth_abbrev_test1" (must be available and populated with relevant content)
65
	 *  (2) Recognises "and", "et", "&" as equivalents (special case for "et al.") - all parsed to ampersand
66
	 *  (3) Recognises (e.g.) "Smith 1980" and "Smith, 1980" as equivalents - comma is removed in these cases
67
	 *  (4) Recognises (e.g.) "F. J. R. Taylor, 1980" and "F.J.R. Taylor, 1980" as equivalents -
68
	 *      extra space after full stops is ignored in these cases
69
	 *  (5) Returns uppercase string, diacritical marks intact
70
	 *
71
	 * @param string $str : authority string
72
	 * @param integer $upcase : convert to uppercase if $upcase = 1
73
	 * @return string : parsed author string
74
	 */
75
	public function parse_auth( $str, $upcase=1 ) {
862 aurelien 76
 
1318 aurelien 77
		$this->debug['parse_auth'][] = "1";
78
		$temp = $str = trim($str);
862 aurelien 79
 
80
  		if ( ($str == NULL) || ($str == '') ) {
81
				$this->debug['parse_auth'][] = "1a";
82
		    return '';
1318 aurelien 83
		}
862 aurelien 84
 
1318 aurelien 85
		if ( ( $temp == null ) || ( $temp == '') ) {
86
			$this->debug['parse_auth'][] = "2a";
87
			return('');
88
		} else {
862 aurelien 89
 
1318 aurelien 90
			$this->debug['parse_auth'][] = "2b";
91
 
92
			// add space after full stops, except at end (NB, will also add spece before some close brackets)
93
			$temp = rtrim( str_replace('.', '. ', $temp) );
94
			$this->debug['parse_auth'][] = "4 (temp:$temp)";
862 aurelien 95
 
1318 aurelien 96
			//normalise "et", "and" to ampersand (et al. is a special case)
97
			// if ( $temp like '% et al%' ) {
98
			if ( preg_match('/ et al/', $temp) ) {
99
				$temp = str_replace(' et al','zzzzz', $temp);
100
				$this->debug['parse_auth'][] = "4a (temp:$temp)";
101
			}
862 aurelien 102
 
1318 aurelien 103
			$temp = str_replace(' et ',' & ', $temp );
104
			$temp = str_replace(' and ',' & ', $temp );
995 aurelien 105
 
1318 aurelien 106
			$temp = str_replace('zzzzz',' et al', $temp);
862 aurelien 107
 
1318 aurelien 108
			$this->debug['parse_auth'][] = "5 (temp:$temp)";
862 aurelien 109
 
1318 aurelien 110
			//remove commas before dates (only)
111
			//	like '%, 17%'
112
			if ( preg_match('/, 17/', $temp) ) {
113
				$temp = str_replace(', 17',' 17', $temp);
114
				$this->debug['parse_auth'][] = "5a (temp:$temp)";
115
			}
116
 
117
			//	like '%, 18%'
118
			if ( preg_match('/, 18/', $temp) ) {
119
				$temp = str_replace(', 18',' 18', $temp);
120
				$this->debug['parse_auth'][] = "5b (temp:$temp)";
121
			}
862 aurelien 122
 
1318 aurelien 123
			//	like '%, 19%'
124
			if ( preg_match('/, 19/', $temp) ) {
125
				$temp = str_replace(', 19',' 19', $temp);
126
				$this->debug['parse_auth'][] = "5c (temp:$temp)";
127
			}
128
 
129
			//	like '%, 20%'
130
			if ( preg_match('/, 20/', $temp) ) {
131
				$temp = str_replace(', 20',' 20', $temp);
132
				$this->debug['parse_auth'][] = "5d (temp:$temp)";
133
			}
862 aurelien 134
 
1318 aurelien 135
			// reduce multiple internal spaces to single space
136
			$temp = $this->reduce_spaces( $temp );
137
 
138
			//	like '% -%'
139
			$temp = str_replace(' -', '-', $temp);
140
 
141
			$this->debug['parse_auth'][] = "6 (temp:$temp)";
142
 
143
			foreach( explode(' ', $temp) as $this_word ) {
144
 
145
				//$this->debug['parse_auth'][] = "7 (this_word:$this_word)";
146
				$elapsed_chars = '';
147
				//	like '(%'
148
				if ( preg_match('/^\(/', $this_word) ) {
149
					$elapsed_chars .= '(';
150
					$this_word = substr( $this_word, 1 );
151
					//$this->debug['parse_auth'][] = "7a (this_word:$this_word) (elapsed_chars:$elapsed_chars)";
862 aurelien 152
				}
153
 
1318 aurelien 154
				// Add back the word to the final translation
155
				$elapsed_chars .= $this_word . ' ';
156
				//$this->debug['parse_auth'][] = "7c (this_word:$this_word) (elapsed_chars:$elapsed_chars)";
862 aurelien 157
			}
1318 aurelien 158
 
159
			$elapsed_chars = $this->reduce_spaces( str_replace(' )', ')', $elapsed_chars) );
160
 
161
			return trim( $elapsed_chars ) ;
162
		}
862 aurelien 163
 
1318 aurelien 164
	}
862 aurelien 165
 
1318 aurelien 166
	/**
167
	 * Function: parse
168
	 * Purpose: Produces parsed version of an input string (scientific name components)
169
	 * @author Tony Rees (Tony.Rees@csiro.au)
170
	 * Date created: June 2007-November 2008
171
	 * Inputs: input string as str (this version presumes genus, genus+species, or
172
	 * genus+species+authority)
173
	 * Outputs: parsed version of input string, for match purposes
174
	 * Remarks:
175
	 *    (1) Removes known text elements e.g.
176
	 *      'aff.', 'cf.', 'subsp.', subgenera if enclosed in brackets, etc. as desired
177
	 *    (2) Removes accented and non A-Z characters other than full stops
178
	 *       (in scientific name portions)
179
	 *    (3) Returns uppercase scientific name (genus + species only)
180
	 *       plus unaltered (presumed) authority
181
	 *     examples;
182
	 *       Anabaena cf. flos-aquae Ralfs ex Born. et Flah. => ANABAENA FLOSAQUAE Ralfs
183
	 *       ex Born. et Flah.
184
	 *       Abisara lemÈe-pauli => ABISARA LEMEEPAULI
185
	 *       Fuc/us Vesiculos2us => FUCUS VESICULOSUS
186
	 *       Buffo ignicolor LacÈpËde, 1788 => BUFFO IGNICOLOR LacÈpËde, 1788
187
	 *       Barbatia (Mesocibota) bistrigata (Dunker, 1866) => BARBATIA BISTRIGATA (Dunker, 1866)
188
	 *    (4) Thus version does not handle genus+author, or genus+species+infraspecies
189
	 *       (second" good" term is presumed to be species epithet, anything after is
190
	 *       considered to be start of the authority), however could be adapted further as required
191
     *         and actually it was done in this version for Tela Botanica
192
	 *    (5) There is a separate function "parse_auth" for normalizing authorities when required
193
	 *      (e.g. for authority comparisons)
194
	 *
195
	 * @param string $str : input string ( genus, genus+species, or genus+species+authority )
196
	 * @return string : parsed string
197
	 */
198
	public function parse( $str = NULL ) {
199
 
200
		unset($this->debug['parse']);
862 aurelien 201
 
1318 aurelien 202
		$temp = '';
203
		$first_str_part = NULL;
204
		$second_str_part = NULL;
205
		$temp_genus = '';
206
		$temp_species = '';
207
		$temp_genus_species = '';
208
		$temp_authority = '';
209
		$temp_infra = '';
862 aurelien 210
 
1318 aurelien 211
		//$this->debug['parse'][] = "1";
862 aurelien 212
 
1318 aurelien 213
		if ( ($str == NULL) || ( trim($str) == '') ) {
214
			//$this->debug[] = "N1a<br>";
215
			return '';
216
		} else {
217
			//	trim any leading, trailing spaces or line feeds
218
			$temp = trim( $str );
219
			//$this->debug['parse'][] = "1b";
220
		}
862 aurelien 221
 
1318 aurelien 222
		if ( $temp == NULL || $temp == '') {
223
			//$this->debug['parse'][] = "2a";
224
			return '';
225
		} else {
226
			//$this->debug['parse'][] = "2b";
862 aurelien 227
 
1318 aurelien 228
			// replace any HTML ampersands
229
			$set = array('%', '&', 'amp;%', 'AMP;%');
230
			$temp = str_replace( $set, '&', $temp );
862 aurelien 231
 
1318 aurelien 232
			//$this->debug['parse'][] = "2b1 (temp:$temp)";
862 aurelien 233
 
1318 aurelien 234
			// remove any content in angle brackets (e.g. html tags - <i>, </i>, etc.)
235
			$html_pattern = "(\<(/?[^\>]+)\>)";
236
			//? This should not just handle html tags but all <*>
237
			$temp = preg_replace( $html_pattern, '', $temp);
238
			//$this->debug['parse'][] = "2b2 (temp:$temp)";
862 aurelien 239
 
1318 aurelien 240
			// if second term (only) is in round brackets, presume it is a subgenus or a comment and remove it
241
			// examples: Barbatia (Mesocibota) bistrigata (Dunker, 1866) => Barbatia bistrigata (Dunker, 1866)
242
			// Barbatia (?) bistrigata (Dunker, 1866) => Barbatia bistrigata (Dunker, 1866)
243
			// (obviously this will not suit genus + author alone, where first part of authorname is in brackets,
244
			// however this is very rare?? and in any case we are not supporting genus+authority in this version)
245
			//if ( $temp like '% (%)%'
246
			$temp = preg_replace( "/ \(\w*\W*\)/", '', $temp, 1 );
247
			//? Not sure if this will catch if
248
			//$this->debug['parse'][] = "2b3 (temp:$temp)";
862 aurelien 249
 
1318 aurelien 250
			// if second term (only) is in square brackets, presume it is a comment and remove it
251
			// example: Aphis [?] ficus Theobald, [1918] => Aphis ficus Theobald, [1918]
252
			//if ( $temp like '% [%]%'
253
			$temp = preg_replace( "/ \[\w*\W*\]/", '', $temp, 1 );
254
			//? Not sure if this will catch if
255
			//$this->debug['parse'][] = "2b4 (temp:$temp)";
862 aurelien 256
 
1318 aurelien 257
			// drop indicators of questionable id's - presume all are lowercase for now (could extend as needed)
258
			$temp = preg_replace( "/ cf /", " ", $temp );
259
			$temp = preg_replace( "/ cf\. /", " ", $temp );
260
			$temp = preg_replace( "/ near /", " ", $temp );
261
			$temp = preg_replace( "/ aff\. /", " ", $temp );
262
			$temp = preg_replace( "/ sp\. /", " ", $temp );
263
			$temp = preg_replace( "/ spp\. /", " ", $temp );
264
			$temp = preg_replace( "/ spp /", " ", $temp );
862 aurelien 265
 
1318 aurelien 266
			//$this->debug['parse'][] = "2b5 (temp:$temp)";
862 aurelien 267
 
1318 aurelien 268
			// eliminate or close up any stray spaces introduced by the above
269
			$temp = $this->reduce_spaces( $temp );
862 aurelien 270
 
1318 aurelien 271
			//$this->debug['parse'][] = "2b6 (temp:$temp)";
862 aurelien 272
 
1318 aurelien 273
			// now presume first element is genus, second (if present) is species, remainder
274
			//   (if present) is authority
275
			// look for genus name
276
			$ar = explode( " ", $temp, 2);
277
			if ( count( $ar ) ) {
278
				$temp_genus = $ar[0];
279
				$temp = @$ar[1];
280
			} else {
281
				$temp_genus = $temp;
282
				$temp = '';
283
			}
862 aurelien 284
 
1318 aurelien 285
			//$this->debug['parse'][] = "2b7 (temp_genus:$temp_genus) (temp:$temp)";
862 aurelien 286
 
1318 aurelien 287
			// look for species epithet and authority
288
			$ar = explode( " ", $temp, 2);
289
			if ( count( $ar ) ) {
290
				$temp_species = $ar[0];
291
				$temp_authority = @$ar[1];
292
			} else {
293
				$temp_species = $temp;
294
				$temp_authority = '';
295
			}
296
            // look for subspecies
862 aurelien 297
 
1318 aurelien 298
            $infras =array('subsp.','var.');
862 aurelien 299
 
1318 aurelien 300
            $temp_authority = preg_replace( "/ssp./", "subsp.", $temp_authority);
301
            $temp_authority = preg_replace( "/ssp /", "subsp.", $temp_authority);
302
            $temp_authority = preg_replace( "/subsp /", "subsp.", $temp_authority);
303
            $temp_authority = preg_replace( "/var /", "var.", $temp_authority);
862 aurelien 304
 
1318 aurelien 305
            $temp_infra_authority = '';
306
            $temp_infra_type = '';
307
            foreach ($infras as $infra) {
308
            	$pos = strpos($temp_authority, $infra);
309
                if ($pos === false) {
310
                	continue;
311
                } else {
312
                	$temp_infra=substr($temp_authority,$pos+strlen($infra));
313
                    $temp_authority=substr($temp_authority,0,$pos);
314
                    $temp_infra=trim($temp_infra);
315
                    $temp_infra_type=$infra;
316
                    // look for infra epithet and authority
317
                    $ar = explode(" ", $temp_infra, 2);
318
                    if ( count( $ar ) ) {
319
                    	$temp_infra = $ar[0];
320
                        $temp_infra_authority = @$ar[1];
862 aurelien 321
                    }
1318 aurelien 322
                    break; // on s'arrete au premier trouve
862 aurelien 323
                }
1318 aurelien 324
			}
862 aurelien 325
 
1318 aurelien 326
			//$this->debug['parse'][] = "2b8 (temp_genus:$temp_genus) (temp_species:$temp_species) (temp_authority:$temp_authority) (temp_infra:$temp_infra) (temp_infra_authority:$temp_infra_authority) (temp:$temp)";
862 aurelien 327
 
1318 aurelien 328
			// replace selected ligatures here (Genus names can contain Æ, OE ligature)
329
			$temp_genus = str_replace( 'Æ', 'AE', $temp_genus);
330
			$temp_species = str_replace( 'Æ', 'AE', $temp_species);
331
			$temp_infra = str_replace( 'Æ', 'AE', $temp_infra );
862 aurelien 332
 
1318 aurelien 333
			//$this->debug['parse'][] = "2b9 (temp_genus:$temp_genus) (temp_species:$temp_species) (temp_authority:$temp_authority) (temp_infra:$temp_infra) (temp_infra_authority:$temp_infra_authority) (temp:$temp)";
862 aurelien 334
 
1318 aurelien 335
            $temp_genus= trim($temp_genus);
336
			$temp_species= trim($temp_species);
337
			$temp_infra= trim($temp_infra );
862 aurelien 338
 
1318 aurelien 339
			// reduce any new multiple internal spaces to single space, if present
340
            $temp_genus= $this->reduce_spaces( $temp_genus );
341
			$temp_species= $this->reduce_spaces( $temp_species );
342
			$temp_infra= $this->reduce_spaces( $temp_infra );
862 aurelien 343
 
1318 aurelien 344
			//$this->debug['parse'][] = "2b10 (temp_genus:$temp_genus) (temp_species:$temp_species) (temp_authority:$temp_authority) (temp_infra:$temp_infra) (temp_infra_authority:$temp_infra_authority) (temp:$temp)";
862 aurelien 345
 
1318 aurelien 346
            if (isset($temp_authority) && ($temp_authority!='') ) {
347
            	$temp_authority=$this->parse_auth($temp_authority);
348
            }
862 aurelien 349
 
1318 aurelien 350
            if (isset($temp_infra_authority) && ($temp_infra_authority!='') ) {
351
            	$temp_infra_authority=$this->parse_auth($temp_infra_authority);
352
            }
353
			//$this->debug['parse'][] = "2b11 (temp_genus:$temp_genus) (temp_species:$temp_species) (temp_authority:$temp_authority) (temp_infra:$temp_infra) (temp_infra_authority:$temp_infra_authority) (temp:$temp)";
354
			return array("genus"=>$temp_genus, "species"=>$temp_species, "authority"=>$temp_authority, "infra"=>$temp_infra, "infra_authority"=>$temp_infra_authority, "infra_type"=>$temp_infra_type);
355
		}
356
	} // End NameParser
357
} // End Class
358
?>