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<?php
// declare(encoding='UTF-8');
/**
 * Classe permettant de convertir une chaine d'un nom scientifique en un format standard.
 *
 * Source orignale :
 * Taxamatch-Webservice PHP v1.0.0
 * @author Michael Giddens
 * @link http://www.silverbiology.com
 *
 *
 * @internal   Mininum PHP version : 5.2
 * @category   CEL
 * @package    Services
 * @subpackage Bibliothèques
 * @version    0.1
 * @author     Mathias CHOUET <mathias@tela-botanica.org>
 * @author     David DELON <david@clapas.net>
 * @author     Jean-Pascal MILCENT <jpm@tela-botanica.org>
 * @author     Aurelien PERONNET <aurelien@tela-botanica.org>
 * @license    GPL v3 <http://www.gnu.org/licenses/gpl.txt>
 * @license    CECILL v2 <http://www.cecill.info/licences/Licence_CeCILL_V2-en.txt>
 * @copyright  1999-2014 Tela Botanica <accueil@tela-botanica.org>
 */
class NameParser {

        /**
         * Whether to debug or nor
         * @var bool|integer
         */
        public $debug_flag;

        /**
         * Sets value to the method property
         * @param mixed $name class property name
         * @param mixed $value class property value
         */
        public function set($name, $value) {
                $this->$name = $value;
        }

        /**
         * Reduce Spaces
         * This will reduce the string to only allow once space between characters
         * @param string $str : string to reduce space
         * @return string : string with only once space between characters
         */
        private function reduce_spaces($str) {
                $str = preg_replace('/ {2,}/', ' ', $str );
                $str = trim( $str );
                return( $str );
        }

        /**
         * Function: parse_auth
         * Purpose: Produce a parsed version of authority of a taxon name
         * @author Tony Rees (Tony.Rees@csiro.au)
         * Date created: March 2008
         * Inputs: authority string as str
         * Remarks:
         *  (1) Performs authority expension of known abbreviated authornames using
         *   table "auth_abbrev_test1" (must be available and populated with relevant content)
         *  (2) Recognises "and", "et", "&" as equivalents (special case for "et al.") - all parsed to ampersand
         *  (3) Recognises (e.g.) "Smith 1980" and "Smith, 1980" as equivalents - comma is removed in these cases
         *  (4) Recognises (e.g.) "F. J. R. Taylor, 1980" and "F.J.R. Taylor, 1980" as equivalents -
         *      extra space after full stops is ignored in these cases
         *  (5) Returns uppercase string, diacritical marks intact
         *
         * @param string $str : authority string
         * @param integer $upcase : convert to uppercase if $upcase = 1
         * @return string : parsed author string
         */
        public function parse_auth($str, $upcase = 1) {
                $this->debug['parse_auth'][] = "1";
                $temp = $str = trim($str);

                if ( ($str == NULL) || ($str == '') ) {
                                $this->debug['parse_auth'][] = "1a";
                    return '';
                }

                if ( ( $temp == null ) || ( $temp == '') ) {
                        $this->debug['parse_auth'][] = "2a";
                        return('');
                } else {

                        $this->debug['parse_auth'][] = "2b";

                        // add space after full stops, except at end (NB, will also add spece before some close brackets)
                        $temp = rtrim( str_replace('.', '. ', $temp) );
                        $this->debug['parse_auth'][] = "4 (temp:$temp)";

                        //normalise "et", "and" to ampersand (et al. is a special case)
                        // if ( $temp like '% et al%' ) {
                        if ( preg_match('/ et al/', $temp) ) {
                                $temp = str_replace(' et al','zzzzz', $temp);
                                $this->debug['parse_auth'][] = "4a (temp:$temp)";
                        }

                        $temp = str_replace(' et ',' & ', $temp );
                        $temp = str_replace(' and ',' & ', $temp );

                        $temp = str_replace('zzzzz',' et al', $temp);

                        $this->debug['parse_auth'][] = "5 (temp:$temp)";

                        //remove commas before dates (only)
                        //      like '%, 17%'
                        if ( preg_match('/, 17/', $temp) ) {
                                $temp = str_replace(', 17',' 17', $temp);
                                $this->debug['parse_auth'][] = "5a (temp:$temp)";
                        }

                        //      like '%, 18%'
                        if ( preg_match('/, 18/', $temp) ) {
                                $temp = str_replace(', 18',' 18', $temp);
                                $this->debug['parse_auth'][] = "5b (temp:$temp)";
                        }

                        //      like '%, 19%'
                        if ( preg_match('/, 19/', $temp) ) {
                                $temp = str_replace(', 19',' 19', $temp);
                                $this->debug['parse_auth'][] = "5c (temp:$temp)";
                        }

                        //      like '%, 20%'
                        if ( preg_match('/, 20/', $temp) ) {
                                $temp = str_replace(', 20',' 20', $temp);
                                $this->debug['parse_auth'][] = "5d (temp:$temp)";
                        }

                        // reduce multiple internal spaces to single space
                        $temp = $this->reduce_spaces( $temp );

                        //      like '% -%'
                        $temp = str_replace(' -', '-', $temp);

                        $this->debug['parse_auth'][] = "6 (temp:$temp)";

                        foreach (explode(' ', $temp) as $this_word) {
                                //$this->debug['parse_auth'][] = "7 (this_word:$this_word)";
                                $elapsed_chars = '';
                                //      like '(%'
                                if ( preg_match('/^\(/', $this_word) ) {
                                        $elapsed_chars .= '(';
                                        $this_word = substr( $this_word, 1 );
                                        //$this->debug['parse_auth'][] = "7a (this_word:$this_word) (elapsed_chars:$elapsed_chars)";
                                }

                                // Add back the word to the final translation
                                $elapsed_chars .= $this_word . ' ';
                                //$this->debug['parse_auth'][] = "7c (this_word:$this_word) (elapsed_chars:$elapsed_chars)";
                        }
                        $elapsed_chars = $this->reduce_spaces( str_replace(' )', ')', $elapsed_chars) );
                        return trim( $elapsed_chars ) ;
                }
        }

        /**
         * Function: parse
         * Purpose: Produces parsed version of an input string (scientific name components)
         * @author Tony Rees (Tony.Rees@csiro.au)
         * Date created: June 2007-November 2008
         * Inputs: input string as str (this version presumes genus, genus+species, or
         * genus+species+authority)
         * Outputs: parsed version of input string, for match purposes
         * Remarks:
         *    (1) Removes known text elements e.g.
         *      'aff.', 'cf.', 'subsp.', subgenera if enclosed in brackets, etc. as desired
         *    (2) Removes accented and non A-Z characters other than full stops
         *       (in scientific name portions)
         *    (3) Returns uppercase scientific name (genus + species only)
         *       plus unaltered (presumed) authority
         *     examples;
         *       Anabaena cf. flos-aquae Ralfs ex Born. et Flah. => ANABAENA FLOSAQUAE Ralfs
         *       ex Born. et Flah.
         *       Abisara lemÈe-pauli => ABISARA LEMEEPAULI
         *       Fuc/us Vesiculos2us => FUCUS VESICULOSUS
         *       Buffo ignicolor LacÈpËde, 1788 => BUFFO IGNICOLOR LacÈpËde, 1788
         *       Barbatia (Mesocibota) bistrigata (Dunker, 1866) => BARBATIA BISTRIGATA (Dunker, 1866)
         *    (4) Thus version does not handle genus+author, or genus+species+infraspecies
         *       (second" good" term is presumed to be species epithet, anything after is
         *       considered to be start of the authority), however could be adapted further as required
     *         and actually it was done in this version for Tela Botanica
         *    (5) There is a separate function "parse_auth" for normalizing authorities when required
         *      (e.g. for authority comparisons)
         *
         * @param string $str : input string ( genus, genus+species, or genus+species+authority )
         * @return string : parsed string
         */
        public function parse( $str = NULL ) {
                unset($this->debug['parse']);
                $temp = '';
                $first_str_part = NULL;
                $second_str_part = NULL;
                $temp_genus = '';
                $temp_species = '';
                $temp_genus_species = '';
                $temp_authority = '';
                $temp_infra = '';

                //$this->debug['parse'][] = "1";

                if ( ($str == NULL) || ( trim($str) == '') ) {
                        //$this->debug[] = "N1a<br>";
                        return '';
                } else {
                        //      trim any leading, trailing spaces or line feeds
                        $temp = trim( $str );
                        //$this->debug['parse'][] = "1b";
                }

                if ( $temp == NULL || $temp == '') {
                        //$this->debug['parse'][] = "2a";
                        return '';
                } else {
                        //$this->debug['parse'][] = "2b";

                        // replace any HTML ampersands
                        $set = array('%', '&', 'amp;%', 'AMP;%');
                        $temp = str_replace( $set, '&', $temp );

                        //$this->debug['parse'][] = "2b1 (temp:$temp)";

                        // remove any content in angle brackets (e.g. html tags - <i>, </i>, etc.)
                        $html_pattern = '(\<(/?[^\>]+)\>)';
                        //? This should not just handle html tags but all <*>
                        $temp = preg_replace( $html_pattern, '', $temp);
                        //$this->debug['parse'][] = "2b2 (temp:$temp)";

                        // if second term (only) is in round brackets, presume it is a subgenus or a comment and remove it
                        // examples: Barbatia (Mesocibota) bistrigata (Dunker, 1866) => Barbatia bistrigata (Dunker, 1866)
                        // Barbatia (?) bistrigata (Dunker, 1866) => Barbatia bistrigata (Dunker, 1866)
                        // (obviously this will not suit genus + author alone, where first part of authorname is in brackets,
                        // however this is very rare?? and in any case we are not supporting genus+authority in this version)
                        //if ( $temp like '% (%)%'
                        $temp = preg_replace( '/ \(\w*\W*\)/', '', $temp, 1 );
                        //? Not sure if this will catch if
                        //$this->debug['parse'][] = "2b3 (temp:$temp)";

                        // if second term (only) is in square brackets, presume it is a comment and remove it
                        // example: Aphis [?] ficus Theobald, [1918] => Aphis ficus Theobald, [1918]
                        //if ( $temp like '% [%]%'
                        $temp = preg_replace( '/ \[\w*\W*\]/', '', $temp, 1 );
                        //? Not sure if this will catch if
                        //$this->debug['parse'][] = "2b4 (temp:$temp)";

                        // drop indicators of questionable id's - presume all are lowercase for now (could extend as needed)
                        $temp = preg_replace('/ cf /', ' ', $temp );
                        $temp = preg_replace('/ cf\. /', ' ', $temp );
                        $temp = preg_replace('/ near /', ' ', $temp );
                        $temp = preg_replace('/ aff\. /', ' ', $temp );
                        $temp = preg_replace('/ sp\. /', ' ', $temp );
                        $temp = preg_replace('/ spp\. /', ' ', $temp );
                        $temp = preg_replace('/ spp /', ' ', $temp );

                        //$this->debug['parse'][] = "2b5 (temp:$temp)";

                        // eliminate or close up any stray spaces introduced by the above
                        $temp = $this->reduce_spaces( $temp );

                        //$this->debug['parse'][] = "2b6 (temp:$temp)";

                        // now presume first element is genus, second (if present) is species, remainder
                        //   (if present) is authority
                        // look for genus name
                        $ar = explode(' ', $temp, 2);
                        if ( count( $ar ) ) {
                                $temp_genus = $ar[0];
                                $temp = @$ar[1];
                        } else {
                                $temp_genus = $temp;
                                $temp = '';
                        }

                        //$this->debug['parse'][] = "2b7 (temp_genus:$temp_genus) (temp:$temp)";

                        // look for species epithet and authority
                        $ar = explode(' ', $temp, 2);
                        if ( count( $ar ) ) {
                                $temp_species = $ar[0];
                                $temp_authority = @$ar[1];
                        } else {
                                $temp_species = $temp;
                                $temp_authority = '';
                        }
                        // look for subspecies

                        $infras =array('subsp.','var.');

                        $temp_authority = preg_replace( "/ssp./", "subsp.", $temp_authority);
                        $temp_authority = preg_replace( "/ssp /", "subsp.", $temp_authority);
                        $temp_authority = preg_replace( "/subsp /", "subsp.", $temp_authority);
                        $temp_authority = preg_replace( "/var /", "var.", $temp_authority);

                        $temp_infra_authority = '';
                        $temp_infra_type = '';
                        foreach ($infras as $infra) {
                                $pos = strpos($temp_authority, $infra);
                                if ($pos === false) {
                                        continue;
                                } else {
                                        $temp_infra=substr($temp_authority,$pos+strlen($infra));
                                        $temp_authority=substr($temp_authority,0,$pos);
                                        $temp_infra=trim($temp_infra);
                                        $temp_infra_type=$infra;
                                        // look for infra epithet and authority
                                        $ar = explode(' ', $temp_infra, 2);
                                        if ( count( $ar ) ) {
                                                $temp_infra = $ar[0];
                                                $temp_infra_authority = @$ar[1];
                                        }
                                        break; // on s'arrete au premier trouve
                                }
                        }

                        //$this->debug['parse'][] = "2b8 (temp_genus:$temp_genus) (temp_species:$temp_species) (temp_authority:$temp_authority) (temp_infra:$temp_infra) (temp_infra_authority:$temp_infra_authority) (temp:$temp)";

                        // replace selected ligatures here (Genus names can contain Æ, OE ligature)
                        $temp_genus = str_replace( 'Æ', 'AE', $temp_genus);
                        $temp_species = str_replace( 'Æ', 'AE', $temp_species);
                        $temp_infra = str_replace( 'Æ', 'AE', $temp_infra );

                        //$this->debug['parse'][] = "2b9 (temp_genus:$temp_genus) (temp_species:$temp_species) (temp_authority:$temp_authority) (temp_infra:$temp_infra) (temp_infra_authority:$temp_infra_authority) (temp:$temp)";

                        $temp_genus= trim($temp_genus);
                        $temp_species= trim($temp_species);
                        $temp_infra= trim($temp_infra );

                        // reduce any new multiple internal spaces to single space, if present
                        $temp_genus= $this->reduce_spaces( $temp_genus );
                        $temp_species= $this->reduce_spaces( $temp_species );
                        $temp_infra= $this->reduce_spaces( $temp_infra );

                        //$this->debug['parse'][] = "2b10 (temp_genus:$temp_genus) (temp_species:$temp_species) (temp_authority:$temp_authority) (temp_infra:$temp_infra) (temp_infra_authority:$temp_infra_authority) (temp:$temp)";

                        if (isset($temp_authority) && ($temp_authority!='') ) {
                                $temp_authority=$this->parse_auth($temp_authority);
                        }

                        if (isset($temp_infra_authority) && ($temp_infra_authority!='') ) {
                                $temp_infra_authority=$this->parse_auth($temp_infra_authority);
                        }
                        //$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)";
                        return array("genus"=>$temp_genus, "species"=>$temp_species, "authority"=>$temp_authority, "infra"=>$temp_infra, "infra_authority"=>$temp_infra_authority, "infra_type"=>$temp_infra_type);
                }
        }
}