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<?php
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<?php
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/**
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/**
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* Taxamatch-Webservice PHP v1.0.0
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* Taxamatch-Webservice PHP v1.0.0
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* @author Michael Giddens
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* @author Michael Giddens
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* @link http://www.silverbiology.com
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* @link http://www.silverbiology.com
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*/
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*/
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/* Adapation par David Delon Decembre 2010 : gestion sous espece
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/* Adapation par David Delon Decembre 2010 : gestion sous espece
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*/
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*/
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/**
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/**
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* Class NameParser
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* Class NameParser
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* Used to convert a string to a standarized format.
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* Used to convert a string to a standarized format.
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*/
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*/
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class NameParser {
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class NameParser {
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/**
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/**
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* Whether to debug or nor
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* Whether to debug or nor
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* @var bool|integer
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* @var bool|integer
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*/
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*/
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public $debug_flag;
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public $debug_flag;
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/**
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/**
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* Constructor
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* Constructor
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*/
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*/
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public function __construct( ) {
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public function __construct( ) {
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}
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}
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/**
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/**
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* Sets value to the method property
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* Sets value to the method property
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* @param mixed $name class property name
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* @param mixed $name class property name
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* @param mixed $value class property value
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* @param mixed $value class property value
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*/
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*/
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public function set($name,$value) {
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public function set($name,$value) {
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$this->$name = $value;
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$this->$name = $value;
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}
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}
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/**
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/**
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* Reduce Spaces
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* Reduce Spaces
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* This will reduce the string to only allow once space between characters
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* This will reduce the string to only allow once space between characters
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* @param string $str : string to reduce space
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* @param string $str : string to reduce space
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* @return string : string with only once space between characters
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* @return string : string with only once space between characters
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*/
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*/
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private function reduce_spaces( $str ) {
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private function reduce_spaces( $str ) {
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$str = preg_replace("/ {2,}/", ' ', $str );
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$str = preg_replace("/ {2,}/", ' ', $str );
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$str = trim( $str );
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$str = trim( $str );
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return( $str );
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return( $str );
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}
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}
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/**
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/**
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* Function: parse_auth
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* Function: parse_auth
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* Purpose: Produce a parsed version of authority of a taxon name
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* Purpose: Produce a parsed version of authority of a taxon name
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* @author Tony Rees (Tony.Rees@csiro.au)
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* @author Tony Rees (Tony.Rees@csiro.au)
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* Date created: March 2008
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* Date created: March 2008
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* Inputs: authority string as str
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* Inputs: authority string as str
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* Remarks:
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* Remarks:
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* (1) Performs authority expension of known abbreviated authornames using
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* (1) Performs authority expension of known abbreviated authornames using
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* table "auth_abbrev_test1" (must be available and populated with relevant content)
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* table "auth_abbrev_test1" (must be available and populated with relevant content)
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* (2) Recognises "and", "et", "&" as equivalents (special case for "et al.") - all parsed to ampersand
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* (2) Recognises "and", "et", "&" as equivalents (special case for "et al.") - all parsed to ampersand
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* (3) Recognises (e.g.) "Smith 1980" and "Smith, 1980" as equivalents - comma is removed in these cases
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* (3) Recognises (e.g.) "Smith 1980" and "Smith, 1980" as equivalents - comma is removed in these cases
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* (4) Recognises (e.g.) "F. J. R. Taylor, 1980" and "F.J.R. Taylor, 1980" as equivalents -
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* (4) Recognises (e.g.) "F. J. R. Taylor, 1980" and "F.J.R. Taylor, 1980" as equivalents -
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* extra space after full stops is ignored in these cases
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* extra space after full stops is ignored in these cases
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* (5) Returns uppercase string, diacritical marks intact
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* (5) Returns uppercase string, diacritical marks intact
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*
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*
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* @param string $str : authority string
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* @param string $str : authority string
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* @param integer $upcase : convert to uppercase if $upcase = 1
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* @param integer $upcase : convert to uppercase if $upcase = 1
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* @return string : parsed author string
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* @return string : parsed author string
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*/
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*/
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public function parse_auth( $str, $upcase=1 ) {
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public function parse_auth( $str, $upcase=1 ) {
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$this->debug['parse_auth'][] = "1";
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$this->debug['parse_auth'][] = "1";
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$temp = $str = trim($str);
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$temp = $str = trim($str);
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if ( ($str == NULL) || ($str == '') ) {
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if ( ($str == NULL) || ($str == '') ) {
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$this->debug['parse_auth'][] = "1a";
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$this->debug['parse_auth'][] = "1a";
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return '';
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return '';
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}
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}
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if ( ( $temp == null ) || ( $temp == '') ) {
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if ( ( $temp == null ) || ( $temp == '') ) {
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$this->debug['parse_auth'][] = "2a";
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$this->debug['parse_auth'][] = "2a";
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return('');
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return('');
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} else {
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} else {
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$this->debug['parse_auth'][] = "2b";
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$this->debug['parse_auth'][] = "2b";
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// add space after full stops, except at end (NB, will also add spece before some close brackets)
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// add space after full stops, except at end (NB, will also add spece before some close brackets)
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$temp = rtrim( str_replace('.', '. ', $temp) );
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$temp = rtrim( str_replace('.', '. ', $temp) );
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$this->debug['parse_auth'][] = "4 (temp:$temp)";
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$this->debug['parse_auth'][] = "4 (temp:$temp)";
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//normalise "et", "and" to ampersand (et al. is a special case)
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//normalise "et", "and" to ampersand (et al. is a special case)
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// if ( $temp like '% et al%' ) {
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// if ( $temp like '% et al%' ) {
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if ( preg_match('/ et al/', $temp) ) {
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if ( preg_match('/ et al/', $temp) ) {
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$temp = str_replace(' et al','zzzzz', $temp);
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$temp = str_replace(' et al','zzzzz', $temp);
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$this->debug['parse_auth'][] = "4a (temp:$temp)";
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$this->debug['parse_auth'][] = "4a (temp:$temp)";
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}
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}
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$temp = str_replace(' et ',' & ', $temp );
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$temp = str_replace(' et ',' & ', $temp );
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$temp = str_replace(' and ',' & ', $temp );
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$temp = str_replace(' and ',' & ', $temp );
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$temp = str_replace('zzzzz',' et al', $temp);
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$temp = str_replace('zzzzz',' et al', $temp);
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$this->debug['parse_auth'][] = "5 (temp:$temp)";
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$this->debug['parse_auth'][] = "5 (temp:$temp)";
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//remove commas before dates (only)
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//remove commas before dates (only)
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// like '%, 17%'
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// like '%, 17%'
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if ( preg_match('/, 17/', $temp) ) {
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if ( preg_match('/, 17/', $temp) ) {
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$temp = str_replace(', 17',' 17', $temp);
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$temp = str_replace(', 17',' 17', $temp);
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$this->debug['parse_auth'][] = "5a (temp:$temp)";
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$this->debug['parse_auth'][] = "5a (temp:$temp)";
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}
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}
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// like '%, 18%'
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// like '%, 18%'
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if ( preg_match('/, 18/', $temp) ) {
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if ( preg_match('/, 18/', $temp) ) {
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$temp = str_replace(', 18',' 18', $temp);
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$temp = str_replace(', 18',' 18', $temp);
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$this->debug['parse_auth'][] = "5b (temp:$temp)";
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$this->debug['parse_auth'][] = "5b (temp:$temp)";
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}
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}
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// like '%, 19%'
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// like '%, 19%'
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if ( preg_match('/, 19/', $temp) ) {
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if ( preg_match('/, 19/', $temp) ) {
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$temp = str_replace(', 19',' 19', $temp);
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$temp = str_replace(', 19',' 19', $temp);
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$this->debug['parse_auth'][] = "5c (temp:$temp)";
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$this->debug['parse_auth'][] = "5c (temp:$temp)";
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}
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}
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// like '%, 20%'
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// like '%, 20%'
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if ( preg_match('/, 20/', $temp) ) {
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if ( preg_match('/, 20/', $temp) ) {
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$temp = str_replace(', 20',' 20', $temp);
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$temp = str_replace(', 20',' 20', $temp);
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$this->debug['parse_auth'][] = "5d (temp:$temp)";
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$this->debug['parse_auth'][] = "5d (temp:$temp)";
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}
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}
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// reduce multiple internal spaces to single space
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// reduce multiple internal spaces to single space
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$temp = $this->reduce_spaces( $temp );
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136 |
$temp = $this->reduce_spaces( $temp );
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137 |
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// like '% -%'
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// like '% -%'
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$temp = str_replace(' -', '-', $temp);
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$temp = str_replace(' -', '-', $temp);
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140 |
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$this->debug['parse_auth'][] = "6 (temp:$temp)";
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$this->debug['parse_auth'][] = "6 (temp:$temp)";
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foreach( explode(' ', $temp) as $this_word ) {
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foreach( explode(' ', $temp) as $this_word ) {
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144 |
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$this->debug['parse_auth'][] = "7 (this_word:$this_word)";
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- |
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//$this->debug['parse_auth'][] = "7 (this_word:$this_word)";
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146 |
$elapsed_chars = '';
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// like '(%'
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147 |
// like '(%'
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if ( preg_match('/^\(/', $this_word) ) {
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148 |
if ( preg_match('/^\(/', $this_word) ) {
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$elapsed_chars .= '(';
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149 |
$elapsed_chars .= '(';
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$this_word = substr( $this_word, 1 );
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150 |
$this_word = substr( $this_word, 1 );
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$this->debug['parse_auth'][] = "7a (this_word:$this_word) (elapsed_chars:$elapsed_chars)";
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151 |
//$this->debug['parse_auth'][] = "7a (this_word:$this_word) (elapsed_chars:$elapsed_chars)";
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}
|
152 |
}
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|
153 |
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// Add back the word to the final translation
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154 |
// Add back the word to the final translation
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$elapsed_chars .= $this_word . ' ';
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155 |
$elapsed_chars .= $this_word . ' ';
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$this->debug['parse_auth'][] = "7c (this_word:$this_word) (elapsed_chars:$elapsed_chars)";
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156 |
//$this->debug['parse_auth'][] = "7c (this_word:$this_word) (elapsed_chars:$elapsed_chars)";
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| 159 |
}
|
157 |
}
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|
158 |
|
| 161 |
$elapsed_chars = $this->reduce_spaces( str_replace(' )', ')', $elapsed_chars) );
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159 |
$elapsed_chars = $this->reduce_spaces( str_replace(' )', ')', $elapsed_chars) );
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|
160 |
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| 163 |
return trim( $elapsed_chars ) ;
|
161 |
return trim( $elapsed_chars ) ;
|
| 164 |
}
|
162 |
}
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|
163 |
|
| 166 |
}
|
164 |
}
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|
165 |
|
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/**
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166 |
/**
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* Function: parse
|
167 |
* Function: parse
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* Purpose: Produces parsed version of an input string (scientific name components)
|
168 |
* Purpose: Produces parsed version of an input string (scientific name components)
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* @author Tony Rees (Tony.Rees@csiro.au)
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169 |
* @author Tony Rees (Tony.Rees@csiro.au)
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| 172 |
* Date created: June 2007-November 2008
|
170 |
* Date created: June 2007-November 2008
|
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* Inputs: input string as str (this version presumes genus, genus+species, or
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171 |
* Inputs: input string as str (this version presumes genus, genus+species, or
|
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* genus+species+authority)
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172 |
* genus+species+authority)
|
| 175 |
* Outputs: parsed version of input string, for match purposes
|
173 |
* Outputs: parsed version of input string, for match purposes
|
| 176 |
* Remarks:
|
174 |
* Remarks:
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| 177 |
* (1) Removes known text elements e.g.
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175 |
* (1) Removes known text elements e.g.
|
| 178 |
* 'aff.', 'cf.', 'subsp.', subgenera if enclosed in brackets, etc. as desired
|
176 |
* 'aff.', 'cf.', 'subsp.', subgenera if enclosed in brackets, etc. as desired
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| 179 |
* (2) Removes accented and non A-Z characters other than full stops
|
177 |
* (2) Removes accented and non A-Z characters other than full stops
|
| 180 |
* (in scientific name portions)
|
178 |
* (in scientific name portions)
|
| 181 |
* (3) Returns uppercase scientific name (genus + species only)
|
179 |
* (3) Returns uppercase scientific name (genus + species only)
|
| 182 |
* plus unaltered (presumed) authority
|
180 |
* plus unaltered (presumed) authority
|
| 183 |
* examples;
|
181 |
* examples;
|
| 184 |
* Anabaena cf. flos-aquae Ralfs ex Born. et Flah. => ANABAENA FLOSAQUAE Ralfs
|
182 |
* Anabaena cf. flos-aquae Ralfs ex Born. et Flah. => ANABAENA FLOSAQUAE Ralfs
|
| 185 |
* ex Born. et Flah.
|
183 |
* ex Born. et Flah.
|
| 186 |
* Abisara lemÈe-pauli => ABISARA LEMEEPAULI
|
184 |
* Abisara lemÈe-pauli => ABISARA LEMEEPAULI
|
| 187 |
* Fuc/us Vesiculos2us => FUCUS VESICULOSUS
|
185 |
* Fuc/us Vesiculos2us => FUCUS VESICULOSUS
|
| 188 |
* Buffo ignicolor LacÈpËde, 1788 => BUFFO IGNICOLOR LacÈpËde, 1788
|
186 |
* Buffo ignicolor LacÈpËde, 1788 => BUFFO IGNICOLOR LacÈpËde, 1788
|
| 189 |
* Barbatia (Mesocibota) bistrigata (Dunker, 1866) => BARBATIA BISTRIGATA (Dunker, 1866)
|
187 |
* Barbatia (Mesocibota) bistrigata (Dunker, 1866) => BARBATIA BISTRIGATA (Dunker, 1866)
|
| 190 |
* (4) Thus version does not handle genus+author, or genus+species+infraspecies
|
188 |
* (4) Thus version does not handle genus+author, or genus+species+infraspecies
|
| 191 |
* (second" good" term is presumed to be species epithet, anything after is
|
189 |
* (second" good" term is presumed to be species epithet, anything after is
|
| 192 |
* considered to be start of the authority), however could be adapted further as required
|
190 |
* considered to be start of the authority), however could be adapted further as required
|
| 193 |
* and actually it was done in this version for Tela Botanica
|
191 |
* and actually it was done in this version for Tela Botanica
|
| 194 |
* (5) There is a separate function "parse_auth" for normalizing authorities when required
|
192 |
* (5) There is a separate function "parse_auth" for normalizing authorities when required
|
| 195 |
* (e.g. for authority comparisons)
|
193 |
* (e.g. for authority comparisons)
|
| 196 |
*
|
194 |
*
|
| 197 |
* @param string $str : input string ( genus, genus+species, or genus+species+authority )
|
195 |
* @param string $str : input string ( genus, genus+species, or genus+species+authority )
|
| 198 |
* @return string : parsed string
|
196 |
* @return string : parsed string
|
| 199 |
*/
|
197 |
*/
|
| 200 |
public function parse( $str = NULL ) {
|
198 |
public function parse( $str = NULL ) {
|
| 201 |
|
199 |
|
| 202 |
unset($this->debug['parse']);
|
200 |
unset($this->debug['parse']);
|
| 203 |
|
- |
|
| 204 |
|
201 |
|
| 205 |
$temp = '';
|
202 |
$temp = '';
|
| 206 |
$first_str_part = NULL;
|
203 |
$first_str_part = NULL;
|
| 207 |
$second_str_part = NULL;
|
204 |
$second_str_part = NULL;
|
| 208 |
$temp_genus = '';
|
205 |
$temp_genus = '';
|
| 209 |
$temp_species = '';
|
206 |
$temp_species = '';
|
| 210 |
$temp_genus_species = '';
|
207 |
$temp_genus_species = '';
|
| 211 |
$temp_authority = '';
|
208 |
$temp_authority = '';
|
| 212 |
$temp_infra = '';
|
209 |
$temp_infra = '';
|
| 213 |
|
210 |
|
| 214 |
$this->debug['parse'][] = "1";
|
211 |
//$this->debug['parse'][] = "1";
|
| 215 |
|
212 |
|
| 216 |
if ( ($str == NULL) || ( trim($str) == '') ) {
|
213 |
if ( ($str == NULL) || ( trim($str) == '') ) {
|
| 217 |
$this->debug[] = "N1a<br>";
|
214 |
//$this->debug[] = "N1a<br>";
|
| 218 |
return '';
|
215 |
return '';
|
| 219 |
} else {
|
216 |
} else {
|
| 220 |
// trim any leading, trailing spaces or line feeds
|
217 |
// trim any leading, trailing spaces or line feeds
|
| 221 |
$temp = trim( $str );
|
218 |
$temp = trim( $str );
|
| 222 |
$this->debug['parse'][] = "1b";
|
219 |
//$this->debug['parse'][] = "1b";
|
| 223 |
}
|
220 |
}
|
| 224 |
|
221 |
|
| 225 |
if ( $temp == NULL || $temp == '') {
|
222 |
if ( $temp == NULL || $temp == '') {
|
| 226 |
$this->debug['parse'][] = "2a";
|
223 |
//$this->debug['parse'][] = "2a";
|
| 227 |
return '';
|
224 |
return '';
|
| 228 |
} else {
|
225 |
} else {
|
| 229 |
$this->debug['parse'][] = "2b";
|
226 |
//$this->debug['parse'][] = "2b";
|
| 230 |
|
227 |
|
| 231 |
// replace any HTML ampersands
|
228 |
// replace any HTML ampersands
|
| 232 |
$set = array('%', '&', 'amp;%', 'AMP;%');
|
229 |
$set = array('%', '&', 'amp;%', 'AMP;%');
|
| 233 |
$temp = str_replace( $set, '&', $temp );
|
230 |
$temp = str_replace( $set, '&', $temp );
|
| 234 |
|
231 |
|
| 235 |
$this->debug['parse'][] = "2b1 (temp:$temp)";
|
232 |
//$this->debug['parse'][] = "2b1 (temp:$temp)";
|
| 236 |
|
233 |
|
| 237 |
// remove any content in angle brackets (e.g. html tags - <i>, </i>, etc.)
|
234 |
// remove any content in angle brackets (e.g. html tags - <i>, </i>, etc.)
|
| 238 |
$html_pattern = "(\<(/?[^\>]+)\>)";
|
235 |
$html_pattern = "(\<(/?[^\>]+)\>)";
|
| 239 |
//? This should not just handle html tags but all <*>
|
236 |
//? This should not just handle html tags but all <*>
|
| 240 |
$temp = preg_replace( $html_pattern, '', $temp);
|
237 |
$temp = preg_replace( $html_pattern, '', $temp);
|
| 241 |
$this->debug['parse'][] = "2b2 (temp:$temp)";
|
238 |
//$this->debug['parse'][] = "2b2 (temp:$temp)";
|
| 242 |
|
239 |
|
| 243 |
// if second term (only) is in round brackets, presume it is a subgenus or a comment and remove it
|
240 |
// if second term (only) is in round brackets, presume it is a subgenus or a comment and remove it
|
| 244 |
// examples: Barbatia (Mesocibota) bistrigata (Dunker, 1866) => Barbatia bistrigata (Dunker, 1866)
|
241 |
// examples: Barbatia (Mesocibota) bistrigata (Dunker, 1866) => Barbatia bistrigata (Dunker, 1866)
|
| 245 |
// Barbatia (?) bistrigata (Dunker, 1866) => Barbatia bistrigata (Dunker, 1866)
|
242 |
// Barbatia (?) bistrigata (Dunker, 1866) => Barbatia bistrigata (Dunker, 1866)
|
| 246 |
// (obviously this will not suit genus + author alone, where first part of authorname is in brackets,
|
243 |
// (obviously this will not suit genus + author alone, where first part of authorname is in brackets,
|
| 247 |
// however this is very rare?? and in any case we are not supporting genus+authority in this version)
|
244 |
// however this is very rare?? and in any case we are not supporting genus+authority in this version)
|
| 248 |
//if ( $temp like '% (%)%'
|
245 |
//if ( $temp like '% (%)%'
|
| 249 |
$temp = preg_replace( "/ \(\w*\W*\)/", '', $temp, 1 );
|
246 |
$temp = preg_replace( "/ \(\w*\W*\)/", '', $temp, 1 );
|
| 250 |
//? Not sure if this will catch if
|
247 |
//? Not sure if this will catch if
|
| 251 |
$this->debug['parse'][] = "2b3 (temp:$temp)";
|
248 |
//$this->debug['parse'][] = "2b3 (temp:$temp)";
|
| 252 |
|
249 |
|
| 253 |
// if second term (only) is in square brackets, presume it is a comment and remove it
|
250 |
// if second term (only) is in square brackets, presume it is a comment and remove it
|
| 254 |
// example: Aphis [?] ficus Theobald, [1918] => Aphis ficus Theobald, [1918]
|
251 |
// example: Aphis [?] ficus Theobald, [1918] => Aphis ficus Theobald, [1918]
|
| 255 |
//if ( $temp like '% [%]%'
|
252 |
//if ( $temp like '% [%]%'
|
| 256 |
$temp = preg_replace( "/ \[\w*\W*\]/", '', $temp, 1 );
|
253 |
$temp = preg_replace( "/ \[\w*\W*\]/", '', $temp, 1 );
|
| 257 |
//? Not sure if this will catch if
|
254 |
//? Not sure if this will catch if
|
| 258 |
$this->debug['parse'][] = "2b4 (temp:$temp)";
|
255 |
//$this->debug['parse'][] = "2b4 (temp:$temp)";
|
| 259 |
|
256 |
|
| 260 |
// drop indicators of questionable id's - presume all are lowercase for now (could extend as needed)
|
257 |
// drop indicators of questionable id's - presume all are lowercase for now (could extend as needed)
|
| 261 |
$temp = preg_replace( "/ cf /", " ", $temp );
|
258 |
$temp = preg_replace( "/ cf /", " ", $temp );
|
| 262 |
$temp = preg_replace( "/ cf\. /", " ", $temp );
|
259 |
$temp = preg_replace( "/ cf\. /", " ", $temp );
|
| 263 |
$temp = preg_replace( "/ near /", " ", $temp );
|
260 |
$temp = preg_replace( "/ near /", " ", $temp );
|
| 264 |
$temp = preg_replace( "/ aff\. /", " ", $temp );
|
261 |
$temp = preg_replace( "/ aff\. /", " ", $temp );
|
| 265 |
$temp = preg_replace( "/ sp\. /", " ", $temp );
|
262 |
$temp = preg_replace( "/ sp\. /", " ", $temp );
|
| 266 |
$temp = preg_replace( "/ spp\. /", " ", $temp );
|
263 |
$temp = preg_replace( "/ spp\. /", " ", $temp );
|
| 267 |
$temp = preg_replace( "/ spp /", " ", $temp );
|
264 |
$temp = preg_replace( "/ spp /", " ", $temp );
|
| 268 |
|
265 |
|
| 269 |
$this->debug['parse'][] = "2b5 (temp:$temp)";
|
266 |
//$this->debug['parse'][] = "2b5 (temp:$temp)";
|
| 270 |
|
267 |
|
| 271 |
// eliminate or close up any stray spaces introduced by the above
|
268 |
// eliminate or close up any stray spaces introduced by the above
|
| 272 |
$temp = $this->reduce_spaces( $temp );
|
269 |
$temp = $this->reduce_spaces( $temp );
|
| 273 |
|
270 |
|
| 274 |
$this->debug['parse'][] = "2b6 (temp:$temp)";
|
271 |
//$this->debug['parse'][] = "2b6 (temp:$temp)";
|
| 275 |
|
272 |
|
| 276 |
// now presume first element is genus, second (if present) is species, remainder
|
273 |
// now presume first element is genus, second (if present) is species, remainder
|
| 277 |
// (if present) is authority
|
274 |
// (if present) is authority
|
| 278 |
// look for genus name
|
275 |
// look for genus name
|
| 279 |
$ar = explode( " ", $temp, 2);
|
276 |
$ar = explode( " ", $temp, 2);
|
| 280 |
if ( count( $ar ) ) {
|
277 |
if ( count( $ar ) ) {
|
| 281 |
$temp_genus = $ar[0];
|
278 |
$temp_genus = $ar[0];
|
| 282 |
$temp = @$ar[1];
|
279 |
$temp = @$ar[1];
|
| 283 |
} else {
|
280 |
} else {
|
| 284 |
$temp_genus = $temp;
|
281 |
$temp_genus = $temp;
|
| 285 |
$temp = '';
|
282 |
$temp = '';
|
| 286 |
}
|
283 |
}
|
| 287 |
|
284 |
|
| 288 |
$this->debug['parse'][] = "2b7 (temp_genus:$temp_genus) (temp:$temp)";
|
285 |
//$this->debug['parse'][] = "2b7 (temp_genus:$temp_genus) (temp:$temp)";
|
| 289 |
|
286 |
|
| 290 |
// look for species epithet and authority
|
287 |
// look for species epithet and authority
|
| 291 |
$ar = explode( " ", $temp, 2);
|
288 |
$ar = explode( " ", $temp, 2);
|
| 292 |
if ( count( $ar ) ) {
|
289 |
if ( count( $ar ) ) {
|
| 293 |
$temp_species = $ar[0];
|
290 |
$temp_species = $ar[0];
|
| 294 |
$temp_authority = @$ar[1];
|
291 |
$temp_authority = @$ar[1];
|
| 295 |
} else {
|
292 |
} else {
|
| 296 |
$temp_species = $temp;
|
293 |
$temp_species = $temp;
|
| 297 |
$temp_authority = '';
|
294 |
$temp_authority = '';
|
| 298 |
}
|
295 |
}
|
| 299 |
// look for subspecies
|
296 |
// look for subspecies
|
| 300 |
|
297 |
|
| 301 |
$infras =array('subsp.','var.');
|
298 |
$infras =array('subsp.','var.');
|
| 302 |
|
299 |
|
| 303 |
$temp_authority = preg_replace( "/ssp./", "subsp.", $temp_authority);
|
300 |
$temp_authority = preg_replace( "/ssp./", "subsp.", $temp_authority);
|
| 304 |
$temp_authority = preg_replace( "/ssp /", "subsp.", $temp_authority);
|
301 |
$temp_authority = preg_replace( "/ssp /", "subsp.", $temp_authority);
|
| 305 |
$temp_authority = preg_replace( "/subsp /", "subsp.", $temp_authority);
|
302 |
$temp_authority = preg_replace( "/subsp /", "subsp.", $temp_authority);
|
| 306 |
$temp_authority = preg_replace( "/var /", "var.", $temp_authority);
|
303 |
$temp_authority = preg_replace( "/var /", "var.", $temp_authority);
|
| - |
|
304 |
|
| - |
|
305 |
$temp_infra_authority = '';
|
| 307 |
|
306 |
$temp_infra_type = '';
|
| 308 |
foreach ($infras as $infra) {
|
307 |
foreach ($infras as $infra) {
|
| 309 |
$pos = strpos($temp_authority, $infra);
|
308 |
$pos = strpos($temp_authority, $infra);
|
| 310 |
if ($pos === false) {
|
309 |
if ($pos === false) {
|
| 311 |
continue;
|
310 |
continue;
|
| 312 |
}
|
- |
|
| 313 |
else {
|
311 |
} else {
|
| 314 |
$temp_infra=substr($temp_authority,$pos+strlen($infra));
|
312 |
$temp_infra=substr($temp_authority,$pos+strlen($infra));
|
| 315 |
$temp_authority=substr($temp_authority,0,$pos);
|
313 |
$temp_authority=substr($temp_authority,0,$pos);
|
| 316 |
$temp_infra=trim($temp_infra);
|
314 |
$temp_infra=trim($temp_infra);
|
| 317 |
$temp_infra_type=$infra;
|
315 |
$temp_infra_type=$infra;
|
| 318 |
// look for infra epithet and authority
|
316 |
// look for infra epithet and authority
|
| 319 |
$ar = explode(" ", $temp_infra, 2);
|
317 |
$ar = explode(" ", $temp_infra, 2);
|
| 320 |
if ( count( $ar ) ) {
|
318 |
if ( count( $ar ) ) {
|
| 321 |
$temp_infra = $ar[0];
|
319 |
$temp_infra = $ar[0];
|
| 322 |
$temp_infra_authority = @$ar[1];
|
320 |
$temp_infra_authority = @$ar[1];
|
| 323 |
}
|
321 |
}
|
| 324 |
break; // on s'arrete au premier trouve
|
322 |
break; // on s'arrete au premier trouve
|
| 325 |
}
|
323 |
}
|
| 326 |
}
|
324 |
}
|
| 327 |
|
325 |
|
| 328 |
$this->debug['parse'][] = "2b8 (temp_genus:$temp_genus) (temp_species:$temp_species) (temp_authority:$temp_authority) (temp_infra:$temp_infra) (temp_infra_authority:$temp_infra_authority) (temp:$temp)";
|
- |
|
| 329 |
|
326 |
//$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)";
|
| 330 |
|
327 |
|
| 331 |
// replace selected ligatures here (Genus names can contain Æ, OE ligature)
|
328 |
// replace selected ligatures here (Genus names can contain Æ, OE ligature)
|
| 332 |
$temp_genus = str_replace( 'Æ', 'AE', $temp_genus);
|
329 |
$temp_genus = str_replace( 'Æ', 'AE', $temp_genus);
|
| 333 |
$temp_species = str_replace( 'Æ', 'AE', $temp_species);
|
330 |
$temp_species = str_replace( 'Æ', 'AE', $temp_species);
|
| 334 |
$temp_infra = str_replace( 'Æ', 'AE', $temp_infra );
|
331 |
$temp_infra = str_replace( 'Æ', 'AE', $temp_infra );
|
| 335 |
|
- |
|
| 336 |
|
332 |
|
| 337 |
$this->debug['parse'][] = "2b9 (temp_genus:$temp_genus) (temp_species:$temp_species) (temp_authority:$temp_authority) (temp_infra:$temp_infra) (temp_infra_authority:$temp_infra_authority) (temp:$temp)";
|
333 |
//$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)";
|
| 338 |
|
334 |
|
| 339 |
$temp_genus= trim($temp_genus);
|
335 |
$temp_genus= trim($temp_genus);
|
| 340 |
$temp_species= trim($temp_species);
|
336 |
$temp_species= trim($temp_species);
|
| 341 |
$temp_infra= trim($temp_infra );
|
337 |
$temp_infra= trim($temp_infra );
|
| 342 |
|
338 |
|
| 343 |
// reduce any new multiple internal spaces to single space, if present
|
339 |
// reduce any new multiple internal spaces to single space, if present
|
| 344 |
$temp_genus= $this->reduce_spaces( $temp_genus );
|
340 |
$temp_genus= $this->reduce_spaces( $temp_genus );
|
| 345 |
$temp_species= $this->reduce_spaces( $temp_species );
|
341 |
$temp_species= $this->reduce_spaces( $temp_species );
|
| 346 |
$temp_infra= $this->reduce_spaces( $temp_infra );
|
342 |
$temp_infra= $this->reduce_spaces( $temp_infra );
|
| 347 |
|
343 |
|
| 348 |
$this->debug['parse'][] = "2b10 (temp_genus:$temp_genus) (temp_species:$temp_species) (temp_authority:$temp_authority) (temp_infra:$temp_infra) (temp_infra_authority:$temp_infra_authority) (temp:$temp)";
|
344 |
//$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)";
|
| 349 |
|
345 |
|
| 350 |
if (isset($temp_authority) && ($temp_authority!='') ) {
|
346 |
if (isset($temp_authority) && ($temp_authority!='') ) {
|
| 351 |
$temp_authority=$this->parse_auth($temp_authority);
|
347 |
$temp_authority=$this->parse_auth($temp_authority);
|
| 352 |
}
|
348 |
}
|
| 353 |
|
349 |
|
| 354 |
if (isset($temp_infra_authority) && ($temp_infra_authority!='') ) {
|
350 |
if (isset($temp_infra_authority) && ($temp_infra_authority!='') ) {
|
| 355 |
$temp_infra_authority=$this->parse_auth($temp_infra_authority);
|
351 |
$temp_infra_authority=$this->parse_auth($temp_infra_authority);
|
| 356 |
}
|
352 |
}
|
| 357 |
|
- |
|
| 358 |
|
- |
|
| 359 |
$this->debug['parse'][] = "2b11 (temp_genus:$temp_genus) (temp_species:$temp_species) (temp_authority:$temp_authority) (temp_infra:$temp_infra) (temp_infra_authority:$temp_infra_authority) (temp:$temp)";
|
353 |
//$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)";
|
| 360 |
|
- |
|
| 361 |
return array("genus"=>$temp_genus, "species"=>$temp_species, "authority"=>$temp_authority, "infra"=>$temp_infra, "infra_authority"=>$temp_infra_authority, "infra_type"=>$temp_infra_type);
|
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);
|
| 362 |
|
- |
|
| 363 |
}
|
355 |
}
|
| 364 |
|
- |
|
| 365 |
} // End NameParser
|
356 |
} // End NameParser
|
| 366 |
|
- |
|
| 367 |
|
- |
|
| 368 |
|
- |
|
| 369 |
} // End Class
|
357 |
} // End Class
|
| 370 |
|
- |
|
| 371 |
?>
|
358 |
?>
|