<?php

/********************************************************************************************************************************************
 *
 *	PubMed Search
 *	~~~~~~~~~~~~~
 *		Maintained by Joe D: joe@cotch.net
 *		This is version 0.3b, released 2009-03-07
 *
 *		The Author Profile Tool is an addition to PET, AssEd and OAFF.
 *
 *
 *	License
 *	~~~~~~~
 *   		This file is part of PET.
 *
 *    		PET is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by
 *    		the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
 *
 *    		PET is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
 *    		MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.
 *
 *    		You should have received a copy of the GNU General Public License along with PET.  If not, see <http://www.gnu.org/licenses/>.
 *
 *
 *  	User defined settings
 *  	~~~~~~~~~~~~~~~~~~~~~
 */
 
$ncbi_Tool	 = "AssEd";

// Default display settings:
$ps_ShowCounts 		= true;		// make a table of search counts in pubmed and PMC
$ps_ShowAuDetails 	= true;		// make an AuthorProfile (if search is for an author)
$ps_ShowJournals 	= true;		// make a list of most popular journals
$ps_ShowPublishers 	= true;		// make a list of most popular publishers
$ps_ShowLanguages 	= true;		// make a list of languages
$ps_ShowTrends 		= true;		// make a bar chart of publishing trends by year
$ps_ShowAuthors 	= true;		// make a list of (co)authors
$ps_ShowCloud 		= true;		// make a tag cloud from abstracts

// Ignore list for the word cloud
$CloudIgnore = array("and","from","that","the","this","was","for","with","has","have","are","both","but","been","not","these","than","those","thus","which","were","any","their","had","its","there","our","they");

/*
 *		You will also need to edit 'lib/Variables.php'
 *
 *
 *	Changelog
 *	~~~~~~~~~
 *	- v0.3b - 2009-03-07
 *		- Completely rearranged code so that various items can be switched on and off as desired, and the file can be adapted for external use
 *		- Added a world cloud option
 *		- Added IsAuthor switch so that the tool can be used for things other than just AuthorProfiles
 *	- v0.2b - 2008-11-02
 *		- Added languages to highlight tool
 *	- v0.1b - 2008-10-25
 *
 *
 *
 ********************************************************************************************************************************************/
 

 
error_reporting(E_ERROR);
ini_set('display_errors', '1');

require_once("lib/Variables.php");
require_once("lib/SupportFunctions.php");
require_once("lib/DoiResolve.php");

include_once("lib/eSearch.php");
include_once("lib/eSummary.php");
include_once("lib/eFetch.php");
@include_once("lib/BioMedCentral.php");

session_start();


$PhpEntrezTool = new PubmedSearch();				// Run the object


class PubmedSearch
{

	var $SearchTerm;	// string - our search term
	
	var $PostData;		// array  - posted input
	var $IsAuthor;		// t/f    - whether we are searching for an author
	var $ShowCounts;	// t/f    - make a table of search counts in pubmed and PMC
	var $ShowAuDetails;	// t/f    - make an AuthorProfile
	var $ShowJournals;	// t/f    - make a list of most popular journals
	var $ShowPublishers;	// t/f	  - make a list of most popular publishers
	var $ShowLanguages;	// t/f    - make a list of languages
	var $ShowTrends;	// t/f    - make a bar chart of publishing trends by year
	var $ShowAuthors;	// t/f    - make a list of (co)authors
	var $ShowCloud;		// t/f	  - make a tag cloud from abstracts
	var $OrderBy;		// string - order by 'score' or 'date'
	var $HighLight;		// array  - strings to HighLight and score
	
	var $QueryKey;		// string - pubmed session query number
	var $WebEnv;		// string - pubmed session variable
	var $IdLists;		// array  - PMIDs for HighLight terms
	var $Weight;		// array  - weights for HighLight Terms

	var $Title;		// string - page title
	var $Html;		// string - page html
	
	var $Publications;	// array  - details of each pub needed for making the HTML, associated to PMIDs
	var $Abstracts;		// array  - abstracts associated to PMIDs
	var $Scores;

	var $Counts;		// array  - counts for publications in pubmed and PMC over various timescales
	var $Journals;		// array  - count for each journal
	var $Dois;		// array  - count for each top-level DOI, to turn into publishers
	var $Languages;		// array  - count for each language
	var $CoAuthors;		// array  - count for each (co)author
	var $Years;		// array  - count for each year published
	var $Cloud;		// array  - counts for each abstract word
	var $OaIdList;

	var $FullName;		// array  - list of full names found, if IsAuthor is switched on
	var $Emails;		// array  - list of emails, if IsAuthor is switched on
	var $Affiliations;	// array  - list of affiliations, if IsAuthor is switched on
	

	
	function PubmedSearch($SearchTerm = null, $Auto = true)
	{
		
		// Find the SearchTerm
		if     (isset($SearchTerm))		$this->SearchTerm = $SearchTerm;			// look for the term in the input variables
		elseif (isset($_GET['SearchTerm'])) 	$this->SearchTerm = $_GET['SearchTerm'];		// look for the term in the postdata
		elseif (isset($_SESSION['SearchTerm']))	$this->SearchTerm = $_SESSION['SearchTerm'];		// look for the term in the saved session variables

		// If no SearchTerm is found, return an error message
		else {
			$this->Title = "PET: Error";
			$this->Html = "<p><b>Error:</b> No search term specified.</p>\n";
			$this->OutputHtml();
		}
		
		$this->SearchTerm = str_replace("%20", " ", str_replace("_", " ", $this->SearchTerm));		// clean up SearchTerm


		// Extract other variables
		// Order by 'date' or 'score' - postdata needs to be given priority here
		if (isset($_GET['OrderBy'])) $this->OrderBy = $_GET['OrderBy']; 				
		else 			     $this->OrderBy = 'guess';
		// Layout variables -- load the defaults, then overrule
		Global $ps_ShowCounts, $ps_ShowJournals, $ps_ShowPublishers, $ps_ShowLanguages, $ps_ShowTrends, $ps_ShowAuthors, $ps_ShowCloud, $ps_ShowAuDetails;	// Global defaults
		$this->ShowCounts	= $ps_ShowCounts;
		$this->ShowJournals	= $ps_ShowJournals;
		$this->ShowPublishers	= $ps_ShowPublishers;
		$this->ShowLanguages	= $ps_ShowLanguages;
		$this->ShowTrends	= $ps_ShowTrends;
		$this->ShowAuthors	= $ps_ShowAuthors;
		$this->ShowCloud	= $ps_ShowCloud;
		$this->ShowAuDetails	= $ps_ShowAuDetails;

		if (!empty($_GET['IsAuthor'])) $this->IsAuthor	   = true;

		if (isset($_SESSION['PostData'])) {
			$this->PostData = $_SESSION['PostData'];						// Get the session data from other PET services
			if (isset($this->PostData['Searches'])) $this->HighLight = $this->PostData['Searches']; // extract the highlight terms
			if (empty($this->OrderBy) or ($this->OrderBy == "guess")) $this->OrderBy = "score";	// automatically assign OrderBy
		}
		if (empty($this->OrderBy) or ($this->OrderBy == "guess")) $this->OrderBy = "year";		// automatically assign OrderBy
		
		
		
		/*********************/
		// If we're in automatic mode, run the functions
		if ($Auto) {
			if ($this->ShowCounts)		$this->GetBasicCounts();				// Make a table of search counts
			if (isset($this->HighLight)) 	$this->MakeIdLists();					// Get PubMed IDs matching HighLight
			$this->RunSearch();								 	// Run the PubMed Search
			if (!empty($this->FullName)) 	$this->GetFullNameCounts();				// Add to this->Counts the counts for full author names
			if (!empty($this->ShowCloud))   $this->MakeCloud();					// Make a word cloud
			
			$this->PrintResults();									// Return the HTML
		}
	}
	
	
	
	
	/**********************************************************************
	 *  Function: GetBasicCounts(  )
	 *   - Get counts for various timescales from PubMed and PMC
	 *   - Runs automatically when $ShowCounts is 'true'
	 */
	function GetBasicCounts() {
		try {
			$eSearch = new eSearch( 'pubmed', "\"" . $this->SearchTerm . "\"", null, null, 20, 'count');
			$eSearch->Run(2);
			$this->Counts['PubMed (all)'] = $eSearch->Count;
			$this->QueryKey = $eSearch->QueryKey;
			$this->WebEnv   = $eSearch->WebEnv;

			$eSearch = new eSearch( 'pubmed', "\"" . $this->SearchTerm . "\" AND (free full text[sb])", null, null, 20 );
			$eSearch->Run(2);
			$this->Counts['Open Access'] = $eSearch->Count;
			$this->OaIdList = $eSearch->IdList;
			
			$eSearch = new eSearch( 'pubmed', "\"" . $this->SearchTerm . "\"", null, null, 20, 'count');
			$eSearch->RelDate = 3652;
			$eSearch->Run(2);
			$this->Counts['PubMed (10yr)']  = $eSearch->Count;
	
			$eSearch = new eSearch( 'pubmed', "\"" . $this->SearchTerm . "\"", null, null, 20, 'count');
			$eSearch->RelDate = 1826;
			$eSearch->Run(2);		
			$this->Counts['PubMed (5yr)']  = $eSearch->Count;
	
			$eSearch = new eSearch( 'pubmed', "\"" . $this->SearchTerm . "\"", null, null, 20, 'count');
			$eSearch->RelDate = 365;
			$eSearch->Run(2);		
			$this->Counts['PubMed (1yr)']  = $eSearch->Count;
	
			$eSearch = new eSearch( 'pmc', "\"" . $this->SearchTerm . "\"", null, null, 20, 'count');
			$eSearch->Run(2);
			$this->Counts['PMC (all)'] = $eSearch->Count;
			
			$eSearch = new eSearch( 'pmc', "\"" . $this->SearchTerm . "\"", null, null, 20, 'count');
			$eSearch->RelDate = 3652;
			$eSearch->Run(2);		
			$this->Counts['PMC (10yr)']  = $eSearch->Count;
	
			$eSearch = new eSearch( 'pmc', "\"" . $this->SearchTerm . "\"", null, null, 20, 'count');
			$eSearch->RelDate = 1826;
			$eSearch->Run(2);		
			$this->Counts['PMC (5yr)']  = $eSearch->Count;
	
			$eSearch = new eSearch( 'pmc', "\"" . $this->SearchTerm . "\"", null, null, 20, 'count');
			$eSearch->RelDate = 365;
			$eSearch->Run(2);		
			$this->Counts['PMC (1yr)']  = $eSearch->Count;
		}
		catch (Exception $e) {
				$this->Html = "<p>Caught an exception while trying to fetch document summaries (".$e->getMessage().").  Reloading the page to try again...</p>\n";
				$this->OutputHtml(true);
		}
	}
	
	
	
	
	/**********************************************************************
	 *  Function: MakeIdLists(   )
	 *   - Fill $IdLists with arrays of PubMed IDs for the $HighLight terms; 
	 *   - Fill $Weight with weights for each HighLight term;
	 *   - Fill $Counts with counts for each HighLight term;
	 *   - Runs automatically when $HighLight is not empty
	 */

/****** CLEANUP NEEDED: extract SearchStrings somewhere before running anything that relies on them *********/
	function MakeIdLists() {
		foreach ($this->HighLight as $Search) {
			$SearchTerm = "\"" . $this->SearchTerm . "\" (" . $Search['SearchString'] . ")";
			
			try { 
				$eSearch = new eSearch( "pubmed", $SearchTerm, "1900/01/01", date('Y/m/01'), $Search['AtMost'] ); 
				$eSearch->Run(2);
			}
			catch (Exception $e) {
				$this->Html .= "<p><b>Warning</b>: caught an exception when trying to retreive the XML data from PubMed.  I am going to reload the page and hope that the problem goes away.  The error given was: " . $e->getMessage() . "</p>\n";
				$this->SaveReload();
				exit;
			}
			
			if (is_array($eSearch->IdList)) $this->IdLists[$Search['SearchString']] = $eSearch->IdList;
			elseif (is_string($eSearch->IdList)) $this->IdLists[$Search['SearchString']][] = $eSearch->IdList;

			// Calculate the weight to be given to each search -- the weight diminishes logarithmically thus giving additional weight to rare terms			
			$weight[$Search['SearchString']] = 2;
			if ($Search['Count'] < 1000000) $this->Weight[$Search['SearchString']] = 3;
			if ($Search['Count'] < 100000) $this->Weight[$Search['SearchString']] = 4;
			if ($Search['Count'] < 10000) $this->Weight[$Search['SearchString']] = 6;
			if ($Search['Count'] < 1000) $this->Weight[$Search['SearchString']] = 9;
			if ($Search['Count'] < 100) $this->Weight[$Search['SearchString']] = 13;
			
			$this->Counts[$Search['SearchString']] = $eSearch->Count;
		}
	}
	
	
	
	
	/**********************************************************************
	 *  Function: RunSearch(   )
	 *   - Gets the array of PubMed results and processes them
	 */
	function RunSearch() {	
	
		// Run the Search, and extract some info from the results
		$SearchTerm = "\"" . $this->SearchTerm . "\"";
		//if ($this->IsAuthor) $SearchTerm .= "[Author]";			// this breaks things
		$eSearch = new eSearch( 'pubmed', $SearchTerm, null, null, 20 );
		$eSearch->Run(2);
		
		if (isset($_SESSION['ps_Publications'])) $this->Publications = $_SESSION['ps_Publications'];	// check to see if we already have some processed publications saved
		
		$CutOff = $eSearch->Count;
		if ($CutOff > 250) $CutOff = 250;
		
		for ($eFs = (isset($this->Publications) ? count($this->Publications) : 0); $eFs < $CutOff; $eFs += 50) {
			try{
				$eFetch = new eFetch( 'pubmed', $eSearch->QueryKey, $eSearch->WebEnv, $eSearch->Translation, $eFs, 50 );
				$eFetch->Run(1);
				$eSummary = new eSummary( 'pubmed', $eSearch->QueryKey, $eSearch->WebEnv, $eFs, 50 );
				$eSummary->Run(1);
			}
			catch (Exception $e) {
				$eSearch->DeleteCache();
				$eSummary->DeleteCache();
				unset($eSearch);
				try{
					$eSearch = new eSearch( 'pubmed', $SearchTerm, null, null, 20 );
					$eSearch->Run(2);
					$eFetch = new eFetch( 'pubmed', $eSearch->QueryKey, $eSearch->WebEnv, $eSearch->Translation, $eFs, 50);
					$eFetch->Run(1);			
					$eSummary = new eSummary( 'pubmed', $eSearch->QueryKey, $eSearch->WebEnv, $eFs, 50 );
					$eSummary->Run(1);
				}
				catch (Exception $f) {
					$this->Html = "<p>Caught an exception while trying to fetch document summaries (".$e->getMessage().").  Reloading the page to try again...</p>\n";
					$this->SaveReload();
				}
			}			
			
			foreach ($eFetch->Array['PubmedArticle'] as &$Pub) {
				
				// Merge the eSummary into the eFetch
				// - unfortunately, there are a few details in eSummary which aren't available in eFetch
				if (!empty($eSummary->Array['DocSum'][$Pub['MedlineCitation']['PMID']])) $Pub = array_merge($Pub, $eSummary->Array['DocSum'][$Pub['MedlineCitation']['PMID']]);
				unset($eSummary->Array['DocSum'][$Pub['MedlineCitation']['PMID']]);
				
				// Send it off to ExtractPaper for processing
				$this->ExtractPaper($Pub);
				unset($Pub);
			}
		}
	}
	
	
	
	
	/**********************************************************************
	 *  Function: ExtractPaper( Pub - merged array of eSummary and eFetch )
	 *   - Gets the array of PubMed results and processes them
	 */
	function ExtractPaper($Pub)
	{
		/*************************/
		//  Make sure we have the correct associations
		$Pub['Id'] = $Pub['MedlineCitation']['PMID'];		// PubMed ID
		if (empty($Pub['Source'])) {							// Journal
			if (!empty($Pub['MedlineCitation']['Article']['Journal']['ISOAbbreviation'])) $Pub['Source'] = $Pub['MedlineCitation']['Article']['Journal']['ISOAbbreviation'];
			else $Pub['Source'] = $Pub['MedlineCitation']['Article']['Journal']['Title'];
		}


				
		/*************************/
		//  Counts: Journals, Publishers, Languages, Years, (co)Authors
				
		// Journals
		if ($this->ShowJournals) {
			if (isset($this->Journals[$Pub['Source']])) $this->Journals[$Pub['Source']] += 1;
			else $this->Journals[$Pub['Source']] = 1;
			$Pub['Classes'][] = str_replace(" ", "_", $Pub['Source']);
		}
		
		// Publishers
		if ($this->ShowPublishers and isset($Pub['PubmedData']['ArticleIdList']['doi'])) {
			$Doi = explode("/", $Pub['PubmedData']['ArticleIdList']['doi']);
			if (isset($this->Dois[$Doi[0]])) $this->Dois[$Doi[0]] += 1;
			else $this->Dois[$Doi[0]] = 1;
			$Pub['Classes'][] = str_replace(".","", $Doi[0]);
		}
		
		// Languages
		if ($this->ShowLanguages and isset($Pub['LangList']['Lang'])) {
			if (isset($this->Languages[$Pub['LangList']['Lang']])) $this->Languages[$Pub['LangList']['Lang']] += 1;
			else $this->Languages[$Pub['LangList']['Lang']] = 1;
			$Pub['Classes'][] = 'lang-' . $Pub['LangList']['Lang'];
		}

		// Years
		if ($this->ShowTrends and isset($Pub['MedlineCitation']['Article']['Journal']['JournalIssue']['PubDate']['Year'])) {
			if (!empty($this->Years[$Pub['MedlineCitation']['Article']['Journal']['JournalIssue']['PubDate']['Year']])) $this->Years[$Pub['MedlineCitation']['Article']['Journal']['JournalIssue']['PubDate']['Year']] += 1;
			else $this->Years[$Pub['MedlineCitation']['Article']['Journal']['JournalIssue']['PubDate']['Year']] = 1;
		}				
				
		
		/*************************/
		// AuthorProfile
		// - if the search is for an author, build their profile
		if ($this->IsAuthor) { 
			if (count($Pub['MedlineCitation']['Article']['AuthorList']) == 1) { $Pub['FirstAu'] = true; $Pub['LastAu']  = true; }	// If this is a single author publication, our author must be the first author!
			else {
				$i = 1;
				foreach ($Pub['MedlineCitation']['Article']['AuthorList'] as $k => $v) {
					unset($l, $m);
					if (isset($l)) unset($l);
					if (($i == 1) and ($k == $this->SearchTerm)) $Pub['FirstAu'] = true;
					if (isset($v['Initials'])) $l = $v['LastName'] . ' ' . substr($v['Initials'], 0, 1);
					if (isset($v['Initials'])) $m = $v['LastName'] . ' ' . substr($v['ForeName'], 0, 1);
					
					// Find some fullnames...
					if (($k == $this->SearchTerm) OR (isset($l) and ($l == $this->SearchTerm)) OR (isset($m) and ($m == $this->SearchTerm))) {
						$FullName = (isset($v['ForeName']) ? $v['ForeName'] : (isset($v['Initials']) ? $v['Initials'] : 'Anon')) . (isset($v['MiddleName']) ? " " . $v['MiddleName'] : '') . " " . $v['LastName'];
						if (isset($this->FullName[$FullName])) $this->FullName[$FullName] += 1;
						else $this->FullName[$FullName] = 1;
					}
					
					// Make a list of (co)Authors
					elseif ($this->ShowAuthors) {
						if (!empty($this->CoAuthors[$k])) $this->CoAuthors[$k] += 1;
						else $this->CoAuthors[$k] = 1;					
					}
					$i++;
				}
				if ($k == $this->SearchTerm) $Pub['LastAu']  = true;
			}
			
			
			// If we're keeping counts, build them for first/last authorship
			if ($this->ShowCounts) {
				// Count for first author
				if (!empty($Pub['FirstAu'])) {
					if (!empty($this->Counts['First Author'])) $this->Counts['First Author'] += 1;
					else $this->Counts['First Author'] = 1;
					$Pub['Classes'][] = "FirstAu";
				}
				
				// Count for last author
				if (!empty($Pub['LastAu'])) {
					if (!empty($this->Counts['Last Author'])) $this->Counts['Last Author'] += 1;
					else $this->Counts['Last Author'] = 1;
					$Pub['Classes'][] = "LastAu";
				}
			}
			
			
			// If we're going to be building an AuthorProfile, keep a record of affiliations and email addresses
			if ($this->ShowAuDetails) {
				// Affiliations
				if (isset($Pub['MedlineCitation']['Article']['Affiliation']) and (empty($this->Affiliations[$FullName]) OR !in_array($Pub['MedlineCitation']['Article']['Affiliation'], $this->Affiliations[$FullName]))) $this->Affiliations[$FullName][] = $Pub['MedlineCitation']['Article']['Affiliation'];

				// Email addresses 
				if (!empty($Pub['FirstAu']) and !empty($Pub['MedlineCitation']['Article']['Affiliation'])) {
					if (strpos($Pub['MedlineCitation']['Article']['Affiliation'], '@', 0)) {
						$email = strtolower(substr($Pub['MedlineCitation']['Article']['Affiliation'], strrpos($Pub['MedlineCitation']['Article']['Affiliation'], ' ')));
						if (empty($this->Emails[$FullName]) OR !in_array($email, $this->Emails[$FullName])) $this->Emails[$FullName][] = $email;
					}
				}
			
				// If BMC module is installed, we can also try and get email addresses from BioMedCentral
				if (class_exists("BioMedCentral")) $this->GetDetailsFromBmc($Doi[1]);
			}
		}
		
		// Otherwise, just make the list of all authors
		elseif ($this->ShowAuthors) {
			foreach ($Pub['MedlineCitation']['Article']['AuthorList'] as $k => $v) {
				if (!empty($this->CoAuthors[$k])) $this->CoAuthors[$k] += 1;
				else $this->CoAuthors[$k] = 1;					
			}
		}
			
		
		
		/***********  SCORES  ***********/
		if (!empty($Pub['FirstAu']) and !empty($this->PostData['ScoreFirstAu']))   $this->Scores[$Pub['MedlineCitation']['PMID']] = $this->PostData['ScoreFirstAu'];
		elseif (!empty($Pub['LastAu']) and !empty($this->PostData['ScoreLastAu'])) $this->Scores[$Pub['MedlineCitation']['PMID']] = $this->PostData['ScoreLastAu'];
		else 									   $this->Scores[$Pub['MedlineCitation']['PMID']] = 1;
			
		if (!empty($this->PostData['WeightJournal']) and (in_array($Pub['MedlineCitation']['Article']['Journal']['ISOAbbreviation'], $this->PostData['ScoreJournal']) OR in_array($Pub['MedlineCitation']['Article']['Journal']['ISSN'], $this->PostData['ScoreJournal']) OR in_array($Pub['MedlineCitation']['Article']['Journal']['ISOAbbreviation'], $this->PostData['FullJournalName']))) $this->Scores[$Pub['MedlineCitation']['PMID']] = $this->Scores[$Pub['MedlineCitation']['PMID']] * $this->PostData['WeightJournal'];
		if (!empty($this->PostData['ScoreDoi']) and isset($Doi) and in_array($Doi[0], $this->PostData['ScoreDoi'])) $this->Scores[$$Pub['MedlineCitation']['PMID']] = $this->Scores[$Pub['MedlineCitation']['PMID']] * $this->PostData['WeightDoi'];
		// Weight the score by age
		if (isset($this->PostData['ScoreAge']) and $this->PostData['ScoreAge']) {
			$Timestamp = strtotime(implode("/", $Pub['MedlineCitation']['Article']['Journal']['JournalIssue']['PubDate']));
			$Age = time() - $Timestamp;
	 		$Age = $Age / 31570560;	
	 		if ($Age < 1) $Weight = 2; 			// If the publication is less than a year old, double the score
	 		else $Weight = 0.5 + (1 / $Age);		// Otherwise, weight it by 0.5 + (1 / Age)
			$this->Scores[$Pub['MedlineCitation']['PMID']] = $this->Scores[$Pub['MedlineCitation']['PMID']] * $Weight;
		}
		// Weight the score by search matches
		if (!empty($this->IdLists)) {
			foreach ($this->IdLists as $String => $IdList) { 
				if (in_array($Pub['MedlineCitation']['PMID'], $IdList)) {
					$this->Scores[$Pub['MedlineCitation']['PMID']] = $this->Scores[$Pub['MedlineCitation']['PMID']] * $this->Weight[$String]; 
					$Pub['Classes'][] = str_replace(" ", "_", $String);
				}
			}
		}
			
			
		/*************************/
		//  Make stripped array
		$this->Publications[$Pub['Id']] = array(
			"Title"	   => $Pub['MedlineCitation']['Article']['ArticleTitle'],
			"Authors"  => $Pub['MedlineCitation']['Article']['AuthorList'],
			"Source"   => $Pub['Source'],
			"PubDate"  => implode("-", $Pub['MedlineCitation']['Article']['Journal']['JournalIssue']['PubDate']),
			"Citation" => "<i>" . $Pub['Source'] . "</i> ". (isset($Pub['SO']) ? $Pub['SO'] : implode("-", $Pub['MedlineCitation']['Article']['Journal']['JournalIssue']['PubDate'])),
			"Doi"      => $Pub['PubmedData']['ArticleIdList']['doi'],
			"Classes"  => $Pub['Classes'],
		);
		//  Save abstract for mining and HTML things
		$this->Abstracts[$Pub['Id']] = $Pub['MedlineCitation']['Article']['Abstract']['AbstractText'];
	}
	
	
	
	/**********************************************************************
	 *  Function: ExtractPaper( Pub - merged array of eSummary and eFetch )
	 *   - Gets the array of PubMed results and processes them
	 */
	function GetDetailsFromBmc($Doi) {
		$Bmc = new BioMedCentral( "10.1186/" . $Doi );
		$Bmc->GetXmlFile();
		if (isset($Bmc->Error)) return 0;
		$Bmc->XmlToArray();
		
		if (isset($Bmc->Array['fm']['bibl']['aug'][$this->SearchTerm])) {
			if (!empty($Bmc->Array['fm']['bibl']['aug'][$this->SearchTerm]['mi'])) $FullName = array($Bmc->Array['fm']['bibl']['aug'][$this->SearchTerm]['fnm'], $Bmc->Array['fm']['bibl']['aug'][$this->SearchTerm]['mi'], $Bmc->Array['fm']['bibl']['aug'][$this->SearchTerm]['snm']);
			else $FullName = array($Bmc->Array['fm']['bibl']['aug'][$this->SearchTerm]['fnm'], $Bmc->Array['fm']['bibl']['aug'][$this->SearchTerm]['snm']);
			$FullName = implode(" ", $FullName);
			if (isset($this->FullName[$FullName])) $this->FullName[$FullName] += 1;
			else $this->FullName[$FullName] = 1;
			
			if (!empty($Bmc->Array['fm']['bibl']['aug'][$this->SearchTerm]['email'])) {
				$email = strtolower($Bmc->Array['fm']['bibl']['aug'][$this->SearchTerm]['email']);
				if (empty($this->Emails[$FullName]) OR !in_array($email, $this->Emails[$FullName])) $this->Emails[$FullName][] = $email;
			}
	
			if (!empty($Bmc->Array['fm']['bibl']['aug'][$this->SearchTerm]['insr'])) {
				if (isset($Bmc->Array['fm']['bibl']['aug'][$this->SearchTerm]['insr']['iid'])) {
					if (is_array($Bmc->Array['fm']['bibl']['aug'][$this->SearchTerm]['insr']['iid'])) {
						foreach ($Bmc->Array['fm']['bibl']['aug'][$this->SearchTerm]['insr']['iid'] as $v) {
							$AffiliationId  = $v;
							if (!empty($Bmc->Array['fm']['bibl']['insg']['ins'][$AffiliationId])) $Affiliation	= $Bmc->Array['fm']['bibl']['insg']['ins'][$AffiliationId];
							if (empty($this->Affiliations[$FullName]) OR !in_array($Affiliation, $this->Affiliations[$FullName])) $this->Affiliations[$FullName][] = $Affiliation;
						}
					}
					else {
						$AffiliationId  = $Bmc->Array['fm']['bibl']['aug'][$this->SearchTerm]['insr']['iid'];
						if (!empty($Bmc->Array['fm']['bibl']['insg']['ins'][$AffiliationId])) $Affiliation	= $Bmc->Array['fm']['bibl']['insg']['ins'][$AffiliationId];
						if (empty($this->Affiliations[$FullName]) OR !in_array($Affiliation, $this->Affiliations[$FullName])) $this->Affiliations[$FullName][] = $Affiliation;
					}
				}
			}
		}
		unset($Bmc);
		return 1;
	}
	
	
	
	/**********************************************************************
	 *  Function: GetFullNameCounts(  )
	 *   - if this is an AuthorProfile, get the counts for each fullname found
	 */
	function GetFullNameCounts() {		
		// Full name counts
		foreach ($this->FullName as $Fn => $Count) {
			$this->Counts[$Fn] = $Count;
			
			$eSearch = new eSearch( 'pubmed', $Fn, null, null, 20 );
			$eSearch->Run(2);
			if (!empty($eSearch->Count)) {
				//$this->Counts[$Fn]  = $eSearch->Count;
				foreach ($eSearch->IdList as $Id) { if (!empty($this->Publications[$Id])) $this->Publications[$Id]['Classes'][] = str_replace(" ", "_", $Fn); }
			}	
			unset($eSearch);
		}
	}
	
	
	
	/**********************************************************************
	 *  Function: MakeCloud(  )
	 *   - make a tag cloud from abstracts
	 */	
	function MakeCloud($Max = 200, $Min = 60, $Div = " &middot; ", $CutOff = 60)
	{
		Global $CloudIgnore;
		
		// Count the number of words
		foreach ($this->Abstracts as $Abstract) {
			$Abstract = strtolower(strip_chars(array(".",",","-","/",";",":","(",")","[","]"), $Abstract));
			$Words = explode(" ",$Abstract);
			foreach ($Words as $Word) {
				if (in_array($Word, $CloudIgnore) or (strlen($Word) < 3)) continue;
				if (isset($Counts[$Word])) $Counts[$Word] += 1;
				else $Counts[$Word] = 1;
			}
		}
		
		
		// Count the number of values
		arsort($Counts);
		$Vals = 0;
		$i = 0;
		foreach ($Counts as $Count) {
			$i += 1;
			if (isset($PrevCount) and ($Count == $PrevCount)) continue;
			$Vals += 1;
			if ($i >= $CutOff) break;
			$PrevCount = $Count;
		}
		
		// Assign sizes
		unset($PrevCount);
		$Step = ($Max - $Min) / $Vals;
		$Size = $Max;
		$i = 1;
		foreach ($Counts as $Word => $Count) {
			if (isset($PrevCount) and ($Count != $PrevCount)) $Size -= $Step;
			$Sizes[$Word] = $Size;
			if ($i >= $CutOff) break;
			$PrevCount = $Count;
			$i += 1;			
		}
		
		ksort($Sizes);
		
		// Make HTML
		$this->Cloud = "";
		$i = 1;
		foreach ($Sizes as $Word => $Size) {
			$this->Cloud .= "<span style=\"font-size: " . $Size . "%;\"><a href=\"PubmedSearch.php?SearchTerm=(" . $this->SearchTerm . ") AND " . $Word . "\">" . $Word . "</a></span>\n";
			if ($i < count($Sizes)) $this->Cloud .= $Div;
			$i += 1;
		}
	}
	
	
/************************************************************************************************************************************************************


		HTML FUNCTIONS

		- Lists
		- Author Profile
		- World Cloud
		
		- Counts
		- Journals
		- Publishers
		- Languages
		- Trends
		- Authors
		
		- Default unified HTML
		- Page maker
		- SaveReload


*************************************************************************************************************************************************************/
	

	/**********************************************************************
	 *  Function: PrintResults(  )
	 *   - make the HTML for the results
	 */
	function PrintResults()
	{
		$this->Title = $this->SearchTerm;
	
		$this->Html = "<table cellpadding=5 cellspacing=4 border=0 style=\"border: 0px;\">";		// > begin layout table
		$this->Html .= "<tr valign=\"top\">\n<td width=690 rowspan=3 valign=\"top\"> ";			// > begin left colum		
		if ($this->IsAuthor and $this->ShowAuDetails) $this->Html .= $this->HtmlProfiles() . "<br>\n";	// Author profile
		if ($this->ShowCloud) {										// Word cloud
			$this->Html .= "<table class=\"nicetable\" cellpadding=5 cellspacing=4 border=0><tr><th>Cloud</th></tr><tr><td><p align=\"center\">" . $this->Cloud . "</p></td></tr></table><br/>\n";
		}
		$this->Html .= $this->HtmlPubLists();								// Publication lists
		$this->Html .= "</td><td width=202 valign=\"top\">";						// > end left column; begin right column
		if ($this->ShowCounts)		$this->Html .= $this->HtmlCounts();				// Counts
		if ($this->ShowJournals)	$this->Html .= $this->HtmlJournals();				// Journals
		if ($this->ShowPublishers)	$this->Html .= $this->HtmlPublishers();				// Publishers
		if ($this->ShowLanguages)	$this->Html .= $this->HtmlLanguages();				// Languages
		if ($this->ShowAuthors)		$this->Html .= $this->HtmlAuthors();				// (Co)Authors
		if ($this->ShowTrends)		$this->Html .= $this->HtmlTrends();				// Trends
		$this->Html .= "</td></tr></table>\n";								// > end layout table
	
		$this->OutputHtml();
	}
	



	/**********************************************************************
	 *  Function: HtmlPubLists(  )
	 *   - make the HTML for the publication lists
	 *   - this function makes two lists: one ordered by date, the other by score
	 */
	function HtmlPubLists() 
	{		
		// By date
		$DateTable = "<table class=\"nicetable\" cellpadding=5 cellspacing=4 border=0><tr><th>Publication list <span style=\"font-size: 60%; text-decoration: none; font-weight: normal;\">(order by: date | <a href=\"JavaScript:RemoveContent('YearTable'); InsertContent('ScoreTable');\">score</a>)</span></th></tr>\n";
		foreach ($this->Publications as $Pmid => $Pub) {
			unset($AuList);
			
			// Highlight text
			if (isset($this->HighLight)) {
				foreach ($this->HighLight as $Search) { 
					$NewTerms = explode(" ", $Search['SearchString']);
					if (!empty($NewTerms)) $HighlightTerms = array_merge($HighlightTerms, $NewTerms);
				}
				foreach ($HighlightTerms as $Term) { $Pub['Title'] = str_replace($Term, "<span style=\"background: yellow;\">" . $Term . "</span>", $Pub['Title']); }
			}
			
			$Doi = explode("/", $Pub['Doi']);
			if (!empty($Pub['Authors'])) {
				foreach ($Pub['Authors'] as $Short => $Full) {
					if (empty($Full['LastName'])) $Au = "<a href=\"AuthorProfile.php?author=" . str_replace(" ", "_", $Short) . "\">" . $Full['CollectiveName'] . "</a>";
					else {
						if ($Short == $this->SearchTerm) $Au = "<b>" . (isset($Full['ForeName']) ? $Full['ForeName'] : $Full['Initials']) . (isset($Full['MiddleName']) ? " " . $Full['MiddleName'] : '') . " " . $Full['LastName'] . "</b>";
						else $Au = "<a href=\"PubmedSearch.php?SearchTerm=" . str_replace(" ", "_", $Short) . "&IsAuthor=true\">" . (isset($Full['ForeName']) ? $Full['ForeName'] : (isset($Full['Initials']) ? $Full['Initials'] : 'Anon')) . (isset($Full['MiddleName']) ? " " . $Full['MiddleName'] : '') . " " . $Full['LastName'] . "</a>";
					}
					$AuList[] = $Au;
				}
				$AuList = implode(", ", $AuList);
			} else $AuList = "Error - could not extract author list.";
			$DateTable .= "<tr><td class=\"" . implode(" ", $Pub['Classes']) . "\" style=\"border: 1px solid #ddd;\">
					<p>Date: <b>" . $Pub['PubDate'] . "</b></p>
					<p><b>" . $Pub['Title'] . "</b></p>
					<p>" . $AuList . "</p>
					<p>" . ((!empty($this->OaIdList) and in_array($Pmid, $this->OaIdList)) ? "<img src=\"images/padlock.gif\" style=\"margin-bottom: -4px;\" height=\"18px\" alt=\"[Open Access]\" title=\"Free full text to this article is available\"/>" : "") . $Pub['Citation'] . "
					" . (isset($Pub['Doi']) ? "<a href=\"http://dx.doi.org/" . $Pub['Doi'] . "\">[doi:" . $Pub['Doi'] . "]</a>" : "") . "
					<a href=\"http://www.ncbi.nlm.nih.gov/pubmed/" . $Pmid . "\">[pmid:" . $Pmid . "]</a></p>
					</td></tr>\n";
		}
		$DateTable .= "</table>\n";
			
			
		// By score
		arsort($this->Scores);
		$ScoreTable = "<table class=\"nicetable\" cellpadding=5 cellspacing=4 border=0><tr><th>Publication list <span style=\"font-size: 60%; text-decoration: none; font-weight: normal;\">(order by: <a href=\"JavaScript:RemoveContent('ScoreTable'); InsertContent('YearTable');\">date</a> | score)</span></th></tr>\n";
		foreach ($this->Scores as $Pmid => $Score) {
			unset($AuList);
			
			$Pub = $this->Publications[$Pmid];
			
			// Highlight text
			if (isset($this->HighLight)) {
				foreach ($this->HighLight as $Search) { 
					$NewTerms = explode(" ", $Search['SearchString']);
					if (!empty($NewTerms)) $HighlightTerms = array_merge($HighlightTerms, $NewTerms);
				}
				foreach ($HighlightTerms as $Term) { $Pub['Title'] = str_replace($Term, "<span style=\"background: yellow;\">" . $Term . "</span>", $Pub['Title']); }
			}
			
			$Doi = explode("/", $Pub['Doi']);
			if (!empty($Pub['Authors'])) {
				foreach ($Pub['Authors'] as $Short => $Full) {
					if (empty($Full['LastName'])) $Au = "<a href=\"AuthorProfile.php?author=" . str_replace(" ", "_", $Short) . "\">" . $Full['CollectiveName'] . "</a>";
					else {
						if ($Short == $this->SearchTerm) $Au = "<b>" . (isset($Full['ForeName']) ? $Full['ForeName'] : $Full['Initials']) . (isset($Full['MiddleName']) ? " " . $Full['MiddleName'] : '') . " " . $Full['LastName'] . "</b>";
						else $Au = "<a href=\"PubmedSearch.php?SearchTerm=" . str_replace(" ", "_", $Short) . "&IsAuthor=true\">" . (isset($Full['ForeName']) ? $Full['ForeName'] : (isset($Full['Initials']) ? $Full['Initials'] : 'Anon')) . (isset($Full['MiddleName']) ? " " . $Full['MiddleName'] : '') . " " . $Full['LastName'] . "</a>";
					}
					$AuList[] = $Au;
				}
				$AuList = implode(", ", $AuList);
			} else $AuList = "Error - could not extract author list.";
			$ScoreTable .= "<tr><td class=\"" . implode(" ", $Pub['Classes']) . "\" style=\"border: 1px solid #ddd;\">
					<p>Score: <b>" . $Score . "</b></p>
					<p><b>" . $Pub['Title'] . "</b></p>
					<p>" . $AuList . "</p>
					<p>" . ((!empty($this->OaIdList) and in_array($Pmid, $this->OaIdList)) ? "<img src=\"images/padlock.gif\" style=\"margin-bottom: -4px;\" height=\"18px\" alt=\"[Open Access]\" title=\"Free full text to this article is available\"/>" : "") . $Pub['Citation'] . "
					" . (isset($Pub['Doi']) ? "<a href=\"http://dx.doi.org/" . $Pub['Doi'] . "\">[doi:" . $Pub['Doi'] . "]</a>" : "") . "
					<a href=\"http://www.ncbi.nlm.nih.gov/pubmed/" . $Pmid . "\">[pmid:" . $Pmid . "]</a></p>
					</td></tr>\n";
		
		}
		$ScoreTable .= "</table>\n";
		
		
		if ($this->OrderBy == "score") {
			$Html = "<div id=\"ScoreTable\">" . $ScoreTable . "</div>\n";
			$Html .= "<div id=\"YearTable\" style=\"display:none;\">" . $DateTable . "</div>\n";
		}		
		else {
			$Html = "<div id=\"ScoreTable\" style=\"display:none;\">" . $ScoreTable . "</div>\n";
			$Html .= "<div id=\"YearTable\">" . $DateTable . "</div>\n";
		}
		
		return $Html;
	}

			
			
	/**********************************************************************
	 *  Function: HtmlProfiles(  )
	 *   - make the HTML for the publication lists
	 *   - this function makes two lists: one ordered by date, the other by score
	 */
	 function HtmlProfiles()
	 {
		$Html = "<table class=\"nicetable\" cellpadding=4 cellspacing=4 border=0><tr valign=\"top\"><th colspan=\"2\" width=690>Suggested names</th></tr>\n";
		if (!empty($this->FullName)) {
			foreach ($this->FullName as $k => $v) {
				$Html .= "<tr><td><b><a href=\"javascript:highLight('". str_replace(" ", "_", $k) . "')\">" . $k . "</a></b></td>\n";
				$Html .= "<td><p>" . (isset($this->Emails[$k]) ? implode("</p><p>", $this->Emails[$k]) : '') . "</p></td></tr>\n";
				$Html .= "<tr><td colspan=\"2\" style=\"border-bottom: 1px solid #000;\">\n";
				$Html .= "<div id=\"link-". str_replace(" ", "_", $k) . "\" " . ((empty($this->Affiliations[$k]) or (count($this->Affiliations[$k]) <= 3)) ? "style=\"display:none;\"" : "") . "><p><a href=\"javascript:InsertContent('" . str_replace(" ", "_", $k) . "'); RemoveContent('link-" . str_replace(" ", "_", $k) . "');\">Show affiliations.</a></p></div>\n";
				$Html .= "<div id=\"". str_replace(" ", "_", $k) . "\" " . ((!empty($this->Affiliations[$k]) and (count($this->Affiliations[$k]) > 3)) ? "style=\"display:none;\"" : "") . "><p><a href=\"javascript:RemoveContent('" . str_replace(" ", "_", $k) . "'); InsertContent('link-" . str_replace(" ", "_", $k) . "');\">Hide affiliations.</a></p><p>" . (!empty($this->Affiliations[$k]) ? implode("</p><p>", $this->Affiliations[$k]) : "No affiliations found.") . "</p></div></td></tr>\n";
			}
		}
		else $Html .= "<tr><td colspan=\"2\"><p>None found.</p></td></tr>";
		
		$Html .= "</td></tr></table>\n";
		
		return $Html;
	}



	/**********************************************************************
	 *  Function: HtmlCounts(  )
	 *   - make the HTML for the counts
	 */
	function HtmlCounts()
	{		
		$Html .= "<table class=\"nicetable\" cellpadding=4 cellspacing=4 border=0 width=202><th colspan=\"2\">Search counts</th>\n";
		$SearchLinks = array(
			"PubMed (all)" => "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22" . $this->Author . "%22",
			"Open Access" => "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22" . $this->Author . "%22 AND (free full text[sb])",
			"PubMed (10yr)" => "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22" . $this->Author . "%22  AND (&quot;last 10 years&quot;[PDat])",
			"PubMed (5yr)" => "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22" . $this->Author . "%22  AND (&quot;last 5 years&quot;[PDat]",
			"PubMed (1yr)" => "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22" . $this->Author . "%22  AND (&quot;last 1 years&quot;[PDat]",
			"PMC (all)" => "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pmc&Cmd=Search&Term=%22" . $this->Author . "%22",
			"PMC (10yr)" => "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pmc&Cmd=Search&Term=%22" . $this->Author . "%22  AND (&quot;last 10 years&quot;[PDat]",
			"PMC (5yr)" => "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pmc&Cmd=Search&Term=%22" . $this->Author . "%22  AND (&quot;last 5 years&quot;[PDat]",
			"PMC (1yr)" => "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pmc&Cmd=Search&Term=%22" . $this->Author . "%22  AND (&quot;last 1 years&quot;[PDat]",
			"First Author" => "javascript:highLight('FirstAu')",
			"Last Author" => "javascript:highLight('LastAu')",
		);
		
		foreach ($this->Counts as $k => $v) {
			$Html .= "<tr><td>" . ((strlen($k) > 26) ? substr($k, 0, 23) . '...' : $k) . "</td><td>" . (isset($SearchLinks[$k]) ? "<a href=\"" . $SearchLinks[$k] . "\">" . $v . "</a>" : "<a href=\"javascript:highLight('" . str_replace(" ", "_", $k) . "')\">" . $v . "</a>") . "</td></tr>";
		}
		
		$Html .= "</table><br/>";
		return $Html;
	}
		



	/**********************************************************************
	 *  Function: HtmlLanguages(  )
	 *   - make the HTML for the languages
	 */
	function HtmlLanguages()
	{
		$Html = "<table class=\"nicetable\" cellpadding=4 cellspacing=4 border=0 width=202><th colspan=\"2\">Languages</th>\n";
		arsort($this->Languages);
		$i = 0;
		foreach ($this->Languages as $k => $v) {
			$Html .= "<tr><td><a href=\"javascript:highLight('lang-" . str_replace(" ", "_", $k) . "');\">" . $k . "</a></td><td>" . $v . "</td></tr>\n";
			$i += 1;
			if ($i > 20) break;
		}
		
		$Html .= "</table><br/>\n";
		return $Html;
	}	
		
		
	/**********************************************************************
	 *  Function: HtmlJournals(  )
	 *   - make the HTML for the journals
	 */
	function HtmlJournals()
	{
		$Html = "<table class=\"nicetable\" cellpadding=4 cellspacing=4 border=0 width=202><th colspan=\"2\">Favourite journals</th>\n";
		arsort($this->Journals);
		$i = 0;
		foreach ($this->Journals as $k => $v) {
			$Html .= "<tr><td><a href=\"javascript:highLight('" . str_replace(" ", "_", $k) . "');\">" . $k . "</a></td><td><a href=\"http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22". $this->Author . "%22  AND (&quot;" . $k . "&quot;[TA])\">" . $v . "</a></td></tr>\n";
			$i += 1;
			if ($i > 20) break;
		}
		
		$Html .= "</table><br/>\n";
		return $Html;		
	}
		
		
	/**********************************************************************
	 *  Function: HtmlPublishers(  )
	 *   - make the HTML for the publishers
	 */
	function HtmlPublishers()
	{
		Global $PublisherTranslation;
		$Html = "<table class=\"nicetable\" cellpadding=4 cellspacing=4 border=0 width=202><tr><th colspan=\"2\">Favourite publishers</th>\n";
		arsort($this->Dois);
		$i = 0;
		foreach ($this->Dois as $k => $v) {
			$Html .= "<tr><td><a href=\"javascript:highLight('" . str_replace(".", "", $k) . "');\">" . (isset($PublisherTranslation[$k]) ? $PublisherTranslation[$k] : $k) . "</a></td><td>". $v . "</a></td></tr>\n";
			$i += 1;
			if ($i > 20) break;
		}
		
		$Html .= "</table><br/>\n";
		return $Html;
	}


	/**********************************************************************
	 *  Function: HtmlAuthors(  )
	 *   - make the HTML for the authors
	 */
	function HtmlAuthors()
	{
		$Html = "<table class=\"nicetable\" cellpadding=4 cellspacing=4 border=0 width=202><tr><th colspan=\"2\">Co-authors</th>\n";
		arsort($this->CoAuthors);
		$i = 0;
		foreach ($this->CoAuthors as $k => $v) {
			$Html .= "<tr><td><a href=\"PubmedSearch.php?SearchTerm=" . $k . "&IsAuthor=true\">" . $k . "</a></td><td>". $v . "</a></td></tr>\n";
			$i += 1;
			if ($i > 20) break;
		}
		
		$Html .= "</table><br/>\n";
		return $Html;
	}


	/**********************************************************************
	 *  Function: HtmlTrends(  )
	 *   - make the HTML for trends
	 */		
	function HtmlTrends()
	{	 
		$Html = "<table class=\"nicetable\" cellpadding=4 cellspacing=4 border=0 width=202><tr><th colspan=\"2\">History</th>\n";
		
		$h = 0;
		for ($y = date('Y'); $y > 1970; $y--) {
			if (empty($this->Years[$y])) { $Years[$y] = 0; continue; }
			if ($this->Years[$y] > $h) $h = $this->Years[$y];
			$Years[$y] = $this->Years[$y];
			$CutOff = $y;
			unset($this->Years[$y]);
		}
		
		$i = 0;
		foreach ($Years as $y => $c) {
			if ($y < $CutOff) break;
			$width = (135 / $h) * $c;
			$Html .= "<tr><td>" . $y . "</td><td><div style=\"width: " . $width . "; background: url('images/greenpixel.png'); text-align: right;\">" . (!empty($c) ? $c : "&nbsp;") . "</div></td></tr>\n";
		}

		$Html .= "</table><br/>\n";
		return $Html;
	}





	/********************************************************************************************************************************************
	 *	Function: OutputHtml( Reload )
	 *		Formats the page as HTML
	 */
	function OutputHtml($Reload = false)
	{
		$Title  = $this->Title;
		$Html   = $this->Html;
		$SearchTerm = $this->SearchTerm;
		
		if ($Reload) $Reload = "<meta http-equiv=\"refresh\" content=\"0;url=PubmedSearch.php?s=" . session_id() . "&SearchTerm=" . $this->SearchTerm . "\">\n";
		else $Reload = "";
		$NavBar = file_get_contents("NavBar.php");
		
		$Time = round((microtime(true) - $_SESSION['began']), 2);	// Calculate the time elapsed

echo <<<END
			<html>
				<head>
					<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
					<title>$Title</title>
					<link rel="stylesheet" type="text/css" href="style.css"/>
					<script language="JavaScript"><!--
						function changeTdColor(searchClass,theColour) {
							var els = document.getElementsByTagName('td');
							var elsLen = els.length;
							var pattern = new RegExp("(^|\\\\s)"+searchClass+"(\\\\s|$)");
							for (i=0; i<elsLen; i++) {
								var curClasses = els[i].className.split(' ');
								for (var k=0; k<curClasses.length; k++) {
									if (pattern.test(curClasses[k])) {
										els[i].setAttribute('bgcolor',theColour);
									}
								}
							}
							return true;
						}

						var highlightedClass = '';
						function highLight(cssClass) {
							if (highlightedClass) { 
								changeTdColor(highlightedClass, 'white');
							}
							changeTdColor(cssClass, 'yellow');
							highlightedClass = cssClass;
						}

						function RemoveContent(d) {
							document.getElementById(d).style.display = "none";
						}
						function InsertContent(d) {
							document.getElementById(d).style.display = "";
						}
					--></script>
					
					
					$Reload
				</head>
				<body>
					$NavBar
					<div id="main">
					<h1>PubMed Search: $SearchTerm</h1>
					$Html
					<p style="text-align: center;">... time elapsed: $Time seconds.</p>
					<p style="text-align: center;">Content from pubmed used under NLM terms of use (<a href="http://www.ncbi.nlm.nih.gov/About/disclaimer.html">NLM disclaimer</a>).  Content from BioMed Central and the Open-Access padlock (PLoS) used under the terms of the <a href="http://creativecommons.org/licenses/by/2.5/">Creative Commons Attribution license.</a></p>
					</div>
				</body>
			<html>
END;
		exit;


	}	
	



	/********************************************************************************************************************************************
	 *	Function: SaveReload(  )
	 *		Saves session variables and reloads the page
	 */
	function SaveReload()
	{
		$_SESSION['ps_Publications'] = $this->Publications;
		$this->OutputHtml(true);
	}
}
?>