var ENAbrowser = require('embl-ebi-rest').ENAbrowser;

/****
 * Retrieval using organism names
 * [http://www.ebi.ac.uk/ena/about/browser#retrieval_organism_name]
 *
 * taxonSearch(<organism :string>)
 * Retieves entry in ENA Taxonomy XML format
 */ 
var enab = new ENAbrowser(),
	query = { id: "Panthera pardus orientalis" };
	
enab.taxonSearch(query, function(){
	console.log(enab.entry)
});


/**
 * Taxonomy Portal Options
 * [http://www.ebi.ac.uk/ena/about/browser#taxonomy_portal_options]
 *
 * taxonSearch( { <id: string>, <result: string>
 *	 			[, <display: string> --default='xml']
 *				[, <subtree: boolean> --default=false] } );
 * Retieves entry in fasta/xml format.
 *
 * valid options for results:
 * --------------------------
 * sequence_release	: Nucleotide Sequences (EMBL-Bank Release)
 * sequence_update	: Nucleotide Sequences (EMBL-Bank Update)
 * sequence_coding	: Protein-coding sequences in EMBL-Bank
 * sample			: Samples in ENA
 * study			: Studies
 * analysis			: Nucleotide sequence analyses in SRA
 * analysis_study	: Nucleotide sequence analyses in SRA (grouped by study)
 * read_run			: Raw reads in SRA
 * read_experiment	: Raw reads in SRA (grouped by experiment)
 * read_study		: Raw reads in SRA (grouped by study)
 * read_trace		: Capillary Traces in Trace Archive
 */
var enab = new ENAbrowser(),
	query = { id:'109974', result: 'sequence_coding', display: 'fasta'};

enab.taxonSearch(query, function(){
	console.log(enab.entry)
});



/****
* Retrieval using single identifiers
* [http://www.ebi.ac.uk/ena/about/browser#retrieval_single_identifier]
*
* idSearch (<id :string> [, <display :string> --default:'fasta'])
*/
var enab = new ENAbrowser(),
	query = { id: 'A00145' }

enab.idSearch(query, function(){
	console.log(enab.entry)
});


/**
 * Retrieval using multiple identifiers
 * [http://www.ebi.ac.uk/ena/about/browser#retrieval_multiple_identifiers]
 */
var enab = new ENAbrowser(),
query = { id: 'A00145,A00146' }

enab.idSearch(query, function(){
	console.log(enab.entry)
}); 
 

/**
 * Retrieval using an array of identifiers, display='xml'
 */
var enab = new ENAbrowser(),
query = { id: ['A00145','A00146'], display: 'xml' }

enab.idSearch(query, function(){
	console.log(enab.entry)
}); 
 

/**
 * Dependencies
 */
var Dbfetch = require('embl-ebi-rest').Dbfetch;

/**
 * Create a Dbfetch instance and a query object,
 * call get() to asynchronously fetch entry in the instance's 'entry' property.
 * 
 */
var dbfetch = new Dbfetch(),
	query = { db:'uniprotkb', id:'WAP_RAT', format: 'fasta', style: 'raw' };

dbfetch.get(query, function(){
	console.log(dbfetch.entry);
});	


/**
 * The callback receives a 'self' argument referencing the Dbfetch instance object.
 * The following code produces the same results of the previous example. 
 * (It's used in nodeunit testing)
 */
dbfetch.get(query, function(self){
	console.log(self.entry);
});	



/**
 * Fetch multiple ids/accessions in raw/fasta format
 */
var dbfetch = new Dbfetch(),
	multiple_query = {
						db: 'embl',
						id: 'M10051, K00650',
						format: 'fasta',
						style: 'raw'
					 };
			
 dbfetch.get(multiple_query, function(){
 	console.log(dbfetch.entry);
 });	
 
/*
 * fasta2json();
 * Synchronous parse of raw-fasta entries into { id, accession, description, seq } objects.
 * An array of entry-objects is returned for multiple fasta records.
 * The method also stores the parsed object in the instance 'jsonEntry' property
 */
var dbfetch = new Dbfetch(),
multiple_query = { 	db: 'embl',
					id: 'M10051, K00650',
					format: 'fasta',
					style: 'raw'  };

dbfetch.get(multiple_query, function(){
	json = dbfetch.fasta2json();  
	console.log( json );
	console.log( json == dbfetch.jsonEntry ); // true;
});	
 



/********************************************************
 * DbfetchInfo
 * introspection of databases meta-informations
 */

var info = require('embl-ebi-rest').DbfetchInfo;
 
/**
 * Get a list of database names
 */
var db_list = info.db()
  
/**
 * Get the db-meta-info object for a named database
 */
var embl = info.db('embl');
   
/**
 * Get the infoFormatList meta-infos for a given db-meta-info object
 */
var embl_formats = info.formats(embl)

/*
 * Get the format-meta-info-obj for a given db-meta-info-obj and a format-name
 */
var embl_fasta = info.format(embl, 'fasta');

/**
 * Get the style-meta-info-obj for a given format-meta-info-obj
 */
 var embl_fasta_styles = info.styles(embl_fasta);