[Biophp-dev] Code for the humunguous IO class

[Serge Gregorio]

Oops, I forgot to send this with my earlier email.  I think
Sean's eFetch etc. code will fall under the category of LIT
parsers and cat-ters (function parse_lit_pubmed() & function
cat_lit_pubmed() the very bottom).

Rgds,

Serge

==================================================================

function autodetect_IO($file, $filetype)
   {
   // code for autodetecting here, returns an array with two elements, the
   // first is the CLASS, and the second element is the IO_FORMAT.
   }

function file_verb($filetype, $operation)
	{	
	switch($filetype)
		{
		case "FILE": return ($operation == "R" ? "parse" : "cat");					
		case "VAR": return ($operation == "R" ? "eval" : "assign");					
		case "SQL": return ($operation == "R" ? "select" : "insert");					 
		case "STDIN": return "input";
		case "STDOUT": return "output";
		}
	}		
	
class IO
   {

        // Constructor function of class IO.
        // Sample usage: $oIO = new IO("gbuna.seq", "file", "R", "Xna", "GenBank");
        //               $oIO = new IO("*", "STDOUT", "W", "Protein", "swp");
 	function IO($file, $filetype, $operation, $class, $IO_format)
	   {
		$filetype = strtoupper($filetype);
		$operation = strtoupper($operation);
		$class = strtoupper($class);
		$IO_format = strtoupper($IO_format);		

                if ( (is_null($class)) or (is_null($IO_format)) )
                   {
                   $auto_result = autodetect_IO($file, $filetype);
                   $class = $auto_result[0];
                   $IO_format = $auto_result[1];
                   }
                elseif ($IO_format == "GENBANK") $IO_format = "GB";
                elseif ($IO_format == "SWISSPROT") $IO_format = "SWP";
           
		if (!(in_array($class, array("SEQ", "XNA", "PROTEIN", "RESTEN", 
                      "SEQALIGN", "ENZYME", "PATHWAY"))))
		   die("ERROR: Invalid value supplied to parameter 'class'!");

		$funcname = file_verb($filetype, $operation) . "_" . strtolower($class) . "_" . $IO_format . "()";
		eval("$funcname;");		
		}				
		
	// XNA readers/writers =======================================================

	// === XNA parsers/cat-ters ==================================================
		
	function parse_xna_gb()
		{
		}
		
	function cat_xna_gb() {}		
		
	// parsers for formats not yet read by GenePHP 2.0
	function parse_xna_srs() {}	
	function cat_xna_srs() {}
	
	// === XNA selectors / insert-ors ==============================================
	
	function select_xna_gphp()
	   {
		}
	
	function insert_xna_gphp()
	 	{
		}		
		
	// === XNA input-ers / output-ers ==============================================		
	
	function input_xna_gb() {}
	function output_xna_gb() {}
	
	function input_xna_srs() {}
	function output_xna_srs() {}	
	
	// Protein readers/writers ====================================================

	// === Protein parsers/cat-ters ===============================================
	
	function parse_protein_gb()
	   {
		}
		
	function cat_protein_gb() {}
	
	function parse_protein_swp() 
		{
		}
		
	function cat_protein_swp() {}		
		
	function parse_protein_pdb()
	   {
		}		
		
	function cat_protein_pdb() {}		
		
	// parsers for formats not yet read by GenePHP 2.0		
	function parse_protein_mmcif() {}
	function cat_protein_mmcif() {}
	
	function parse_protein_pir() {}
	function cat_protein_pir() {}
	
	// === Protein selectors and insert-ors ========================================
		
	function select_protein_gphp()
		{
		}	
		
	function insert_protein_gphp()
		{
		}		
		
	// === Protein input-er and output-ers ========================================		
	
	function input_protein_gb() {}
	function output_protein_gb() {}
	
	function input_protein_swp() {}
	function output_protein_swp() {}
	
	function input_protein_pdb() {}
	function output_protein_pdb() {}
	
	function input_protein_mmcif() {}
	function output_protein_mmcif() {}
	
	function input_protein_pir() {}
	function output_protein_pir() {}	
	
	// SeqAlign readers/writers ====================================================

	// === SeqAlign parsers/cat-ers ===============================================		
				
	function parse_seqalign_aln() 
		{
		}	

	function cat_seqalign_aln() {}
	
	// === SeqAlign input-ers / output-ers ==========================================
	
	function input_seqalign_aln() {}
	function output_seqalign_aln() {}
	
	// RestEn readers/writers ====================================================	
	
	// === RestEn parsers/cat-ers ===============================================		
		
	function eval_resten_gphp()
	   {
		}	
		
   function assign_resten_gphp()
	   {
		}			
		
	// === RestEn selectors/insert-ors =============================================
	
	function select_resten_gphp()
		{
		}
		
	function insert_resten_gphp()
		{
		}		

	// Lit readers/writers =========================================================

	// === Lit parsers/cat-ters ====================================================		
	
        function parse_lit_pubmed() {}		
	function cat_lit_pubmed() {}		
	
	// === Lit parsers/cat-ters ====================================================	
	
	function select_lit_gphp() {}
	function insert_lit_gphp() {}
	
	// === Lit input-ers / output-ers ==============================================
	
	function input_lit_pubmed() {}
	function output_lit_pubmed() {}			
	}	


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