/* *******************************************************************
 * The contents of this file are subject to the Mozilla Public License
 * Version 1.1 (the "License"); you may not use this file except in
 * compliance with the License. You may obtain a copy of the License at
 * http://www.mozilla.org/MPL/
 *
 * Software distributed under the License is distributed on an "AS IS"
 * basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See
 * the License for the specific language governing rights and
 * limitations under the License.
 *
 * The Original Code is the BioWarehouse.
 *
 * The Initial Developer of the Original Code is SRI International.
 * Portions created by SRI International are Copyright (C) 2004.
 * All Rights Reserved.
 ******************************************************************* */
/*
 * MYSQL functions
 */

#ifndef _WH_MYSQL_H
#define _WH_MYSQL_H 1

#include "compound-parse.h"
#include "protein-parse.h"

void
wh_mysql_make_biocyc_dataset(char * name, char * version, char * release_date);
void
wh_mysql_make_biocyc_organism (void);
 
void
wh_mysql_insert_all_subpathway_predecessors();

void
wh_mysql_insert_into_chemical(int compound_wid,
			      struct compound_entry *entry,
			      char * systematic_name,
			      char * cas_registry_numbers,
			      char * smiles,
			      char * formula);

void
wh_mysql_insert_class_into_chemical(int compound_wid, char * class_name);

int
wh_mysql_select_chemical_wid(char * name);

void
wh_mysql_into_reaction(int wid,
		       char * delta_g0, short delta_g0_ind,
		       char * ec_number, short ec_number_ind, short ec_number_proposed_ind,
		       char spontaneous, short spontaneous_ind);
void
wh_mysql_insert_into_reactant(int reaction_wid, int chemical_wid, double coefficient);
void
wh_mysql_insert_into_product(int reaction_wid,int chemical_wid, double coefficient);
int
wh_mysql_select_reaction(char * name);
 
void
wh_mysql_insert_into_protein(int wid, struct protein_entry *entry,
			     double molecular_weight, double molecular_weight_exp);
int
wh_mysql_select_protein(char* name);

void
wh_mysql_update_protein_full(int wid, struct protein_entry *entry,
			     double molecular_weight, double molecular_weight_exp, double pi_calc);

void
wh_mysql_update_protein_aasequence(int wid, char * aa_sequence);

void
wh_mysql_insert_into_enzymatic_reaction(int enzrxn_wid,
					int reaction_wid,
					int protein_wid,
					int complex_wid, short complex_ind,
					char * reaction_direction, short reaction_direction_ind);
int
wh_mysql_select_enzrxn(char* name);

void
wh_mysql_insert_into_feature(int feature_wid, char * class, char * geometry, char * point_type,
                             char * common_name, short common_name_ind,
                             int startpos, short startpos_ind,
                             int endpos, short endpos_ind);
void
wh_mysql_insert_into_gene(int gene_wid,
			  char * common_name,
			  char * unique_id,
			  char direction,
			  char * startpos, short startpos_ind,
			  char * endpos, short endpos_ind,
			  char interrupted, short interrupted_ind);
int
wh_mysql_select_gene(char * name);


void
wh_mysql_insert_into_pathway(int wid, char * name);
void
wh_mysql_update_pathway(int wid, char * name);
void
wh_mysql_insert_into_pathwaylink(int pathway1_wid, int pathway2_wid, int chemical_wid);
void
wh_mysql_insert_into_superpathway(int sub_pathway_wid, int super_pathway_wid);
void
wh_mysql_insert_into_pathwayreaction(int pathway_wid, int reaction_wid, char hypothetical,
				     int prior_reaction_wid, short prior_reaction_wid_ind);
int
wh_mysql_select_pathway(char * name);
#endif