table_structure.h

/*
 * table_structure.h
 *
 * License: Artistic License, see file LICENSE.TXT or 
 *          https://opensource.org/licenses/artistic-license-1.0
 */
 
#ifndef _TABLE_STRUCTURE
#define _TABLE_STRUCTURE
 
#include <mysql++/mysql++.h>
#include <mysql++/ssqls.h>
#include <string>
#include <cstring>
#include <stdlib.h>
using namespace std;
 
/*
 * tables structure for comparative gene prediction, all in one table, one database for all species
 */
sql_create_6(genomes,
         1,6,
         int,seqid,
         string,dnaseq,
         string,seqname,
         int,start,
         int,end,
         string,species)
sql_create_2(speciesnames,
         1,2,
         int,speciesid,
         string,speciesname)
sql_create_3(seqnames,
         1,3,
         int,seqnr,
         int,speciesid,
         string,seqname)
sql_create_14(hints,
          1,14,
          int,hintid,
          int,speciesid,
          int,seqnr,
          string,source,
          int,start,
          int,end,
          double,score,
          int,type,
          string,strand,
          string,frame,
          int,priority,
          string,grp,
          int,mult,
          string,esource)
// The database schema is an excerpt from ENSEMBL:
// http://www.ensembl.org/info/docs/api/core/core_schema.html
// The following is calling a very complex macro which will create
// the table structure row in a STL container.
sql_create_2(dna,
         1, 2,
         int,seq_region_id,
         std::string, sequence)  
sql_create_4(seq_region,
         1,4,
         int,seq_region_id,
         std::string,name,
         std::string,coord_system_id,
         int,length)
sql_create_6(assembly,
         1, 6,
         int, asm_seq_region_id,
         int, cmp_seq_region_id,
         int, asm_start,
         int, asm_end,
         int, cmp_start,
         int, cmp_end)
// omit species name, assume every species has its own database,
// 'name' is the shared key in 'seq_region' table which refers to 'chrName' in augustus
// it could also be scaffold.'query_region' is defined in database 'cmpproject', so is 'augustus-gff'
 
 
#endif //_TABLE_STRUCTURE