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#ifndef _TABLE_STRUCTURE
#define _TABLE_STRUCTURE
#include <mysql++.h>
#include <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
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