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// =============================================================== //
// //
// File : adGene.h //
// Purpose : Specific defines for ARB genome //
// //
// Coded by Ralf Westram (coder@reallysoft.de) in July 2002 //
// Institute of Microbiology (Technical University Munich) //
// http://www.arb-home.de/ //
// //
// =============================================================== //
#ifndef ADGENE_H
#define ADGENE_H
#ifndef _GLIBCXX_CSTDLIB
#include <cstdlib>
#endif
#define GENOM_ALIGNMENT "ali_genom"
#define GENOM_DB_TYPE "genom_db" // main flag (true = genom db, false/missing=normal db)
#define ARB_HIDDEN "ARB_display_hidden"
/* GEN_position is interpreted as
*
* join( complement[0](start_pos[0]..stop_pos[0]),
* complement[1](start_pos[1]..stop_pos[1]),
* complement[2](start_pos[2], stop_pos[2]),
* ... )
*
* start_pos is always lower than stop_pos
* joined genes on complementary strand are normally ordered backwards
* (i.e. part with highest positions comes first)
*/
struct GEN_position {
int parts;
bool joinable; // true = join(...), false = order(...) aka not joinable or unknown
size_t *start_pos;
size_t *stop_pos;
unsigned char *complement; // ASCII 0 = normal or ASCII 1 = complementary
// [optional elements]
// start_uncertain/stop_uncertain contain one char per part (or NULL which means "all positions are certain")
// meaning of characters:
// '<' = position MIGHT be lower
// '=' = position is certain
// '>' = position MIGHT be higher
// '+' = position is directly BEHIND (but before next base position, i.e. specifies a location between to base positions)
// '-' = position is BEFORE
unsigned char *start_uncertain;
unsigned char *stop_uncertain;
};
#else
#error adGene.h included twice
#endif // ADGENE_H
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