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// =============================================================== //
// //
// File : RNA3D_StructureData.hxx //
// Purpose : //
// //
// Institute of Microbiology (Technical University Munich) //
// http://www.arb-home.de/ //
// //
// =============================================================== //
#ifndef RNA3D_STRUCTUREDATA_HXX
#define RNA3D_STRUCTUREDATA_HXX
#ifndef ARBDB_H
#include <arbdb.h>
#endif
#define SAI 0
#define SEARCH 1
#define SSU_16S 1
#define LSU_23S 2
#define LSU_5S 3
#define _1PNU 1
#define _1VOR 2
#define _1C2W 3
// DisplayLists
enum {
STRUCTURE_BACKBONE = 300,
STRUCTURE_BACKBONE_CLR,
HELIX_NUMBERS,
HELIX_NUMBERS_POINTS,
HELIX_A, HELIX_G, HELIX_C, HELIX_U,
UNPAIRED_HELIX_A, UNPAIRED_HELIX_G, UNPAIRED_HELIX_C, UNPAIRED_HELIX_U,
NON_HELIX_A, NON_HELIX_G, NON_HELIX_C, NON_HELIX_U,
STRUCTURE_POS,
STRUCTURE_POS_ANCHOR,
MAP_SPECIES_BASE_DIFFERENCE,
MAP_SPECIES_BASE_DIFFERENCE_POS, MAP_SPECIES_BASE_DIFFERENCE_POS_ANCHOR,
MAP_SPECIES_BASE_A, MAP_SPECIES_BASE_G, MAP_SPECIES_BASE_C, MAP_SPECIES_BASE_U,
MAP_SPECIES_DELETION, MAP_SPECIES_MISSING,
MAP_SPECIES_INSERTION_POINTS, MAP_SPECIES_INSERTION_BASES, MAP_SPECIES_INSERTION_BASES_ANCHOR,
MAP_SAI_TO_STRUCTURE,
MAP_SEARCH_STRINGS_TO_STRUCTURE, MAP_SEARCH_STRINGS_BACKBONE,
ECOLI_CURSOR_POSITION,
ECOLI_TERTIARY_INTRACTION_PSEUDOKNOTS,
ECOLI_TERTIARY_INTRACTION_TRIPLE_BASES
};
struct Struct2Dplus3D {
char base;
char mask;
char code;
int pos;
int helixNr;
float x;
float y;
float z;
struct Struct2Dplus3D *next;
};
struct Struct2Dinfo {
char base; // Nucleotide
char mask; // Helix mask [..<<<..>>>]
char code; // Helix code (H)elix (N)on-helix (S)tart (E)nd
int pos; // Base Position
int helixNr; // Helix Number
struct Struct2Dinfo *next;
};
struct Struct3Dinfo {
float x;
float y;
float z;
char base;
int pos;
struct Struct3Dinfo *next;
};
struct HelixNrInfo {
float x, y, z;
int helixNr;
struct HelixNrInfo *next;
};
struct CurrSpecies {
float x;
float y;
float z;
int pos;
char base;
struct CurrSpecies *next;
};
struct Insertions {
int pos;
char base;
struct Insertions *next;
};
struct Vector3;
class ED4_sequence_terminal;
class BI_ecoli_ref;
struct ED4_plugin_host;
struct Structure3D : virtual Noncopyable {
Vector3 *strCen;
int iInterval;
int iMapSAI;
int iMapSearch;
int iMapEnable;
int iStartPos, iEndPos;
int iEColiStartPos, iEColiEndPos;
int iTotalSubs, iTotalDels, iTotalIns;
int LSU_molID;
int HelixBase; // to create display lists storing helix information
static GBDATA *gb_main;
BI_ecoli_ref *EColiRef;
ED4_plugin_host& Host;
OpenGLGraphics *GRAPHICS; // not really a good place - it better should be passed from callers
Structure3D(ED4_plugin_host& host_);
~Structure3D();
void ReadCoOrdinateFile();
void StoreCoordinates(float x, float y, float z, char base, unsigned int pos);
void GetSecondaryStructureInfo();
void Store2Dinfo(char *info, int pos, int helixNr);
void PrepareSecondaryStructureData();
void Combine2Dand3DstructureInfo();
void Store2D3Dinfo(Struct2Dinfo *s2D, Struct3Dinfo *s3D);
static int FindTypeOfRNA();
void DeleteOldMoleculeData();
void GenerateMoleculeSkeleton();
void ComputeBasePositions();
void PositionsToCoordinatesDispList(int listID, int *pos, int len);
void PointsToQuads(float x, float y, float z);
void StoreHelixNrInfo(float x, float y, float z, int helixNr);
void GenerateDisplayLists();
void GenerateHelixDispLists(int HELIX_NR_ID, int HELIX_NR);
void GenerateHelixNrDispList(int startHx, int endHx);
void GenerateSecStructureHelixRegions();
void GenerateSecStructureNonHelixRegions();
void GenerateSecStructureUnpairedHelixRegions();
void GenerateTertiaryInteractionsDispLists();
void MapCurrentSpeciesToEcoliTemplate(AW_root *awr);
void StoreCurrSpeciesDifference(char base, int pos);
void DeleteOldSpeciesData();
void BuildDisplayList(int listID, int *pos, int len);
void GenerateBaseDifferenceDisplayList();
void GenerateBaseDifferencePositionDisplayList();
void StoreInsertions(char base, int pos);
void DeleteOldInsertionData();
void GenerateInsertionDisplayList();
void GenerateCursorPositionDispList(long pos);
void MapSaiToEcoliTemplate();
void MapSearchStringsToEcoliTemplate(AW_root *awr);
};
#else
#error RNA3D_StructureData.hxx included twice
#endif
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