ARB
|
#include <RNA3D_StructureData.hxx>
Static Public Member Functions | |
static int | FindTypeOfRNA () |
Public Attributes | |
Vector3 * | strCen |
int | iInterval |
int | iMapSAI |
int | iMapSearch |
int | iMapEnable |
int | iStartPos |
int | iEndPos |
int | iEColiStartPos |
int | iEColiEndPos |
int | iTotalSubs |
int | iTotalDels |
int | iTotalIns |
int | LSU_molID |
int | HelixBase |
BI_ecoli_ref * | EColiRef |
ED4_plugin_host & | Host |
OpenGLGraphics * | GRAPHICS |
Static Public Attributes | |
static GBDATA * | gb_main = NULp |
Definition at line 109 of file RNA3D_StructureData.hxx.
Structure3D::Structure3D | ( | ED4_plugin_host & | host_ | ) |
Definition at line 56 of file RNA3D_StructureData.cxx.
Structure3D::~Structure3D | ( | ) |
Definition at line 76 of file RNA3D_StructureData.cxx.
void Structure3D::ReadCoOrdinateFile | ( | ) |
Definition at line 205 of file RNA3D_StructureData.cxx.
References _1C2W, _1PNU, _1VOR, RNA3D_Global::bDisplayComments, find_data_file(), FindTypeOfRNA(), iEColiEndPos, iEColiStartPos, line, LSU_23S, LSU_5S, LSU_molID, NULp, RNA3D, SSU_16S, StoreCoordinates(), strCen, throw_IO_error(), Vector3::x, Vector3::y, Z, and Vector3::z.
Referenced by Change3DMolecule_CB(), and InitializeOpenGLEngine().
Definition at line 82 of file RNA3D_StructureData.cxx.
References Struct3Dinfo::base, Struct3Dinfo::next, NULp, Struct3Dinfo::pos, start3D, Struct3Dinfo::x, Struct3Dinfo::y, y, and Struct3Dinfo::z.
Referenced by ReadCoOrdinateFile().
void Structure3D::GetSecondaryStructureInfo | ( | ) |
Definition at line 322 of file RNA3D_StructureData.cxx.
References find_data_file(), FindTypeOfRNA(), info, LSU_23S, LSU_5S, NULp, SSU_16S, Store2Dinfo(), and throw_IO_error().
Referenced by Change3DMolecule_CB(), and InitializeOpenGLEngine().
Definition at line 296 of file RNA3D_StructureData.cxx.
References Struct2Dinfo::base, Struct2Dinfo::code, Struct2Dinfo::helixNr, Struct2Dinfo::mask, Struct2Dinfo::next, NULp, Struct2Dinfo::pos, and start2D.
Referenced by GetSecondaryStructureInfo().
void Structure3D::Combine2Dand3DstructureInfo | ( | ) |
Definition at line 415 of file RNA3D_StructureData.cxx.
References RNA3D_Global::bDisplayComments, Struct2Dinfo::next, Struct3Dinfo::next, Struct2Dinfo::pos, Struct3Dinfo::pos, RNA3D, start2D, start3D, and Store2D3Dinfo().
Referenced by Change3DMolecule_CB(), and InitializeOpenGLEngine().
void Structure3D::Store2D3Dinfo | ( | Struct2Dinfo * | s2D, |
Struct3Dinfo * | s3D | ||
) |
Definition at line 389 of file RNA3D_StructureData.cxx.
References Struct2Dplus3D::base, Struct2Dinfo::base, Struct2Dplus3D::code, Struct2Dinfo::code, Struct2Dplus3D::helixNr, Struct2Dinfo::helixNr, Struct2Dplus3D::mask, Struct2Dinfo::mask, Struct2Dplus3D::next, NULp, Struct2Dplus3D::pos, Struct2Dinfo::pos, start2D3D, Struct2Dplus3D::x, Struct3Dinfo::x, Struct2Dplus3D::y, Struct3Dinfo::y, Struct2Dplus3D::z, and Struct3Dinfo::z.
Referenced by Combine2Dand3DstructureInfo().
|
static |
Definition at line 106 of file RNA3D_StructureData.cxx.
References aw_message_if(), error(), GB_await_error(), GB_end_transaction(), GB_entry(), gb_main, GB_push_transaction(), GB_read_char_pntr(), GBT_find_SAI(), GBT_get_default_alignment(), is_Gap(), LSU_23S, LSU_5S, NULp, and SSU_16S.
Referenced by calc_helix_count(), CreateDisplayHelices_window(), CreateRNA3DMainWindow(), GenerateDisplayLists(), GenerateTertiaryInteractionsDispLists(), GetSecondaryStructureInfo(), and ReadCoOrdinateFile().
void Structure3D::DeleteOldMoleculeData | ( | ) |
Definition at line 153 of file RNA3D_StructureData.cxx.
References DeleteOldInsertionData(), DeleteOldSpeciesData(), Struct2Dplus3D::next, Struct2Dinfo::next, Struct3Dinfo::next, HelixNrInfo::next, and NULp.
Referenced by Change3DMolecule_CB().
void Structure3D::GenerateMoleculeSkeleton | ( | ) |
Definition at line 894 of file RNA3D_StructureData.cxx.
References GRAPHICS, Struct2Dplus3D::helixNr, Struct2Dplus3D::mask, Struct2Dplus3D::next, RNA3D_GC_BASES_HELIX, RNA3D_GC_BASES_NON_HELIX, RNA3D_GC_BASES_UNPAIRED_HELIX, start2D3D, STRUCTURE_BACKBONE, STRUCTURE_BACKBONE_CLR, Struct2Dplus3D::x, Struct2Dplus3D::y, and Struct2Dplus3D::z.
Referenced by GenerateDisplayLists().
void Structure3D::ComputeBasePositions | ( | ) |
Definition at line 957 of file RNA3D_StructureData.cxx.
References GRAPHICS, iInterval, Struct3Dinfo::next, Struct3Dinfo::pos, start3D, STRUCTURE_POS, STRUCTURE_POS_ANCHOR, Struct3Dinfo::x, Struct3Dinfo::y, and Struct3Dinfo::z.
Referenced by DisplayPostionsIntervalChanged_CB(), and GenerateDisplayLists().
Definition at line 498 of file RNA3D_StructureData.cxx.
References RNA3D_Global::bPointSpritesSupported, Struct2Dplus3D::next, PointsToQuads(), Struct2Dplus3D::pos, RNA3D, start2D3D, Struct2Dplus3D::x, Struct2Dplus3D::y, and Struct2Dplus3D::z.
Referenced by GenerateSecStructureHelixRegions(), GenerateSecStructureNonHelixRegions(), and GenerateSecStructureUnpairedHelixRegions().
void Structure3D::PointsToQuads | ( | float | x, |
float | y, | ||
float | z | ||
) |
Definition at line 451 of file RNA3D_StructureData.cxx.
References RNA3D_Global::bPointSpritesSupported, and RNA3D.
Referenced by BuildDisplayList(), GenerateBaseDifferenceDisplayList(), GenerateHelixNrDispList(), GenerateInsertionDisplayList(), MapSaiToEcoliTemplate(), MapSearchStringsToEcoliTemplate(), and PositionsToCoordinatesDispList().
void Structure3D::StoreHelixNrInfo | ( | float | x, |
float | y, | ||
float | z, | ||
int | helixNr | ||
) |
Definition at line 717 of file RNA3D_StructureData.cxx.
References HelixNrInfo::helixNr, HelixNrInfo::next, NULp, start, HelixNrInfo::x, y, HelixNrInfo::y, and HelixNrInfo::z.
Referenced by GenerateHelixDispLists().
void Structure3D::GenerateDisplayLists | ( | ) |
Definition at line 854 of file RNA3D_StructureData.cxx.
References ComputeBasePositions(), FindTypeOfRNA(), GenerateHelixDispLists(), GenerateMoleculeSkeleton(), GenerateSecStructureHelixRegions(), GenerateSecStructureNonHelixRegions(), GenerateSecStructureUnpairedHelixRegions(), GenerateTertiaryInteractionsDispLists(), HelixBase, LSU_23S, LSU_5S, and SSU_16S.
Referenced by Change3DMolecule_CB(), and InitializeOpenGLEngine().
Definition at line 737 of file RNA3D_StructureData.cxx.
References Struct2Dinfo::helixNr, Struct2Dinfo::mask, Struct2Dplus3D::next, Struct2Dinfo::next, Struct2Dplus3D::pos, Struct2Dinfo::pos, start2D, start2D3D, StoreHelixNrInfo(), Struct2Dplus3D::x, Struct2Dplus3D::y, and Struct2Dplus3D::z.
Referenced by GenerateDisplayLists().
Definition at line 814 of file RNA3D_StructureData.cxx.
References RNA3D_Global::bPointSpritesSupported, GRAPHICS, HELIX_NUMBERS, HELIX_NUMBERS_POINTS, HelixNrInfo::helixNr, HelixNrInfo::next, PointsToQuads(), RNA3D, start, HelixNrInfo::x, HelixNrInfo::y, and HelixNrInfo::z.
Referenced by update_HelixNrDispList().
void Structure3D::GenerateSecStructureHelixRegions | ( | ) |
Definition at line 552 of file RNA3D_StructureData.cxx.
References Struct2Dplus3D::base, HELIX_A, HELIX_C, HELIX_G, HELIX_U, Struct2Dplus3D::helixNr, Struct2Dplus3D::mask, Struct2Dplus3D::next, Struct2Dplus3D::pos, PositionsToCoordinatesDispList(), and start2D3D.
Referenced by GenerateDisplayLists().
void Structure3D::GenerateSecStructureNonHelixRegions | ( | ) |
Definition at line 525 of file RNA3D_StructureData.cxx.
References Struct2Dplus3D::base, Struct2Dplus3D::helixNr, Struct2Dplus3D::next, NON_HELIX_A, NON_HELIX_C, NON_HELIX_G, NON_HELIX_U, Struct2Dplus3D::pos, PositionsToCoordinatesDispList(), and start2D3D.
Referenced by GenerateDisplayLists().
void Structure3D::GenerateSecStructureUnpairedHelixRegions | ( | ) |
Definition at line 581 of file RNA3D_StructureData.cxx.
References Struct2Dplus3D::base, Struct2Dplus3D::helixNr, Struct2Dplus3D::mask, Struct2Dplus3D::next, Struct2Dplus3D::pos, PositionsToCoordinatesDispList(), start2D3D, UNPAIRED_HELIX_A, UNPAIRED_HELIX_C, UNPAIRED_HELIX_G, and UNPAIRED_HELIX_U.
Referenced by GenerateDisplayLists().
void Structure3D::GenerateTertiaryInteractionsDispLists | ( | ) |
Definition at line 618 of file RNA3D_StructureData.cxx.
References ECOLI_TERTIARY_INTRACTION_PSEUDOKNOTS, ECOLI_TERTIARY_INTRACTION_TRIPLE_BASES, find_data_file(), FindTypeOfRNA(), K, LSU_23S, LSU_5S, Struct2Dplus3D::next, NULp, Struct2Dplus3D::pos, SSU_16S, start2D3D, throw_IO_error(), Struct2Dplus3D::x, Struct2Dplus3D::y, and Struct2Dplus3D::z.
Referenced by GenerateDisplayLists().
void Structure3D::MapCurrentSpeciesToEcoliTemplate | ( | AW_root * | awr | ) |
Definition at line 1268 of file RNA3D_StructureData.cxx.
References ED4_plugin_host::announce_current_species(), aw_message_if(), AW_root::awar(), AWAR_3D_SELECTED_SPECIES, AWAR_SPECIES_NAME, RNA3D_Global::bEColiRefInitialized, bEndPosStored, bOldInsertionDataExists, bOldSpeciesDataExists, bStartPosStored, DeleteOldInsertionData(), DeleteOldSpeciesData(), EColiRef, error(), GB_await_error(), GB_end_transaction(), GB_entry(), gb_main, GB_push_transaction(), GB_read_char_pntr(), GB_read_string(), GBS_global_string(), GBT_find_SAI(), GBT_find_sequence(), GBT_find_species(), GBT_get_default_alignment(), GenerateBaseDifferenceDisplayList(), GenerateInsertionDisplayList(), Host, iEndPos, BI_ecoli_ref::init(), is_Gap(), iStartPos, NULp, AW_awar::read_string(), RNA3D, StoreCurrSpeciesDifference(), StoreInsertions(), and AW_awar::write_string().
Referenced by MapDisplayParameters(), and MapSelectedSpeciesChanged_CB().
Definition at line 1002 of file RNA3D_StructureData.cxx.
References CurrSpecies::base, bOldSpeciesDataExists, Struct2Dplus3D::next, CurrSpecies::next, NULp, Struct2Dplus3D::pos, CurrSpecies::pos, start2D3D, startSp, Struct2Dplus3D::x, CurrSpecies::x, Struct2Dplus3D::y, CurrSpecies::y, Struct2Dplus3D::z, and CurrSpecies::z.
Referenced by MapCurrentSpeciesToEcoliTemplate().
void Structure3D::DeleteOldSpeciesData | ( | ) |
Definition at line 1033 of file RNA3D_StructureData.cxx.
References bOldSpeciesDataExists, CurrSpecies::next, and NULp.
Referenced by DeleteOldMoleculeData(), and MapCurrentSpeciesToEcoliTemplate().
Definition at line 1083 of file RNA3D_StructureData.cxx.
References RNA3D_Global::bPointSpritesSupported, CurrSpecies::next, PointsToQuads(), CurrSpecies::pos, RNA3D, startSp, CurrSpecies::x, CurrSpecies::y, and CurrSpecies::z.
Referenced by GenerateBaseDifferenceDisplayList().
void Structure3D::GenerateBaseDifferenceDisplayList | ( | ) |
Definition at line 1110 of file RNA3D_StructureData.cxx.
References CurrSpecies::base, RNA3D_Global::bPointSpritesSupported, BuildDisplayList(), GenerateBaseDifferencePositionDisplayList(), iTotalDels, iTotalSubs, MAP_SPECIES_BASE_A, MAP_SPECIES_BASE_C, MAP_SPECIES_BASE_DIFFERENCE, MAP_SPECIES_BASE_G, MAP_SPECIES_BASE_U, MAP_SPECIES_DELETION, MAP_SPECIES_MISSING, CurrSpecies::next, PointsToQuads(), CurrSpecies::pos, RNA3D, startSp, CurrSpecies::x, CurrSpecies::y, and CurrSpecies::z.
Referenced by MapCurrentSpeciesToEcoliTemplate().
void Structure3D::GenerateBaseDifferencePositionDisplayList | ( | ) |
Definition at line 1045 of file RNA3D_StructureData.cxx.
References GRAPHICS, MAP_SPECIES_BASE_DIFFERENCE_POS, MAP_SPECIES_BASE_DIFFERENCE_POS_ANCHOR, Struct3Dinfo::next, CurrSpecies::next, Struct3Dinfo::pos, CurrSpecies::pos, Struct3Dinfo::x, Struct3Dinfo::y, and Struct3Dinfo::z.
Referenced by GenerateBaseDifferenceDisplayList().
Definition at line 1164 of file RNA3D_StructureData.cxx.
References Insertions::base, bOldInsertionDataExists, Insertions::next, NULp, Insertions::pos, and startIns.
Referenced by MapCurrentSpeciesToEcoliTemplate().
void Structure3D::DeleteOldInsertionData | ( | ) |
Definition at line 1184 of file RNA3D_StructureData.cxx.
References bOldInsertionDataExists, Insertions::next, and NULp.
Referenced by DeleteOldMoleculeData(), and MapCurrentSpeciesToEcoliTemplate().
void Structure3D::GenerateInsertionDisplayList | ( | ) |
Definition at line 1196 of file RNA3D_StructureData.cxx.
References Insertions::base, RNA3D_Global::bPointSpritesSupported, buffer, GRAPHICS, iTotalIns, MAP_SPECIES_INSERTION_BASES, MAP_SPECIES_INSERTION_BASES_ANCHOR, MAP_SPECIES_INSERTION_POINTS, Struct3Dinfo::next, Insertions::next, PointsToQuads(), Struct3Dinfo::pos, Insertions::pos, RNA3D, Struct3Dinfo::x, Struct3Dinfo::y, and Struct3Dinfo::z.
Referenced by MapCurrentSpeciesToEcoliTemplate().
void Structure3D::GenerateCursorPositionDispList | ( | long | pos | ) |
Definition at line 935 of file RNA3D_StructureData.cxx.
References ECOLI_CURSOR_POSITION, Struct3Dinfo::next, Struct3Dinfo::pos, start3D, Struct3Dinfo::x, Struct3Dinfo::y, and Struct3Dinfo::z.
Referenced by CursorPositionChanged_CB().
void Structure3D::MapSaiToEcoliTemplate | ( | ) |
Definition at line 1452 of file RNA3D_StructureData.cxx.
References BasePosition::abs_2_rel(), RNA3D_Global::bEColiRefInitialized, RNA3D_Global::bMapSaiDispListCreated, RNA3D_Global::bPointSpritesSupported, RNA3D_Global::cGraphics, EColiRef, ED4_plugin_host::get_SAI_background(), Host, iEndPos, iMapSAI, iStartPos, long, MAP_SAI_TO_STRUCTURE, Struct3Dinfo::next, NULp, PointsToQuads(), RNA3D, SAI, SAICOLORS, ED4_plugin_host::SAIs_visualized(), and ValidSearchColor().
Referenced by MapDisplayParameters(), and MapSaiToEcoliTemplateChanged_CB().
void Structure3D::MapSearchStringsToEcoliTemplate | ( | AW_root * | awr | ) |
Definition at line 1382 of file RNA3D_StructureData.cxx.
References BasePosition::abs_2_rel(), RNA3D_Global::bEColiRefInitialized, RNA3D_Global::bMapSearchStringsDispListCreated, RNA3D_Global::bPointSpritesSupported, RNA3D_Global::cGraphics, COLORLINK, EColiRef, ED4_plugin_host::get_search_background(), Host, iEndPos, iMapSearch, iStartPos, long, MAP_SEARCH_STRINGS_BACKBONE, MAP_SEARCH_STRINGS_TO_STRUCTURE, Struct3Dinfo::next, NULp, PointsToQuads(), RNA3D, SEARCH, ValidSearchColor(), Vector3::x, Vector3::y, and Vector3::z.
Referenced by MapDisplayParameters(), and MapSearchStringsToEcoliTemplateChanged_CB().
|
inline |
Definition at line 174 of file RNA3D_StructureData.hxx.
References arb_assert, FindTypeOfRNA(), LSU_23S, LSU_5S, and SSU_16S.
Referenced by DisplayHelixNrsChanged_CB(), and MapDisplayParameters().
Vector3* Structure3D::strCen |
Definition at line 110 of file RNA3D_StructureData.hxx.
Referenced by ReadCoOrdinateFile(), RenderOpenGLScene(), and ~Structure3D().
int Structure3D::iInterval |
Definition at line 112 of file RNA3D_StructureData.hxx.
Referenced by ComputeBasePositions(), and MapDisplayParameters().
int Structure3D::iMapSAI |
Definition at line 113 of file RNA3D_StructureData.hxx.
Referenced by MapDisplayParameters(), MapSaiToEcoliTemplate(), and MapSaiToEcoliTemplateChanged_CB().
int Structure3D::iMapSearch |
Definition at line 114 of file RNA3D_StructureData.hxx.
Referenced by MapDisplayParameters(), MapSearchStringsToEcoliTemplate(), and MapSearchStringsToEcoliTemplateChanged_CB().
int Structure3D::iMapEnable |
Definition at line 115 of file RNA3D_StructureData.hxx.
Referenced by MapDisplayParameters(), MapSaiToEcoliTemplateChanged_CB(), MapSearchStringsToEcoliTemplateChanged_CB(), and MapSelectedSpeciesChanged_CB().
int Structure3D::iStartPos |
Definition at line 116 of file RNA3D_StructureData.hxx.
Referenced by MapCurrentSpeciesToEcoliTemplate(), MapSaiToEcoliTemplate(), and MapSearchStringsToEcoliTemplate().
int Structure3D::iEndPos |
Definition at line 116 of file RNA3D_StructureData.hxx.
Referenced by MapCurrentSpeciesToEcoliTemplate(), MapSaiToEcoliTemplate(), and MapSearchStringsToEcoliTemplate().
int Structure3D::iEColiStartPos |
Definition at line 117 of file RNA3D_StructureData.hxx.
Referenced by ReadCoOrdinateFile().
int Structure3D::iEColiEndPos |
Definition at line 117 of file RNA3D_StructureData.hxx.
Referenced by ReadCoOrdinateFile().
int Structure3D::iTotalSubs |
Definition at line 118 of file RNA3D_StructureData.hxx.
Referenced by GenerateBaseDifferenceDisplayList().
int Structure3D::iTotalDels |
Definition at line 118 of file RNA3D_StructureData.hxx.
Referenced by GenerateBaseDifferenceDisplayList().
int Structure3D::iTotalIns |
Definition at line 118 of file RNA3D_StructureData.hxx.
Referenced by GenerateInsertionDisplayList().
int Structure3D::LSU_molID |
Definition at line 119 of file RNA3D_StructureData.hxx.
Referenced by Change3DMolecule_CB(), and ReadCoOrdinateFile().
int Structure3D::HelixBase |
Definition at line 120 of file RNA3D_StructureData.hxx.
Referenced by GenerateDisplayLists().
Definition at line 122 of file RNA3D_StructureData.hxx.
Referenced by CreateRNA3DMainWindow(), FindTypeOfRNA(), and MapCurrentSpeciesToEcoliTemplate().
BI_ecoli_ref* Structure3D::EColiRef |
Definition at line 123 of file RNA3D_StructureData.hxx.
Referenced by CursorPositionChanged_CB(), MapCurrentSpeciesToEcoliTemplate(), MapSaiToEcoliTemplate(), and MapSearchStringsToEcoliTemplate().
ED4_plugin_host& Structure3D::Host |
Definition at line 124 of file RNA3D_StructureData.hxx.
Referenced by MapCurrentSpeciesToEcoliTemplate(), MapSaiToEcoliTemplate(), and MapSearchStringsToEcoliTemplate().
OpenGLGraphics* Structure3D::GRAPHICS |
Definition at line 126 of file RNA3D_StructureData.hxx.
Referenced by ComputeBasePositions(), GenerateBaseDifferencePositionDisplayList(), GenerateHelixNrDispList(), GenerateInsertionDisplayList(), GenerateMoleculeSkeleton(), and ~Structure3D().