#include "RNA3D_GlobalHeader.hxx"#include "RNA3D_Global.hxx"#include "RNA3D_OpenGLGraphics.hxx"#include "RNA3D_Graphics.hxx"#include "RNA3D_StructureData.hxx"#include <cerrno>#include <string>#include <iostream>#include <fstream>#include <arbdbt.h>#include <aw_msg.hxx>#include <aw_awars.hxx>#include <aw_root.hxx>#include <ed4_extern.hxx>#include <ed4_plugins.hxx>#include <BI_basepos.hxx>#include <arb_global_defs.h>
Go to the source code of this file.
Macros | |
| #define | COLORLINK (ED4_G_SBACK_0 - RNA3D_GC_SBACK_0) |
| #define | SAICOLORS (ED4_G_CBACK_0 - RNA3D_GC_CBACK_0) |
Functions | |
| bool | is_Gap (char c) |
| static char * | find_data_file (const char *name) |
| static void | throw_IO_error (const char *filename) __ATTR__NORETURN |
| static bool | ValidSearchColor (int iColor, int mode) |
Variables | |
| static Struct3Dinfo * | start3D = NULp |
| static Struct2Dinfo * | start2D = NULp |
| static Struct2Dplus3D * | start2D3D = NULp |
| static HelixNrInfo * | start = NULp |
| static CurrSpecies * | startSp = NULp |
| static bool | bOldSpeciesDataExists = false |
| static Insertions * | startIns = NULp |
| static bool | bOldInsertionDataExists = false |
| static bool | bStartPosStored = false |
| static bool | bEndPosStored = false |
| static char | globalComment [1000] |
Macro Definition Documentation
| #define COLORLINK (ED4_G_SBACK_0 - RNA3D_GC_SBACK_0) |
Definition at line 22 of file RNA3D_StructureData.cxx.
Referenced by Structure3D::MapSearchStringsToEcoliTemplate().
| #define SAICOLORS (ED4_G_CBACK_0 - RNA3D_GC_CBACK_0) |
Definition at line 23 of file RNA3D_StructureData.cxx.
Referenced by Structure3D::MapSaiToEcoliTemplate().
Function Documentation
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Definition at line 38 of file RNA3D_StructureData.cxx.
References GAP::is_std_gap().
Referenced by Structure3D::FindTypeOfRNA(), and Structure3D::MapCurrentSpeciesToEcoliTemplate().
Definition at line 42 of file RNA3D_StructureData.cxx.
References GB_lib_file(), and string().
Referenced by Structure3D::GenerateTertiaryInteractionsDispLists(), Structure3D::GetSecondaryStructureInfo(), and Structure3D::ReadCoOrdinateFile().
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Definition at line 49 of file RNA3D_StructureData.cxx.
References error(), and string().
Referenced by Structure3D::GenerateTertiaryInteractionsDispLists(), Structure3D::GetSecondaryStructureInfo(), and Structure3D::ReadCoOrdinateFile().
Definition at line 1372 of file RNA3D_StructureData.cxx.
References RNA3D_GC_CBACK_0, RNA3D_GC_MAX, RNA3D_GC_SBACK_0, SAI, and SEARCH.
Referenced by Structure3D::MapSaiToEcoliTemplate(), and Structure3D::MapSearchStringsToEcoliTemplate().
Variable Documentation
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Definition at line 27 of file RNA3D_StructureData.cxx.
Referenced by Structure3D::Combine2Dand3DstructureInfo(), Structure3D::ComputeBasePositions(), Structure3D::GenerateCursorPositionDispList(), and Structure3D::StoreCoordinates().
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Definition at line 28 of file RNA3D_StructureData.cxx.
Referenced by Structure3D::Combine2Dand3DstructureInfo(), Structure3D::GenerateHelixDispLists(), and Structure3D::Store2Dinfo().
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Definition at line 29 of file RNA3D_StructureData.cxx.
Referenced by Structure3D::GenerateHelixDispLists(), Structure3D::GenerateMoleculeSkeleton(), Structure3D::GenerateSecStructureHelixRegions(), Structure3D::GenerateSecStructureNonHelixRegions(), Structure3D::GenerateSecStructureUnpairedHelixRegions(), Structure3D::GenerateTertiaryInteractionsDispLists(), Structure3D::PositionsToCoordinatesDispList(), Structure3D::Store2D3Dinfo(), and Structure3D::StoreCurrSpeciesDifference().
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Definition at line 30 of file RNA3D_StructureData.cxx.
Referenced by Feature::addQualifiedEntry(), ARB_executable(), ARB_strpartdup(), AW_openURL(), awt_create_input_mask(), ED4_SearchResults::buildColorString(), BaseFrequencies::changed_range(), check_no_parameter(), AliDataSlice::cmp_data(), FINAL_TYPE< SEQTYPE >::cmp_data(), SpecificGap< T >::cmp_data(), SpecificAliData< char >::cmp_data(), copy_to_buf(), ED4_getSaiColorString(), ED4_pfold_calculate_secstruct_match(), ED4_pfold_extend_nucleation_sites(), ED4_pfold_resolve_overlaps(), etog_convert_references(), Helpfile::extractInternalLinks(), StringParser::extractWord(), File_selection::fill(), gb_commit_transaction_local_rek(), gb_untouch_children(), gbcms_talking_unfold(), gbl_head(), GBP_charPtr_2_GB_alignment_type(), GBP_charPtr_2_GB_CASE(), GBP_charPtr_2_GB_SEARCH_TYPE(), GBP_charPtr_2_GB_TYPES(), GBP_charPtr_2_GB_UNDO_TYPE(), GBS_regreplace(), GBT_read_gene_sequence_and_length(), GEN_write_position(), Structure3D::GenerateHelixNrDispList(), ST_ML::get_color_string(), ED4_SearchResults::get_first_at(), get_ident(), get_nn_range_from_awars(), ED4_host::get_SAI_background(), ED4_host::get_search_background(), SEC_base_part::getNextAbspos(), GroupIterator::GroupIterator(), gtoe_reference(), init_gene_species_xfer_fields_subconfig(), ali_aligner_last_cell::insert_left(), ali_aligner_last_cell::insert_up(), intersection(), AWT_translator::isStartCodon(), chartable::SepBaseFreq::lastDifference(), MG_export_fields(), MG_update_selection_list_on_field_transfers(), AliDataSlice::operate_on_mem(), FINAL_TYPE< SEQTYPE >::operate_on_mem(), SpecificGap< T >::operate_on_mem(), SpecificAliData< char >::operate_on_mem(), parseCounter(), ConfigMapping::parseFrom(), GroupSearch::perform_search(), ALI_PROFILE::print(), AW_awar::run_callbacks(), run_command(), scan_flag_parameter(), scan_identifier(), scan_keyword_parameter(), scan_long_parameter(), scan_string_parameter(), SEC_region::set_sequence_portion(), AliDataSlice::slice_down(), FINAL_TYPE< SEQTYPE >::slice_down(), st_ml_add_sequence_part_to_stat(), start_remote_command_for_application(), Structure3D::StoreHelixNrInfo(), string2enum(), chartable::SepBaseFreq::sub_and_add(), to_printable(), translateSAItoColors(), and wait_for_dbentry().
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Definition at line 31 of file RNA3D_StructureData.cxx.
Referenced by Structure3D::BuildDisplayList(), Structure3D::GenerateBaseDifferenceDisplayList(), and Structure3D::StoreCurrSpeciesDifference().
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Definition at line 32 of file RNA3D_StructureData.cxx.
Referenced by Structure3D::DeleteOldSpeciesData(), Structure3D::MapCurrentSpeciesToEcoliTemplate(), and Structure3D::StoreCurrSpeciesDifference().
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Definition at line 33 of file RNA3D_StructureData.cxx.
Referenced by Structure3D::StoreInsertions().
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Definition at line 34 of file RNA3D_StructureData.cxx.
Referenced by Structure3D::DeleteOldInsertionData(), Structure3D::MapCurrentSpeciesToEcoliTemplate(), and Structure3D::StoreInsertions().
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Definition at line 35 of file RNA3D_StructureData.cxx.
Referenced by Structure3D::MapCurrentSpeciesToEcoliTemplate().
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Definition at line 36 of file RNA3D_StructureData.cxx.
Referenced by Structure3D::MapCurrentSpeciesToEcoliTemplate().
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Definition at line 203 of file RNA3D_StructureData.cxx.
