update_viewer.cpp File Reference

#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>
#include <corelib/ncbistl.hpp>
#include <objtools/readers/fasta.hpp>
#include <util/line_reader.hpp>
#include <objects/cdd/Cdd.hpp>
#include <objects/cdd/Update_align.hpp>
#include <objects/cdd/Update_comment.hpp>
#include <objects/seq/Seq_annot.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objects/seqloc/PDB_seq_id.hpp>
#include <objects/seqset/Seq_entry.hpp>
#include <objects/seqset/Bioseq_set.hpp>
#include <objects/ncbimime/Ncbi_mime_asn1.hpp>
#include <objects/ncbimime/Biostruc_seq.hpp>
#include <objects/mmdb2/Model_type.hpp>
#include <objects/mmdb2/Biostruc_model.hpp>
#include <objects/mmdb1/Biostruc_graph.hpp>
#include <objects/mmdb1/Biostruc_descr.hpp>
#include <objects/general/Dbtag.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/mmdb1/Biostruc_id.hpp>
#include <objects/mmdb1/Mmdb_id.hpp>
#include <objects/mmdb1/Biostruc_annot_set.hpp>
#include <objects/mmdb3/Biostruc_feature_set.hpp>
#include <objects/mmdb3/Chem_graph_alignment.hpp>
#include <objects/mmdb3/Chem_graph_pntrs.hpp>
#include <objects/mmdb3/Residue_pntrs.hpp>
#include <objects/mmdb3/Residue_interval_pntr.hpp>
#include <objects/mmdb1/Molecule_id.hpp>
#include <objects/mmdb1/Residue_id.hpp>
#include <objects/mmdb3/Biostruc_feature_set_id.hpp>
#include <objects/mmdb3/Biostruc_feature_id.hpp>
#include <memory>
#include <algorithm>
#include "remove_header_conflicts.hpp"
#include "update_viewer.hpp"
#include "asn_reader.hpp"
#include "update_viewer_window.hpp"
#include "messenger.hpp"
#include "sequence_display.hpp"
#include "cn3d_colors.hpp"
#include "alignment_manager.hpp"
#include "cn3d_threader.hpp"
#include "structure_set.hpp"
#include "molecule.hpp"
#include "cn3d_tools.hpp"
#include "cn3d_blast.hpp"
#include "molecule_identifier.hpp"
#include "cn3d_cache.hpp"
#include "cn3d_ba_interface.hpp"
#include "cn3d_pssm.hpp"
#include <wx/tokenzr.h>

Include dependency graph for update_viewer.cpp:

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Typedefs
typedef bool(*	CompareUpdates) (BlockMultipleAlignment *a, BlockMultipleAlignment *b)

Functions
	USING_SCOPE (objects)
static BlockMultipleAlignment *	MakeEmptyAlignment (const Sequence *master, const Sequence *dependent)
static void	MapDependentToMaster (const BlockMultipleAlignment *alignment, int dependentRow, vector< int > *dependent2master)
static BlockMultipleAlignment *	GetAlignmentByBestNeighbor (const BlockMultipleAlignment *multiple, const BLASTer::AlignmentList rowAlignments)
static bool	CompareUpdatesByIdentifier (BlockMultipleAlignment *a, BlockMultipleAlignment *b)
static bool	CompareUpdatesByScore (BlockMultipleAlignment *a, BlockMultipleAlignment *b)

Variables
	USING_NCBI_SCOPE
static CompareUpdates	updateComparisonFunction = NULL

Typedef Documentation

CompareUpdates

typedef bool(* CompareUpdates) (BlockMultipleAlignment *a, BlockMultipleAlignment *b)

Definition at line 1166 of file update_viewer.cpp.

Function Documentation

CompareUpdatesByIdentifier()

static bool CompareUpdatesByIdentifier ( BlockMultipleAlignment *  a, BlockMultipleAlignment *  b  )

static

Definition at line 1168 of file update_viewer.cpp.

References a, b, and MoleculeIdentifier::CompareIdentifiers().

Referenced by UpdateViewer::SortByIdentifier().

CompareUpdatesByScore()

static bool CompareUpdatesByScore ( BlockMultipleAlignment *  a, BlockMultipleAlignment *  b  )

static

Definition at line 1176 of file update_viewer.cpp.

References a, and b.

Referenced by UpdateViewer::SortByPSSM().

GetAlignmentByBestNeighbor()

static BlockMultipleAlignment* GetAlignmentByBestNeighbor ( const BlockMultipleAlignment *  multiple, const BLASTer::AlignmentList  rowAlignments  )

static

Definition at line 994 of file update_viewer.cpp.

References BlockMultipleAlignment::AddAlignedBlockAtEnd(), Messenger::AddHighlights(), BlockMultipleAlignment::AddUnalignedBlocks(), StructureSet::alignmentManager, b, BlockMultipleAlignment::Clone(), ERRORMSG, BlockMultipleAlignment::GetMaster(), BlockMultipleAlignment::GetRowDouble(), BlockMultipleAlignment::GetSequenceOfRow(), GlobalMessenger(), Sequence::identifier, INFOMSG, int, len, Sequence::Length(), MapDependentToMaster(), BlockMultipleAlignment::NRows(), NULL, StructureBase::parentSet, Messenger::RemoveAllHighlights(), Block::SetRangeOfRow(), MoleculeIdentifier::ToString(), BlockMultipleAlignment::UpdateBlockMapAndColors(), WARNINGMSG, and Block::width.

Referenced by UpdateViewer::BlastNeighbor().

MakeEmptyAlignment()

static BlockMultipleAlignment* MakeEmptyAlignment ( const Sequence *  master, const Sequence *  dependent  )

static

Definition at line 376 of file update_viewer.cpp.

References BlockMultipleAlignment::AddUnalignedBlocks(), StructureSet::alignmentManager, ERRORMSG, NULL, StructureBase::parentSet, and BlockMultipleAlignment::UpdateBlockMapAndColors().

Referenced by UpdateViewer::GetVASTAlignments(), and UpdateViewer::MakeEmptyAlignments().

MapDependentToMaster()

static void MapDependentToMaster ( const BlockMultipleAlignment *  alignment, int  dependentRow, vector< int > *  dependent2master  )

static

Definition at line 977 of file update_viewer.cpp.

References b, Block::Range::from, BlockMultipleAlignment::GetSequenceOfRow(), BlockMultipleAlignment::GetUngappedAlignedBlocks(), i, and Sequence::Length().

Referenced by GetAlignmentByBestNeighbor().

USING_SCOPE()

USING_SCOPE

(

objects

)

Variable Documentation

updateComparisonFunction

CompareUpdates updateComparisonFunction = NULL

static

Definition at line 1181 of file update_viewer.cpp.

Referenced by UpdateViewer::SortByIdentifier(), UpdateViewer::SortByPSSM(), and UpdateViewer::SortUpdates().

USING_NCBI_SCOPE

USING_NCBI_SCOPE

Definition at line 93 of file update_viewer.cpp.