#include <ncbi_pch.hpp>
#include <corelib/ncbifile.hpp>
#include <corelib/ncbiexec.hpp>
#include <objmgr/seq_vector.hpp>
#include <objmgr/util/sequence.hpp>
#include <objtools/readers/fasta.hpp>
#include <serial/iterator.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objects/seq/Annotdesc.hpp>
#include <algo/phy_tree/dist_methods.hpp>
#include <gui/objutils/label.hpp>
#include <objects/gbproj/AbstractProjectItem.hpp>
#include <gui/packages/pkg_alignment/msa_tool_job.hpp>
#include <gui/widgets/wx/wx_utils.hpp>
#include <gui/widgets/wx/async_call.hpp>
#include <wx/filename.h>
#include <wx/utils.h>
#include <wx/msgdlg.h>

Include dependency graph for msa_tool_job.cpp:

Go to the SVN repository for this file.

Classes
struct	STreeNodeMapper

Typedefs
typedef map< CSeq_id_Handle, bool >	TSeqTypeMap

typedef CMSAToolJob::TLocPair	TLocPair

typedef CMSAToolJob::TIdMap	TIdMap

Functions
	USING_SCOPE (objects)

static void	s_DumpSequences_wRange (CNcbiOstream &ostr, TConstScopedObjects &locations, TSeqTypeMap &seq_types, CMappingRanges &ranges, map< string, TLocPair > &idmap)

Typedef Documentation

◆ TIdMap

typedef CMSAToolJob::TIdMap TIdMap

Definition at line 70 of file msa_tool_job.cpp.

◆ TLocPair

typedef CMSAToolJob::TLocPair TLocPair

Definition at line 69 of file msa_tool_job.cpp.

◆ TSeqTypeMap

typedef map<CSeq_id_Handle, bool> TSeqTypeMap

Definition at line 68 of file msa_tool_job.cpp.

Function Documentation

◆ s_DumpSequences_wRange()

static void s_DumpSequences_wRange	(	CNcbiOstream &	ostr,
		TConstScopedObjects &	locations,
		TSeqTypeMap &	seq_types,
		CMappingRanges &	ranges,
		map< string, TLocPair > &	idmap
	)

static

Definition at line 102 of file msa_tool_job.cpp.

References CMappingRanges::AddConversion(), data, CSeq_id_Base::e_Local, CBioseq_Handle::eCoding_Iupac, eNa_strand_plus, eNa_strand_unknown, CScope::GetBioseqHandle(), CSeq_id_Handle::GetHandle(), CSeq_loc::GetId(), GetLength(), CSeqVector::GetSeqData(), GetStart(), CBioseq_Handle::IsNucleotide(), NON_CONST_ITERATE, CSeqVector::size(), and NStr::SizetToString().

Referenced by CMSAToolJob::BeforeRun().

◆ USING_SCOPE()

USING_SCOPE ( objects )

Classes

Typedefs