src/algo/sequence/demo/xcompareannotsdemo.cpp File Reference

#include <ncbi_pch.hpp>
#include <vector>
#include <map>
#include <list>
#include <corelib/ncbistd.hpp>
#include <corelib/ncbiapp.hpp>
#include <corelib/ncbienv.hpp>
#include <corelib/ncbiargs.hpp>
#include <corelib/ncbiobj.hpp>
#include <corelib/ncbiexpt.hpp>
#include <corelib/plugin_manager.hpp>
#include <objmgr/object_manager.hpp>
#include <objmgr/scope.hpp>
#include <objects/seqset/gb_release_file.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objects/seqalign/Seq_align_set.hpp>
#include <objects/seqalign/Dense_seg.hpp>
#include <objects/seqfeat/RNA_ref.hpp>
#include <objects/seqfeat/Feat_id.hpp>
#include <objects/seqfeat/SeqFeatXref.hpp>
#include <objects/seq/MolInfo.hpp>
#include <objects/general/Dbtag.hpp>
#include <objects/general/Object_id.hpp>
#include <util/compress/stream.hpp>
#include <util/compress/zlib.hpp>
#include <objtools/data_loaders/genbank/gbloader.hpp>
#include <objtools/data_loaders/lds/lds_dataloader.hpp>
#include <objtools/data_loaders/genbank/readers.hpp>
#include <objtools/alnmgr/alnmix.hpp>
#include <algo/sequence/loc_mapper.hpp>
#include <algo/sequence/compare_feats.hpp>
#include <dbapi/driver/drivers.hpp>
#include <limits>

Include dependency graph for xcompareannotsdemo.cpp:

Go to the source code of this file.

Classes
class	CLocMapper_Default
class	CLocMapper_Default::CGappedRange
class	CGbScopeLoader
class	CXcompareAnnotsApplication
Typedefs
typedef int	TLoadScopeMethod
Enumerations
enum	ELoadScopeMethod {   eLoadScope_Failed, eLoadScope_LDS, eLoadScope_SeqEntry, eLoadScope_SeqAnnot,   eLoadScope_GBR }
Functions
	USING_SCOPE (objects)
bool	IsManualScope (CScope &scope)
bool	IsInScope (CScope &scope, const CSeq_id &id)
string	GetProductLabel (const CSeq_feat &feat, CScope &scope)
ESerialDataFormat	StringToSerialFormat (string str)
string	GetIdStartStopStrandStr (const CSeq_loc &loc, CScope &scope, bool use_long_label)
void	AddSpanningSentinelFeat (CScope &scope, const CSeq_id &id, CSeqFeatData::E_Choice type, string title="Sentinel")
void	AddSentinelRNASeq (CScope &scope, const CSeq_id &id)
void	AddDefaultSentinelFeats (CScope &scope, const CSeq_loc &loc)
auto_ptr< CObjectIStream >	GetIStream (string path, ESerialDataFormat serial_format)
TLoadScopeMethod	LoadScope (string arg_path, CScope &scope, ESerialDataFormat serial_format)
int	main (int argc, const char *argv[])
Variables
	USING_NCBI_SCOPE

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Typedef Documentation

typedef int TLoadScopeMethod

Definition at line 608 of file xcompareannotsdemo.cpp.

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Enumeration Type Documentation

enum ELoadScopeMethod

Enumerator: eLoadScope_Failed  eLoadScope_LDS  eLoadScope_SeqEntry  eLoadScope_SeqAnnot  eLoadScope_GBR  Definition at line 607 of file xcompareannotsdemo.cpp.

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Function Documentation

void AddDefaultSentinelFeats (  CScope &  scope, const CSeq_loc &  loc )

Definition at line 511 of file xcompareannotsdemo.cpp. References AddSpanningSentinelFeat(), CSeqFeatData_Base::e_Gene, CMolInfo_Base::eBiomol_genomic, CMolInfo_Base::eBiomol_other, CMolInfo_Base::eBiomol_other_genetic, CMolInfo_Base::eBiomol_peptide, CMolInfo_Base::eBiomol_unknown, NStr::eFirst, NStr::eNocase, NStr::Find(), CMolInfo_Base::GetBiomol(), CScope::GetBioseqHandle(), GetId(), GetMolInfo(), GetTitle(), NPOS, SAnnotSelector::SetFeatType(), SAnnotSelector::SetOverlapTotalRange(), SAnnotSelector::SetResolveAll(), and SAnnotSelector::SetResolveDepth().

void AddSentinelRNASeq (  CScope &  scope, const CSeq_id &  id )

Definition at line 489 of file xcompareannotsdemo.cpp. References AddSpanningSentinelFeat(), CScope::AddTopLevelSeqEntry(), CSeqFeatData_Base::e_Gene, CSeqFeatData_Base::e_Rna, CSeq_inst_Base::eMol_rna, CSeq_inst_Base::eRepr_virtual, and CScope::ResetHistory().

void AddSpanningSentinelFeat (  CScope &  scope, const CSeq_id &  id, CSeqFeatData::E_Choice  type, string  title = "Sentinel" )

Definition at line 445 of file xcompareannotsdemo.cpp. References CScope::AddSeq_annot(), CSeqFeatData_Base::e_Gene, CSeqFeatData_Base::e_Rna, CRNA_ref_Base::eType_other, eUnknown, and NCBI_THROW. Referenced by AddDefaultSentinelFeats(), and AddSentinelRNASeq().

string GetIdStartStopStrandStr (  const CSeq_loc &  loc, CScope &  scope, bool  use_long_label )

Definition at line 408 of file xcompareannotsdemo.cpp. References CSeq_id::AsFastaString(), eGetId_ForceAcc, CSeq_loc::fMerge_SingleRange, GetId(), CSeq_loc::GetLabel(), CSeq_loc_Base::IsWhole(), out(), and Seq_loc_Merge().

auto_ptr<CObjectIStream> GetIStream (  string  path, ESerialDataFormat  serial_format )

Definition at line 586 of file xcompareannotsdemo.cpp. References NStr::EndsWith(), CZipCompression::fCheckFileHeader, CCompressionStream::fOwnAll, CObjectIStream::Open(), and auto_ptr< X >::reset().

string GetProductLabel (  const CSeq_feat &  feat, CScope &  scope )

Definition at line 376 of file xcompareannotsdemo.cpp. References CSeq_feat_Base::CanGetProduct(), eGetId_ForceAcc, GetId(), CSeq_feat_Base::GetProduct(), and id.

bool IsInScope (  CScope &  scope, const CSeq_id &  id )

Definition at line 334 of file xcompareannotsdemo.cpp. References CSeqFeatData_Base::e_Cdregion, CSeqFeatData_Base::e_Gene, CSeqFeatData_Base::e_Rna, SAnnotSelector::eSortOrder_None, CSeqFeatData::eSubtype_exon, SAnnotSelector::IncludeFeatSubtype(), SAnnotSelector::IncludeFeatType(), IsManualScope(), SAnnotSelector::SetMaxSize(), SAnnotSelector::SetResolveAll(), SAnnotSelector::SetSearchUnresolved(), and SAnnotSelector::SetSortOrder().

bool IsManualScope (  CScope &  scope  )

Definition at line 327 of file xcompareannotsdemo.cpp. References CScope::eManualTSEs, and CScope::GetAllTSEs(). Referenced by IsInScope().

TLoadScopeMethod LoadScope (  string  arg_path, CScope &  scope, ESerialDataFormat  serial_format )

Definition at line 609 of file xcompareannotsdemo.cpp. References _TRACE, CScope::AddDataLoader(), eLoadScope_LDS, CObjectManager::eNonDefault, CLDS_Database::eReadOnly, CObjectManager::GetInstance(), CLDS_DataLoader::GetLoaderNameFromArgs(), CLDS_Database::Open(), and CLDS_DataLoader::RegisterInObjectManager(). Referenced by CXcompareAnnotsApplication::Run().

int main (  int  argc, const char *  argv[] )

Definition at line 1902 of file xcompareannotsdemo.cpp. References eDS_Default.

ESerialDataFormat StringToSerialFormat (  string  str  )

Definition at line 398 of file xcompareannotsdemo.cpp. References eSerial_AsnBinary, eSerial_AsnText, eSerial_Json, eSerial_None, and eSerial_Xml. Referenced by CXcompareAnnotsApplication::Run(), and CXcompareAnnotsApplication::x_ProcessSeqAlignSetFromFile().

USING_SCOPE (  objects   )

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Variable Documentation

USING_NCBI_SCOPE

Definition at line 79 of file xcompareannotsdemo.cpp.

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