src/algo/align/ngalign/sequence_set.cpp File Reference

#include <ncbi_pch.hpp>
#include <corelib/ncbiexpt.hpp>
#include <math.h>
#include <algo/align/ngalign/sequence_set.hpp>
#include <objmgr/scope.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objects/seqalign/Seq_align_set.hpp>
#include <objects/seqalign/Dense_seg.hpp>
#include <algo/align/util/score_builder.hpp>
#include <algo/blast/api/blast_types.hpp>
#include <algo/blast/api/bl2seq.hpp>
#include <algo/blast/api/blast_options_handle.hpp>
#include <algo/blast/api/blast_nucl_options.hpp>
#include <algo/blast/api/disc_nucl_options.hpp>
#include <objtools/readers/fasta.hpp>
#include <algo/blast/blastinput/blast_scope_src.hpp>
#include <algo/blast/blastinput/blast_fasta_input.hpp>
#include <algo/blast/blastinput/blast_input_aux.hpp>
#include <algo/dustmask/symdust.hpp>

Include dependency graph for sequence_set.cpp:

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Functions
	USING_SCOPE (objects)
	USING_SCOPE (blast)
CRef< CSeq_loc >	s_GetMaskLoc (const CSeq_id &Id, CSeqMasker *SeqMasker, CScope &Scope)

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Function Documentation

CRef<CSeq_loc> s_GetMaskLoc (  const CSeq_id &  Id, CSeqMasker *  SeqMasker, CScope &  Scope )

Definition at line 132 of file sequence_set.cpp. References CBioseq_Handle::eCoding_Iupac, ERR_POST, CBioseq_Handle::eStrand_Plus, CScope::GetBioseqHandle(), CBioseq_Handle::GetSeqVector(), CException::ReportAll(), and auto_ptr< X >::reset().

USING_SCOPE (  blast   )

USING_SCOPE (  objects   )

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