1 #ifndef SEQ_LOC_MAPPER__HPP
2 #define SEQ_LOC_MAPPER__HPP
103 EFeatMapDirection dir,
150 ESeqMapDirection direction,
162 ESeqMapDirection direction,
175 ESeqMapDirection direction,
176 const CSeq_id* top_level_id = 0,
192 ESeqMapDirection direction,
194 const CSeq_id* top_level_id = 0,
207 ESeqMapDirection direction,
222 ESeqMapDirection direction,
223 const CSeq_id* top_level_id = 0,
249 EGCAssemblyAlias to_alias,
251 EScopeFlag scope_flag = eCopyScope);
254 ESeqMapDirection direction,
257 EScopeFlag scope_flag = eCopyScope,
271 void x_InitializeSeqMap(
const CSeqMap& seq_map,
274 void x_InitializeSeqMap(
const CSeqMap& seq_map,
278 void x_InitializeSeqMap(
const CSeqMap& seq_map,
287 void x_InitializeSeqMapDown(
CSeqMap_CI seg_it,
289 void x_InitializeSeqMapSingleLevel(
CSeqMap_CI seg_it,
Storage for multiple mapping ranges.
Class used to map seq-alignments.
namespace ncbi::objects::
CSeq_loc_Mapper_Options –.
Include a standard set of the NCBI C++ Toolkit most basic headers.
static unsigned char depth[2 *(256+1+29)+1]
CSeq_loc_Mapper & operator=(const CSeq_loc_Mapper &)
EGCAssemblyAlias
Destination of seq-id mapping through a GC-Assembly.
EScopeFlag
Using CScope for virtual bioseqs created from GC-Assemblies.
virtual CSeq_align_Mapper_Base * InitAlignMapper(const CSeq_align &src_align)
CSeq_loc_Mapper(const CSeq_loc_Mapper &)
@ eGCA_Genbank
Map to GenBank alias, prefer GI.
@ eGCA_UCSC
Map to UCSC alias.
@ eGCA_Refseq
Map to RefSeq alias, prefer GI.
@ eGCA_GenbankAcc
Map to GenBank alias, prefer acc.ver.
@ eGCA_RefseqAcc
Map to RefSeq alias, prefer acc.ver.
@ eOriginalScope
Put the generated bioseqs into the original scope.
@ eSeqMap_Up
map from segments to the top level bioseq
#define END_NCBI_SCOPE
End previously defined NCBI scope.
#define END_SCOPE(ns)
End the previously defined scope.
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
#define BEGIN_SCOPE(ns)
Define a new scope.
#define NCBI_XOBJMGR_EXPORT
const CharType(& source)[N]
Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.
Selector used in CSeqMap methods returning iterators.