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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/seq__loc__mapper_8hpp_source.html below:

NCBI C++ ToolKit: include/objmgr/seq_loc_mapper.hpp Source File

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,

295  void

x_InitGCAssembly(

const CGC_Assembly

& gc_assembly,

Storage for multiple mapping ranges.

Class used to map seq-alignments.

namespace ncbi::objects::

CSeq_loc_Mapper_Base –.

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.

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