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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/align__group_8hpp_source.html below:

NCBI C++ ToolKit: include/algo/sequence/align_group.hpp Source File

1 #ifndef GUI_PLUGINS_ALGO_ALIGN___ALIGN_GROUP__HPP 2 #define GUI_PLUGINS_ALGO_ALIGN___ALIGN_GROUP__HPP 76 const string

& annot_base_name,

77

objects::CScope& scope);

83 void

GroupByLikeTaxIds(

const TAlignList

& aligns,

85 const string

& annot_base_name,

86

objects::CScope& scope);

95

fRefSeqPredicted = 0x02,

100

fGB_EMBL_DDBJ = 0x40,

102

fSequenceDefaults = fRefSeq | fEST | fGB_EMBL_DDBJ

107 void

GroupBySequenceType(

const TAlignList

& aligns,

109 const string

& annot_base_name,

110

objects::CScope& scope,

120 void

GroupBySeqIds(

const TAlignList

& aligns,

122 const string

& annot_base_name,

123

objects::CScope& scope,

127 void

GroupByStrand(

const TAlignList

& aligns,

129 const string

& annot_base_name,

130

objects::CScope& scope);

141 void

x_SeparateByTaxId(

const TAlignList

& alignments,

143

objects::CScope& scope);

147

objects::CScope& scope);

148 TTaxId

x_GetTaxId(

const

objects::CSeq_id_Handle&

id

149

objects::CScope& scope);

map< TTaxId, CConstRef< objects::COrg_ref > > TTaxInfoMap

map< objects::CSeq_id_Handle, TTaxId > TTaxIdMap

typedefs for caching of taxonomic information

set< TTaxId > TTaxIds

typedefs for dealing with separations by tax-id

CAlignGroup & operator=(const CAlignGroup &)

unique_ptr< objects::CTaxon1 > m_Taxon1

map< TTaxIds, list< CRef< objects::CSeq_align > > > TTaxAlignMap

CAlignGroup(const CAlignGroup &)

forbidden!

CConstRef< objects::COrg_ref > x_GetOrgRef(const objects::CSeq_id_Handle &id, objects::CScope &scope)

list< CRef< objects::CSeq_align > > TAlignList

list< CRef< objects::CSeq_annot > > TAnnotList

SStrictId_Tax::TId TTaxId

Taxon id type.

#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_XALGOSEQ_EXPORT

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

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