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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/id__mapper_8hpp_source.html below:

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

1 #ifndef ALGO_ID_MAPPER___ID_MAPPER__HPP 2 #define ALGO_ID_MAPPER___ID_MAPPER__HPP 82 typedef

objects::CGC_TypedSeqId::E_Choice

E_Choice

;

83 typedef

objects::CGC_SeqIdAlias::E_AliasTypes

E_Alias

;

104 operator string

()

const

;

109 bool

IsSpecMet(

const SIdSpec

& Guessed)

const

;

113 bool

Guess(

const

objects::CSeq_loc&

Loc

, SIdSpec& Spec)

const

;

119 bool

CanMeetSpec(

const

objects::CSeq_loc&

Loc

const

SIdSpec& Spec)

const

;

129

E_Gap IsLocInAGap(

const

objects::CSeq_loc&

Loc

)

const

;

133 void

GetSynonyms(

const

objects::CSeq_id& BaseId,

135 bool

NcbiOnly =

true

)

const

;

140 void

x_Init_SeqLocMappers(

void

)

const

;

142 bool

x_NCBI34_Guess(

const

objects::CSeq_id& Id, SIdSpec& Spec)

const

;

146 void

x_StripPseudoSeq(objects::CGC_Sequence& Seq);

147 void

x_RecursiveSeqFix(objects::CGC_Sequence& Seq);

148 void

x_FillGpipeTopRole(objects::CGC_Sequence& Seq);

149 void

x_RemoveHiddenAccessions(objects::CGC_Sequence& Seq);

150 void

x_FillChromosomeIds(

void

);

151 void

x_PrioritizeIds(

void

);

156 bool

x_IsExactIdInAssembly(

const

objects::CSeq_id& Id)

const

;

157 bool

x_IsFuzzyIdInAssembly(

const

objects::CSeq_id& Id)

const

;

166 int

x_GetRole(

const

objects::CGC_Sequence& Seq)

const

;

168 void

x_AddSeqToMap(

const

objects::CSeq_id& Id,

176 bool

x_DoesSeqContainSyn(

const

objects::CGC_Sequence& Seq,

const

objects::CSeq_id& Id)

const

;

179

x_GetIdFromSeqAndSpec(

const

objects::CGC_Sequence& Seq,

183 enum

{ e_No,

e_Yes

, e_Up, e_Down };

185 int

x_CanSeqMeetSpec(

const

objects::CGC_Sequence& Seq,

190 bool

x_MakeSpecForSeq(

const

objects::CSeq_id& Id,

191 const

objects::CGC_Sequence& Seq,

196

x_FindChromosomeSequence(

const

objects::CSeq_id& Id,

201

x_FindParentSequence(

const

objects::CSeq_id& Id,

202 const

objects::CGC_Assembly& Assembly,

206 bool

x_IsParentSequence(

const

objects::CSeq_id& Id,

207 const

objects::CGC_Sequence& Parent

212 const

objects::CGC_Sequence& Seq,

217 const

objects::CGC_Sequence& Seq,

222 const

objects::CGC_Sequence& Seq,

228

E_Gap x_Merge_E_Gaps(E_Gap First, E_Gap Second)

const

;

229

E_Gap x_IsLoc_Int_InAGap(

const

objects::CSeq_interval& Int)

const

;

TSeqLocMapperRef m_UpMapper

void x_BuildSeqMap(const objects::CGC_AssemblyUnit &assm)

map< objects::CSeq_id_Handle, TGC_SequenceCRef > TChildToParentMap

TAccToVerMap m_AccToVerMap

void x_PrioritizeIds(objects::CGC_Sequence &Sequence)

CConstRef< objects::CGC_Sequence > TGC_SequenceCRef

void x_BuildSeqMap(const objects::CGC_Assembly &assm)

vector< string > m_Chromosomes

void x_BuildSeqMap(const objects::CGC_Sequence &Seq, int Depth=1)

map< objects::CSeq_id_Handle, TGC_SequenceCRef > TIdToSeqMap

TChildToParentMap m_ChildToParentMap

CRef< objects::CSeq_loc_Mapper > TSeqLocMapperRef

CRef< objects::CGC_Assembly > m_Assembly

map< string, int > TAccToVerMap

bool operator<(const CEquivRange &A, const CEquivRange &B)

bool operator==(const CEquivRange &A, const CEquivRange &B)

CRange< Position > Map(const CRange< Position > &target, const CRange< Position > &range)

#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_XALGOID_MAPPER_EXPORT

@ eGC_SequenceRole_top_level

objects::CGC_TypedSeqId::E_Choice E_Choice

objects::CGC_SeqIdAlias::E_AliasTypes E_Alias

string ToString(const wxRect &rc)

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