NCBI C++ ToolKit
Functions | Variables
tabular.cpp File Reference

Formatting of pairwise sequence alignments in tabular form. More...

#include <ncbi_pch.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objtools/alnmgr/alnmix.hpp>
#include <objtools/align_format/tabular.hpp>
#include <objtools/align_format/showdefline.hpp>
#include <objtools/align_format/align_format_util.hpp>
#include <serial/iterator.hpp>
#include <objects/general/Object_id.hpp>
#include <objmgr/util/sequence.hpp>
#include <objects/blastdb/Blast_def_line.hpp>
#include <objmgr/seqdesc_ci.hpp>
#include <objects/seqfeat/Org_ref.hpp>
#include <map>
+ Include dependency graph for tabular.cpp:

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 USING_SCOPE (objects)
static string s_GetSeqIdListString (const list< CRef< CSeq_id > > &id, CBlastTabularInfo::ESeqIdType id_type)
CRef< CSeq_ids_ReplaceLocalId (const CBioseq_Handle &bh, CConstRef< CSeq_id > sid_in, bool parse_local)
bool s_IsValidName (const string &name)
static void s_FillJunctionalInfo (int left_stop, int right_start, int &junction_len, string &junction_seq, const string &query_seq)
static void s_GetCigarString (const CSeq_align &align, string &cigar, int query_len, CScope &scope)
static string s_InsertGap (const string &nuc_without_gap, const string &nuc, const string &prot, char gap_char)
static void s_GetGermlineTranslation (const CRef< blast::CIgAnnotation > &annot, CAlnVec &alnvec, const string &aligned_query_string, const string &aligned_germline_string, string &query_translation_string, string &germline_translation_string)
static void s_SetAirrAlignmentInfo (const CRef< CSeq_align > &align_v, const CRef< CSeq_align > &align_d, const CRef< CSeq_align > &align_j, const CRef< CSeq_align > &align_c, const CRef< blast::CIgAnnotation > &annot, CScope &scope, map< string, string > &airr_data)
static void SetCdrFwrSeq (const string &nuc_seq, string &translated_seq, bool is_first_domain, int region_start, int frame_start, string &next_trans_addition, bool &next_trans_substract, string extra_from_next_region)


static const string NA = "N/A"

Detailed Description

Formatting of pairwise sequence alignments in tabular form.

One line is printed for each alignment with tab-delimited fielalnVec.

Definition in file tabular.cpp.

Function Documentation

◆ s_FillJunctionalInfo()

static void s_FillJunctionalInfo ( int  left_stop,
int  right_start,
int junction_len,
string junction_seq,
const string query_seq 

Definition at line 1506 of file tabular.cpp.

Referenced by CIgBlastTabularInfo::SetAirrFormatData().

◆ s_GetCigarString()

static void s_GetCigarString ( const CSeq_align align,
string cigar,
int  query_len,
CScope scope 

◆ s_GetGermlineTranslation()

static void s_GetGermlineTranslation ( const CRef< blast::CIgAnnotation > &  annot,
CAlnVec alnvec,
const string aligned_query_string,
const string aligned_germline_string,
string query_translation_string,
string germline_translation_string 

◆ s_GetSeqIdListString()

static string s_GetSeqIdListString ( const list< CRef< CSeq_id > > &  id,
CBlastTabularInfo::ESeqIdType  id_type 

◆ s_InsertGap()

static string s_InsertGap ( const string nuc_without_gap,
const string nuc,
const string prot,
char  gap_char 

Definition at line 1611 of file tabular.cpp.

References i, int, nuc, and prot.

Referenced by s_GetGermlineTranslation().

◆ s_IsValidName()

bool s_IsValidName ( const string name)

◆ s_ReplaceLocalId()

CRef<CSeq_id> s_ReplaceLocalId ( const CBioseq_Handle bh,
CConstRef< CSeq_id sid_in,
bool  parse_local 

◆ s_SetAirrAlignmentInfo()

static void s_SetAirrAlignmentInfo ( const CRef< CSeq_align > &  align_v,
const CRef< CSeq_align > &  align_d,
const CRef< CSeq_align > &  align_j,
const CRef< CSeq_align > &  align_c,
const CRef< blast::CIgAnnotation > &  annot,
CScope scope,
map< string, string > &  airr_data 

◆ SetCdrFwrSeq()

static void SetCdrFwrSeq ( const string nuc_seq,
string translated_seq,
bool  is_first_domain,
int  region_start,
int  frame_start,
string next_trans_addition,
bool next_trans_substract,
string  extra_from_next_region 


USING_SCOPE ( objects  )

Variable Documentation

◆ NA

const string NA = "N/A"
Modified on Sun Jun 16 04:31:21 2024 by rev. 669887