NCBI C++ ToolKit
Classes | Functions | Variables
vecscreen_run.cpp File Reference

Run vecscreen, produce output. More...

#include <ncbi_pch.hpp>
#include <algo/blast/format/blast_format.hpp>
#include <objects/seq/Seq_annot.hpp>
#include <algo/blast/api/sseqloc.hpp>
#include <algo/blast/api/objmgr_query_data.hpp>
#include <algo/blast/api/local_blast.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objmgr/util/seq_loc_util.hpp>
#include <objmgr/util/sequence.hpp>
#include <objtools/align_format/showdefline.hpp>
#include <objtools/blast/seqdb_reader/seqdb.hpp>
#include <objtools/readers/fasta.hpp>
#include <algo/blast/format/vecscreen_run.hpp>
#include <misc/jsonwrapp/jsonwrapp.hpp>
+ Include dependency graph for vecscreen_run.cpp:

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Classes

struct  SVecscreenMatchFinder
 

Functions

 USING_SCOPE (blast)
 
 USING_SCOPE (objects)
 
 USING_SCOPE (sequence)
 
string s_PopIdPart (const string &in_str)
 
void s_MakeFastaSubStrs (const string &in_str, list< string > &out_strs)
 
void s_MakeFastaSubIds (const CSeq_id &in_id, list< CRef< CSeq_id > > &out_ids)
 
CRef< CSeq_ids_ReplaceLocalId (const CBioseq_Handle &bh, CConstRef< CSeq_id > sid_in, bool parse_local)
 
list< CRef< CSeq_id > > s_SetIdList (const CBioseq_Handle &bh, string &title)
 

Variables

 USING_NCBI_SCOPE
 
map< string, intmatch_type_ints = { {"Strong",0}, {"Moderate",1}, {"Weak",2}, {"Suspect",3},{"Absent",4} }
 
map< int, stringmatch_type_strs = { {0,"Strong"}, {1,"Moderate"}, {2,"Weak"}, {3,"Suspect"},{4,"Absent"} }
 

Detailed Description

Run vecscreen, produce output.

Definition in file vecscreen_run.cpp.

Function Documentation

◆ s_MakeFastaSubIds()

void s_MakeFastaSubIds ( const CSeq_id in_id,
list< CRef< CSeq_id > > &  out_ids 
)

Definition at line 87 of file vecscreen_run.cpp.

References CSeq_id::GetSeqIdString(), ITERATE, s_MakeFastaSubStrs(), and CSeq_id::Set().

Referenced by s_SetIdList().

◆ s_MakeFastaSubStrs()

void s_MakeFastaSubStrs ( const string in_str,
list< string > &  out_strs 
)

Definition at line 78 of file vecscreen_run.cpp.

References s_PopIdPart().

Referenced by s_MakeFastaSubIds().

◆ s_PopIdPart()

string s_PopIdPart ( const string in_str)

Definition at line 65 of file vecscreen_run.cpp.

References min(), and NPOS.

Referenced by s_MakeFastaSubStrs().

◆ s_ReplaceLocalId()

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

◆ s_SetIdList()

list<CRef<CSeq_id> > s_SetIdList ( const CBioseq_Handle bh,
string title 
)

◆ USING_SCOPE() [1/3]

USING_SCOPE ( blast  )

◆ USING_SCOPE() [2/3]

USING_SCOPE ( objects  )

◆ USING_SCOPE() [3/3]

USING_SCOPE ( sequence  )

Variable Documentation

◆ match_type_ints

map<string, int> match_type_ints = { {"Strong",0}, {"Moderate",1}, {"Weak",2}, {"Suspect",3},{"Absent",4} }

Definition at line 61 of file vecscreen_run.cpp.

Referenced by CVecscreenRun::CFormatter::FormatResults().

◆ match_type_strs

map<int, string> match_type_strs = { {0,"Strong"}, {1,"Moderate"}, {2,"Weak"}, {3,"Suspect"},{4,"Absent"} }

Definition at line 62 of file vecscreen_run.cpp.

Referenced by CVecscreenRun::CFormatter::FormatResults().

◆ USING_NCBI_SCOPE

USING_NCBI_SCOPE

Definition at line 55 of file vecscreen_run.cpp.

Modified on Fri Feb 23 11:47:37 2024 by modify_doxy.py rev. 669887