NCBI C++ ToolKit
Macros | Functions | Variables
utilfeat.cpp File Reference
#include <ncbi_pch.hpp>
#include "ftacpp.hpp"
#include <objects/seqfeat/BioSource.hpp>
#include <objects/seqset/Bioseq_set.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objects/seq/Seq_descr.hpp>
#include <objects/seqfeat/Org_ref.hpp>
#include <objects/seqfeat/OrgName.hpp>
#include <objects/seqfeat/SubSource.hpp>
#include "index.h"
#include <objtools/flatfile/flatdefn.h>
#include "ftaerr.hpp"
#include "asci_blk.h"
#include "add.h"
#include "utilfeat.h"
#include "utilfun.h"
+ Include dependency graph for utilfeat.cpp:

Go to the source code of this file.

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Macros

#define THIS_FILE   "utilfeat.cpp"
 

Functions

char ValidAminoAcid (const string &abbrev)
 
 USING_SCOPE (objects)
 
bool SeqLocHaveFuzz (const CSeq_loc &loc)
 
char * CpTheQualValue (const TQualVector &qlist, const Char *qual)
 
char * GetTheQualValue (TQualVector &qlist, const Char *qual)
 
bool DeleteQual (TQualVector &qlist, const Char *qual)
 
Uint1 GetQualValueAa (char *qval, bool checkseq)
 
bool GetGenomeInfo (CBioSource &bsp, const Char *bptr)
 
static void GetTaxnameNameFromDescrs (const TSeqdescList &descrs, vector< string > &names)
 
static void GetTaxnameName (TEntryList &seq_entries, vector< string > &names)
 
static void CheckDelGbblockSourceFromDescrs (TSeqdescList &descrs, const vector< string > &names)
 
static void CheckDelGbblockSource (TEntryList &seq_entries, const vector< string > &names)
 
void MaybeCutGbblockSource (TEntryList &seq_entries)
 
void MakeLocStrCompatible (string &str)
 
string location_to_string (const CSeq_loc &loc)
 

Variables

const char * ParFlat_GImod []
 
const char * valid_organelle []
 

Macro Definition Documentation

◆ THIS_FILE

#define THIS_FILE   "utilfeat.cpp"

Definition at line 59 of file utilfeat.cpp.

Function Documentation

◆ CheckDelGbblockSource()

static void CheckDelGbblockSource ( TEntryList seq_entries,
const vector< string > &  names 
)
static

Definition at line 443 of file utilfeat.cpp.

References Begin(), CheckDelGbblockSourceFromDescrs(), and names.

Referenced by MaybeCutGbblockSource().

◆ CheckDelGbblockSourceFromDescrs()

static void CheckDelGbblockSourceFromDescrs ( TSeqdescList descrs,
const vector< string > &  names 
)
static

◆ CpTheQualValue()

char* CpTheQualValue ( const TQualVector qlist,
const Char qual 
)

◆ DeleteQual()

bool DeleteQual ( TQualVector qlist,
const Char qual 
)

◆ GetGenomeInfo()

bool GetGenomeInfo ( CBioSource bsp,
const Char bptr 
)

◆ GetQualValueAa()

Uint1 GetQualValueAa ( char *  qval,
bool  checkseq 
)

◆ GetTaxnameName()

static void GetTaxnameName ( TEntryList seq_entries,
vector< string > &  names 
)
static

Definition at line 332 of file utilfeat.cpp.

References Begin(), GetTaxnameNameFromDescrs(), and names.

Referenced by MaybeCutGbblockSource().

◆ GetTaxnameNameFromDescrs()

static void GetTaxnameNameFromDescrs ( const TSeqdescList descrs,
vector< string > &  names 
)
static

◆ GetTheQualValue()

char* GetTheQualValue ( TQualVector qlist,
const Char qual 
)

◆ location_to_string()

string location_to_string ( const CSeq_loc loc)

◆ MakeLocStrCompatible()

void MakeLocStrCompatible ( string str)

Definition at line 467 of file utilfeat.cpp.

References last(), and str().

Referenced by GetLocationStr(), and location_to_string().

◆ MaybeCutGbblockSource()

void MaybeCutGbblockSource ( TEntryList seq_entries)

Definition at line 454 of file utilfeat.cpp.

References CheckDelGbblockSource(), ctll::empty(), GetTaxnameName(), and names.

Referenced by GenBankAsciiOrig(), OutputEmblAsn(), and XMLAscii().

◆ SeqLocHaveFuzz()

bool SeqLocHaveFuzz ( const CSeq_loc loc)

Definition at line 105 of file utilfeat.cpp.

References CSeq_loc::GetLabel().

Referenced by InternalStopCodon(), ProcFeatBlk(), SPFeatGeneral(), and SpProcFeatBlk().

◆ USING_SCOPE()

USING_SCOPE ( objects  )

◆ ValidAminoAcid()

char ValidAminoAcid ( const string abbrev)

Definition at line 632 of file cleanup_utils.cpp.

Referenced by GetQualValueAa().

Variable Documentation

◆ ParFlat_GImod

const char* ParFlat_GImod[]
Initial value:
= {
"Mitochondr",
"Chloroplast",
"Kinetoplas",
"Cyanelle",
"Chromoplast",
"Plastid",
"Macronuclear",
"Extrachrom",
"Plasmid",
"Leucoplast",
"Apicoplast",
nullptr
}

Definition at line 73 of file utilfeat.cpp.

Referenced by GetGenomeInfo().

◆ valid_organelle

const char* valid_organelle[]
Initial value:
= {
"apicoplast",
"chloroplast",
"chromatophore",
"chromoplast",
"cyanelle",
"hydrogenosome",
"kinetoplast",
"leucoplast",
"mitochondrion",
"nucleomorph",
"plastid",
"proplastid",
nullptr
}

Definition at line 88 of file utilfeat.cpp.

Referenced by CheckDelGbblockSourceFromDescrs().

Modified on Sun Mar 03 03:16:56 2024 by modify_doxy.py rev. 669887