NCBI C++ ToolKit
Macros | Functions
fcleanup.cpp File Reference
#include <ncbi_pch.hpp>
#include <objmgr/scope.hpp>
#include <objmgr/seqdesc_ci.hpp>
#include <objects/seq/Seq_descr.hpp>
#include <objects/seq/Bioseq.hpp>
#include <serial/iterator.hpp>
#include <objects/seq/MolInfo.hpp>
#include <objtools/cleanup/cleanup.hpp>
#include <objmgr/bioseq_ci.hpp>
#include <objmgr/feat_ci.hpp>
#include <objmgr/seq_entry_handle.hpp>
#include <objmgr/util/sequence.hpp>
#include <objmgr/util/feature.hpp>
#include <objtools/edit/cds_fix.hpp>
#include <objtools/flatfile/flatfile_parse_info.hpp>
#include <objtools/flatfile/flatfile_parser.hpp>
#include "utilfun.h"
#include "loadfeat.h"
#include "fcleanup.h"
+ Include dependency graph for fcleanup.cpp:

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Macros

#define THIS_FILE   "fcleanup.cpp"
 

Functions

 USING_SCOPE (objects)
 
static void MoveSourceDescrToTop (CSeq_entry &entry)
 
static bool IsEmptyMolInfo (const CMolInfo &mol_info)
 
static void MoveAnnotToTop (CSeq_entry &seq_entry)
 
static void MoveBiomolToTop (CSeq_entry &seq_entry)
 
static void LookForProductName (CSeq_feat &feat)
 
static bool IsConversionPossible (const vector< pair< TSeqPos, TSeqPos >> &ranges)
 
static void SetNewInterval (const CSeq_interval *first, const CSeq_interval *last, const TSeqPos &from, TSeqPos &to, CSeq_loc &loc)
 
static void ConvertMixToInterval (CSeq_loc &loc)
 
static void ConvertPackedIntToInterval (CSeq_loc &loc)
 
void g_InstantiateMissingProteins (CSeq_entry_Handle entryHandle)
 
void FinalCleanup (TEntryList &seq_entries)
 

Macro Definition Documentation

◆ THIS_FILE

#define THIS_FILE   "fcleanup.cpp"

Definition at line 61 of file fcleanup.cpp.

Function Documentation

◆ ConvertMixToInterval()

static void ConvertMixToInterval ( CSeq_loc loc)
static

◆ ConvertPackedIntToInterval()

static void ConvertPackedIntToInterval ( CSeq_loc loc)
static

◆ FinalCleanup()

void FinalCleanup ( TEntryList seq_entries)

◆ g_InstantiateMissingProteins()

void g_InstantiateMissingProteins ( CSeq_entry_Handle  entryHandle)

◆ IsConversionPossible()

static bool IsConversionPossible ( const vector< pair< TSeqPos, TSeqPos >> &  ranges)
static

Definition at line 236 of file fcleanup.cpp.

References convert(), first(), and i.

Referenced by ConvertMixToInterval(), and ConvertPackedIntToInterval().

◆ IsEmptyMolInfo()

static bool IsEmptyMolInfo ( const CMolInfo mol_info)
static

◆ LookForProductName()

static void LookForProductName ( CSeq_feat feat)
static

◆ MoveAnnotToTop()

static void MoveAnnotToTop ( CSeq_entry seq_entry)
static

◆ MoveBiomolToTop()

static void MoveBiomolToTop ( CSeq_entry seq_entry)
static

◆ MoveSourceDescrToTop()

static void MoveSourceDescrToTop ( CSeq_entry entry)
static

◆ SetNewInterval()

static void SetNewInterval ( const CSeq_interval first,
const CSeq_interval last,
const TSeqPos from,
TSeqPos to,
CSeq_loc loc 
)
static

◆ USING_SCOPE()

USING_SCOPE ( objects  )
Modified on Thu Jul 18 16:04:01 2024 by modify_doxy.py rev. 669887