A RetroSearch Logo

Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Search Query:

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/blastdb__dataextract_8cpp.html below:

NCBI C++ ToolKit: src/objtools/blast/blastdb_format/blastdb_dataextract.cpp File Reference

Defines classes which extract data from a BLAST database. More...

#include <ncbi_pch.hpp>
#include <objtools/blast/blastdb_format/invalid_data_exception.hpp>
#include <objtools/blast/blastdb_format/blastdb_dataextract.hpp>
#include <objects/seq/Seqdesc.hpp>
#include <objects/seq/Seq_descr.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/seqloc/PDB_seq_id.hpp>
#include <corelib/ncbiutil.hpp>
#include <util/sequtil/sequtil_manip.hpp>
#include <util/checksum.hpp>
#include <objmgr/object_manager.hpp>
#include <objmgr/scope.hpp>

Include dependency graph for blastdb_dataextract.cpp:

Go to the source code of this file.

Go to the SVN repository for this file.

Macros #define  NOT_AVAILABLE   "N/A"   #define  SEPARATOR   ";"   #define  CTRL_A   "\001"   Functions   USING_SCOPE (objects)   string  GetBareId (const CSeq_id &id)   static void  s_ReplaceCtrlAsInTitle (CRef< CBioseq > bioseq)   static string  s_GetTitle (const CBioseq &bioseq)   static string  s_ConfigureDeflineTitle (const string &title, bool use_ctrl_a)   Auxiliary function to format the defline for FASTA output format. More...
  static string  s_CheckName (const string &name)   Variables static const string  kNoMasksFound = "none"   Detailed Description

Defines classes which extract data from a BLAST database.

Definition in file blastdb_dataextract.cpp.

Macro Definition Documentation ◆ CTRL_A #define CTRL_A   "\001"

Definition at line 604 of file blastdb_dataextract.cpp.

◆ NOT_AVAILABLE #define NOT_AVAILABLE   "N/A"

Definition at line 49 of file blastdb_dataextract.cpp.

◆ SEPARATOR #define SEPARATOR   ";"

Definition at line 50 of file blastdb_dataextract.cpp.

Function Documentation ◆ GetBareId() string GetBareId ( const CSeq_id &  id )

Definition at line 256 of file seq_writer.cpp.

Referenced by CBlastDBExtractor::ExtractSeqId(), s_ConfigureDeflineTitle(), and CBlastDBExtractor::x_SetGi2SeqIdMap().

◆ s_CheckName() static string s_CheckName ( const string &  name ) static

Definition at line 821 of file blastdb_dataextract.cpp.

◆ s_ConfigureDeflineTitle() static string s_ConfigureDeflineTitle ( const string &  title, bool  use_ctrl_a  ) static

Auxiliary function to format the defline for FASTA output format.

Definition at line 631 of file blastdb_dataextract.cpp.

References CTRL_A, FindBestChoice(), CSeq_id::fParse_PartialOK, NStr::fSplit_ByPattern, GetBareId(), kSeparator, NPOS, CSeq_id::ParseIDs(), CSeq_id::Score(), and NStr::Split().

◆ s_GetTitle() static string s_GetTitle ( const CBioseq &  bioseq ) static

Definition at line 618 of file blastdb_dataextract.cpp.

References _ASSERT, CBioseq_Base::CanGetDescr(), CSeqdesc_Base::e_Title, CSeq_descr_Base::Get(), CBioseq_Base::GetDescr(), ITERATE, and string.

Referenced by CBlastDBExtractor::ExtractFasta().

◆ s_ReplaceCtrlAsInTitle() static void s_ReplaceCtrlAsInTitle ( CRef< CBioseq >  bioseq ) static

Definition at line 606 of file blastdb_dataextract.cpp.

References CTRL_A, CSeqdesc_Base::e_Title, NON_CONST_ITERATE, NStr::ReplaceInPlace(), CBioseq_Base::SetDescr(), and string.

Referenced by CBlastDBExtractor::ExtractFasta().

◆ USING_SCOPE() USING_SCOPE ( objects  ) Variable Documentation ◆ kNoMasksFound const string kNoMasksFound = "none" static

Definition at line 551 of file blastdb_dataextract.cpp.

Referenced by CBlastDBExtractor::ExtractMaskingData().

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4