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/splign__app_8cpp.html below:

NCBI C++ ToolKit: src/app/splign/splign_app.cpp File Reference

#include <ncbi_pch.hpp>
#include "splign_app.hpp"
#include "splign_app_exception.hpp"
#include <corelib/ncbistd.hpp>
#include <corelib/ncbi_system.hpp>
#include <serial/objostrasn.hpp>
#include <serial/serial.hpp>
#include <algo/align/nw/align_exception.hpp>
#include <algo/align/nw/nw_spliced_aligner16.hpp>
#include <algo/align/splign/splign_cmdargs.hpp>
#include <algo/align/util/hit_comparator.hpp>
#include <algo/blast/api/bl2seq.hpp>
#include <algo/blast/api/local_blast.hpp>
#include <algo/blast/api/objmgr_query_data.hpp>
#include <algo/blast/api/local_db_adapter.hpp>
#include <objmgr/seq_vector.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqalign/Score_set.hpp>
#include <objects/seqalign/Score.hpp>
#include <objtools/readers/fasta.hpp>
#include <objtools/readers/reader_exception.hpp>
#include <objtools/data_loaders/blastdb/bdbloader.hpp>
#include <objtools/data_loaders/genbank/gbloader.hpp>
#include <objtools/lds2/lds2.hpp>
#include <objtools/data_loaders/lds2/lds2_dataloader.hpp>
#include <objtools/alnmgr/score_builder_base.hpp>
#include <algorithm>
#include <memory>

Include dependency graph for splign_app.cpp:

Go to the source code of this file.

Go to the SVN repository for this file.

Classes struct   SComplement   Enumerations enum   ERunMode { eNotSet , ePairwise , eBatch1 , eBatch2 }   Functions void  ReadCompartment (istream &istr, CSplign::THitRefs *phitrefs)   string  GetLdsDbDir (const string &fasta_dir)   size_t  GetNonConsensusSpliceCount (const CSplign::TResults &splign_results)   int  main (int argc, const char *argv[])   Variables const char  kSplignLdsDb [] = "splign.lds2db"     USING_NCBI_SCOPE   Enumeration Type Documentation ◆ ERunMode enum ERunMode Enumerator eNotSet  ePairwise  eBatch1  eBatch2 

Definition at line 549 of file splign_app.cpp.

Function Documentation ◆ GetLdsDbDir() string GetLdsDbDir ( const string &  fasta_dir )

Definition at line 560 of file splign_app.cpp.

References CDirEntry::GetPathSeparator().

Referenced by CSplignApp::Run().

◆ GetNonConsensusSpliceCount() size_t GetNonConsensusSpliceCount ( const CSplign::TResults &  splign_results )

Definition at line 908 of file splign_app.cpp.

References isdigit(), ITERATE, CSplign::SAlignedCompartment::m_Segments, n, and CNWFormatter::SSegment::s_IsConsensusSplice().

Referenced by CSplignApp::x_ProcessPair().

◆ main() int main ( int  argc, const char *  argv[]  )

Definition at line 1182 of file splign_app.cpp.

◆ ReadCompartment() void ReadCompartment ( istream &  istr, CSplign::THitRefs *  phitrefs  )

Definition at line 364 of file splign_app.cpp.

Referenced by CSplignApp::x_GetNextComp().

Variable Documentation ◆ kSplignLdsDb const char kSplignLdsDb[] = "splign.lds2db"

Definition at line 558 of file splign_app.cpp.

Referenced by CSplignApp::Run().

◆ USING_NCBI_SCOPE USING_NCBI_SCOPE

Definition at line 1180 of file splign_app.cpp.

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