#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 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[])