splign.hpp File Reference

#include <corelib/ncbistd.hpp>
#include <corelib/version_api.hpp>
#include <objmgr/scope.hpp>
#include <objmgr/bioseq_handle.hpp>
#include <objects/seq/seq_id_handle.hpp>
#include <util/range_coll.hpp>
#include <algo/align/nw/nw_formatter.hpp>
#include <algo/align/util/blast_tabular.hpp>

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Classes
class	CSplign
	CSplign is the central library object for computing spliced cDNA-to-genomic alignments. More...
struct	CSplign::SAlignedCompartment
struct	CSplign::SAlnMapElem

Variables
const string	kTestType_20_28_plus = "20_28_plus"
const string	kTestType_20_28 = "20_28_90_cut20"
const string	kTestType_production_default = "production_default"

Variable Documentation

kTestType_20_28

const string kTestType_20_28 = "20_28_90_cut20"

Definition at line 55 of file splign.hpp.

Referenced by CSplign::Run(), CSplignArgUtil::SetupArgDescriptions(), CSplign::x_Run(), and CSplign::x_RunOnCompartment().

kTestType_20_28_plus

const string kTestType_20_28_plus = "20_28_plus"

Definition at line 54 of file splign.hpp.

Referenced by CSplign::Run(), CSplignArgUtil::SetupArgDescriptions(), CSplign::x_Run(), and CSplign::x_RunOnCompartment().

kTestType_production_default

const string kTestType_production_default = "production_default"

Definition at line 56 of file splign.hpp.

Referenced by CSplignArgUtil::ArgsToSplign(), and CSplign::x_ProcessTermSegm().