#include <ncbi_pch.hpp>#include <objmgr/object_manager.hpp>#include <objmgr/seq_vector.hpp>#include <objects/seqalign/Dense_seg.hpp>#include <objtools/data_loaders/blastdb/bdbloader.hpp>#include <objtools/readers/fasta.hpp>#include <serial/iterator.hpp>#include <algo/cobalt/cobalt.hpp>
Include dependency graph for cobalt_test_util.cpp:
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Functions | |
| USING_SCOPE (cobalt) | |
| USING_SCOPE (objects) | |
| int | ReadFastaQueries (const string &filename, vector< CRef< objects::CSeq_loc > > &seqs, CRef< objects::CScope > &scope, bool parse_deflines, objects::CSeqIdGenerator *id_generator) |
| int | ReadMsa (const string &filename, CRef< CSeq_align > &align, CRef< CScope > scope, bool parse_deflines, objects::CSeqIdGenerator *id_generator) |
Variables | |
| USING_NCBI_SCOPE | |
Function Documentation
◆ ReadFastaQueries()
| int ReadFastaQueries | ( | const string & | filename, |
| vector< CRef< objects::CSeq_loc > > & | seqs, | ||
| CRef< objects::CScope > & | scope, | ||
| bool | parse_deflines, | ||
| objects::CSeqIdGenerator * | id_generator | ||
| ) |
Definition at line 51 of file cobalt_test_util.cpp.
References CStreamLineReader::AtEOF(), ConstBegin(), ILineError::eProblem_ModifierFoundButNoneExpected, CFastaReader::fAssumeProt, CFastaReader::fForceType, flags, CFastaReader::fNoParseID, CFastaReader::IgnoreProblem(), CFastaReader::ReadOneSeq(), CFastaReader::SetIDGenerator(), and CSeq_loc::SetWhole().
Referenced by BOOST_AUTO_TEST_CASE(), and CMultiAlignerFixture::x_ReadSequences().
◆ ReadMsa()
| int ReadMsa | ( | const string & | filename, |
| CRef< CSeq_align > & | align, | ||
| CRef< CScope > | scope, | ||
| bool | parse_deflines, | ||
| objects::CSeqIdGenerator * | id_generator | ||
| ) |
Definition at line 99 of file cobalt_test_util.cpp.
References CScope::AddTopLevelSeqEntry(), CStreamLineReader::AtEOF(), CRef< C, Locker >::Empty(), ILineError::eProblem_ModifierFoundButNoneExpected, CFastaReader::fAssumeProt, CFastaReader::fForceType, flags, CFastaReader::fNoParseID, CFastaReader::fValidate, CSeq_entry::GetAnnot(), CFastaReader::IgnoreProblem(), CFastaReader::ReadAlignedSet(), and CFastaReader::SetIDGenerator().
Referenced by BOOST_AUTO_TEST_CASE(), and CMultiAlignerFixture::x_ReadAlignments().
◆ USING_SCOPE() [1/2]
| USING_SCOPE | ( | cobalt | ) |
◆ USING_SCOPE() [2/2]
| USING_SCOPE | ( | objects | ) |
Variable Documentation
◆ USING_NCBI_SCOPE
| USING_NCBI_SCOPE |
Definition at line 46 of file cobalt_test_util.cpp.
