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NCBI C++ ToolKit: include/algo/cobalt/base.hpp File Reference

Definitions used by all COBALT aligner components. More...

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Definitions used by all COBALT aligner components.

Definition in file base.hpp.

Basic data type for offsets into a sequence.

By convention, all offsets are zero-based

Definition at line 49 of file base.hpp.

Basic type specifying a range on a sequence.

Definition at line 52 of file base.hpp.

define for the fundamental building block of sequence ranges

Definition at line 115 of file base.hpp.

The aligner internally works only with the ncbistdaa alphabet.

Definition at line 119 of file base.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), CSequence::CompressSequences(), CSequence::CreateMsa(), CSequence::InsertGaps(), CProfileData::Load(), CSequence::PropagateGaps(), CSequence::Reset(), TKmerMethods< TKmerCounts >::SetParams(), CMultiAligner::x_AlignProfileProfile(), CMultiAligner::x_AssignDefaultResFreqs(), CMultiAligner::x_AssignRPSResFreqs(), CMultiAligner::x_ComputeProfileRangeAlignment(), x_FillResidueFrequencies(), x_GetProfile(), x_GetSelfScore(), CMultiAligner::x_MakeClusterResidueFrequencies(), x_NormalizeResidueFrequencies(), and x_ScoreFromTranscriptCore().

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