Definitions used by all COBALT aligner components. More...
#include <util/range.hpp>
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Classes | |
| class | CLocalRange< Position > |
| Sufficient extra functionality is needed from CRange that it justifies extending the class. More... | |
Typedefs | |
| typedef int | TOffset |
| Basic data type for offsets into a sequence. More... | |
| typedef pair< TOffset, TOffset > | TOffsetPair |
| Basic type specifying a range on a sequence. More... | |
| typedef CLocalRange< TOffset > | TRange |
| define for the fundamental building block of sequence ranges More... | |
Variables | |
| static const int | kAlphabetSize = 28 |
| The aligner internally works only with the ncbistdaa alphabet. More... | |
Detailed Description
Definitions used by all COBALT aligner components.
Definition in file base.hpp.
Typedef Documentation
◆ TOffset
◆ TOffsetPair
| typedef pair<TOffset, TOffset> TOffsetPair |
◆ TRange
| typedef CLocalRange<TOffset> TRange |
Variable Documentation
◆ kAlphabetSize
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().
