#include <GappedAlignment.h>
Inheritance diagram for mems::GappedAlignment:
Public Member Functions | |
| GappedAlignment * | Clone () const |
| GappedAlignment * | Copy () const |
| creates a copy of this using a boost::pool::fast_pool_allocator | |
| virtual void | CropEnd (gnSeqI crop_amount) |
Deprecated: Use CropLeft and CropRight instead Removes the last crop_amount base pairs from the end of the match. | |
| virtual void | CropLeft (gnSeqI crop_amount, uint seqI) |
Crop this match from the left Removes the first crop_amount positions from the left side of the match. | |
| virtual void | CropRight (gnSeqI crop_amount, uint seqI) |
Crop this match from the right Removes the last crop_amount positions from the right side of the match. | |
| virtual void | CropStart (gnSeqI crop_amount) |
Deprecated: Use CropLeft and CropRight instead Removes the first crop_amount base pairs from the beginning of the match. | |
| virtual void | Free () |
| frees storage used by this object in a boost::pool::fast_pool_allocator | |
| GappedAlignment (uint seq_count, gnSeqI align_length) | |
| GappedAlignment () | |
| void | GetAlignment (std::vector< bitset_t > &align_matrix) const |
| Gets a copy of the alignment as an array of dynamic_bitsets. | |
| void | GetColumn (gnSeqI col, std::vector< gnSeqI > &pos, std::vector< bool > &column) const |
| Given an alignment column index, this function returns the corresponding sequence coordinates and whether each sequence is aligned in that column If a given sequence is not represented in the requested column, the position returned in pos should be that of the first nucleotide to the left of the requested column. | |
| virtual void | Invert () |
| Inverts the coordinates of this match. | |
| virtual bool | IsGap (uint seq, gnSeqI col) const |
| returns true if the given row,column of the alignment has a gap character | |
| void | SetAlignment (const std::vector< std::string > &seq_align) |
| Sets the alignment. | |
| virtual AbstractMatch * | Split (gnSeqI before_column) |
| Splits the alignment before the specified column. | |
| void | swap (GappedAlignment &other) |
Protected Member Functions | |
| void | CropEndCoords (gnSeqI crop_amount) |
| void | CropStartCoords (gnSeqI crop_amount) |
| void | swap (GappedAlignment *other) |
Protected Attributes | |
| std::vector< std::string > | align_matrix |
Friends | |
| const std::vector< std::string > & | GetAlignment (const GappedAlignment &ga, const std::vector< genome::gnSequence * > &seq_table) |
| std::ostream & | operator<< (std::ostream &os, const GappedAlignment &ga) |
| Writes this GappedAlignment to the specified output stream (e.g. | |
| std::istream & | operator>> (std::istream &is, GappedAlignment &ga) |
| Reads a GappedAlignment from the specified input stream (e.g. | |
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Definition at line 23 of file GappedAlignment.cpp. Referenced by Clone(). |
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Definition at line 27 of file GappedAlignment.cpp. References uint. |
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Definition at line 31 of file GappedAlignment.h. References GappedAlignment(). |
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creates a copy of this using a boost::pool::fast_pool_allocator
Implements mems::AbstractMatch. Definition at line 86 of file GappedAlignment.h. References mems::m_allocateAndCopy(). Referenced by mems::AlignLCBInParallel(), mems::removeLargeGapsPP(), and Split(). |
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Deprecated: Use CropLeft and CropRight instead Removes the last
Implements mems::AbstractMatch. Definition at line 150 of file GappedAlignment.h. References mems::AbstractGappedAlignment< SparseAbstractMatch<> >::AlignmentLength(), CropEndCoords(), mems::SparseAbstractMatch<>::SeqCount(), std::swap(), and uint. Referenced by CropLeft(), and Split(). |
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Crop this match from the left Removes the first
Implements mems::AbstractMatch. Definition at line 165 of file GappedAlignment.h. References mems::AbstractGappedAlignment< SparseAbstractMatch<> >::AlignmentLength(), CropEnd(), CropStart(), mems::SparseAbstractMatch<>::Orientation(), and uint. Referenced by CropRight(). |
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Crop this match from the right Removes the last
Implements mems::AbstractMatch. Definition at line 186 of file GappedAlignment.h. References CropLeft(), Invert(), and uint. |
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Deprecated: Use CropLeft and CropRight instead Removes the first
Implements mems::AbstractMatch. Definition at line 123 of file GappedAlignment.h. References CropStartCoords(), mems::SparseAbstractMatch<>::SeqCount(), and uint. Referenced by CropLeft(). |
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frees storage used by this object in a boost::pool::fast_pool_allocator
Implements mems::AbstractMatch. Definition at line 91 of file GappedAlignment.h. References mems::m_free(). |
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Gets a copy of the alignment as an array of dynamic_bitsets.
Implements mems::AbstractMatch. Definition at line 195 of file GappedAlignment.h. References mems::bitset_t, and mems::SparseAbstractMatch<>::LeftEnd(). |
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Given an alignment column index, this function returns the corresponding sequence coordinates and whether each sequence is aligned in that column If a given sequence is not represented in the requested column, the position returned in pos should be that of the first nucleotide to the left of the requested column. If no nucleotides exist to the left of the requested column, then a NO_MATCH is returned in pos for that sequence. Implements mems::AbstractMatch. Definition at line 240 of file GappedAlignment.h. References mems::SparseAbstractMatch<>::LeftEnd(), mems::SparseAbstractMatch<>::Orientation(), mems::AbstractMatch::RightEnd(), mems::SparseAbstractMatch<>::SeqCount(), and uint. |
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Inverts the coordinates of this match.
Reimplemented from mems::SparseAbstractMatch<>. Definition at line 97 of file GappedAlignment.h. References mems::SparseAbstractMatch<>::SeqCount(), and uint. Referenced by CropRight(). |
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returns true if the given row,column of the alignment has a gap character
Implements mems::AbstractMatch. Definition at line 265 of file GappedAlignment.h. References uint. |
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Sets the alignment.
Implements mems::AbstractGappedAlignment< SparseAbstractMatch<> >. Definition at line 33 of file GappedAlignment.cpp. References mems::AbstractGappedAlignment< SparseAbstractMatch<> >::SetAlignmentLength(). Referenced by mems::MuscleInterface::Align(), mems::ClustalInterface::Align(), mems::MuscleInterface::ProfileAlign(), mems::MuscleInterface::ProfileAlignFast(), mems::GenericIntervalList< MatchType >::ReadList(), mems::GenericIntervalList< MatchType >::ReadStandardAlignment(), mems::GenericIntervalList< MatchType >::ReadStandardAlignmentCompact(), mems::MuscleInterface::Refine(), mems::ProgressiveAligner::refineAlignment(), mems::MuscleInterface::RefineFast(), and mems::GenericInterval< GappedBaseImpl >::SetAlignment(). |
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Splits the alignment before the specified column. The left-side remains in "this" GappedAlignment, and the right side is returned as a new GappedAlignment Definition at line 209 of file GappedAlignment.h. References align_matrix, mems::AbstractGappedAlignment< SparseAbstractMatch<> >::AlignmentLength(), Copy(), CropEnd(), CropStartCoords(), mems::AbstractGappedAlignment< SparseAbstractMatch<> >::Length(), mems::SparseAbstractMatch<>::SeqCount(), mems::AbstractGappedAlignment< SparseAbstractMatch<> >::SetAlignmentLength(), mems::AbstractGappedAlignment< SparseAbstractMatch<> >::SetLength(), mems::SparseAbstractMatch<>::SetStart(), mems::SparseAbstractMatch<>::Start(), and std::swap(). Referenced by mems::removeLargeGapsPP(). |
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Definition at line 73 of file GappedAlignment.h. References align_matrix, and std::swap(). |
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Definition at line 69 of file GappedAlignment.h. Referenced by std::swap(). |
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Writes this GappedAlignment to the specified output stream (e.g. cout). |
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Reads a GappedAlignment from the specified input stream (e.g. cin). |
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Definition at line 78 of file GappedAlignment.h. Referenced by mems::GetAlignment(), mems::operator<<(), mems::operator>>(), Split(), and swap(). |
1.3.6