Represents a range of traces.
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#include <trace_controller.hh>
Represents a range of traces.
Represents a range of possible traces in a dynamic programming matrix for aligning two sequences
- See also
- TraceController
Construct from pair of alignment strings.
construct trace range of two sequences given two alignment strings of the sequences and the allowed deviation delta the sequences can contain gaps themselves (which happens, when sequences orignate from a sequence profile).
- Parameters
-
pseqA | SeqEntry of sequence A |
pseqB | SeqEntry of sequence B |
aliA | alignment SeqEntry for sequence A |
aliB | alignment SeqEntry for sequence B |
delta | the allowed deviation |
side conditions: remove_gaps(seqA) == remove_gaps(aliA) && remove_gaps(seqB) == remove_gaps(aliB) where remove_gaps is a function that removes all gap symbols length(aliA)==length(aliB)
Construct as consensus trace range from a set of traces.
Constructs object as consensus trace ranges of the traces trs. The construction follows an idea of relaxing the deviation constraints by computing a trace with minimal accumulated distance to all traces and then determining its delta environment.
- Parameters
-
lenA | length of sequence A |
lenB | length of sequence B |
trs | set of traces |
delta | deviation |
Computes cost of a cut in the consensus trace of a trace range set.
- Parameters
-
i | cut.first |
j | cut.second |
trs | set of trace ranges |
- Returns
- cost of cut (i,j) in consensus of trs
size_t LocARNA::TraceRange::max_col |
( |
size_t |
i | ) |
const |
|
inline |
Maximal column of trace in a row.
- Parameters
-
- Returns
- maximal valid trace cell in the row i
size_t LocARNA::TraceRange::min_col |
( |
size_t |
i | ) |
const |
|
inline |
Minimal column of trace in a row.
- Parameters
-
- Returns
- minimal valid trace cell in the row i
void LocARNA::TraceRange::print_debug |
( |
std::ostream & |
out | ) |
const |
Print object to ouptut stream for debugging
- Parameters
-
Remove common gaps in pairwise alignment
- Parameters
-
aliA | alignment string A with name (SeqEntry) |
aliB | alignment string B with name (SeqEntry) |
- Returns
- pair of "sequence entries" that represent the pairwise alignment given by aliA and aliB where gap-only columns are removed
size_t LocARNA::TraceRange::rows |
( |
| ) |
const |
|
inline |
Read number of rows.
- Returns
- length of seqA, i.e. the maximal row of the trace
std::vector<size_t> LocARNA::TraceRange::max_col_vector_ |
|
protected |
The documentation for this class was generated from the following files: