SequenceAlignment

Represents an alignment of two sequences.

struct SequenceAlignment (

S

alias scoreFun = "a == b ? 0 : 1"

) {

alias getScore = binaryFun!scoreFun;

score_t score;

EditOp[] editPath;

score_t indelPenalty;

Flag!"freeShift" freeShift;

score_t computeScore();

bool isValid();

auto stripInsertions(Strip strip);

auto partial(size_t begin, size_t end, Strip stripInsertions);

auto opDollar();

auto opIndex(size_t[2] slice);

size_t[2] opSlice(size_t begin, size_t end);

string toString(size_t width);

}

Members

Aliases

getScore alias getScore = binaryFun!scoreFun: Undocumented in source.

Functions

computeScore score_t computeScore(): Compute alignment score.
isValid bool isValid(): Undocumented in source. Be warned that the author may not have intended to support it.
opDollar auto opDollar(): Undocumented in source. Be warned that the author may not have intended to support it.
opIndex auto opIndex(size_t[2] slice): Get a partial alignment with respect to reference.
opSlice size_t[2] opSlice(size_t begin, size_t end): Undocumented in source. Be warned that the author may not have intended to support it.
partial auto partial(size_t begin, size_t end, Strip stripInsertions): Get a partial alignment with respect to reference.
stripInsertions auto stripInsertions(Strip strip): Strip leading/trailing insertions.
toString string toString(size_t width): Get a string representation of this alignment. Visual alignment breaks unless elements of the sequences convert to single chars via to!string.

Variables

editPath EditOp[] editPath;: Undocumented in source.
freeShift Flag!"freeShift" freeShift;: Undocumented in source.
indelPenalty score_t indelPenalty;: Undocumented in source.
query S query;: Undocumented in source.
reference S reference;: Undocumented in source.
score score_t score;: Undocumented in source.

Meta

Source

See Implementation

dalicious string aliases

score_t

classes

AlignmentException

enums

functions

structs

SequenceAlignment