Spec ExactReversableFragment
A type for ungapped, pairwise segment matches that maybe in reverse orientation.

Extends Fragment
All Extended Fragment
Defined in <seqan/align.h>
Signature template <[typename TSize[, typename TSpec]]> class Fragment<TSize, ExactReversableFragment<TSpec> >;

Template Parameters

TSize The size type of the underlying sequence. Default: Size<CharString>Type.
TSpec Specializing type. Default: ExactFragment<>.

Member Function Overview

Interface Function Overview

Interface Functions Inherited From Fragment

Detailed Description

Compared to the ExactFragment specialzing type of Fragment, a ExactReversableFragment stores an additional bool value to indicate whether a match is in reverse orientation or not.

Member Functions Detail

Fragment::Fragment(); Fragment::Fragment(seqID1, beg1, seqID2, beg2, l[, reversed]);



seqID1 ID of the first sequence. Type: TId.
beg1 Begin position of segment match in first sequence. Type: TSize.
seqID2 ID of the second sequence. Type: TId.
beg2 Begin position of segment match in second sequence. Type: TSize.
l The length of the segment match. Type: TSize.
reversed A bool; true if the segments match in reverse orientation, false otherwise.

Interface Functions Detail

bool isReversed(frag);

Return whether a segment match is in reverse orientation.


frag The Fragment to query for reverseness.


bool true if the fragment is reversed and false otherwise.