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 ExactReversableFragment is a specialized 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]);

Constructor.

Parameters

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.

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

Interface Functions Detail

bool isReversed(frag);

Return whether a segment match is in reverse orientation.

Parameters

frag The Fragment to query for reverseness.

Returns

bool true if the fragment is reversed and false otherwise.

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.