Class Fragment
A type for pairwise segment matches.

All Subcl's ExactFragment, ExactReversableFragment
Defined in <seqan/align.h>
Signature template <[typename TSize[, typename TSpec]]> class Fragment;

Template Parameters

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

Interface Function Overview

Detailed Description

Examples

// Construct fragment.
unsigned seqId1 = 0, beg1 = 0, seqId2 = 32, beg2 = 42, len = 33;
Fragment<> fragment(seqId1, beg1, seqId2, beg2, len);

// Update fragment's properties.
fragmentBegin(fragment, 0) = 10;
fragmentBegin(fragment, 1) = 10;
sequenceId(fragment, 0) = 33;
sequenceId(fragment, 1) = 44;
fragmentLength(fragment) += 42;

Interface Functions Detail

TSize fragmentBegin(frag, seqId);

Return fragment begin.

Parameters

frag The Fragment to query.
seqId The id of the sequence to get the begin for.

Returns

TSize Reference to the fragment begin position member.

Data Races

Thread safety unknown!

TSize fragmentLength(frag);

Return fragment begin.

Parameters

frag The Fragment to query for its length.

Returns

TSize Reference to the Fragment's length.

Data Races

Thread safety unknown!

TInfix label(frag, stringSet, seqID);

Access to the Fragment's label.

Parameters

frag The Fragment to query.
stringSet The StringSet with the sequences.
seqID The id of the sequence for which the label should be retrieved.

Data Races

Thread safety unknown!

TId sequenceId(frag, seqNum);

Access to the sequence ID of a fragment.

Parameters

frag A Fragment.
seqNum The sequence number for which the id should be retrieved. Note that Fragment stores information about exactly two sequences which can be accessed with seqNum 0 or 1 but whose ids may differ from their seqNum.

Returns

TId Reference to the sequence fragment id member.

Data Races

Thread safety unknown!