Class
FragmentA type for pairwise segment matches.
A type for pairwise segment matches.
All Subcl's | ExactFragment, ExactReversableFragment |
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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. |
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TSpec |
Specializing type. Default: ExactFragment<>. |
Interface Function Overview
-
TSize fragmentBegin(frag, seqId);
Return fragment begin. -
TSize fragmentLength(frag);
Return fragment begin. -
TInfix label(frag, stringSet, seqID);
Access to the Fragment's label. -
TId sequenceId(frag, seqNum);
Access to the sequence ID of a fragment.
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. |
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seqId
|
The id of the sequence to get the begin for. |
Returns
TSize |
Reference to the fragment begin position member. |
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Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
TSize fragmentLength(frag);
Return fragment begin.
Parameters
frag
|
The Fragment to query for its length. |
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Returns
TSize |
Reference to the Fragment's length. |
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Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
TInfix label(frag, stringSet, seqID);
Access to the Fragment's label.
Parameters
frag
|
The Fragment to query. |
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stringSet
|
The StringSet with the sequences. |
seqID
|
The id of the sequence for which the label should be retrieved. |
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
TId sequenceId(frag, seqNum);
Access to the sequence ID of a fragment.
Parameters
frag
|
A Fragment. |
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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. |
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Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.