Class
Align
An alignment of sequences.
Align<TSource, TSpec>
Include Headers
seqan/align.h
Parameters

TSource | Type of the ungapped sequences. Metafunctions: Source
TSpec | The specializing type. Metafunctions: Spec Default: ArrayGaps

Remarks
The default implementation of Align stores the alignment in a set of Gaps<TSource,TSpec> objects. Hence, the default implementation is row-based, so it will be faster to access the alignment row-wise than column-wise.
Metafunctions

Col | Type of a column in an alignment.
Cols | Type of column container of an alignment.
GetValue | Type for reading values.
Reference | Reference type.
Row | Type of a row in an alignment.
Rows | Type of row container of an alignment.
Source | Return underlying sequence of Gaps/Alignments.
StringSetType | Return type of stringSet function.
Value | Type of the items in the container or behind an iterator.

Functions

bamRecordToAlignment | Convert BamAlignmentRecord to an Align object.
bandedChainAlignment | Computes the best global pairwise alignment between two sequences given a non-empty seed chain.
col | A column in an alignment.
cols | The container of columns in an alignment.
detach | Makes an object independent from other objects.
globalAlignment | Computes the best global pairwise alignment.
integrateAlign | Integrates an alignment into another by copying the gaps.
localAlignment | Computes the best pairwise local alignment using the Smith-Waterman algorithm.
matchRefinement | Refines (i.e. cuts into smaller parts) a set of pairwise segment matches in such a way that none of the segments partly overlap. They are either identical (fully overlapping) or non-overlapping.
nextLocalAlignment | Compute next suboptimal local alignment.
row | A row in an alignment.
rows | The container of rows in an alignment.
setStrings | Loads the sequences of a stringset into an alignment.
splitAlignment | Compute split alignments.
stringSet | Gets the string set of an alignment graph.

Examples
File "align.cpp"

1 | #include <seqan/basic.h>
2 | #include <seqan/sequence.h>
3 | #include <seqan/file.h> // for I/O
4 | #include <seqan/align.h>
5 | #include <seqan/score.h>
6 |
7 | using namespace seqan;
8 |
9 | int main()
10 | {
11 | StringSet<DnaString> stringSet;
12 | appendValue(stringSet, "AGTTTAATCA");
13 | appendValue(stringSet, "AGTATACGA");
14 |
15 | Align<DnaString> align(stringSet); // Initialize the Align object using a StringSet.
16 |
17 | int score = globalAlignment(align, EditDistanceScore()); // Compute a global alingment using the Align object.
18 |
19 | std::cout << "score = " << score << std::endl;
20 | std::cout << "align\n" << align << std::endl;
21 |
22 | return 0;
23 | }

The output is as follows:
score = -4
align
0 . :
AGTTTAATCA
||| | | |
AGTAT-ACGA
Example Programs
Local Alignments, Global Alignments
See Also
AlignCols
SeqAn - Sequence Analysis Library - www.seqan.de

Page built @2014/10/13 16:12:56