Segment

Class

Segment

A contiguous part of a sequence.

Segment


InfixSegment		PrefixSegment		SuffixSegment

Segment<THost, TSpec>

Include Headers

seqan/sequence.h

Parameters

THost	Type of the whole sequence. Instances of Segment<THost, TSpec> are subsequences of THost objects. Metafunctions: Host
TSpec	The specializing type. Metafunctions: Spec Default: InfixSegment.

Specializations

InfixSegment	An arbitrary segment.
PrefixSegment	First part of a sequence.
SuffixSegment	End part segment of a sequence.

Metafunctions

DefaultOverflowExplicit	The default overflow strategy for explicit resize.
DefaultOverflowImplicit	The default overflow strategy for implicit resize.
GetValue	Type for reading values.
Host	Type of the object a given object depends on.
IsContiguous	Determines whether a container stores its elements in a contiguous array.
IsSequence	Determines whether a container stores its elements in sequential order.
Iterator	Type of iterator objects that are used to traverse the container.
Reference	Reference type.
Size	Type of an object that is suitable to hold size information.
Spec	The spec of a class.
Value	Type of the items in the container or behind an iterator.

Functions

assign	Assigns one object to another object.
atBegin	Determines whether an iterator is at the beginning position.
atEnd	Determines whether an iterator is at the end position.
begin	The begin of a container.
beginPosition	Begin position of object in host.
capacity	The maximal length.
complement	Complement a sequence or a StringSet in-place.
empty	Test a container for being empty.
endPosition	End position of object in host.
getObjectId	A value that identifies the underlying sequence.
goBegin	Iterates to the first position of a container.
goDown	Iterates down one edge or a path in a tree.
goEnd	Iterates to the last position of a container.
goNext	Iterates to next position.
goPrevious	Iterates to pevious position.
host	The object a given object depends on.
length	The number of items/characters.
reverseComplement	Reverse and complement a sequence or a StringSet in-place.
setHost	Sets the host of an object.
shareResources	Determines whether two sequences share the same resource.
toLower	Convert characters in sequence or StringSet to lower case in-place.
toUpper	Convert characters in sequence or StringSet to lower case in-place.
value	Reference to the value.

Examples

File "infix.cpp"

1	#include <seqan/basic.h>
2	#include <seqan/sequence.h>
3	#include <seqan/file.h> // for I/O
4
5
6	using namespace seqan;
7
8	int main()
9	{
10	String<Dna> dnaSeq = "TATACGCGAAAA";
11	Infix<String<Dna> >::Type inf = infix(dnaSeq, 4, 8);
12	std::cout << "Infix: " << inf << std::endl;
13
14	return 0;
15	}

The output is as follows:

Infix: CGCG

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