Sequence::ClustalW< T > Class Template Reference

ClustalW streams. More...

#include <Sequence/Clustalw.hpp>

Inheritance diagram for Sequence::ClustalW< T >:

Public Types
typedef std::vector< T >::size_type	size_type
typedef std::vector< T >::reference	reference
typedef std::vector< T >::const_reference	const_reference
typedef std::vector< T >::iterator	iterator
typedef std::vector< T >::const_iterator	const_iterator

Public Member Functions
	ClustalW (const AlignStream< T > &a)
	ClustalW (const ClustalW< T > &a)
	ClustalW (const std::vector< T > &a)
	ClustalW (AlignStream< T > &&a)
	ClustalW (ClustalW< T > &&a)
	ClustalW (std::vector< T > &&a)
std::istream &	read (std::istream &s)
std::ostream &	print (std::ostream &s) const
ClustalW< T > &	operator= (const AlignStream< T > &rhs)
bool	empty () const
size_type	size (void) const
reference	operator[] (const size_type &i)
const_reference	operator[] (const size_type &i) const
iterator	begin ()
const_iterator	begin () const
iterator	end ()
const_iterator	end () const
bool	IsAlignment (void)
bool	Gapped (void)
unsigned	UnGappedLength (void)
void	RemoveGaps (void)
void	RemoveTerminalGaps (void)
std::vector< T >	Trim (std::vector< int >sites)
std::vector< T >	TrimComplement (std::vector< int >sites)
const std::vector< T >	Data (void)
void	assign (const_iterator beg, const_iterator end)
void	assign (std::vector< T > &&_data)

Detailed Description

template<typename T>
class Sequence::ClustalW< T >

ClustalW streams.

This class defines an input routine for alignments in ClustalW format. This class template can be instantiated with the following types:

Sequence::ClustalW< Sequence::Fasta >; //or anything derived from Sequence::Seq
Sequence::ClustalW< std::pair<std::string, std::string> >;

//example: a std::pair<std::string,std::string>
#include<utility>
#include <string>
#include <iostream>
#include <Sequence/Clustalw.hpp>

//using namespace std;
using namespace Sequence;

int main()
{
//instantiate the template
ClustalW< std::pair<string,string> > x;
//read in an object from stdin
cin >> x;
for (int i = 0 ; i < x.size() ; ++i)
{
//output each element in Fasta format
//but without using Sequence::Fasta
cout << '>'
<< x[i].name
<< '\n'
<< x[i].seq
<< '\n';
}
}

Definition at line 77 of file Clustalw.hpp.

Member Typedef Documentation

const_iterator

template<typename T>

typedef std::vector<T>::const_iterator Sequence::AlignStream< T >::const_iterator

inherited

value type is std::vector<T>::const_iterator

Definition at line 124 of file AlignStream.hpp.

iterator

template<typename T>

typedef std::vector<T>::iterator Sequence::AlignStream< T >::iterator

inherited

value type is std::vector<T>::iterator

Definition at line 120 of file AlignStream.hpp.

Member Function Documentation

assign() [1/2]

template<typename T>

void Sequence::AlignStream< T >::assign ( const_iterator  beg, const_iterator  end  )

inherited

Assign data to object. Since the value type for these iterators evaluates to std::vector<T>::const_iterator, any vector<T> can be the data source

Exceptions

std::runtime_error

is thrown if all data elements in the range (beg,end] are not of the same length

assign() [2/2]

template<typename T>

void Sequence::AlignStream< T >::assign ( std::vector< T > &&  _data )

inherited

Assign via a move operation

Exceptions

std::runtime_error

is thrown if all data elements are not of the same length

empty()

template<typename T>

bool Sequence::AlignStream< T >::empty ( ) const

inlineinherited

Returns data.empty()

Definition at line 85 of file AlignStream.hpp.

operator[]() [1/2]

template<typename T>

reference Sequence::AlignStream< T >::operator[] ( const size_type &  i )

inlineinherited

Returns the i-th object of type T in the vector data

Definition at line 101 of file AlignStream.hpp.

operator[]() [2/2]

template<typename T>

const_reference Sequence::AlignStream< T >::operator[] ( const size_type &  i ) const

inlineinherited

Returns the i-th object of type T in the vector data

Definition at line 109 of file AlignStream.hpp.

print()

template<typename T>

std::ostream& Sequence::ClustalW< T >::print ( std::ostream &  s ) const

virtual

To define a non-abstract AlignStream, print must be defined

Implements Sequence::AlignStream< T >.

read()

template<typename T>

std::istream& Sequence::ClustalW< T >::read ( std::istream &  s )

virtual

To define a non-abstract AlignStream, read must be defined

Implements Sequence::AlignStream< T >.

size()

template<typename T>

size_type Sequence::AlignStream< T >::size ( void  ) const

inlineinherited

Returns data.size()

Definition at line 93 of file AlignStream.hpp.

---

The documentation for this class was generated from the following file:

• Clustalw.hpp