Virtual interface to alignment streams. More...
#include <Sequence/AlignStream.hpp>
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 | |
| AlignStream (const std::vector< T > &_data) | |
| AlignStream (std::vector< T > &&_data) | |
| AlignStream (const AlignStream< T > &a) | |
| AlignStream (AlignStream< T > &&a) | |
| bool | empty () const |
| size_type | size (void) const |
| reference | operator[] (const size_type &i) |
| const_reference | operator[] (const size_type &i) const |
| iterator | begin () |
| iterator | end () |
| const_iterator | begin () const |
| 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) |
| virtual std::istream & | read (std::istream &s)=0 |
| virtual std::ostream & | print (std::ostream &s) const =0 |
| void | assign (const_iterator beg, const_iterator end) |
| void | assign (std::vector< T > &&_data) |
Detailed Description
template<typename T>
class Sequence::AlignStream< T >
Virtual interface to alignment streams.
This template defines a virtual base class for input of sequences in aligned block formats, such as ClustalW.
This class doesn't really define any operations on alignments. It is merely an interface for input/output and some simple basic manipulations.
- Note
- The only valid template parameters for this class are types in the inheritance hierarchy of Sequence::Seq. std::pair<std::string,std::string> is also supported.
Definition at line 61 of file AlignStream.hpp.
Member Typedef Documentation
◆ const_iterator
| typedef std::vector<T>::const_iterator Sequence::AlignStream< T >::const_iterator |
value type is std::vector<T>::const_iterator
Definition at line 124 of file AlignStream.hpp.
◆ iterator
| typedef std::vector<T>::iterator Sequence::AlignStream< T >::iterator |
value type is std::vector<T>::iterator
Definition at line 120 of file AlignStream.hpp.
Member Function Documentation
◆ assign() [1/2]
| void Sequence::AlignStream< T >::assign | ( | const_iterator | beg, |
| const_iterator | end | ||
| ) |
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]
| void Sequence::AlignStream< T >::assign | ( | std::vector< T > && | _data | ) |
Assign via a move operation
- Exceptions
-
std::runtime_error is thrown if all data elements are not of the same length
◆ empty()
|
inline |
Returns data.empty()
Definition at line 85 of file AlignStream.hpp.
◆ operator[]() [1/2]
|
inline |
Returns the i-th object of type T in the vector data
Definition at line 101 of file AlignStream.hpp.
◆ operator[]() [2/2]
|
inline |
Returns the i-th object of type T in the vector data
Definition at line 109 of file AlignStream.hpp.
◆ print()
|
pure virtual |
To define a non-abstract AlignStream, print must be defined
Implemented in Sequence::ClustalW< T >, and Sequence::phylipData< T >.
◆ read()
|
pure virtual |
To define a non-abstract AlignStream, read must be defined
Implemented in Sequence::ClustalW< T >, and Sequence::phylipData< T >.
◆ size()
|
inline |
Returns data.size()
Definition at line 93 of file AlignStream.hpp.
The documentation for this class was generated from the following file:
