ppALIGN API documentation

AlignOverlap Class Reference

#include <alignoverlap.hpp>

Inheritance diagram for AlignOverlap:
AlignHandler

List of all members.

Classes

struct  AlignCol
class  AlignSegment
class  AlternativeSegment

Public Types

typedef std::map
< AlternativeSegment, int >
::iterator 		alternative_iterator
typedef std::map
< AlternativeSegment, int >
::const_iterator 		alternative_const_iterator
typedef std::vector
< AlignSegment >::iterator 		segment_iterator
typedef std::vector
< AlignSegment >
::const_iterator 		segment_const_iterator

Public Member Functions

 AlignOverlap (const Align &ref, Sequence &_seq1, Sequence &_seq2)
void Add (const std::string &generator, const Align &a)
void StreamOutPartition (std::ostream &ost, Pair seq_offset=Pair(0, 0))
void BuildOverlapSegments ()
Segments in the reference alignment.



segment_iterator BeginSegments ()
segment_iterator EndSegments ()

Detailed Description

Determine the overlap between a reference alignment and a set of alternative alignments. The constructor of AlignOverlap expects an reference alignment ref and a pair of sequences. Alternative alignments are added via Add and Results can be displayed by StreamOutPartition.

Examples:

alternative_alignments.cpp.

Definition at line 82 of file alignoverlap.hpp.

Member Typedef Documentation

typedef std::map<AlternativeSegment,int>::const_iterator AlignOverlap::alternative_const_iterator

iterator through the map of segments -> number of occurencies

Definition at line 192 of file alignoverlap.hpp.

typedef std::map<AlternativeSegment,int>::iterator AlignOverlap::alternative_iterator

iterator through the map of segments -> number of occurencies

Examples:
alternative_alignments.cpp.

Definition at line 188 of file alignoverlap.hpp.

typedef std::vector<AlignSegment>::const_iterator AlignOverlap::segment_const_iterator

A const iterator for the segments of the reference alignment.

Definition at line 286 of file alignoverlap.hpp.

typedef std::vector<AlignSegment>::iterator AlignOverlap::segment_iterator

An iterator for the segments of the reference alignment.

Examples:
alternative_alignments.cpp.

Definition at line 282 of file alignoverlap.hpp.

Constructor & Destructor Documentation

AlignOverlap::AlignOverlap ( const Align &  ref,
Sequence &  _seq1,
Sequence &  _seq2 
)

Constructor.

Parameters:
ref a reference alignment
_seq1 the first sequence
_seq2 the second sequence

Member Function Documentation

void AlignOverlap::Add ( const std::string &  generator,
const Align &  a 
) [virtual]

Add an alternative alignment to be compared

Parameters:
generator Unique name of the generator (e.g. PartitionDriverBase::Name())
a alignment

Implements AlignHandler.

Examples:
alternative_alignments.cpp.
AlignOverlap::segment_iterator AlignOverlap::BeginSegments (  )  [inline]

The begin of the vector of alignment segments.

Examples:
alternative_alignments.cpp.

Definition at line 355 of file alignoverlap.hpp.

AlignOverlap::segment_iterator AlignOverlap::EndSegments (  )  [inline]

The end of the vector of alignment segments.

Examples:
alternative_alignments.cpp.

Definition at line 360 of file alignoverlap.hpp.

void AlignOverlap::StreamOutPartition ( std::ostream &  ost,
Pair  seq_offset = Pair(0, 0) 
)

Stream out result in XML format

Parameters:
ost outstream object
seq_offset offset of the sequence pair (start positions of the BLAST hit for example)
Examples:
alternative_alignments.cpp.
The documentation for this class was generated from the following file: