mems::GenericIntervalList< MatchType > Class Template Reference

This class represents a set Intervals, each of which is a collinear aligned region There are functions to read and write an GenericIntervalList. More...

#include <IntervalList.h>

List of all members.

Public Member Functions

void Clear ()

Deletes the objects associated with this GenericIntervalList.

GenericIntervalList (const GenericIntervalList &ml)

GenericIntervalList ()

GenericIntervalList & operator= (const GenericIntervalList &ml)

void ReadList (std::istream &match_stream)

Reads a GenericIntervalList from an input stream Sequence and SML file names are read into the seq_filename and sml_filename vectors, but the actual files are not opened.

void ReadStandardAlignment (std::istream &in_stream)

Reads in a set of intervals that are in xmfa (eXtended MultiFastA) format.

void ReadStandardAlignmentCompact (std::istream &in_stream)

Reads in a set of intervals that are in xmfa (eXtended MultiFastA) format and stores them in CompactGappedAlignments<>.

void WriteAlignedSequences (std::ostream &match_file) const

Writes a gapped alignment of sequences to the output stream.

void WriteList (std::ostream &match_stream) const

Writes a GenericIntervalList to the designated output stream.

void WriteStandardAlignment (std::ostream &out_file) const

Writes a gapped alignment of sequences in a standard format.

~GenericIntervalList ()

Public Attributes

std::string backbone_filename

The name of an associated backbone file, or empty if none exists.

std::vector< std::string > seq_filename

The names of files associated with the sequences used by this alignment.

std::vector< genome::gnSequence * > seq_table

The actual sequences used in this alignment.

Detailed Description

template<class MatchType = Interval>
class mems::GenericIntervalList< MatchType >

This class represents a set Intervals, each of which is a collinear aligned region There are functions to read and write an GenericIntervalList.

See also:: Interval

Definition at line 39 of file IntervalList.h.

Constructor & Destructor Documentation

template<class MatchType = Interval>

mems::GenericIntervalList< MatchType >::GenericIntervalList ( ) [inline]

Definition at line 41 of file IntervalList.h.

template<class MatchType>

mems::GenericIntervalList< MatchType >::GenericIntervalList ( const GenericIntervalList< MatchType > & ml )

Definition at line 101 of file IntervalList.h.

template<class MatchType = Interval>

mems::GenericIntervalList< MatchType >::~GenericIntervalList ( ) [inline]

Definition at line 44 of file IntervalList.h.

Member Function Documentation

template<class MatchType>

void mems::GenericIntervalList< MatchType >::Clear ( )

Deletes the objects associated with this GenericIntervalList.

Definition at line 116 of file IntervalList.h.
References mems::GenericIntervalList< MatchType >::seq_filename, mems::GenericIntervalList< MatchType >::seq_table, and uint.
Referenced by mems::GenericIntervalList< MatchType >::ReadStandardAlignment().

template<class MatchType>

GenericIntervalList< MatchType > & mems::GenericIntervalList< MatchType >::operator= ( const GenericIntervalList< MatchType > & ml )

Definition at line 107 of file IntervalList.h.
References mems::GenericIntervalList< MatchType >::seq_filename, and mems::GenericIntervalList< MatchType >::seq_table.

template<class MatchType>

void mems::GenericIntervalList< MatchType >::ReadList ( std::istream & match_stream )

Reads a GenericIntervalList from an input stream Sequence and SML file names are read into the seq_filename and sml_filename vectors, but the actual files are not opened.
The calling function should load them after using this method.
Parameters:

match_stream The input stream to read from

Definition at line 127 of file IntervalList.h.
References mems::UngappedLocalAlignment< AbstractMatchImpl >::Copy(), mems::Interval, mems::Match, mems::GenericIntervalList< MatchType >::seq_filename, mems::GappedAlignment::SetAlignment(), mems::UngappedLocalAlignment< AbstractMatchImpl >::SetLength(), mems::AbstractGappedAlignment< SparseAbstractMatch<> >::SetLength(), mems::SparseAbstractMatch<>::SetStart(), and uint.

template<class MatchType>

void mems::GenericIntervalList< MatchType >::ReadStandardAlignment ( std::istream & in_stream )

Reads in a set of intervals that are in xmfa (eXtended MultiFastA) format.

Definition at line 392 of file IntervalList.h.
References mems::AbstractGappedAlignment< SparseAbstractMatch<> >::AlignmentLength(), mems::GenericIntervalList< MatchType >::Clear(), mems::GetAlignment(), mems::Interval, mems::AbstractGappedAlignment< SparseAbstractMatch<> >::Length(), mems::GenericIntervalList< MatchType >::seq_filename, mems::GenericIntervalList< MatchType >::seq_table, mems::GappedAlignment::SetAlignment(), mems::AbstractGappedAlignment< SparseAbstractMatch<> >::SetLength(), mems::SparseAbstractMatch<>::SetStart(), mems::SparseAbstractMatch<>::Start(), and uint.

template<class MatchType>

void mems::GenericIntervalList< MatchType >::ReadStandardAlignmentCompact ( std::istream & in_stream )

Reads in a set of intervals that are in xmfa (eXtended MultiFastA) format and stores them in CompactGappedAlignments<>.

Definition at line 564 of file IntervalList.h.
References mems::AbstractGappedAlignment< SparseAbstractMatch<> >::AlignmentLength(), mems::GetAlignment(), mems::Interval, mems::AbstractGappedAlignment< SparseAbstractMatch<> >::Length(), mems::GenericIntervalList< MatchType >::seq_filename, mems::GenericIntervalList< MatchType >::seq_table, mems::SparseAbstractMatch<>::SeqCount(), mems::CompactGappedAlignment< BaseType >::SetAlignment(), mems::GappedAlignment::SetAlignment(), mems::AbstractGappedAlignment< SparseAbstractMatch<> >::SetLength(), mems::SparseAbstractMatch<>::SetStart(), mems::SparseAbstractMatch<>::Start(), and uint.

template<class MatchType>

void mems::GenericIntervalList< MatchType >::WriteAlignedSequences ( std::ostream & match_file ) const

Writes a gapped alignment of sequences to the output stream.

Definition at line 740 of file IntervalList.h.
References mems::GetAlignment(), mems::GenericIntervalList< MatchType >::seq_filename, mems::GenericIntervalList< MatchType >::seq_table, and uint.

template<class MatchType>

void mems::GenericIntervalList< MatchType >::WriteList ( std::ostream & match_stream ) const

Writes a GenericIntervalList to the designated output stream.

Parameters:

match_stream The outptu stream to write to

Definition at line 248 of file IntervalList.h.
References mems::GetAlignment(), mems::AbstractGappedAlignment< SparseAbstractMatch<> >::Length(), mems::Match, mems::GenericIntervalList< MatchType >::seq_filename, mems::GenericIntervalList< MatchType >::seq_table, mems::SparseAbstractMatch<>::Start(), and uint.

template<class MatchType>

void mems::GenericIntervalList< MatchType >::WriteStandardAlignment ( std::ostream & out_file ) const

Writes a gapped alignment of sequences in a standard format.

Definition at line 300 of file IntervalList.h.
References mems::GenericIntervalList< MatchType >::backbone_filename, mems::GetAlignment(), mems::GenericIntervalList< MatchType >::seq_filename, mems::GenericIntervalList< MatchType >::seq_table, and uint.

Member Data Documentation

template<class MatchType = Interval>

std::string mems::GenericIntervalList< MatchType >::backbone_filename

The name of an associated backbone file, or empty if none exists.

Definition at line 92 of file IntervalList.h.
Referenced by mems::GenericIntervalList< MatchType >::WriteStandardAlignment().

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

libMems/IntervalList.h

Generated on Fri Mar 14 06:01:40 2008 for libMems by

1.3.6


Public Member Functions
void	Clear ()
	Deletes the objects associated with this GenericIntervalList.
	GenericIntervalList (const GenericIntervalList &ml)
	GenericIntervalList ()
GenericIntervalList &	operator= (const GenericIntervalList &ml)
void	ReadList (std::istream &match_stream)
	Reads a GenericIntervalList from an input stream Sequence and SML file names are read into the seq_filename and sml_filename vectors, but the actual files are not opened.
void	ReadStandardAlignment (std::istream &in_stream)
	Reads in a set of intervals that are in xmfa (eXtended MultiFastA) format.
void	ReadStandardAlignmentCompact (std::istream &in_stream)
	Reads in a set of intervals that are in xmfa (eXtended MultiFastA) format and stores them in CompactGappedAlignments<>.
void	WriteAlignedSequences (std::ostream &match_file) const
	Writes a gapped alignment of sequences to the output stream.
void	WriteList (std::ostream &match_stream) const
	Writes a GenericIntervalList to the designated output stream.
void	WriteStandardAlignment (std::ostream &out_file) const
	Writes a gapped alignment of sequences in a standard format.
	~GenericIntervalList ()
Public Attributes
std::string	backbone_filename
	The name of an associated backbone file, or empty if none exists.
std::vector< std::string >	seq_filename
	The names of files associated with the sequences used by this alignment.
std::vector< genome::gnSequence * >	seq_table
	The actual sequences used in this alignment.

mems::GenericIntervalList< MatchType > Class Template Reference

Public Member Functions

Public Attributes

Detailed Description

template<class MatchType = Interval> class mems::GenericIntervalList< MatchType >

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<class MatchType = Interval>
class mems::GenericIntervalList< MatchType >