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 ()
GenericIntervalListoperator= (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().

template<class MatchType = Interval>
std::vector<std::string> mems::GenericIntervalList< MatchType >::seq_filename
 

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

Definition at line 89 of file IntervalList.h.

Referenced by mems::Aligner::align(), mems::GenericIntervalList< MatchType >::Clear(), mems::collapseCollinear(), mems::GenericIntervalList< MatchType >::operator=(), mems::GenericIntervalList< MatchType >::ReadList(), mems::GenericIntervalList< MatchType >::ReadStandardAlignment(), mems::GenericIntervalList< MatchType >::ReadStandardAlignmentCompact(), mems::Aligner::RecursiveAnchorSearch(), mems::GenericIntervalList< MatchType >::WriteAlignedSequences(), mems::GenericIntervalList< MatchType >::WriteList(), and mems::GenericIntervalList< MatchType >::WriteStandardAlignment().

template<class MatchType = Interval>
std::vector<genome::gnSequence*> mems::GenericIntervalList< MatchType >::seq_table
 

The actual sequences used in this alignment.

Definition at line 90 of file IntervalList.h.

Referenced by mems::addUnalignedIntervals(), mems::Aligner::align(), mems::checkForAllGapColumns(), mems::GenericIntervalList< MatchType >::Clear(), mems::collapseCollinear(), mems::detectAndApplyBackbone(), mems::findIslandsBetweenLCBs(), mems::IdentityMatrix(), mems::makeAllPairwiseGenomeHSS(), mems::GenericIntervalList< MatchType >::operator=(), mems::GenericIntervalList< MatchType >::ReadStandardAlignment(), mems::GenericIntervalList< MatchType >::ReadStandardAlignmentCompact(), mems::Aligner::RecursiveAnchorSearch(), mems::unalignIslands(), mems::GenericIntervalList< MatchType >::WriteAlignedSequences(), mems::GenericIntervalList< MatchType >::WriteList(), mems::WritePermutationCoordinates(), and mems::GenericIntervalList< MatchType >::WriteStandardAlignment().


The documentation for this class was generated from the following file:
Generated on Fri Mar 14 06:01:40 2008 for libMems by doxygen 1.3.6