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RegionPrediction Class Reference

Responsibilities:
Manage all available evidence for a given sequence region

Collaborators:
DataSetAbstractProduct, SpliceSite, AnnotationScore
More...

#include <RegionPrediction.h>

List of all members.

Public Member Functions

 RegionPrediction (const SeqLoc &, const string &)
const string & getSeq () const
bool noData () const
bool noStrndData (dsu::Strand_t) const
virtual void print (std::ostream &, const CustomScore &) const
const string & getTypeStr () const
bool isValid (EvScores::Bnd_t, dsu::Strand_t) const
bool isAccpBndry (dsu::Strand_t strnd) const
 returns true if region falls on a valid acceptor boundry

bool isDonrBndry (dsu::Strand_t strnd) const
 returns true if region falls on a valid donor boundry

bool isValidAcceptorSignals (dsu::Strand_t strnd) const
bool isValidDonorSignals (dsu::Strand_t strnd) const
void score (const CustomScore &, const string &)
 Precondition:
takes as input a valid reference to the genmoic sequence.

Postcondition:
returns a score for each exon model type.

virtual void insert (const PlaceHolder *)
 Needs to track only the 5' 3' region for
which all of the available evidence have in common
e.g.

void storeRelaventData (InputData::const_iterator &, const InputData::const_iterator &)
void setScores (dsu::Strand_t, const EvScores &)
bool hasStart (dsu::Strand_t strnd) const
 falls on a valid start boundary

bool hasStop (dsu::Strand_t strnd) const
 falls on a valid stop boundary

bool isEndOfSeq () const
 check to see if interval is right up against the end of the sequence

void scoreHelp (const string &, dsu::Strand_t)
const EvScores & getScores (dsu::Strand_t strnd) const
const AnnotationScore & getScore (unsigned, dsu::Strand_t strnd) const

Static Public Member Functions

bool is_igr (const RegionPrediction &, const RegionPrediction &, dsu::Strand_t, int)
bool is_intron (const RegionPrediction &, const RegionPrediction &, dsu::Strand_t)

Detailed Description

Responsibilities:
Manage all available evidence for a given sequence region

Collaborators:
DataSetAbstractProduct, SpliceSite, AnnotationScore

Member Function Documentation

void RegionPrediction::insert (  const PlaceHolder *   )  [virtual]
 

Needs to track only the 5' 3' region for
which all of the available evidence have in common
e.g.

only the overlapping region

bool RegionPrediction::isAccpBndry (  dsu::Strand_t  strnd  )  const [inline]
 

returns true if region falls on a valid acceptor boundry

Parameters:
- strnd = dna strnd of interest

bool RegionPrediction::isDonrBndry (  dsu::Strand_t  strnd  )  const [inline]
 

returns true if region falls on a valid donor boundry

Parameters:
- strnd = dna strnd of interest

void RegionPrediction::score (  const CustomScore &  ,
const string & 
) 
 

Precondition:
takes as input a valid reference to the genmoic sequence.

Postcondition:
returns a score for each exon model type.

it is possible that
none of the exon model type's will be scored, if the available
information doesn't "warrant" providing a score, this is basically
saying not enough information to indicate an exon of anytype. CustomScore does all the work now, essentially now it is plugged into this method which use to do all the work. Now you can test different scoring methods through CustomScore implementations without changing the framework code

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