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Annotation Class Reference


Purpose:
Holds all possible gene annotations given a set of input annotations This structure will be used by the dynamic prog.
algorithm to record the optimal annotation with respect to the scoring system.
This class is mainly a wrapper around the AnnotationMatrix object and is responsible for inserting into the matrix and extracting the optimal parse from the matrix
Collaborators:
AnnotationMatrix, AnnotationItem, AnnotationScore, Combine
More...

#include <Annotation.h>

Collaboration diagram for Annotation:

Collaboration graph
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List of all members.

Public Types

typedef std::pair< AnnotationScore,
int > 		aipair_t

Public Member Functions

 Annotation (const string &theSequence, bool forceWholeGeneModel, int cutOff)
 initialize variables


const MatrixItemContents getBestStart (const CustomScore &) const
void insert (const std::vector< RegionPrediction * > &, const CustomScore &)
 Pre Cond:
RegionPrediction's are inserted 'left to right'.
Both sequences are annotated at the same time , so left to right means 5' to 3' on positive side and 3' to 5' on negative side

aipair_t scoreHelp (int end5, int end3, dsu::Strand_t strnd, int mid, const CustomScore &cs) const
bool forceWholeGeneModel () const
bool empty () const
const AnnotationMatrix & getMatrix () const
void print (std::ostream &, const CustomScore &) const
std::list< GffFeature * > * getGeneList (int &, const CustomScore &) const
 Predcond:
presumes scoring matrix is complete.

void scoreGeneList (std::list< GffFeature * > &flst, const CustomScore &cs) const

Protected Attributes

AnnotationMatrix _matrix
const string & _theSeq
const DnaStr _posSeq
const DnaStr _negSeq

Detailed Description


Purpose:
Holds all possible gene annotations given a set of input annotations This structure will be used by the dynamic prog.
algorithm to record the optimal annotation with respect to the scoring system.
This class is mainly a wrapper around the AnnotationMatrix object and is responsible for inserting into the matrix and extracting the optimal parse from the matrix
Collaborators:
AnnotationMatrix, AnnotationItem, AnnotationScore, Combine

Constructor & Destructor Documentation

Annotation::Annotation (  const string &  theSequence,
bool  forceWholeGeneModel,
int  cutOff
)  [inline]
 

initialize variables

Parameters:
theSequence: reference to the raw dna sequence
forceWholeGeneModel: when set to true, while constructing the parse require all coding sequences to begin with a start and end with a stop when false, only check that no inframe stop codons exist

Member Function Documentation

const MatrixItemContents Annotation::getBestStart (  const CustomScore &   )  const
 

list< GffFeature * > * Annotation::getGeneList (  int &  ,
const CustomScore & 
)  const
 

Predcond:
presumes scoring matrix is complete.

identical to printOptimalParse but returns results in list instead of directly to ostream

void Annotation::insert (  const std::vector< RegionPrediction * > &  ,
const CustomScore & 
) 
 

Pre Cond:
RegionPrediction's are inserted 'left to right'.
Both sequences are annotated at the same time , so left to right means 5' to 3' on positive side and 3' to 5' on negative side

Parameters:
const CustomScore& is used to check splice connections and add additional weight
Post Cond:
New piece of evidence is inserted into the annotation matrix

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