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AnnotationItem Class Reference

Purpose:
The annotation matrix is made up of a linked list of this object One instance of this class records all the necessary information
for one unique genomic region. More...

#include <AnnotationItem.h>

Collaboration diagram for AnnotationItem:

Collaboration graph
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List of all members.

Public Types

typedef pair< const AnnotationItem *,
AnnotationScore > 		apair_t
typedef pair< int, apair_t > bpair_t
typedef pair< dsu::Strand_t,
int > 		strnd_frm_t

Public Member Functions

 AnnotationItem (const std::vector< RegionPrediction * > &, const DnaStr &, const DnaStr &)
pair< AnnotationScore, MatrixItemContents > endScore (const CustomScore &, const AnnotationScore &, bool) const
int getEnd5AdjForStop (int model, dsu::Strand_t strnd) const
int getEnd3AdjForStop (int model, dsu::Strand_t strnd) const
dsu::Strand_t getStrnd () const
int getEnd5 () const
int getEnd3 () const
int length () const
const RegionPrediction & getRegionPrediction () const
const DnaStr & getSeq (dsu::Strand_t strnd) const
tback getPred (int, dsu::Strand_t, dsu::side_t, int) const
void print (std::ostream &, const CustomScore &) const
void dpUpdate (const AnnotationItem &, std::vector< scr_pr > &, bool)
 Precond:
Takes as input a valid iterator reference to a downstream
previously scored region
Postcond:
Score the connection of "this" region with the input region
update the best score for "this" region.
This can be a fairly involved process, becuase it checks for legal
exon types, and scores only legal orfs for each of the possible 3
reading frames.


void dpUpdate (std::vector< scr_pr > &, bool, bool)
AnnotationScore computeNonCodingScore () const
void update (const MatrixIdx &, const MatrixIdx &, const int, const AnnotationScore &, const AnnotationItem &)
void update (const MatrixIdx &, const MatrixIdx &, const int, const AnnotationScore &)
pair< int, dsu::Strand_t > getPrevExonType (const MatrixIdx &) const
const MatrixItemContents & getBest (const MatrixIdx &) const
const RegionPrediction * getLeft () const
const RegionPrediction * getRght () const

Static Public Member Functions

bool checkOrf (const AnnotationItem *, const MatrixIdx &, int, int, const DnaStr &)

Detailed Description

Purpose:
The annotation matrix is made up of a linked list of this object One instance of this class records all the necessary information
for one unique genomic region.

This is a manager class that delegates
a lot of responsibility to other objects, for scoring and gene prediction evidence
management. The actual code for recording the optimal parse is done here, nested in dynamicProgrammingUpdateScore
this class contains a RegionPrediction object that refers to the associated evidence and an AnnotationScoreMatrix which records the possible 6 frame scores and their predecessor pointers

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