Main Page | Class Hierarchy | Class List | File List | Class Members

GenePrediction Class Reference

GenePrediction is derived from Prediction and is designed to record whole exon genes. More...

#include <GenePrediction.h>

Inheritance diagram for GenePrediction:

Inheritance graph
[legend]
Collaboration diagram for GenePrediction:

Collaboration graph
[legend]
List of all members.

Public Member Functions

 GenePrediction (const SeqLoc &sl, AnnotationScore d, int modelId, const string &source, const GeneModelType &mt, int frame=-1)
 same construction as Prediction, but also takes as input an exon type identifier currently there are 4 types, initial, terminal, internal, single.

virtual ~GenePrediction ()
 no dynamic memory management

virtual void del ()
void print (std::ostream &, const std::string &) const
 standard display of this object

const string & getTypeStr () const
 type identifier for this object

const int getScoreIdx () const
 get the unique integer index associated with this exon model.

DataStorageType * makePlaceHolders () const
int getFrame () const

Static Public Attributes

const int NUM_ANNOTATION_SCORED_TYPES = 4
const int NOT_GENE_ID = 4

Detailed Description

GenePrediction is derived from Prediction and is designed to record whole exon genes.

(should have called it ExonPrediction oh well) A GenePrediction is a prediction that is made up of Initial,Internal,Single and Terminal exons.

Constructor & Destructor Documentation

GenePrediction::GenePrediction (  const SeqLoc &  sl,
AnnotationScore  d,
int  modelId,
const string &  source,
const GeneModelType &  mt,
int  frame = -1
)  [inline]
 

same construction as Prediction, but also takes as input an exon type identifier currently there are 4 types, initial, terminal, internal, single.

becuase there currently is not enough information on this, I've kept the GeneModelType private under the assumption that it will not be used for now I want to keep it in the framework, however, in case it can become usefull

Member Function Documentation

int GenePrediction::getFrame (   )  const [inline]
 

Returns:
coding frame

const string& GenePrediction::getTypeStr (   )  const [virtual]
 

type identifier for this object

Returns:
the exon model type

Reimplemented from SeqLoc.

DataStorageType* GenePrediction::makePlaceHolders (   )  const [virtual]
 

Returns:
list of exons

Implements Prediction.

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