DataSetAbstractProduct Class Reference

Responsibilities:
Defines the basic behavior of all input data sets, whether it be
gene prediction data, splice site site data, EST matches or some as of
yet undetermined source. More...

#include <DataSetAbstractProduct.h>

Inheritance diagram for DataSetAbstractProduct:

[legend]Collaboration diagram for DataSetAbstractProduct:

[legend]List of all members.

Public Types
typedef DataStorageType::iterator	iterator
typedef DataStorageType::const_iterator	const_iterator
Public Member Functions
	DataSetAbstractProduct (const SeqLoc &, int, const string &, AnnotationScore)
void	sort ()
virtual void	del_temp ()
	some derived times store temporary hash tables to speed up reading in data method provides a universal way of removing temp data
virtual	~DataSetAbstractProduct ()
	stores a linked list
virtual void	del ()
	deletes contents from memory
DataStorageType *	makePlaceHolders () const
	all prediction type objects must be able convert themselfs into a list of pointers that contain each coding sequence seperately
const Prediction *	getLast () const
	interface to the list return the last element
iterator	begin ()
	interface to the list of associated predictions
const_iterator	begin () const
	interface to the list of associated predictions
const_iterator	end () const
	interface to the list of associated predictions
iterator	end ()
	interface to the list of associated predictions
unsigned	size () const
	number of elements in prediction list
bool	empty () const
	true if no prediction list
virtual void	print (std::ostream &, const string &) const
	standard print display
void	insert (Prediction *)
	add a new prediction
void	sort_insert (Prediction *)
virtual void	add_introns ()
	When this container represents a collection of gene predictions from a program that does not explicitely report the introns we want to try making the intron regions explicit.
const Prediction *	getClosestEnd3Exon (int, int) const
int	getClosestEnd5 (int) const
	returns 5' (derived classes overide this behavior)
const Prediction *	getClosestEnd5Exon (int) const
void	getRelatedPrediction (int, int, std::list< const Prediction * > &) const
void	getRelatedPrediction5 (int, std::list< const Prediction * > &) const
void	getRelatedPrediction3 (int, std::list< const Prediction * > &) const
pair< const Prediction *, const Prediction * >	getRelatedPredictionInterval (int, int) const
pair< const Prediction *, const Prediction * >	getIntronBoundaries (int, int) const
const Prediction *	getRelatedPrediction (int) const
int	getListPos (const Prediction *) const
Protected Member Functions
virtual void	add_introns_help ()
Protected Attributes
DataStorageType	lnkSeqLoc
	0..*
Friends
std::ostream &	operator<< (std::ostream &, const DataSetAbstractProduct &)

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Detailed Description

Responsibilities:
Defines the basic behavior of all input data sets, whether it be
gene prediction data, splice site site data, EST matches or some as of
yet undetermined source.

This class is a container class meaning that
it is both a Sequence Location in of itself and a collection of Sequence Locations.
It is a sequence location that stores the boundaries of the collection of sequence
locations. The main algorithm interfaces with this class via the class InputData
which is just a aggregation of these objects. The purpose of this object is to shield the
dynamic programming algorithm from dealing with specific data sources.
Pattern: Container (Design Patterns Gamma et. al) Collaborators:
SeqLoc, DataSetAbstractFactory, InputData. container

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Constructor & Destructor Documentation

DataSetAbstractProduct::DataSetAbstractProduct (  const SeqLoc &  , int  , const string &  , AnnotationScore  )

Parameters: SeqLoc  - associated sequence location int  - id usually 0 or -1, needs to be phased out string  - a source identifier, user defined AnnotationScore  - initialize to badVal usually

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Member Function Documentation

const Prediction* DataSetAbstractProduct::getClosestEnd5Exon (  int   )  const

Parameters: int  X - 5' index returns the closest 5' index <= X

void DataSetAbstractProduct::getRelatedPrediction (  int  , int  , std::list< const Prediction * > &  )  const

Parameters: int  - a 5' index int  - a 3' index return the prediction that overlaps a particular input index location, returns null if none exists

void DataSetAbstractProduct::getRelatedPrediction3 (  int  , std::list< const Prediction * > &  )  const

Parameters: int  - 3' index, look for match

void DataSetAbstractProduct::getRelatedPrediction5 (  int  , std::list< const Prediction * > &  )  const

Parameters: int  - 5' index, look for match

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

• DataSetAbstractProduct.h