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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>

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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 PredictiongetLast () 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 PredictiongetClosestEnd3Exon (int, int) const
int getClosestEnd5 (int) const
 returns 5' (derived classes overide this behavior)

const PredictiongetClosestEnd5Exon (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 PredictiongetRelatedPrediction (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 &)

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


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


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


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