#include <DataSetAbstractProduct.h>
Inheritance diagram for DataSetAbstractProduct:
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 &) |
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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