Uses of Package
AFLPcore

Packages that use AFLPcore

AFLPcore
AFLPgui

Classes in AFLPcore used by AFLPcore

AnalysisMgr
This class contains a list of AnalysisOps which can be used to read in different files.

AnalysisOp
This abstract class represents methods used to analyize a gel.

Bin
This class represents a bin, which is simply a region defined in a gel.

BinOpMgr
This class contains a list of BinOperations which can be used to read in different files.

Cutoff
This class represents different cutoffs for a lane.

CutoffFunction
An abstract class that is used to represent different functions for cutting off noise from data peaks.

CutoffMgr
This class contains a list of CutoffFunctions which can be used to read create different functions for the cutoff.

Data
A class that holds all of the data for the program.

DataList
This is an expandable list that can be used to store objects of type Data.

Gel
A gel contains most of the information needed by the program.

GelOperation
This is an abstract class that represents operations on a gel.

GelOpMgr
This class contains a list of GelOperations which can be used to read in different files.

ImportFilter
This is an abstract class that should be extended to create filters that read data from files.

ImportMgr
This class contains a list of ImportFilters which can be used to read in different files.

Lane
This class represents a lane.

LaneOpMgr
This class contains a list of LaneOperations which can be used to read in different files.

Manager
This class contains a list of Operations which can be used to perform different functions in the program.

Operation
This is an abstract class that should be extended to add functionality to the program.

Option
This class provides a way for other class to specify options and parameters.

Peak
This class represents a peak.

PeakLocate
This is an abstract class that should be extended to provide different ways of finding the peaks in a lane.

PeakMgr
This class contains a list of PeakLocates which can be used to find peaks in the lanes/gel.

ScoreFunction
This class represents functions used to score a bin.

ScoreManager
This class contains a list of ScoreFunctions which can be used to score a bin in different ways.

SearchReturn
This class contains a pair of values used in searches.

SizeFunction
This is an abstract class that is used by Lane and anything else that needs to convert back and forth between scan numbers and sizes, in bp.

SizeMgr
This class contains a list of SizeFunctions which can be used to size a lane.

SortableData
This class allows subclasses that extend it to be sorted into an order.

StandardMgr
This class contains a list of SizeStandards which define different size standards.

TracePoint
Represents a point on the trace, in the form (size, height).

Classes in AFLPcore used by AFLPgui

Bin
This class represents a bin, which is simply a region defined in a gel.

Cutoff
This class represents different cutoffs for a lane.

CutoffFunction
An abstract class that is used to represent different functions for cutting off noise from data peaks.

DataList
This is an expandable list that can be used to store objects of type Data.

Gel
A gel contains most of the information needed by the program.

ImportFilter
This is an abstract class that should be extended to create filters that read data from files.

Lane
This class represents a lane.

Manager
This class contains a list of Operations which can be used to perform different functions in the program.

Option
This class provides a way for other class to specify options and parameters.

ScoringFailure
Thrown to indicate that the scoring function could not function properly.