Uses of Class
AFLPcore.Operation

Packages that use Operation

AFLPcore

Uses of Operation in AFLPcore

Subclasses of Operation in AFLPcore

class	ABI3x00Filter This class reads data from a ABI 3100 and a 3700 capillary machine.
class	ABILaneFilter This class reads data from a lane file produced by extracting lanes from a gel run on an ABI377.
class	AnalysisOp This abstract class represents methods used to analyize a gel.
class	BinAnalysis This class is an AnalysisOp which outputs information about all of the bins in the gel.
class	BinOperation This is an abstract class that represents operations on a bin.
class	CEQLaneFilter This class reads data from a fragment results text file produced by a Beckman Coulter, Inc.
class	CutoffFunction An abstract class that is used to represent different functions for cutting off noise from data peaks.
class	GelOperation This is an abstract class that represents operations on a gel.
class	HighestPeakLocate This class can be used to find peaks in lanes.
class	ImportFilter This is an abstract class that should be extended to create filters that read data from files.
class	LaneOperation This is an abstract class that represents operations on a set of Lanes.
class	LinearCutoff This cutoff function represents a horizontal line.
class	LocalSouthern This class implements the Local Southern sizing method described by E.M.
class	MapMakerAnalysis This class is an AnalysisOp which outputs information about all of the bins in the gel.
class	NoSize This class will not provide any sizing.
class	PartialSigNorm This class normalizes a gel.
class	PeakLocate This is an abstract class that should be extended to provide different ways of finding the peaks in a lane.
class	RawView This class resets the display so that the original data is used instead of normalized data.
class	SCFFilter This class reads data from an SCF file, which are fairly common.
class	ScoreFunction This class represents functions used to score a bin.
class	SegregatingScore This scores each bin by assigning different labels to the differnet cutoff regions.
class	SignalNorm This class normalizes a gel.
class	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.
class	SizeStandard This class is used to define a size standard.

Methods in AFLPcore that return Operation

Operation	Manager.get(java.lang.String opName) Retrieves the operation associated with the given name.
Operation	Manager.getDefault() Gives the default operation for this manager.

Methods in AFLPcore with parameters of type Operation

void	Manager.add(java.lang.String name, Operation operation) Adds the specified operation with the given name to the Manager.
abstract boolean	Manager.classTypeOk(Operation op) Checks to see if the specified operation is compatible with the manager.
boolean	StandardMgr.classTypeOk(Operation op) Checks to see if the specified operation is a SizeStandard.
boolean	PeakMgr.classTypeOk(Operation op) Checks to see if the specified operation is a PeakLocate.
boolean	SizeMgr.classTypeOk(Operation op) Checks to see if the specified operation is an SizeFunction.
boolean	ScoreManager.classTypeOk(Operation op) Checks to see if the specified operation is a ScoreFunction.
boolean	CutoffMgr.classTypeOk(Operation op) Checks to see if the specified operation is a CutoffFunction.
boolean	BinOpMgr.classTypeOk(Operation op) Checks to see if the specified operation is an BinOperation.
boolean	ImportMgr.classTypeOk(Operation op) Checks to see if the specified operation is an ImportFilter.
boolean	AnalysisMgr.classTypeOk(Operation op) Checks to see if the specified operation is an AnalysisOp.
boolean	LaneOpMgr.classTypeOk(Operation op) Checks to see if the specified operation is an LaneOperation.
boolean	GelOpMgr.classTypeOk(Operation op) Checks to see if the specified operation is an GelOperation.