Package AFLPcore

Class Summary

ABI3x00Filter	This class reads data from a ABI 3100 and a 3700 capillary machine.
ABILaneFilter	This class reads data from a lane file produced by extracting lanes from a gel run on an ABI377.
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.
BinAnalysis	This class is an AnalysisOp which outputs information about all of the bins in the gel.
BinOperation	This is an abstract class that represents operations on a bin.
BinOpMgr	This class contains a list of BinOperations which can be used to read in different files.
CEQLaneFilter	This class reads data from a fragment results text file produced by a Beckman Coulter, Inc.
Constants	This class simply contains constants that are used elsewhere in the program.
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.
FeatureList	This is a static class that provides a list of all of the features in the program.
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.
HighestPeakLocate	This class can be used to find peaks in lanes.
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.
LaneOperation	This is an abstract class that represents operations on a set of Lanes.
LaneOpMgr	This class contains a list of LaneOperations which can be used to read in different files.
LinearCutoff	This cutoff function represents a horizontal line.
LocalSouthern	This class implements the Local Southern sizing method described by E.M.
Manager	This class contains a list of Operations which can be used to perform different functions in the program.
MapMakerAnalysis	This class is an AnalysisOp which outputs information about all of the bins in the gel.
NoSize	This class will not provide any sizing.
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.
PartialSigNorm	This class normalizes a gel.
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.
ProgOptions	This class contains static methods and variables that provide several features to the program.
RawView	This class resets the display so that the original data is used instead of normalized data.
SCFFilter	This class reads data from an SCF file, which are fairly common.
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.
SegregatingScore	This scores each bin by assigning different labels to the differnet cutoff regions.
SignalNorm	This class normalizes a gel.
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.
SizeStandard	This class is used to define a size standard.
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.
TracePeakFinder	This is a simple algorithm that is used to find peaks in a set of trace data.
TracePoint	Represents a point on the trace, in the form (size, height).

Error Summary

ListNotSearchableError	Thrown when a list cannot be sorted or searched.
MissingParameterError	Thrown to indicate that a method does not have all of the required parameters to run.
NoBrowserException	Thrown to indicate that the browser needed to display the program help could not be found or accessed.
NoDataError	Thrown to indicate that the data required to perform a function was not present.
PrettyInsignificantError	Thrown to indicate that a miscellanious error has run, but nothing that might harm the running of the program.
ScanCalcError	Thrown to indicate that a method cannot determine the scan number from a given size.
ScoringFailure	Thrown to indicate that the scoring function could not function properly.