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.