Genographer Source Documentation (ver 1.6): Index

Overview

Package

Class

Use

Tree

Deprecated

Index

Help

PREV NEXT

FRAMES NO FRAMES

A B C D E F G H I K L M N O P R S T U V W Y

A

ABI3x00Filter - class AFLPcore.ABI3x00Filter.: This class reads data from a ABI 3100 and a 3700 capillary machine.
ABI3x00Filter() - Constructor for class AFLPcore.ABI3x00Filter: Creates a new filter to read in ABI files.
ABILaneFilter - class AFLPcore.ABILaneFilter.: This class reads data from a lane file produced by extracting lanes from a gel run on an ABI377.
ABILaneFilter() - Constructor for class AFLPcore.ABILaneFilter: Creates a new filter to read in ABI lane files.
ABOUT_STR - Static variable in class AFLPcore.Constants
AboutDialog - class AFLPgui.AboutDialog.: This is the about dialog box for the program.
AboutDialog(Frame) - Constructor for class AFLPgui.AboutDialog: Creates a new about dialog with the
AboutDialog(Frame, String) - Constructor for class AFLPgui.AboutDialog: Creates a new about dialog with the specified parameters
aboutItem - Variable in class AFLPgui.FragmentMap
actionPerformed(ActionEvent) - Method in class AFLPgui.OptionDialog: Handles the buttons.
actionPerformed(ActionEvent) - Method in class AFLPgui.MultiFileDialog: Handle the button clicks as well as double clicks on the list.
actionPerformed(ActionEvent) - Method in class AFLPgui.TraceView: Handles the buttons in the button bar.
actionPerformed(ActionEvent) - Method in class AFLPgui.AboutDialog: Closes the dialog box when ok is hit.
actionPerformed(ActionEvent) - Method in class AFLPgui.Thumbnail: Handles the buttons in the button bar.
actionPerformed(ActionEvent) - Method in class AFLPgui.FragmentMap: Handles the events from buttons and menu items.
actionPerformed(ActionEvent) - Method in class AFLPgui.ControlBar: Handles the button events by calling switchTo(String) in the parent.
actionPerformed(ActionEvent) - Method in class AFLPgui.EntryDialog: Handles the events from buttons.
actionPerformed(ActionEvent) - Method in class AFLPgui.CutoffDialog: Handles the events generated by the buttons.
actionPerformed(ActionEvent) - Method in class AFLPgui.GraphView: Handles the buttons in the button bar.
actionPerformed(ActionEvent) - Method in class AFLPgui.BinDialog: Handles all of the action event, which come mostly from the buttons in the dialog box.
actionPerformed(ActionEvent) - Method in class AFLPgui.GelView: Deal with action events.
add(double) - Method in class AFLPcore.SizeStandard: Adds the specified value to the defintion.
add(String, Operation) - Method in class AFLPcore.Manager: Adds the specified operation with the given name to the Manager.
addBin(Bin) - Method in class AFLPcore.Gel: Adds the specified bin to the gel.
addCutoff(Cutoff) - Method in class AFLPcore.Lane: Adds the specified cutoff to the list of known cutoffs for this lane.
addCutoffFunction(CutoffFunction) - Method in class AFLPgui.CutoffSlider: Adds the specified CutoffFucntion to all of the lanes known to this class.
addData(Data) - Method in class AFLPcore.DataList: Adds the specified data to the list.
addFile(int) - Method in class AFLPgui.MultiFileDialog: Adds an entry to the list of files to be opened/imported.
addFile(int[]) - Method in class AFLPgui.MultiFileDialog: Adds entries to the list of files to be opened/imported.
addFunction(CutoffFunction) - Method in class AFLPcore.Cutoff: Adds the specified function to this cutoff.
addLane(Lane) - Method in class AFLPcore.Gel: Adds a lane to this gel.
addMenu(Menu, Manager) - Method in class AFLPgui.FragmentMap: Adds Operations from the specified Manager to the specified menu and stores the menu items.
addOption(Option, int, int) - Method in class AFLPgui.OptionDialog: Creates a GUI component for the specified option and places it at the specified position.
adjustLocation(double) - Method in class AFLPcore.Bin: Moves the bin to a new location based on it's present location.
adjustRange(double) - Method in class AFLPcore.Bin: Changes the range relative to the current value of the range.
AFLPcore - package AFLPcore
AFLPgui - package AFLPgui
ALL - Static variable in class AFLPcore.SCFFilter
ALL - Static variable in class AFLPcore.ABILaneFilter
ALL - Static variable in class AFLPcore.ABI3x00Filter
analysis - Variable in class AFLPgui.FragmentMap
ANALYSIS - Static variable in class AFLPgui.FragmentMap
AnalysisMgr - class AFLPcore.AnalysisMgr.: This class contains a list of AnalysisOps which can be used to read in different files.
AnalysisMgr() - Constructor for class AFLPcore.AnalysisMgr: Creates a new AnalysisMgr, with a default capacity of 4 and a loadFactor of 1.0.
AnalysisMgr(int, float) - Constructor for class AFLPcore.AnalysisMgr: Creates a new AnalysisMgr with the specified values.
AnalysisOp - class AFLPcore.AnalysisOp.: This abstract class represents methods used to analyize a gel.
AnalysisOp() - Constructor for class AFLPcore.AnalysisOp
AnalysisView - class AFLPgui.AnalysisView.: This class is responsible for displaying methods to analyze a gel and the results of the analysis.
AnalysisView(Frame) - Constructor for class AFLPgui.AnalysisView: Create a new analysis view with the specified parent window.
analyze(Gel) - Method in class AFLPcore.AnalysisOp: This method should provide some sort of information about the gel.
analyze(Gel) - Method in class AFLPcore.BinAnalysis: Provides an anlysis for the the specified gel.
analyze(Gel) - Method in class AFLPcore.MapMakerAnalysis: Provides an anlysis for the the specified gel.
AREA - Static variable in class AFLPcore.Cutoff

B

Bar - class AFLPgui.Bar.: This class will provide a panel that automatically includes lines seperating it on the top and bottom.
BAR_HEIGHT - Static variable in class AFLPgui.FragmentMap
Bar() - Constructor for class AFLPgui.Bar: Creates a new Bar, which will draw both the top and bottom borders.
Bar(boolean, boolean) - Constructor for class AFLPgui.Bar: Creates a new Bar, drawing the specified borders.
BarGraph - class AFLPgui.BarGraph.: This class will draw a graph given a set of lanes and an area in those lanes.
BarGraph() - Constructor for class AFLPgui.BarGraph: Create a new BarGraph.
BarGraph(Color, Color) - Constructor for class AFLPgui.BarGraph: Create a new BarGraph with the specified colors.
Bin - class AFLPcore.Bin.: This class represents a bin, which is simply a region defined in a gel.
Bin(double) - Constructor for class AFLPcore.Bin: Creates a new bin with the specified parameters.
Bin(double, double) - Constructor for class AFLPcore.Bin: Creates a new bin with the specified parameters.
Bin(double, double, ScoreFunction) - Constructor for class AFLPcore.Bin: Creates a new bin with the specified parameters.
BinAnalysis - class AFLPcore.BinAnalysis.: This class is an AnalysisOp which outputs information about all of the bins in the gel.
BinAnalysis() - Constructor for class AFLPcore.BinAnalysis: Creates a new BinAnalysis object.
binAtSize(double) - Method in class AFLPcore.Gel: Gives the bin at the specified location.
BinDialog - class AFLPgui.BinDialog.: This is a dialog box that shows a list of bins.
BinDialog(Frame, String, boolean) - Constructor for class AFLPgui.BinDialog: Create a new Bin Dialog with the specified parameters.
BinOperation - class AFLPcore.BinOperation.: This is an abstract class that represents operations on a bin.
BinOperation() - Constructor for class AFLPcore.BinOperation
binOpItem - Variable in class AFLPgui.FragmentMap
BinOpMgr - class AFLPcore.BinOpMgr.: This class contains a list of BinOperations which can be used to read in different files.
BinOpMgr() - Constructor for class AFLPcore.BinOpMgr: Creates a new BinOpMgr, with a default capacity of 4 and a loadFactor of 1.0.
BinOpMgr(int, float) - Constructor for class AFLPcore.BinOpMgr: Creates a new BinOpMgr with the specified values.
binRedrawItem - Variable in class AFLPgui.FragmentMap
BLANK - Static variable in class AFLPgui.Thumbnail
BLUE - Static variable in class AFLPcore.SCFFilter: color channel
BLUE - Static variable in class AFLPcore.CEQLaneFilter
BLUE - Static variable in class AFLPcore.ABILaneFilter: color channel
BLUE - Static variable in class AFLPcore.Lane: Constant for lane color
BLUE - Static variable in class AFLPcore.ABI3x00Filter: color channel
bottomP - Variable in class AFLPgui.FragmentMap
BUTTON_HEIGHT - Static variable in class AFLPgui.ButtonBar
BUTTON_WIDTH - Static variable in class AFLPgui.ButtonBar
buttonBar - Variable in class AFLPgui.FragmentMap
ButtonBar - class AFLPgui.ButtonBar.: This class extends the bar class and adds four buttons to a bar.
ButtonBar() - Constructor for class AFLPgui.ButtonBar: Create a new button bar with both top and bottom border lines.
ButtonBar(boolean, boolean) - Constructor for class AFLPgui.ButtonBar: Create a new button bar with the specified top and bottom borders.

C

CEQLaneFilter - class AFLPcore.CEQLaneFilter.: This class reads data from a fragment results text file produced by a Beckman Coulter, Inc.
CEQLaneFilter() - Constructor for class AFLPcore.CEQLaneFilter: Creates a new filter to read in CEQ lane files.
CHOICE - Static variable in class AFLPcore.Option
classTypeOk(Operation) - Method in class AFLPcore.Manager: Checks to see if the specified operation is compatible with the manager.
classTypeOk(Operation) - Method in class AFLPcore.StandardMgr: Checks to see if the specified operation is a SizeStandard.
classTypeOk(Operation) - Method in class AFLPcore.PeakMgr: Checks to see if the specified operation is a PeakLocate.
classTypeOk(Operation) - Method in class AFLPcore.SizeMgr: Checks to see if the specified operation is an SizeFunction.
classTypeOk(Operation) - Method in class AFLPcore.ScoreManager: Checks to see if the specified operation is a ScoreFunction.
classTypeOk(Operation) - Method in class AFLPcore.CutoffMgr: Checks to see if the specified operation is a CutoffFunction.
classTypeOk(Operation) - Method in class AFLPcore.BinOpMgr: Checks to see if the specified operation is an BinOperation.
classTypeOk(Operation) - Method in class AFLPcore.ImportMgr: Checks to see if the specified operation is an ImportFilter.
classTypeOk(Operation) - Method in class AFLPcore.AnalysisMgr: Checks to see if the specified operation is an AnalysisOp.
classTypeOk(Operation) - Method in class AFLPcore.LaneOpMgr: Checks to see if the specified operation is an LaneOperation.
classTypeOk(Operation) - Method in class AFLPcore.GelOpMgr: Checks to see if the specified operation is an GelOperation.
clone() - Method in class AFLPcore.Data
clone() - Method in class AFLPcore.Gel: Clones the gel Not Implemented.
clone() - Method in class AFLPcore.SizeFunction: Gives an object where every field has been copied from this object to the new object.
clone() - Method in class AFLPcore.ScoreFunction: Gives an object where every field has been copied from this object to the new object.
clone() - Method in class AFLPcore.CutoffFunction: Gives an object where every field has been copied from this object to the new object.
clone() - Method in class AFLPcore.Lane: Clones this lane Not implemented
clone() - Method in class AFLPcore.Peak: Clones this peak Not implemented
clone() - Method in class AFLPcore.AnalysisOp: Gives an object where every field has been copied from this object to the new object.
clone() - Method in class AFLPcore.Cutoff: Gives an object where all of the data is the same as this one.
clone() - Method in class AFLPcore.Bin: Produces a new bin identical to this one, except it has not been scored.
completeClone() - Method in class AFLPcore.DataList: Creates a new list that is identical to this one with a completely seperate copy of the data in the list.
Constants - class AFLPcore.Constants.: This class simply contains constants that are used elsewhere in the program.
Constants() - Constructor for class AFLPcore.Constants
contains(double) - Method in class AFLPcore.SizeStandard: Tells whether or not the specified value is included in this size standard definition.
ControlBar - class AFLPgui.ControlBar.: This class displays buttons on a panel.
ControlBar(FragmentMap) - Constructor for class AFLPgui.ControlBar: Create a new ControlBar with the specified parent.
copyList(DataList) - Method in class AFLPcore.DataList: Copies the data in this list to the specified destination.
createArrow() - Method in class AFLPgui.CutoffSlider: Creates a polygon that is in the shape of the arrow used to indicate different levels.
createManagerList(Manager, PrintWriter) - Static method in class AFLPcore.FeatureList
currentBin - Variable in class AFLPgui.FragmentMap
currentDir - Variable in class AFLPgui.FragmentMap
currentFile - Variable in class AFLPgui.FragmentMap
currentView - Variable in class AFLPgui.FragmentMap
Cutoff - class AFLPcore.Cutoff.: This class represents different cutoffs for a lane.
Cutoff(double, int) - Constructor for class AFLPcore.Cutoff: Creates a new cutoff with the specified number of levels and starting at the specified position.
CutoffDialog - class AFLPgui.CutoffDialog.: This dialog box will display a cutoff.
CutoffDialog(Frame, String, boolean) - Constructor for class AFLPgui.CutoffDialog: Create a new CutoffDialog with the specified parameters.
CutoffFunction - class AFLPcore.CutoffFunction.: An abstract class that is used to represent different functions for cutting off noise from data peaks.
CutoffFunction() - Constructor for class AFLPcore.CutoffFunction
CutoffMgr - class AFLPcore.CutoffMgr.: This class contains a list of CutoffFunctions which can be used to read create different functions for the cutoff.
CutoffMgr() - Constructor for class AFLPcore.CutoffMgr: Creates a new CutoffMgr, with a default capacity of 4 and a loadFactor of 1.0.
CutoffMgr(int, float) - Constructor for class AFLPcore.CutoffMgr: Creates a new CutoffMgr with the specified values.
CutoffSlider - class AFLPgui.CutoffSlider.: This class provides a way to manipulate a cutoff with the mouse.
CutoffSlider() - Constructor for class AFLPgui.CutoffSlider: Create a new cutoff slider.
cutoffUnder(double) - Method in class AFLPcore.Lane: Gives the first cutoff in the lane that is less than or equal to the specified size.

D

Data - class AFLPcore.Data.: A class that holds all of the data for the program.
Data() - Constructor for class AFLPcore.Data
dataAt(int) - Method in class AFLPcore.DataList: Retrieve the data at the specified index.
DataList - class AFLPcore.DataList.: This is an expandable list that can be used to store objects of type Data.
DataList() - Constructor for class AFLPcore.DataList: Constructs an empty DataList.
DataList(int) - Constructor for class AFLPcore.DataList: Constructs an empty DataList with the specified initial capacity.
DataList(int, int) - Constructor for class AFLPcore.DataList: Constructs an empty DataList with the specified initial capacity and capacity increment.
DEFAULT_PERCENT - Static variable in class AFLPcore.PartialSigNorm
defaultCutoff - Variable in class AFLPgui.FragmentMap
deleteFunction(int) - Method in class AFLPcore.Cutoff: Removes the specified level from this cutoff.
descript - Variable in class AFLPcore.Operation
displayDirectory(File) - Method in class AFLPgui.MultiFileDialog: Displays the specified directory on the left side of the dialog.
doBinOp(Bin) - Method in class AFLPcore.BinOperation: This performs some sort of operation on the bin.
doBinOp(DataList) - Method in class AFLPcore.BinOperation: This performs some sort of operation on all of the bins
doGelOp(Gel) - Method in class AFLPcore.GelOperation: This performs some sort of operation on a gel.
doGelOp(Gel) - Method in class AFLPcore.SignalNorm: This normalizes all of the lanes in the Gel based on the signal stength of each lane.
doGelOp(Gel) - Method in class AFLPcore.PartialSigNorm: This normalizes all of the lanes in the Gel based on the signal stength of each lane.
doGelOp(Gel) - Method in class AFLPcore.RawView: This normalizes all of the lanes in the Gel based on the signal stength of each lane.
doLaneOp(DataList) - Method in class AFLPcore.LaneOperation: This performs some sort of operation on a set of lanes.
drawBins(Graphics) - Method in class AFLPgui.GelView: Draws all the bins in the gel onto the specified graphics object.
drawGraph(Graphics, int, int, int, int, int, double, double, double, DataList) - Method in class AFLPgui.Graph: Draw some sort of graph given the specified parameters.
drawGraph(Graphics, int, int, int, int, int, double, double, double, DataList) - Method in class AFLPgui.BarGraph: Draws the graph described in the class description.
drawGraph(Graphics, int, int, int, int, int, double, double, double, DataList) - Method in class AFLPgui.ScatterGraph: Draw the scatter graph with the specified properties.
drawLaneHeaders(Graphics) - Method in class AFLPgui.GelView: Draws the headers for the lanes, (the little grey tabs at the top of the gel).
drawTrace(Graphics, Lane, int, int) - Method in class AFLPgui.Thumbnail: Draws the trace portion of the thumbnail.

E

EntryDialog - class AFLPgui.EntryDialog.: This is a dialog that can be used to have the user enter a value.
EntryDialog(Frame, String, boolean) - Constructor for class AFLPgui.EntryDialog: Create a new EntryDialog with the specified parameters.
errorDialog - Variable in class AFLPgui.FragmentMap
exitItem - Variable in class AFLPgui.FragmentMap
exportItem - Variable in class AFLPgui.FragmentMap
exportView(int) - Method in class AFLPgui.FragmentMap: This will export the specified data view out to a file.

F

FeatureList - class AFLPcore.FeatureList.: This is a static class that provides a list of all of the features in the program.
FeatureList() - Constructor for class AFLPcore.FeatureList
fileDialog - Variable in class AFLPgui.FragmentMap
filetype - Variable in class AFLPcore.ImportFilter
finalize() - Method in class AFLPgui.GelView: Cleans up before this class is disposed off.
find(double) - Method in class AFLPcore.DataList: Finds the location of the specified key.
find(double[]) - Static method in class AFLPcore.TracePeakFinder
find(double[], int) - Static method in class AFLPcore.TracePeakFinder
find(double[], int, double) - Static method in class AFLPcore.TracePeakFinder
find(double[], int, double, double) - Static method in class AFLPcore.TracePeakFinder: This is the one method in this class, really.
findLaneAt(int) - Method in class AFLPgui.GelView: Gives the position in the gel of the lane at the given size.
findMax(DataList) - Method in class AFLPgui.BarGraph: Finds the maximum height in a list of peaks.
findMax(DataList) - Method in class AFLPgui.ScatterGraph: Gives the maximum height for all of the peaks in the given list.
findNearestUnder(double) - Method in class AFLPcore.DataList: Gives the SortableData element which is less than or equal to the given value.
findPeak(DataList, double, double) - Method in class AFLPcore.PeakLocate: Finds the peaks in the given lanes and only finds those whose size is greater than or equal to minSize and less than or equal to maxSize.
findPeak(DataList, double, double) - Method in class AFLPcore.HighestPeakLocate: Finds a peak in each lane and saves it in the lane.
findPositionInfo(int, int) - Method in class AFLPgui.Thumbnail: Gives the size and intensity for the given point.
findSizeAt(int) - Method in class AFLPgui.GelView: Calculates the size in bp that corresponds to the screen location given.
FragmentMap - class AFLPgui.FragmentMap.: This is the main GenoGrapher program window.
FragmentMap() - Constructor for class AFLPgui.FragmentMap: Create a new FragmentMap.
FragmentMap(String[]) - Constructor for class AFLPgui.FragmentMap: Create a new FragmentMap.

G

gel - Variable in class AFLPgui.FragmentMap
Gel - class AFLPcore.Gel.: A gel contains most of the information needed by the program.
GEL - Variable in class AFLPcore.ImportFilter: constant to determine type of file filter is used on
GEL - Static variable in class AFLPgui.FragmentMap
Gel() - Constructor for class AFLPcore.Gel: Create a new Gel.
GelOperation - class AFLPcore.GelOperation.: This is an abstract class that represents operations on a gel.
GelOperation() - Constructor for class AFLPcore.GelOperation
gelOpItem - Variable in class AFLPgui.FragmentMap
GelOpMgr - class AFLPcore.GelOpMgr.: This class contains a list of GelOperations which can be used to read in different files.
GelOpMgr() - Constructor for class AFLPcore.GelOpMgr: Creates a new GelOpMgr, with a default capacity of 4 and a loadFactor of 1.0.
GelOpMgr(int, float) - Constructor for class AFLPcore.GelOpMgr: Creates a new GelOpMgr with the specified values.
gelRedrawItem - Variable in class AFLPgui.FragmentMap
gelView - Variable in class AFLPgui.FragmentMap
GelView - class AFLPgui.GelView.: Displays the gel as an image and provides the methods used to allow user interaction with the gel, such as placing bins and zooming.
GelView(Gel, Frame) - Constructor for class AFLPgui.GelView: Creates a new viewable object of the specified gel
generateFileList() - Static method in class AFLPcore.FeatureList
get(String) - Method in class AFLPcore.Manager: Retrieves the operation associated with the given name.
getAnalysisMgr() - Static method in class AFLPcore.FeatureList: Gives a manager that contains all of the functions used to analyize a gel known to the program.
getArea() - Method in class AFLPcore.Peak: Gives the area of this peek.
getBackGroundColor() - Method in class AFLPcore.Gel: Gives the color of the background for the gel.
getBin() - Method in class AFLPgui.Thumbnail: Gives the bin displayed.
getBin() - Method in class AFLPgui.GraphView: Gives the bin that was used to produce the graph.
getBinOpMgr() - Static method in class AFLPcore.FeatureList: Gives a manager that contains all of the operations on bins known to the program.
getBins() - Method in class AFLPcore.Gel: Gives a list of all the bins in the gel.
getButtonBar() - Method in class AFLPgui.TraceView: Gives the ButtonBar associated with the trace.
getButtonBar() - Method in class AFLPgui.Thumbnail: Gives the ButtonBar associated with the thumbnails.
getButtonBar() - Method in class AFLPgui.AnalysisView: Gives the button bar used by this class.
getButtonBar() - Method in class AFLPgui.GraphView: Gives the ButtonBar associated with the graph.
getButtonBar() - Method in class AFLPgui.GelView: Gives the button bar that should be used with this object.
getChoices() - Method in class AFLPcore.Option: Gives the list of possiblities for a choice option.
getChoices(int) - Method in class AFLPcore.ScoreFunction: Gives the possible values that score will return.
getChoices(int) - Method in class AFLPcore.SegregatingScore: Gives the labels that the scoring function can assign.
getColor() - Method in class AFLPcore.Lane: Gives the color of the data in this lane.
getConfidence() - Method in class AFLPcore.Peak: Gives the confidence associated with this peak.
getCurrentBin() - Method in class AFLPgui.GelView: Gives the bin that is currently selected on the gel.
getCutoff(double) - Method in class AFLPcore.CutoffFunction: Returns the cutoff value for the specified position
getCutoff(double) - Method in class AFLPcore.LinearCutoff: Gives the cutoff point for this function.
getCutoff(double, int) - Method in class AFLPcore.Cutoff: Gives the value for the height/area above which all peaks should be counted with a confidence relative to the level.
getCutoffFunction(int) - Method in class AFLPcore.Cutoff: Gives the cutoff function for the specified level.
getCutoffMgr() - Static method in class AFLPcore.FeatureList: Gives a manager that contains all of the cutoff functions known to the program.
getCutoffs() - Method in class AFLPcore.Lane: Returns the list of cutoffs associated with this lane.
getDefault() - Method in class AFLPcore.Manager: Gives the default operation for this manager.
getDefaultChoice() - Method in class AFLPcore.Option: Gives the default choice for this option.
getDefaultName() - Method in class AFLPcore.Manager: Gives the name of the default operation for this manager.
getDescription() - Method in class AFLPcore.Operation: Retrieves a short, approximately one sentence, description of the operation.
getDescription() - Method in class AFLPcore.NoSize: Gives a brief description of this sizing function.
getDescription() - Method in class AFLPcore.SignalNorm: Gives a one sentence description of this gel operation.
getDescription() - Method in class AFLPcore.SizeStandard: Defined to satisfy abstract parent class, but not really applicable in this case.
getDescription() - Method in class AFLPcore.SCFFilter: Retrieves a short, approximately one sentence, description of the filter.
getDescription() - Method in class AFLPcore.LinearCutoff: Gives a brief description of the linear filter.
getDescription() - Method in class AFLPcore.CEQLaneFilter: Retrieves a short, approximately one sentence, description of the filter.
getDescription() - Method in class AFLPcore.ABILaneFilter: Retrieves a short, approximately one sentence, description of the filter.
getDescription() - Method in class AFLPcore.BinAnalysis: Gives a one sentence description of this analysis operation.
getDescription() - Method in class AFLPcore.PartialSigNorm: Gives a one sentence description of this gel operation.
getDescription() - Method in class AFLPcore.SegregatingScore: Gives a one sentence description of this score function.
getDescription() - Method in class AFLPcore.HighestPeakLocate: Gives a brief description of the peak location function/algorithm.
getDescription() - Method in class AFLPcore.RawView: Gives a one sentence description of this gel operation.
getDescription() - Method in class AFLPcore.ABI3x00Filter: Retrieves a short, approximately one sentence, description of the filter.
getDescription() - Method in class AFLPcore.MapMakerAnalysis: Gives a one sentence description of this analysis operation.
getDescription() - Method in class AFLPcore.LocalSouthern: Gives a brief description of this sizing function.
getFiles() - Method in class AFLPgui.MultiFileDialog: Gives a list of files selected by the user.
getFileType() - Method in class AFLPcore.ImportFilter: Returns the type of input file supported by this filter, options are ImportFilter.LANE or ImportFilter.GEL.
getFileType() - Method in class AFLPcore.SCFFilter: Returns the type of input file supported by this filter In this case ImportFilter.LANE, since the filter reads in lane data.
getFileType() - Method in class AFLPcore.CEQLaneFilter: Returns the type of input file supported by this filter In this case ImportFilter.LANE, since the filter reads in lane data.
getFileType() - Method in class AFLPcore.ABILaneFilter: Returns the type of input file supported by this filter In this case ImportFilter.LANE, since the filter reads in lane data.
getFileType() - Method in class AFLPcore.ABI3x00Filter: Returns the type of input file supported by this filter In this case ImportFilter.LANE, since the filter reads in lane data.
getFilter() - Method in class AFLPgui.MultiFileDialog: Gives the filter selected in the dialog box.
getFreeHorzPos() - Method in class AFLPgui.ButtonBar: Gives the location of the first space not occupied by a button.
getGelName() - Method in class AFLPcore.Lane: Gives the name of the Gel that this lane was extracted from.
getGelOpMgr() - Static method in class AFLPcore.FeatureList: Gives a manager that contains all of the operations on a gel known to the program.
getGelTopBorder() - Method in class AFLPcore.Gel: Gives the height of the border on the top and bottom of the gel image.
getGlobalMaxIntensity() - Method in class AFLPcore.Gel: Gives the maximum intensity of the gel.
getGraphWidth() - Method in class AFLPgui.GraphView: Gets the width of the graph, which does not include borders.
getHeight() - Method in class AFLPcore.Peak: Gives the height of the peak.
getHeight() - Method in class AFLPgui.TraceView: Gives the height of the trace, excluding borders.
getHeight() - Method in class AFLPgui.GraphView: Gives the height of the graph display area, including borders.
getHeightAt(double) - Method in class AFLPcore.Lane: Gives the intensity of the light for the color at the specified size.
getHelpFile() - Method in class AFLPcore.Operation: Each operation should have a help file that describes its actions, types of files it works on, and an explination of any options that the filter supports.
getHelpFile() - Method in class AFLPcore.NoSize: Gives the help file that describes the function in more detail
getHelpFile() - Method in class AFLPcore.SignalNorm: Gives a file that is the help file for this gel operation
getHelpFile() - Method in class AFLPcore.SizeStandard: Defined to satisfy abstract parent class, but not really applicable in this case.
getHelpFile() - Method in class AFLPcore.SCFFilter: The help file describes which files the filter reads and the options that this filter accepts.
getHelpFile() - Method in class AFLPcore.LinearCutoff: Gives help for the linear cutoff.
getHelpFile() - Method in class AFLPcore.CEQLaneFilter: The help file describes which files the filter reads and the options that this filter accepts.
getHelpFile() - Method in class AFLPcore.ABILaneFilter: The help file describes which files the filter reads and the options that this filter accepts.
getHelpFile() - Method in class AFLPcore.BinAnalysis: Gives a file that is the help file for this analysis operation
getHelpFile() - Method in class AFLPcore.PartialSigNorm: Gives a file that is the help file for this gel operation
getHelpFile() - Method in class AFLPcore.SegregatingScore: Gives a file that is the help file for this scoring function
getHelpFile() - Method in class AFLPcore.HighestPeakLocate: Gives the help file for the Highest peak location function
getHelpFile() - Method in class AFLPcore.RawView: Gives a file that is the help file for this gel operation
getHelpFile() - Method in class AFLPcore.ABI3x00Filter: The help file describes which files the filter reads and the options that this filter accepts.
getHelpFile() - Method in class AFLPcore.MapMakerAnalysis: Gives a file that is the help file for this analysis operation
getHelpFile() - Method in class AFLPcore.LocalSouthern: Gives the help file that describes the function in more detail
getImportMgr() - Static method in class AFLPcore.FeatureList: Gives a manager that contains all of the import filters known to the program.
getInfo(String[], DataList) - Method in class AFLPcore.ScoreFunction: Should provide overall information about a bin scored with this method.
getInfo(String[], DataList) - Method in class AFLPcore.SegregatingScore: This returns a set of strings that describes the overall scoring of the bin.
getInfoBar() - Method in class AFLPgui.TraceView: Returns a bar that displays information about the trace.
getInfoBar() - Method in class AFLPgui.Thumbnail: Returns a bar that displays information about the thumbnails.
getInfoBar() - Method in class AFLPgui.AnalysisView: Gives the label that this class uses to provide status information.
getInfoBar() - Method in class AFLPgui.GraphView: Returns a bar that displays information about the graph.
getInfoBar() - Method in class AFLPgui.GelView: Returns a bar that displays information about the gel.
getIntensity() - Method in class AFLPcore.Gel: Gives the height to which all values will be scaled to transform them into colors.
getLabel() - Method in class AFLPcore.Option: Gives a label for this option that serves as an identifier for the option.
getLaneBorder() - Method in class AFLPcore.Gel: Gives the spacing between two lanes in the gel image.
getLaneIndex() - Method in class AFLPcore.Lane: Gives an integer that is unique to this lane.
getLaneNumber() - Method in class AFLPcore.Lane: Gives the number of the lane on the gel that contianed this information.
getLaneOpMgr() - Static method in class AFLPcore.FeatureList: Gives a manager that contains all of the operations on lanes known to the program.
getLanes() - Method in class AFLPcore.Gel: Gives a list of all of the lanes in the gel.
getLanes() - Method in class AFLPgui.Thumbnail: Gives the lanes that are being displayed.
getLaneWidth() - Method in class AFLPcore.Gel: Gives the width of a lane, in pixels.
getLocation() - Method in class AFLPcore.Peak: Gives the location of the peek in the data.
getLocation() - Method in class AFLPcore.Bin: Gives the position of this bin in the gel.
getMaxGlobalHeight() - Method in class AFLPcore.Lane: Gives the maximum height in the lane
getMaxHeight(double, double) - Method in class AFLPcore.Lane: Gives the maximum height in the specified range.
getMaxIntensity(double, double) - Method in class AFLPcore.Gel: Gives the maximum intensity in the gel between the two specified sizes.
getMaxPoint(double, double) - Method in class AFLPcore.Lane: Gives the maximum point, (size, height) ,in the specified range.
getMaxSize() - Method in class AFLPcore.Gel: Gives the largest size that will be included in the gel image when it is produced.
getMaxSize() - Method in class AFLPcore.Lane: Gives the largest size, in bp, represented by this lane.
getMessage() - Method in class AFLPgui.CutoffSlider: Gets a message describing the current state of the slider.
getMinSize() - Method in class AFLPcore.Gel: Gives the smallest size that will be included in the gel image when it is produced.
getMinSize() - Method in class AFLPcore.Lane: Gives the smallest size, in bp, represented by this lane.
getMode() - Method in class AFLPcore.Cutoff: Gives the current cutoff mode, either height or area.
getName() - Method in class AFLPcore.Operation: Access the name of the operation.
getName() - Method in class AFLPcore.NoSize: Gives the name describing this sizing function.
getName() - Method in class AFLPcore.SignalNorm: Gives the name of this gel operation
getName() - Method in class AFLPcore.SizeStandard: Gives the name of this size standard.
getName() - Method in class AFLPcore.SCFFilter: Access the name of the filter.
getName() - Method in class AFLPcore.LinearCutoff: Gives the name of this linear function.
getName() - Method in class AFLPcore.CEQLaneFilter: Access the name of the filter.
getName() - Method in class AFLPcore.ABILaneFilter: Access the name of the filter.
getName() - Method in class AFLPcore.Lane: Gives the name of the sample run on this lane.
getName() - Method in class AFLPcore.BinAnalysis: Gives the name of this bin analysis operation
getName() - Method in class AFLPcore.PartialSigNorm: Gives the name of this gel operation
getName() - Method in class AFLPcore.Bin: Gives the name of this bin.
getName() - Method in class AFLPcore.SegregatingScore: Gives the name of this segregating score function.
getName() - Method in class AFLPcore.HighestPeakLocate: Gives the name of this peak location function
getName() - Method in class AFLPcore.RawView: Gives the name of this gel operation
getName() - Method in class AFLPcore.ABI3x00Filter: Access the name of the filter.
getName() - Method in class AFLPcore.MapMakerAnalysis: Gives the name of this bin analysis operation
getName() - Method in class AFLPcore.LocalSouthern: Gives the name describing this sizing function.
getNames() - Method in class AFLPcore.Manager: Gets the names of all of the Operations known to the Manager.
getNewButton() - Method in class AFLPgui.ButtonBar: Gives the "new" button on the bar.
getNumLanes() - Method in class AFLPcore.Gel: Gives the number of lanes stored in this gel.
getNumLevels() - Method in class AFLPcore.Cutoff: Gives the number of different cutoff levels supported by this object.
getNumPoints() - Method in class AFLPcore.Lane: This returns the number of points in the trace.
getNumValue() - Method in class AFLPcore.Option: Gives the numerical value associated with this option.
getOpenButton() - Method in class AFLPgui.ButtonBar: Gives the "open" button on the bar.
getOptions() - Method in class AFLPcore.Operation: Retrieves the options associated with this operation.
getOptions() - Method in class AFLPcore.NoSize: There are no options for this sizing function.
getOptions() - Method in class AFLPcore.SignalNorm: No options for this operation, so null is returned.
getOptions() - Method in class AFLPcore.SizeStandard: Defined to satisfy abstract parent class, but not really applicable in this case.
getOptions() - Method in class AFLPcore.SCFFilter: Returns the options for this filter.
getOptions() - Method in class AFLPcore.LinearCutoff: Returns the options/parameters for this Cutoff function.
getOptions() - Method in class AFLPcore.CEQLaneFilter: Returns the options for this filter, which includes the color of the data, the size function to use, and the size standard.
getOptions() - Method in class AFLPcore.ABILaneFilter: Returns the options for this filter, which includes the color of the data, the size function to use, and the size standard.
getOptions() - Method in class AFLPcore.BinAnalysis: No options for this operation, so null is returned.
getOptions() - Method in class AFLPcore.PartialSigNorm: No options for this operation, so null is returned.
getOptions() - Method in class AFLPcore.SegregatingScore: Gives the options for this scoring.
getOptions() - Method in class AFLPcore.HighestPeakLocate: Gives the options, but since there aren't any, this is always null.
getOptions() - Method in class AFLPcore.RawView: No options for this operation, so null is returned.
getOptions() - Method in class AFLPcore.ABI3x00Filter: Returns the options for this filter, which includes the color of the data, the size function to use, and the size standard.
getOptions() - Method in class AFLPcore.MapMakerAnalysis: No options for this operation, so null is returned.
getOptions() - Method in class AFLPcore.LocalSouthern: There are no options for this sizing function.
getOptions() - Method in class AFLPgui.OptionDialog: Gives the options as they were set by the user in the dialog box.
getPeakLocation(int) - Method in class AFLPcore.SizeStandard: Returns the location of a peak at a given index
getPeakMgr() - Static method in class AFLPcore.FeatureList: Gives a manager that contains all of the peak locating algorithms known to the program.
getPeaks() - Method in class AFLPcore.Lane: Gives the list of peaks in the lane.
getPeaksInRange(double, double) - Method in class AFLPcore.Lane: Produces a list of peaks that are in the given range.
getPercentage() - Method in class AFLPgui.EntryDialog: Shows the dialog box and prompts the user for a percentage.
getPixels(double, double, int, double) - Method in class AFLPcore.Gel: Gives an array of pixels that represents the gel as an image.
getPixels(int) - Method in class AFLPcore.Gel: Gives an array of pixels that represents the gel as an image.
getPreferredWidth() - Method in class AFLPgui.Graph: Gives the ideal size of the graph.
getPreferredWidth() - Method in class AFLPgui.BarGraph: Give the ideal width for this graph, which is -1.
getPreferredWidth() - Method in class AFLPgui.ScatterGraph: Gives the preferred width of this graph.
getPrintButton() - Method in class AFLPgui.ButtonBar: Gives the "print" button on the bar.
getRange() - Method in class AFLPcore.Bin: Gives the range of the bin.
getSaveButton() - Method in class AFLPgui.ButtonBar: Gives the "save" button on the bar.
getScan(double) - Method in class AFLPcore.SizeFunction: Gives the index into the trace array, which should correspond to the scan number for any given size.
getScan(double) - Method in class AFLPcore.NoSize: Gives the input value back as the scan number since the size is the scan number in this case.
getScan(double) - Method in class AFLPcore.LocalSouthern: Gives the scan number that will produce the specified size.
getScore(Lane) - Method in class AFLPcore.Bin: Gives the string representing how the given lane was scored.
getScoreInfo() - Method in class AFLPcore.Bin: Gives the overall score info for the bin.
getScoreMethod() - Method in class AFLPcore.Bin: Gives the method used to score a bin.
getScoreMgr() - Static method in class AFLPcore.FeatureList: Gives a manager that contains all of the scoring methods known to the program.
getSearchKey() - Method in class AFLPcore.SortableData: This method returns a value for this object that can be used to order the object.
getSearchKey() - Method in class AFLPcore.Peak: This gives the location of the peek, and is used when searching or sorting objects of this type.
getSearchKey() - Method in class AFLPcore.Cutoff: Gives the starting position for this cutoff.
getSearchKey() - Method in class AFLPcore.Bin: Gives the value used to search/sort bins.
getSelectedLanes() - Method in class AFLPcore.Gel: Gives a list of all of the selected lanes in the gel.
getSize() - Method in class AFLPcore.SizeStandard: Returns the number of elements conained within the datalist
getSize(int) - Method in class AFLPcore.SizeFunction: Gives the size that corresponds to the scan number using some sort of size curve.
getSize(int) - Method in class AFLPcore.NoSize: Gives the scan number back as the size.
getSize(int) - Method in class AFLPcore.LocalSouthern: Gives the size in bp from the scan number, using the method described in the class description.
getSizeFunction() - Method in class AFLPcore.Lane: Gives the object that represents the conversion between size in bp and scan number (trace index).
getSizeInc() - Method in class AFLPcore.Gel: Gives the size in bp represented by each pixel in the pixel array.
getSizeMgr() - Static method in class AFLPcore.FeatureList: Gives a manager that contains all of the functions used to size a lane known to the program.
getStandardMgr() - Static method in class AFLPcore.FeatureList: Gives a manager that contains all of the size standard definitions known to the program.
getStartPos() - Method in class AFLPcore.Cutoff: Gives the starting position for this cutoff.
getStringValue() - Method in class AFLPcore.Option: Gives the string that represents the value of this option.
getText() - Method in class AFLPgui.AnalysisView: Gives the text currently displayed in the output text area.
getThumbnailSize() - Method in class AFLPgui.Thumbnail: Gives the size of an individual thumbnail, including the border around it.
getTotalSignal() - Method in class AFLPcore.Lane: Gives the strength of the signal for this lane.
getTrace() - Method in class AFLPcore.Lane: Gives the current trace for this lane, which is either the normalized trace or the raw trace.
getType() - Method in class AFLPcore.Option: Gives the type of option for this class.
getWidth() - Method in class AFLPgui.TraceView: Gives the width of the trace.
getWidth() - Method in class AFLPgui.GraphView: Gives the width of the graph display area, including borders.
graph - Variable in class AFLPgui.FragmentMap
Graph - class AFLPgui.Graph.: This abstract class provides a way for other parts of the program to draw graphs easily.
GRAPH - Static variable in class AFLPgui.FragmentMap
Graph() - Constructor for class AFLPgui.Graph
GraphView - class AFLPgui.GraphView.: Displays a graph of a bin.
GraphView(DataList, DataList, Frame) - Constructor for class AFLPgui.GraphView: Create a new GraphView with the specified parameters.
GREEN - Static variable in class AFLPcore.SCFFilter: color channel
GREEN - Static variable in class AFLPcore.CEQLaneFilter
GREEN - Static variable in class AFLPcore.ABILaneFilter: color channel
GREEN - Static variable in class AFLPcore.Lane: Constant for lane color
GREEN - Static variable in class AFLPcore.ABI3x00Filter: color channel

H

handleScoreError(ScoringFailure) - Method in class AFLPgui.Thumbnail: Shows an options dialog if an error occurs when scoring a bin.
handleScoreError(ScoringFailure) - Method in class AFLPgui.GraphView: Shows an options dialog if an error occurs when scoring a bin.
hasBottomBorder() - Method in class AFLPgui.Bar: Tells whether or not this bar has a bottom border.
hashCode() - Method in class AFLPcore.Lane: Gives an integer that is equivalent to the lane index, which is a unique number for this lane.
hasTopBorder() - Method in class AFLPgui.Bar: Tells whether or not this bar has a top border.
height - Variable in class AFLPcore.TracePoint: The intensisty of the trace corresponding to the location
HEIGHT - Static variable in class AFLPcore.Cutoff
helpFile - Variable in class AFLPcore.Operation
helpItem - Variable in class AFLPgui.FragmentMap
HighestPeakLocate - class AFLPcore.HighestPeakLocate.: This class can be used to find peaks in lanes.
HighestPeakLocate() - Constructor for class AFLPcore.HighestPeakLocate: Creats a new peak locating class that finds the highest value in a range and calls it a peak.
homePath - Static variable in class AFLPcore.ProgOptions: This is the path that points to the program directory.
HORZ_INSET - Static variable in class AFLPgui.ButtonBar
HORZ_SPACE - Static variable in class AFLPgui.ButtonBar

I

image - Variable in class AFLPgui.ImgButton
ImgButton - class AFLPgui.ImgButton.: A button with an image on it.
ImgButton(Image) - Constructor for class AFLPgui.ImgButton: Creates a new ImgButton with the specified image.
importDialog - Variable in class AFLPgui.FragmentMap
ImportFilter - class AFLPcore.ImportFilter.: This is an abstract class that should be extended to create filters that read data from files.
ImportFilter() - Constructor for class AFLPcore.ImportFilter
importItem - Variable in class AFLPgui.FragmentMap
ImportMgr - class AFLPcore.ImportMgr.: This class contains a list of ImportFilters which can be used to read in different files.
ImportMgr() - Constructor for class AFLPcore.ImportMgr: Creates a new ImportManager, with a default capacity of 4 and a loadFactor of 1.0.
ImportMgr(int, float) - Constructor for class AFLPcore.ImportMgr: Creates a new ImportManager with the specified values.
include(SortableData) - Method in class AFLPcore.DataList: Places the given data in the list so that the order of the list is maintained.
infoBar - Variable in class AFLPgui.FragmentMap
init() - Method in class AFLPgui.Thumbnail: Performs calculations neccessary to display the thumbnails.
init(Bin, DataList, DataList) - Method in class AFLPgui.GraphView: Initialize the graph view.
init(Cutoff, DataList, double) - Method in class AFLPgui.CutoffDialog: Initializes the CutoffDialog with important information.
init(DataList) - Method in class AFLPcore.SizeFunction: This should be used to initialize the sizing function with a set of known peaks.
init(DataList) - Method in class AFLPcore.NoSize: Since this class does not really perform any sizing and instead just assumes that size=scan#, there is no need to initialize it with known points.
init(DataList) - Method in class AFLPcore.LocalSouthern: This takes a list of peaks with the location containing the size in base pairs, and the AREA must contain the scan number of that peak.
init(Gel) - Method in class AFLPgui.AnalysisView: This runs whatever analysis operation is selected, or the default if none has been choosen yet.
init(Lane, DataList) - Method in class AFLPgui.TraceView: Sets the trace to the specified lane and sets the scales.
insertIndex - Variable in class AFLPcore.SearchReturn: The position where the value would go if it is not in the list
invert() - Method in class AFLPcore.ScoreFunction: Changes the score method so that the scoring is opposite of the normal scoring, for example, A becomes B and B becomes A.
invert() - Method in class AFLPcore.SegregatingScore: This switches the labels that will be used to there opposite.
isCanceled() - Method in class AFLPgui.OptionDialog: Tells whether the dialog was canceled or not.
isMarked() - Method in class AFLPcore.Peak: Tells whether or not this peak is marked.
isMultiBin() - Method in class AFLPcore.BinOperation: Tells wether the this operation supports a single bin, or a multi-bin operation.
isRequired() - Method in class AFLPcore.Option: Tells whether or not this option is required by an Operation
isScored() - Method in class AFLPcore.Bin: Used to tell whether or not the score method has been called on this bins current configuration.
isSet() - Method in class AFLPcore.Option: Tells whether or not this option has been set to a value.
isSizeSet() - Method in class AFLPgui.GelView
itemStateChanged(ItemEvent) - Method in class AFLPgui.AnalysisView: Called to handle item events.
itemStateChanged(ItemEvent) - Method in class AFLPgui.CutoffDialog: Loads the selected function when something in the list is changed.
itemStateChanged(ItemEvent) - Method in class AFLPgui.GraphView: Changes the graph to the one selected in the choice box.
itemStateChanged(ItemEvent) - Method in class AFLPgui.BinDialog: This handles events generated when the list is manipulated or when the check box is changed.
itemStateChanged(ItemEvent) - Method in class AFLPgui.GelView: Handle events for the choice box, which adjusts the zoom.

K

keyPressed(KeyEvent) - Method in class AFLPgui.EntryDialog: Unused
keyPressed(KeyEvent) - Method in class AFLPgui.CutoffDialog: Unused
keyPressed(KeyEvent) - Method in class AFLPgui.BinDialog: Unused
keyPressed(KeyEvent) - Method in class AFLPgui.GelView: Unused
keyReleased(KeyEvent) - Method in class AFLPgui.EntryDialog: This mehtod does do things: look for the Enter key and add the '%' sign.
keyReleased(KeyEvent) - Method in class AFLPgui.CutoffDialog: Used to store the info when enter is pressed in the text field.
keyReleased(KeyEvent) - Method in class AFLPgui.BinDialog: This is used to cause the dialog box to store changes made when the Enter key is pushed in one of the fields.
keyReleased(KeyEvent) - Method in class AFLPgui.GelView: Watches for the enter key to be pushed in a text field, and then refreshes the gel when it is.
keyTyped(KeyEvent) - Method in class AFLPgui.EntryDialog: Unused
keyTyped(KeyEvent) - Method in class AFLPgui.CutoffDialog: Unused
keyTyped(KeyEvent) - Method in class AFLPgui.BinDialog: Unused
keyTyped(KeyEvent) - Method in class AFLPgui.GelView: Unused

L

LABEL - Static variable in class AFLPcore.Option
Lane - class AFLPcore.Lane.: This class represents a lane.
LANE - Variable in class AFLPcore.ImportFilter: constant to determine type of file filter is used on
Lane(double[]) - Constructor for class AFLPcore.Lane: Create a new lane with the specified trace.
laneAt(int) - Method in class AFLPcore.Gel: Gives the lane at the specified index.
laneDeleteItem - Variable in class AFLPgui.FragmentMap
LaneOperation - class AFLPcore.LaneOperation.: This is an abstract class that represents operations on a set of Lanes.
LaneOperation() - Constructor for class AFLPcore.LaneOperation
laneOpItem - Variable in class AFLPgui.FragmentMap
LaneOpMgr - class AFLPcore.LaneOpMgr.: This class contains a list of LaneOperations which can be used to read in different files.
LaneOpMgr() - Constructor for class AFLPcore.LaneOpMgr: Creates a new LaneOpMgr, with a default capacity of 4 and a loadFactor of 1.0.
LaneOpMgr(int, float) - Constructor for class AFLPcore.LaneOpMgr: Creates a new LaneOpMgr with the specified values.
LinearCutoff - class AFLPcore.LinearCutoff.: This cutoff function represents a horizontal line.
LinearCutoff() - Constructor for class AFLPcore.LinearCutoff: Creates a new linear function with the value specified in value.
ListNotSearchableError - error AFLPcore.ListNotSearchableError.: Thrown when a list cannot be sorted or searched.
ListNotSearchableError() - Constructor for class AFLPcore.ListNotSearchableError: Constructs a ListNotSearchableError with no detailed message.
ListNotSearchableError(String) - Constructor for class AFLPcore.ListNotSearchableError: Constructs a ListNotSearchableError with the specified detailed message.
LocalSouthern - class AFLPcore.LocalSouthern.: This class implements the Local Southern sizing method described by E.M.
LocalSouthern() - Constructor for class AFLPcore.LocalSouthern
location - Variable in class AFLPcore.TracePoint: The size in bp
location - Variable in class AFLPcore.SearchReturn: The location of value in a list

M

mainPanel - Variable in class AFLPgui.FragmentMap
Manager - class AFLPcore.Manager.: This class contains a list of Operations which can be used to perform different functions in the program.
Manager() - Constructor for class AFLPcore.Manager: Creates a new Manager, with a default capacity of 4 and a loadFactor of 1.0.
Manager(int, float) - Constructor for class AFLPcore.Manager: Creates a new Manager with the specified values.
MapMakerAnalysis - class AFLPcore.MapMakerAnalysis.: This class is an AnalysisOp which outputs information about all of the bins in the gel.
MapMakerAnalysis() - Constructor for class AFLPcore.MapMakerAnalysis: Creates a new MapMakerAnalysis object.
MAX - Static variable in class AFLPcore.PeakLocate: Specifies the largest value in a lane is to be used.
MIN - Static variable in class AFLPcore.PeakLocate: Specifies the smallest value in a lane is to be used.
MissingParameterError - error AFLPcore.MissingParameterError.: Thrown to indicate that a method does not have all of the required parameters to run.
MissingParameterError() - Constructor for class AFLPcore.MissingParameterError: Constructs a MissingParameterError with no detailed message.
MissingParameterError(String) - Constructor for class AFLPcore.MissingParameterError: Constructs a MissingParameterError with the specified detailed message.
modified - Variable in class AFLPgui.FragmentMap
mouseClicked(MouseEvent) - Method in class AFLPgui.CutoffSlider: Handles the mouse clicks.
mouseClicked(MouseEvent) - Method in class AFLPgui.Thumbnail: Adjusts the scoring for a lane if the mouse is over the trace.
mouseClicked(MouseEvent) - Method in class AFLPgui.ImgButton: Unused
mouseClicked(MouseEvent) - Method in class AFLPgui.GraphView: Unused
mouseClicked(MouseEvent) - Method in class AFLPgui.GelView: Handle the click of the mouse.
mouseDragged(MouseEvent) - Method in class AFLPgui.CutoffSlider: If the mouse is over an arrow, it moves the associated function to the new location.
mouseDragged(MouseEvent) - Method in class AFLPgui.Thumbnail: Refreshes the display if the mouse is on the slider.
mouseDragged(MouseEvent) - Method in class AFLPgui.GraphView: Called when the mouse is dragged.
mouseDragged(MouseEvent) - Method in class AFLPgui.GelView: Handle the dragging of the mouse.
mouseEntered(MouseEvent) - Method in class AFLPgui.CutoffSlider: Unused
mouseEntered(MouseEvent) - Method in class AFLPgui.Thumbnail: Unused
mouseEntered(MouseEvent) - Method in class AFLPgui.ImgButton: Unused
mouseEntered(MouseEvent) - Method in class AFLPgui.GraphView: Unused
mouseEntered(MouseEvent) - Method in class AFLPgui.GelView: Don't care about this event.
mouseExited(MouseEvent) - Method in class AFLPgui.CutoffSlider: Unused
mouseExited(MouseEvent) - Method in class AFLPgui.Thumbnail: Unused
mouseExited(MouseEvent) - Method in class AFLPgui.ImgButton: Moves the image position back to it's normal state.
mouseExited(MouseEvent) - Method in class AFLPgui.GraphView: Unused
mouseExited(MouseEvent) - Method in class AFLPgui.GelView: Don't care about this event.
mouseMoved(MouseEvent) - Method in class AFLPgui.CutoffSlider: Determines if the mouse is over an arrow or a blank spot.
mouseMoved(MouseEvent) - Method in class AFLPgui.Thumbnail: Determines what the mouse is over and displays info in the info bar.
mouseMoved(MouseEvent) - Method in class AFLPgui.GraphView: Unused
mouseMoved(MouseEvent) - Method in class AFLPgui.GelView: Handle moving the mouse.
mouseOverType(int, int) - Method in class AFLPgui.GelView: Determines what the mouse is pointing to.
mousePressed(MouseEvent) - Method in class AFLPgui.CutoffSlider: Unused
mousePressed(MouseEvent) - Method in class AFLPgui.Thumbnail: Unused
mousePressed(MouseEvent) - Method in class AFLPgui.ImgButton: Shifts the image position down and to the right.
mousePressed(MouseEvent) - Method in class AFLPgui.GraphView: Unused
mousePressed(MouseEvent) - Method in class AFLPgui.GelView: Handle the event of the mouse button being pressed.
mouseReleased(MouseEvent) - Method in class AFLPgui.CutoffSlider: Unused
mouseReleased(MouseEvent) - Method in class AFLPgui.Thumbnail: Rescores the bin if the mouse was on the slider.
mouseReleased(MouseEvent) - Method in class AFLPgui.ImgButton: Moves the image position back to it's normal state.
mouseReleased(MouseEvent) - Method in class AFLPgui.GraphView: Called when the mouse is released.
mouseReleased(MouseEvent) - Method in class AFLPgui.GelView: Handle the event of the mouse button being released.
MultiFileDialog - class AFLPgui.MultiFileDialog.: This class allows the user to select multiple files.
MultiFileDialog(Frame) - Constructor for class AFLPgui.MultiFileDialog: Creates a new dialog with the specified parameters
MultiFileDialog(Frame, String) - Constructor for class AFLPgui.MultiFileDialog: Creates a new dialog with the specified parameters

N

name - Variable in class AFLPcore.Operation
newButton - Variable in class AFLPgui.FragmentMap
newItem - Variable in class AFLPgui.FragmentMap
nextLine(BufferedReader) - Static method in class AFLPcore.ProgOptions: Gets a line from the specified input stream.
nextLine(BufferedReader) - Static method in class AFLPcore.FeatureList: Gets a line from the specified input stream.
NoBrowserException - error AFLPcore.NoBrowserException.: Thrown to indicate that the browser needed to display the program help could not be found or accessed.
NoBrowserException() - Constructor for class AFLPcore.NoBrowserException: Constructs a NoBrowserException with no detailed message.
NoBrowserException(String) - Constructor for class AFLPcore.NoBrowserException: Constructs a NoBrowserException with the specified detailed message.
NoDataError - error AFLPcore.NoDataError.: Thrown to indicate that the data required to perform a function was not present.
NoDataError() - Constructor for class AFLPcore.NoDataError: Constructs a NoDataError with no detailed message.
NoDataError(String) - Constructor for class AFLPcore.NoDataError: Constructs a NoDataError with the specified detailed message.
NORMALIZED - Static variable in class AFLPcore.Lane: Constant to tell which type of trace the lane is using.
NoSize - class AFLPcore.NoSize.: This class will not provide any sizing.
NoSize() - Constructor for class AFLPcore.NoSize: Create a new NoSize object, which will just use scan numbers as the size.
NUMBER - Static variable in class AFLPcore.Option

O

openButton - Variable in class AFLPgui.FragmentMap
openItem - Variable in class AFLPgui.FragmentMap
Operation - class AFLPcore.Operation.: This is an abstract class that should be extended to add functionality to the program.
Operation() - Constructor for class AFLPcore.Operation
Option - class AFLPcore.Option.: This class provides a way for other class to specify options and parameters.
Option(String, int, boolean) - Constructor for class AFLPcore.Option
Option(String, int, boolean, int) - Constructor for class AFLPcore.Option: Create a new option of the specified type with the specified label.
Option(String, int, boolean, String) - Constructor for class AFLPcore.Option: Create a new option of the specified type with the specified label.
Option(String, int, boolean, String[]) - Constructor for class AFLPcore.Option: Create a new option of the specified type with the specified label.
Option(String, int, boolean, String[], String) - Constructor for class AFLPcore.Option: Create a new option of the specified type with the specified label.
OptionDialog - class AFLPgui.OptionDialog.: This class will display options in a dialog box.
OptionDialog(Option[], Frame) - Constructor for class AFLPgui.OptionDialog: Creates a new option dialog with the specified parameters.
OptionDialog(Option[], Frame, String) - Constructor for class AFLPgui.OptionDialog: Creates a new option dialog with the specified parameters
options - Variable in class AFLPcore.Operation
ORIGINAL - Static variable in class AFLPcore.Lane: Constant to tell which type of trace the lane is using.
overType(int, int) - Method in class AFLPgui.CutoffSlider: Determines if the given point is in a blank area or in an arrow.

P

paint(Graphics) - Method in class AFLPgui.CutoffSlider: Draws a bar with arrows at the different cutoff levels.
paint(Graphics) - Method in class AFLPgui.TraceView: Draws the trace to the specified graphics.
paint(Graphics) - Method in class AFLPgui.Thumbnail: Draws the thumbnails.
paint(Graphics) - Method in class AFLPgui.Bar: This method is used to draw the border and then it calls the paint method of the super so components get drawn properly.
paint(Graphics) - Method in class AFLPgui.ImgButton: Draws the button.
paint(Graphics) - Method in class AFLPgui.ControlBar: Draws a verical line down the right side.
paint(Graphics) - Method in class AFLPgui.AnalysisView: This is used to resize the text area.
paint(Graphics) - Method in class AFLPgui.GraphView: Draws the graph.
paint(Graphics) - Method in class AFLPgui.GelView: Manages the display area and is called automatically when needed.
PartialSigNorm - class AFLPcore.PartialSigNorm.: This class normalizes a gel.
PartialSigNorm() - Constructor for class AFLPcore.PartialSigNorm: Creates a new PartialSigNorm object.
Peak - class AFLPcore.Peak.: This class represents a peak.
Peak(double, double, double) - Constructor for class AFLPcore.Peak: Creates a new peak with the specified parameters.
PeakLocate - class AFLPcore.PeakLocate.: This is an abstract class that should be extended to provide different ways of finding the peaks in a lane.
PeakLocate() - Constructor for class AFLPcore.PeakLocate
PeakMgr - class AFLPcore.PeakMgr.: This class contains a list of PeakLocates which can be used to find peaks in the lanes/gel.
PeakMgr() - Constructor for class AFLPcore.PeakMgr: Creates a new PeakMgr, with a default capacity of 4 and a loadFactor of 1.0.
PeakMgr(int, float) - Constructor for class AFLPcore.PeakMgr: Creates a new PeakMgr with the specified values.
PrettyInsignificantError - error AFLPcore.PrettyInsignificantError.: Thrown to indicate that a miscellanious error has run, but nothing that might harm the running of the program.
PrettyInsignificantError() - Constructor for class AFLPcore.PrettyInsignificantError: Constructs a MissingParameterError with no detailed message.
PrettyInsignificantError(String) - Constructor for class AFLPcore.PrettyInsignificantError: Constructs a MissingParameterError with the specified detailed message.
printButton - Variable in class AFLPgui.FragmentMap
printItem - Variable in class AFLPgui.FragmentMap
printString(String, Graphics) - Method in class AFLPgui.TextPrinter: Prints the given string to the destination of the print job given in the constructor.
ProgOptions - class AFLPcore.ProgOptions.: This class contains static methods and variables that provide several features to the program.
ProgOptions() - Constructor for class AFLPcore.ProgOptions

R

RawView - class AFLPcore.RawView.: This class resets the display so that the original data is used instead of normalized data.
RawView() - Constructor for class AFLPcore.RawView: Creates a new RawView object.
read(DataInputStream) - Method in class AFLPcore.Gel: Reads in the properties of this class from the specified input stream.
read(DataInputStream) - Method in class AFLPcore.SizeFunction: Reads in the properties of this class from the specified input stream.
read(DataInputStream) - Method in class AFLPcore.NoSize: Reads in the properties of this class from the specified input stream.
read(DataInputStream) - Method in class AFLPcore.ScoreFunction: Reads in the properties of this class from the specified input stream.
read(DataInputStream) - Method in class AFLPcore.CutoffFunction: Reads in the properties of this class from the specified input stream.
read(DataInputStream) - Method in class AFLPcore.LinearCutoff: Reads in the properties of this class from the specified input stream.
read(DataInputStream) - Method in class AFLPcore.Lane: Reads in the properties of this class from the specified input stream.
read(DataInputStream) - Method in class AFLPcore.Peak: Reads in the properties of this class from the specified input stream.
read(DataInputStream) - Method in class AFLPcore.Cutoff: Reads in the properties of this class from the specified input stream.
read(DataInputStream) - Method in class AFLPcore.Bin: Reads in the properties of this class from the specified input stream.
read(DataInputStream) - Method in class AFLPcore.SegregatingScore: Reads in the properties of this class from the specified input stream.
read(DataInputStream) - Method in class AFLPcore.LocalSouthern: Reads in the properties of this class from the specified input stream.
readFile(String) - Method in class AFLPgui.FragmentMap: Reads the specified file in to the program.
readGel(File) - Method in class AFLPcore.ImportFilter: This is the method that is called to preform the actual reading of the file.
readGel(File) - Method in class AFLPcore.SCFFilter: This filter does not read gels.
readGel(File) - Method in class AFLPcore.CEQLaneFilter: This filter does not read gels.
readGel(File) - Method in class AFLPcore.ABILaneFilter: This filter does not read gels.
readGel(File) - Method in class AFLPcore.ABI3x00Filter: This filter does not read gels.
readLane(File) - Method in class AFLPcore.ImportFilter: This is the method that is called to preform the actual reading of the file.
readLane(File) - Method in class AFLPcore.SCFFilter: This is the method that is called to preform the actual reading of the file.
readLane(File) - Method in class AFLPcore.CEQLaneFilter: Read the data from the file and use it to create a Lane.
readLane(File) - Method in class AFLPcore.ABILaneFilter: This is the method that is called to preform the actual reading of the file.
readLane(File) - Method in class AFLPcore.ABI3x00Filter: This is the method that is called to preform the actual reading of the file.
readOptions() - Static method in class AFLPcore.ProgOptions: Reads in the options form the configuration file.
readPeak(RandomAccessFile) - Method in class AFLPcore.ABILaneFilter: Read in a peak from the file.
readPeak(RandomAccessFile) - Method in class AFLPcore.ABI3x00Filter: Read in a peak from the file.
rebuild() - Method in class AFLPgui.GelView: Recreates the gel image from the data.
RED - Static variable in class AFLPcore.SCFFilter: color channel
RED - Static variable in class AFLPcore.CEQLaneFilter
RED - Static variable in class AFLPcore.ABILaneFilter: color channel
RED - Static variable in class AFLPcore.Lane: Constant for lane color
RED - Static variable in class AFLPcore.ABI3x00Filter: color channel
refresh() - Method in class AFLPgui.CutoffSlider: Causes any changes in the underlying data to be shown on the screen.
refresh() - Method in class AFLPgui.TraceView: Update the display so that it matches the data.
refresh() - Method in class AFLPgui.Thumbnail: Updates the display so that it matches the data, which may have changed.
refresh() - Method in class AFLPgui.GraphView: Updates the display so that it matches the data.
refresh(boolean) - Method in class AFLPgui.GelView: Called when the image on screen should be redrawn.
removeBin(Bin) - Method in class AFLPcore.Gel: Removes the specified bin from the list of bins for this gel.
removeFile(int) - Method in class AFLPgui.MultiFileDialog: Removes the specified file from the list of files to open/import.
removeLane(Lane) - Method in class AFLPcore.Gel
retrieve(String) - Static method in class AFLPcore.ProgOptions: Gives the value of a parameter specified in the input file.
retrieveImage(String) - Static method in class AFLPgui.ButtonBar: Get an image from the specified file.

S

saveAsItem - Variable in class AFLPgui.FragmentMap
saveButton - Variable in class AFLPgui.FragmentMap
saveItem - Variable in class AFLPgui.FragmentMap
ScanCalcError - error AFLPcore.ScanCalcError.: Thrown to indicate that a method cannot determine the scan number from a given size.
ScanCalcError() - Constructor for class AFLPcore.ScanCalcError: Constructs a ScanCalcError with no detailed message.
ScanCalcError(String) - Constructor for class AFLPcore.ScanCalcError: Constructs a ScanCalcError with the specified detailed message.
ScatterGraph - class AFLPgui.ScatterGraph.: This class provides a way to draw a graph on a graphics object.
ScatterGraph() - Constructor for class AFLPgui.ScatterGraph: Creates a new graph where those lanes with one peak in the defined region will be black and those with more than one peak will be red.
ScatterGraph(Color, Color) - Constructor for class AFLPgui.ScatterGraph: Creates a new graph with the specified parameters.
SCFFilter - class AFLPcore.SCFFilter.: This class reads data from an SCF file, which are fairly common.
SCFFilter() - Constructor for class AFLPcore.SCFFilter: CONSTRUCTOR for new SCFFilter.
score(Cutoff, DataList) - Method in class AFLPcore.ScoreFunction: Gives a label for a lane with the specified cutoff and the specified peaks.
score(Cutoff, DataList) - Method in class AFLPcore.SegregatingScore: Scores a lane by seeing if any of the peaks cross the highest cutoff, and then labeling it appropriately.
score(DataList) - Method in class AFLPcore.Bin: Scores this bin using the scoring method set and the lanes specified.
ScoreFunction - class AFLPcore.ScoreFunction.: This class represents functions used to score a bin.
ScoreFunction() - Constructor for class AFLPcore.ScoreFunction
ScoreManager - class AFLPcore.ScoreManager.: This class contains a list of ScoreFunctions which can be used to score a bin in different ways.
ScoreManager() - Constructor for class AFLPcore.ScoreManager: Creates a new ScoreManager, with a default capacity of 4 and a loadFactor of 1.0.
ScoreManager(int, float) - Constructor for class AFLPcore.ScoreManager: Creates a new ScoreManager with the specified values.
scoreOverall(DataList) - Method in class AFLPcore.Bin: Sets the overall scoring information for the bin.
ScoringFailure - error AFLPcore.ScoringFailure.: Thrown to indicate that the scoring function could not function properly.
ScoringFailure() - Constructor for class AFLPcore.ScoringFailure: Constructs a ScoringFailure with no detailed message.
ScoringFailure(String) - Constructor for class AFLPcore.ScoringFailure: Constructs a ScoringFailure with the specified detailed message.
SearchReturn - class AFLPcore.SearchReturn.: This class contains a pair of values used in searches.
SegregatingScore - class AFLPcore.SegregatingScore.: This scores each bin by assigning different labels to the differnet cutoff regions.
SegregatingScore() - Constructor for class AFLPcore.SegregatingScore: Creates a new segregating score function.
sendActionEventsTo(ActionListener) - Method in class AFLPgui.ButtonBar: Sets the specified target so that it recieves action events from the four buttons.
set(double, double, double) - Method in class AFLPcore.Peak: Changes this peak so that the location, height, and size are set to the values given.
setBackGroundColor(int) - Method in class AFLPcore.Gel: Set the background color to the specified value.
setBin(Bin) - Method in class AFLPgui.Thumbnail: Sets the bin for the thumbnails to the specified one.
setBinList(DataList) - Method in class AFLPgui.Thumbnail: Sets the bins for the thumbnail.
setBins(DataList) - Method in class AFLPgui.BinDialog: The bins to display.
setBorders(boolean, boolean) - Method in class AFLPgui.Bar: Sets the borders for the bar.
setColor(int) - Method in class AFLPcore.Lane: Set the color channel used with this lane to the specified value.
setConfidence(double) - Method in class AFLPcore.Peak: Sets the confidence to the specified value.
setCurrentBin(Bin) - Method in class AFLPgui.GelView: Sets the selection to the specified bin.
setCutoff(Cutoff) - Method in class AFLPgui.CutoffSlider: Sets the cutoff that this slider is based on.
setCutoffFunction(CutoffFunction, int) - Method in class AFLPcore.Cutoff: Sets the cutoff function for the specified level.
setDefault(String) - Method in class AFLPcore.Manager: Sets the default operation to the one specified.
setFunction(int, int) - Method in class AFLPgui.CutoffSlider: Adjusts the cutoff function at level so that it's height matches the height represented by pos.
setGelLength(int) - Method in class AFLPgui.GelView: Set the length of the gel image to the specified value.
setGelName(String) - Method in class AFLPcore.Lane: Set the name of the gel that the lane was on to the specified value.
setGelSizeToMax(int) - Method in class AFLPgui.GelView
setGelTopBorder(int) - Method in class AFLPcore.Gel: Sets the border on the top and bottom of the gel image to the specified value.
setGraphWidth(int) - Method in class AFLPgui.GraphView: Sets the width of the actual graph, which does not include the border.
setHeight(int) - Method in class AFLPgui.TraceView: Sets the height of the trace, including borders to the specified value.
setHeight(int) - Method in class AFLPgui.GraphView: Sets the height of the graph display area, including borders, to the specified value.
setIntensity(double) - Method in class AFLPcore.Gel: Sets the intensity to the specified value.
setLaneBorder(int) - Method in class AFLPcore.Gel: Sets the spacing between lanes as well as the left and right border on the gel image.
setLaneNumber(int) - Method in class AFLPcore.Lane: Set the lane number of this lane to the specified value.
setLanes(DataList) - Method in class AFLPgui.CutoffSlider: Sets the lanes known to the cutoff.
setLanes(DataList) - Method in class AFLPgui.Thumbnail: Sets the lanes for which to display thumbnails to the specified value.
setLaneWidth(int) - Method in class AFLPcore.Gel: Sets the width of a lane in the gel image.
setLocation(double) - Method in class AFLPcore.Bin: Sets the position/location of this bin to the one specified.
setMarkedState(boolean) - Method in class AFLPcore.Peak: Sets the peak as specified.
setMaxScan(int) - Method in class AFLPcore.SizeFunction: Sets the maximum scan number to be returned to the specified value.
setMaxScan(int) - Method in class AFLPcore.NoSize: This class simply interprests the size number as the scan number, so the maximum scan number is not really needed.
setMaxScan(int) - Method in class AFLPcore.LocalSouthern: Sets the maximum scan number to the specified value.
setMaxSize(double) - Method in class AFLPcore.Gel: Sets the largest size that will be included in the gel image when it is produced.
setMinSize(double) - Method in class AFLPcore.Gel: Sets the smallest size that will be included in the gel image when it is produced.
setMode(int) - Method in class AFLPcore.Cutoff: Sets the cutoff so that it applies either to peak height or to peak area.
setName(String) - Method in class AFLPcore.Lane: Set the name of the sample run on this lane to the specified string.
setName(String) - Method in class AFLPcore.Bin: Sets the name of the bin to the specified value.
setNormTrace(double[]) - Method in class AFLPcore.Lane: Set the normalized trace to the specified trace.
setOptions(Option[]) - Method in class AFLPcore.Operation: This is used to set the options to the specified values.
setOptions(Option[]) - Method in class AFLPcore.NoSize: Since there are no options, this method doesn't do much.
setOptions(Option[]) - Method in class AFLPcore.SignalNorm: Since there are no options for this operation, this method will do absolutely nothing.
setOptions(Option[]) - Method in class AFLPcore.SizeStandard: Defined to satisfy abstract parent class, but not really applicable in this case.
setOptions(Option[]) - Method in class AFLPcore.SCFFilter: Sets the parameters for the filter to the specified values.
setOptions(Option[]) - Method in class AFLPcore.LinearCutoff: Set the value for the cutoff.
setOptions(Option[]) - Method in class AFLPcore.CEQLaneFilter: Sets the parameters for the filter to the specified values, including color.
setOptions(Option[]) - Method in class AFLPcore.ABILaneFilter: Sets the parameters for the filter to the specified values, including color.
setOptions(Option[]) - Method in class AFLPcore.BinAnalysis: Since there are no options for this operation, this method will do absolutely nothing.
setOptions(Option[]) - Method in class AFLPcore.PartialSigNorm: Since there are no options for this operation, this method will do absolutely nothing.
setOptions(Option[]) - Method in class AFLPcore.SegregatingScore: Sets the option to the specified values.
setOptions(Option[]) - Method in class AFLPcore.HighestPeakLocate: Since this operations does not have any options, the method does not do anything.
setOptions(Option[]) - Method in class AFLPcore.RawView: Since there are no options for this operation, this method will do absolutely nothing.
setOptions(Option[]) - Method in class AFLPcore.ABI3x00Filter: Sets the parameters for the filter to the specified values, including color.
setOptions(Option[]) - Method in class AFLPcore.MapMakerAnalysis: Since there are no options for this operation, this method will do absolutely nothing.
setOptions(Option[]) - Method in class AFLPcore.LocalSouthern: Since there are no options, this method doesn't do much.
setRange(double) - Method in class AFLPcore.Bin: Sets the range of the bin to the specified value.
setScale(double) - Method in class AFLPgui.CutoffSlider: Sets the scale for the cutoff slider.
setScore(boolean) - Method in class AFLPcore.Bin: Sets the bin so that the current scoring is either accepted as valid or invalidated.
setScore(Lane, String) - Method in class AFLPcore.Bin: Changes the scoring for the specified lane.
setScoreMethod(ScoreFunction) - Method in class AFLPcore.Bin: Sets the scoring method to the one specified.
setSize(double) - Method in class AFLPgui.CutoffSlider: This determines where the cutoff should be applied in the lanes.
setSizeFunction(SizeFunction) - Method in class AFLPcore.Lane: Set the size curve/function to be used by this lane.
setStartPos(double) - Method in class AFLPcore.Cutoff: Adjusts the starting position.
setValue(double) - Method in class AFLPcore.Option: Sets the numerical value of this option to the specified value.
setValue(String) - Method in class AFLPcore.Option: Sets the string value of this option to the specified value.
setViewWidth(int) - Method in class AFLPgui.Thumbnail: Sets the width of the display area.
setVisible(boolean) - Method in class AFLPgui.MultiFileDialog: Controls the visibility of this dialog.
setVisible(boolean) - Method in class AFLPgui.CutoffDialog: Shows or hides this dialog box.
setVisible(boolean) - Method in class AFLPgui.BinDialog: Controls wether or not the dialog box is visible.
setWidth(int) - Method in class AFLPgui.TraceView: Sets the width of the trace, including borders, to the specified value.
setWidth(int) - Method in class AFLPgui.GraphView: Sets the width of the graph display area, including borders, to the specified value.
showAbout() - Method in class AFLPgui.FragmentMap: Displays an about dialog box for the program.
showHelp(String) - Static method in class AFLPcore.ProgOptions: This displays the specified helpfile in a web browser.
SignalNorm - class AFLPcore.SignalNorm.: This class normalizes a gel.
SignalNorm() - Constructor for class AFLPcore.SignalNorm: Creates a new SignalNorm object.
SizeFunction - class AFLPcore.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.
SizeFunction() - Constructor for class AFLPcore.SizeFunction
SizeMgr - class AFLPcore.SizeMgr.: This class contains a list of SizeFunctions which can be used to size a lane.
SizeMgr() - Constructor for class AFLPcore.SizeMgr: Creates a new SizeMgr, with a default capacity of 4 and a loadFactor of 1.0.
SizeMgr(int, float) - Constructor for class AFLPcore.SizeMgr: Creates a new SizeMgr with the specified values.
SizeStandard - class AFLPcore.SizeStandard.: This class is used to define a size standard.
SortableData - class AFLPcore.SortableData.: This class allows subclasses that extend it to be sorted into an order.
SortableData() - Constructor for class AFLPcore.SortableData
StandardMgr - class AFLPcore.StandardMgr.: This class contains a list of SizeStandards which define different size standards.
StandardMgr() - Constructor for class AFLPcore.StandardMgr: Creates a new StandardMgr, with a default capacity of 4 and a loadFactor of 1.0.
StandardMgr(int, float) - Constructor for class AFLPcore.StandardMgr: Creates a new StandardMgr with the specified values.
statusBar - Variable in class AFLPgui.FragmentMap
statusLabel - Variable in class AFLPgui.FragmentMap
storeInfo(int) - Method in class AFLPgui.CutoffDialog: Reads in the height from the text field and stores it into the cutoff.
storeInfo(int) - Method in class AFLPgui.BinDialog: This will read in the values from the display and store them appropriatly.
STRING - Static variable in class AFLPcore.Option: Constant for denoting option type
switchTo(String) - Method in class AFLPgui.FragmentMap: Change the program display so that it displays the type specified.
syncDisplay() - Method in class AFLPgui.GelView

T

TextPrinter - class AFLPgui.TextPrinter.: This class will take a printjob and a string and print that string to the printer, wrapping lines that are to long and moving to a new page when neccessary.
TextPrinter(PrintJob) - Constructor for class AFLPgui.TextPrinter: Creates a new textprinter with a font of Sans Serif, 12pt.
thumbnail - Variable in class AFLPgui.FragmentMap
Thumbnail - class AFLPgui.Thumbnail.: This class displays thumbnails for a bin.
THUMBNAIL - Static variable in class AFLPgui.FragmentMap
Thumbnail(DataList, DataList, Frame) - Constructor for class AFLPgui.Thumbnail: Creates thumbnails with the specified parameters.
toggleSelectedLane(Lane) - Method in class AFLPcore.Gel: Changes the selection state of the specified lane.
trace - Variable in class AFLPgui.FragmentMap
TRACE - Static variable in class AFLPgui.Thumbnail
TRACE - Static variable in class AFLPgui.FragmentMap
TracePeakFinder - class AFLPcore.TracePeakFinder.: This is a simple algorithm that is used to find peaks in a set of trace data.
TracePeakFinder() - Constructor for class AFLPcore.TracePeakFinder
TracePoint - class AFLPcore.TracePoint.: Represents a point on the trace, in the form (size, height).
TracePoint() - Constructor for class AFLPcore.TracePoint: Creates a new point (0,0).
TracePoint(double, double) - Constructor for class AFLPcore.TracePoint: Creates a new point at the specified location.
TraceView - class AFLPgui.TraceView.: Displays the trace of a lane.
TraceView(Frame) - Constructor for class AFLPgui.TraceView: Create a new TraceView with the specified parameters.

U

update(Graphics) - Method in class AFLPgui.TraceView: Called by JVM to refresh screen, but it simply calls paint.
update(Graphics) - Method in class AFLPgui.Thumbnail: Updates the display and is called by java.
update(Graphics) - Method in class AFLPgui.GraphView: Called to update the screen by Java.
update(Graphics) - Method in class AFLPgui.GelView: Called when the screen needs to be updated.
useTrace(int) - Method in class AFLPcore.Lane: Sets the trace to be used when retrieving height, finding peaks, etc.

V

VERT_INSET - Static variable in class AFLPgui.ButtonBar
viewAnalysisItem - Variable in class AFLPgui.FragmentMap
viewGelItem - Variable in class AFLPgui.FragmentMap
viewGraphItem - Variable in class AFLPgui.FragmentMap
viewThumbnailItem - Variable in class AFLPgui.FragmentMap
viewTraceItem - Variable in class AFLPgui.FragmentMap

W

windowActivated(WindowEvent) - Method in class AFLPgui.OptionDialog: Unused
windowActivated(WindowEvent) - Method in class AFLPgui.MultiFileDialog: Unused
windowActivated(WindowEvent) - Method in class AFLPgui.AboutDialog: Unused
windowActivated(WindowEvent) - Method in class AFLPgui.FragmentMap: Unused
windowActivated(WindowEvent) - Method in class AFLPgui.EntryDialog: Unused
windowActivated(WindowEvent) - Method in class AFLPgui.CutoffDialog: Unused
windowActivated(WindowEvent) - Method in class AFLPgui.BinDialog: Unused
windowClosed(WindowEvent) - Method in class AFLPgui.OptionDialog: Unused
windowClosed(WindowEvent) - Method in class AFLPgui.MultiFileDialog: Unused
windowClosed(WindowEvent) - Method in class AFLPgui.AboutDialog: Unused
windowClosed(WindowEvent) - Method in class AFLPgui.FragmentMap: Unused
windowClosed(WindowEvent) - Method in class AFLPgui.EntryDialog: Unused
windowClosed(WindowEvent) - Method in class AFLPgui.CutoffDialog: Unused
windowClosed(WindowEvent) - Method in class AFLPgui.BinDialog: Unused
windowClosing(WindowEvent) - Method in class AFLPgui.OptionDialog: Closes the dialog and is equivalent to pressing cancel.
windowClosing(WindowEvent) - Method in class AFLPgui.MultiFileDialog: Closes the dialog and is equivalent to clicking cancel.
windowClosing(WindowEvent) - Method in class AFLPgui.AboutDialog: Closes the dialog and is equivalent to clicking ok.
windowClosing(WindowEvent) - Method in class AFLPgui.FragmentMap: exits the program when the window is closed.
windowClosing(WindowEvent) - Method in class AFLPgui.EntryDialog: Closes the window and cancels the dialog box.
windowClosing(WindowEvent) - Method in class AFLPgui.CutoffDialog: Closes the dialog box.
windowClosing(WindowEvent) - Method in class AFLPgui.BinDialog: Allows the window to close and has the same affect as pressing the cancel button.
windowDeactivated(WindowEvent) - Method in class AFLPgui.OptionDialog: Unused
windowDeactivated(WindowEvent) - Method in class AFLPgui.MultiFileDialog: Unused
windowDeactivated(WindowEvent) - Method in class AFLPgui.AboutDialog: Unused
windowDeactivated(WindowEvent) - Method in class AFLPgui.FragmentMap: Unused
windowDeactivated(WindowEvent) - Method in class AFLPgui.EntryDialog: Unused
windowDeactivated(WindowEvent) - Method in class AFLPgui.CutoffDialog: Unused
windowDeactivated(WindowEvent) - Method in class AFLPgui.BinDialog: Unused
windowDeiconified(WindowEvent) - Method in class AFLPgui.OptionDialog: Unused
windowDeiconified(WindowEvent) - Method in class AFLPgui.MultiFileDialog: Unused
windowDeiconified(WindowEvent) - Method in class AFLPgui.AboutDialog: Unused
windowDeiconified(WindowEvent) - Method in class AFLPgui.FragmentMap: Unused
windowDeiconified(WindowEvent) - Method in class AFLPgui.EntryDialog: Unused
windowDeiconified(WindowEvent) - Method in class AFLPgui.CutoffDialog: Unused
windowDeiconified(WindowEvent) - Method in class AFLPgui.BinDialog: Unused
windowIconified(WindowEvent) - Method in class AFLPgui.OptionDialog: Unused
windowIconified(WindowEvent) - Method in class AFLPgui.MultiFileDialog: Unused
windowIconified(WindowEvent) - Method in class AFLPgui.AboutDialog: Unused
windowIconified(WindowEvent) - Method in class AFLPgui.FragmentMap: Unused
windowIconified(WindowEvent) - Method in class AFLPgui.EntryDialog: Unused
windowIconified(WindowEvent) - Method in class AFLPgui.CutoffDialog: Unused
windowIconified(WindowEvent) - Method in class AFLPgui.BinDialog: Unused
windowOpened(WindowEvent) - Method in class AFLPgui.OptionDialog: Unused
windowOpened(WindowEvent) - Method in class AFLPgui.MultiFileDialog: Unused
windowOpened(WindowEvent) - Method in class AFLPgui.AboutDialog: Unused
windowOpened(WindowEvent) - Method in class AFLPgui.FragmentMap: Unused
windowOpened(WindowEvent) - Method in class AFLPgui.EntryDialog: Unused
windowOpened(WindowEvent) - Method in class AFLPgui.CutoffDialog: Unused
windowOpened(WindowEvent) - Method in class AFLPgui.BinDialog: Unused
write(DataOutputStream) - Method in class AFLPcore.Gel: Writes all of the information this class needs to store in order to be recreated.
write(DataOutputStream) - Method in class AFLPcore.SizeFunction: Writes all of the information this class needs to store in order to be recreated.
write(DataOutputStream) - Method in class AFLPcore.NoSize: Writes all of the information this class needs to store in order to be recreated.
write(DataOutputStream) - Method in class AFLPcore.ScoreFunction: Writes all of the information this class needs to store in order to be recreated.
write(DataOutputStream) - Method in class AFLPcore.CutoffFunction: Writes all of the information this class needs to store in order to be recreated.
write(DataOutputStream) - Method in class AFLPcore.LinearCutoff: Writes all of the information this class needs to store in order to be recreated.
write(DataOutputStream) - Method in class AFLPcore.Lane: Writes all of the information this class needs to store in order to be recreated.
write(DataOutputStream) - Method in class AFLPcore.Peak: Writes all of the information this class needs to store in order to be recreated.
write(DataOutputStream) - Method in class AFLPcore.Cutoff: Writes all of the information this class needs to store in order to be recreated.
write(DataOutputStream) - Method in class AFLPcore.Bin: Writes all of the information this class needs to store in order to be recreated.
write(DataOutputStream) - Method in class AFLPcore.SegregatingScore: Writes all of the information this class needs to store in order to be recreated.
write(DataOutputStream) - Method in class AFLPcore.LocalSouthern: Writes all of the information this class needs to store in order to be recreated.
writeFile(String) - Method in class AFLPgui.FragmentMap: Writes the gel out to the specified file name.
writeLane(int[], int, Lane, int, int, double, double) - Method in class AFLPcore.Gel: Writes the specified lane data into the specified pixel array at the given location.
writePNG(DataOutputStream) - Method in class AFLPcore.Gel: Writes the gel image in a PNG format to the specified output stream.
writePPM(DataOutputStream) - Method in class AFLPcore.Gel: Writes the gel image in a PPM format to the specified output stream.

Y

YELLOW - Static variable in class AFLPcore.SCFFilter: color channel - note: these probably only correspond to the channels of an SCF file in an arbitrary way.
YELLOW - Static variable in class AFLPcore.CEQLaneFilter
YELLOW - Static variable in class AFLPcore.ABILaneFilter: color channel
YELLOW - Static variable in class AFLPcore.Lane: Constant for lane color
YELLOW - Static variable in class AFLPcore.ABI3x00Filter: color channel

A B C D E F G H I K L M N O P R S T U V W Y

Overview

Package

Class

Use

Tree

Deprecated

Index

Help

PREV NEXT

FRAMES NO FRAMES