Uses of Class
AFLPcore.DataList

Packages that use DataList

AFLPcore
AFLPgui

Uses of DataList in AFLPcore

Methods in AFLPcore that return DataList

DataList	Gel.getLanes() Gives a list of all of the lanes in the gel.
DataList	Gel.getSelectedLanes() Gives a list of all of the selected lanes in the gel.
DataList	Gel.getBins() Gives a list of all the bins in the gel.
DataList	Lane.getPeaksInRange(double min, double max) Produces a list of peaks that are in the given range.
DataList	Lane.getPeaks() Gives the list of peaks in the lane.
DataList	Lane.getCutoffs() Returns the list of cutoffs associated with this lane.
DataList	DataList.completeClone() Creates a new list that is identical to this one with a completely seperate copy of the data in the list.

Methods in AFLPcore with parameters of type DataList

abstract void	SizeFunction.init(DataList standardPoints) This should be used to initialize the sizing function with a set of known peaks.
void	NoSize.init(DataList standardPeaks) 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.
abstract java.lang.String[]	ScoreFunction.getInfo(java.lang.String[] labels, DataList peaks) Should provide overall information about a bin scored with this method.
abstract java.lang.String	ScoreFunction.score(Cutoff cutoff, DataList peaks) Gives a label for a lane with the specified cutoff and the specified peaks.
void	DataList.copyList(DataList dest) Copies the data in this list to the specified destination.
void	Bin.score(DataList lanes) Scores this bin using the scoring method set and the lanes specified.
void	Bin.scoreOverall(DataList lanes) Sets the overall scoring information for the bin.
java.lang.String	SegregatingScore.score(Cutoff cutoff, DataList peaks) Scores a lane by seeing if any of the peaks cross the highest cutoff, and then labeling it appropriately.
java.lang.String[]	SegregatingScore.getInfo(java.lang.String[] tags, DataList peaks) This returns a set of strings that describes the overall scoring of the bin.
abstract void	PeakLocate.findPeak(DataList lanes, double minSize, double maxSize) 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.
void	HighestPeakLocate.findPeak(DataList lanes, double minSize, double maxSize) Finds a peak in each lane and saves it in the lane.
abstract void	LaneOperation.doLaneOp(DataList lanes) This performs some sort of operation on a set of lanes.
abstract void	BinOperation.doBinOp(DataList bins) This performs some sort of operation on all of the bins
void	LocalSouthern.init(DataList standardPeaks) 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.

Uses of DataList in AFLPgui

Methods in AFLPgui that return DataList

DataList

Thumbnail.getLanes() Gives the lanes that are being displayed.

Methods in AFLPgui with parameters of type DataList

void	CutoffSlider.setLanes(DataList lanes) Sets the lanes known to the cutoff.
void	TraceView.init(Lane ln, DataList lanes) Sets the trace to the specified lane and sets the scales.
void	Thumbnail.setLanes(DataList lanes) Sets the lanes for which to display thumbnails to the specified value.
void	Thumbnail.setBinList(DataList bins) Sets the bins for the thumbnail.
abstract void	Graph.drawGraph(java.awt.Graphics g, int x, int y, int width, int height, int bottom_border, double scale, double minSize, double maxSize, DataList lanes) Draw some sort of graph given the specified parameters.
void	BarGraph.drawGraph(java.awt.Graphics g, int x, int y, int width, int height, int bottom_border, double scale, double minSize, double maxSize, DataList lanes) Draws the graph described in the class description.
protected double	BarGraph.findMax(DataList peakList) Finds the maximum height in a list of peaks.
void	ScatterGraph.drawGraph(java.awt.Graphics g, int x, int y, int width, int height, int bottom_border, double scale, double minSize, double maxSize, DataList lanes) Draw the scatter graph with the specified properties.
protected double	ScatterGraph.findMax(DataList peakList) Gives the maximum height for all of the peaks in the given list.
void	CutoffDialog.init(Cutoff ct, DataList lanes, double startPos) Initializes the CutoffDialog with important information.
void	GraphView.init(Bin bin, DataList lanes, DataList bins) Initialize the graph view.
void	BinDialog.setBins(DataList bins) The bins to display.

Constructors in AFLPgui with parameters of type DataList

Thumbnail(DataList lanes, DataList bins, java.awt.Frame parentWindow)
Creates thumbnails with the specified parameters.

GraphView(DataList lanes, DataList bins, java.awt.Frame parentWindow)
Create a new GraphView with the specified parameters.