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edu.stanford.genetics.treeview.karyoview: Javadoc index of package edu.stanford.genetics.treeview.karyoview.
KaryoPanel: This class encapsulates a dendrogram view, which is the classic Eisen treeview. It uses a drag grid panel to lay out a bunch of linked visualizations of the data, a la Eisen. In addition to laying out components, it also manages the GlobalZoomMap. This is necessary since both the GTRView (gene tree) and GlobalView need to know where to lay out genes using the same map. The zoom map is managed by the ViewFrame- it represents the selected genes, and potentially forms a link between different views, only one of which is the DendroView.
KaryoViewExportPanel: This class is a superclass which implements a GUI for selection of options relating to output. It makes most of the relevant variables accessible to subclasses through protected methods. The chooseable widgets should consist of a - listbox full of chromosomes to choose from initially with just the visible ones chosen. - field values to indicate the x scale and y scale, relative to the current displayed image. - non-editable field values indicating the predicted total size.
KaryoView: This class is a model view that displays the karyoscope view for a single experiment in the dataset. There is really quite a lot of complexity involved. I have decided to factor out all knowledge of where things are positioned into the KaryoDrawer class. I have retained knowledge of averaging in this class, as well as most of the component mechanics. This is to facilitate the use of KaryoDrawer for drawing to images with configurable parameters.
ChromosomeLocus: The purpose of this class is purely to hold information about the location of various loci. It does not hold any exporession data directly, although it hold a unique integer, the cdtIndex, which ought to be used to look up any values in a table.
KaryoExportPanel: This class is a superclass which implements a GUI for selection of options relating to output. It makes most of the relevant variables accessible to subclasses through protected methods.
NeighborAverager: average by neighbors. k must be an odd integer. Returns the average of the locus, the (k-1)/2 loci on the left, and the (k-1)/2 loci on the right.
CoordinatesPresets: This class encapsulates a list of Coordinates presets, which is really just FileSets. This is the class to edit the default presets in...
KaryoColorPresetEditor: This class allows graphical editing of KaryoColorPresets Also included is a class to pop up a configuration window.
CoordinatesPresetEditor: This class allows graphical editing of ColorPresets Also included is a class to pop up a configuration window.
Genome: this class encapsulates the position of things. No expression data or headers or other such nonsense allowed.
ChromosomeLoci: this class encapsulates the position of things. No expression data or headers or other such nonsense allowed.
NearestAverager: average k-nearest neighbors of point. If two points are equally close, an unspecified one will be picked.
KaryoViewParameterPanel: This class graphically represents the state of the KaryoView, and allows the user to muck with it.
KaryoDrawer: This is observable because it signals changes to the drawer it is an observer of the selection.
Averager: this base class doesn't actually average. All other methods should subclass.
GroupAverager: encapsulates routines common to averagers of groups of things
IntervalAverager: average all points which are closer than width/2 units away.
KaryoColorPresets: This class encapsulates a list of KaryoColorSet presets.
Chromosome: represents the loci in just one chromosome...