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• edu.stanford.genetics.treeview.dendroview: Javadoc index of package edu.stanford.genetics.treeview.dendroview.


Package Samples:

• edu.stanford.genetics.treeview.dendroview

Classes:

• ArrayDrawer: Class for Drawing A Colored Grid Representation of a Data Matrix. Each cell in the view corresponds to an element in the array. The color of the pixels is determined by the ColorExtractor, which is passed in the value to be converted. The ArrayDrawer is Observable. It setsChanged() itself when the data array is changed, but you have to call notifyObservers() yourself. Notifications from the ColorExtractor, however, are immediately passed on to listeners. Upon setting a data array, ArrayDrawer will set a reference to the data array, and may refer to it when it asked to draw things. Of course, it ...
• DendroView: 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. The intention here is that you create this from a model, and never ...
• KnnDendroView: 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 KnnGlobalView 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 KnnDendroView.
• ATRZoomView: Draws an array tree to show the relations between arrays This object requires a MapContainer to figure out the offsets for the arrays. Furthermore, it sets up a scrollbar to scroll the tree, although there is currently no way to specify how large you would like the scrollable area to be, so the height is just set to match the available space.
• ColorSet: This class represents a set of colors which can be used by a color extractor to translate data values into colors. NOTE: This class has been superceded by the ConfigColorSet in the edu.stanford.genetics.treeview package, although I am not likely to actually rewrite any of this code spontaneously.
• ATRView: Draws an array tree to show the relations between arrays This object requires a MapContainer to figure out the offsets for the arrays. Furthermore, it sets up a scrollbar to scroll the tree, although there is currently no way to specify how large you would like the scrollable area to be.
• PostScriptMaker: This class is designed to save lists of genes to a file. For now, must pass in a yMap. The class will pop up a window and prompt the user for further interaction before killing itself like a good slave.
• ColorSetEditor: This class allows editing of a color set... NOTE: This is superceded by the ConfigColorSet stuff in edu.stanford.genetics.treeview, although this code is still used within the dendroview package.
• ColorBarExportPanel: 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.
• ExportPanel: 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.
• IntegerMap: This class is a contract for maps between indexes and pixels. It would be an interface, except there are some common routines which are worth implementing in the superclass.
• DendroPSWriter: Inner class which outputs a postscript version of Dendroview like things It is loosely coupled in that it only calls protected methods in the ExporPanel superclass.
• MapContainer: MapContainers tell the views which pixel offset to draw each array or gene index at. the scrollbars "scroll" by communicating with the maps.
• ArrayNameView: Renders the names of the arrays. Actually, renders the first element in a HeaderInfo as vertical text. Could easily be generalized.
• GTRView: Draws a gene tree to show the relations between genes This object requires a MapContainer to figure out the offsets for the genes.
• FUOptionsPanel: This class allows selection of Font and Url options. It requires a FontSelectable, a UrlExtractor, and optionally a UrlPresets
• ColorPresetEditor: This class allows graphical editing of ColorPresets Also included is a class to pop up a configuration window.
• ColorPresets: This class encapsulates a list of Color presets. This is the class to edit the default presets in...
• PixelSettingsSelector: A popup to allow interactive changing of the pixel scaling and contrast settings of an array view.

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