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Package Samples:

edu.stanford.ejalbert
edu.stanford.genetics.treeview.app
edu.stanford.genetics.treeview.applet
edu.stanford.genetics.treeview
edu.stanford.genetics.treeview.dendroview
edu.stanford.genetics.treeview.karyoview
edu.stanford.genetics.treeview.model
edu.stanford.genetics.treeview.scatterview
edu.stanford.smi.protege.ui
edu.stanford.smi.protege.storage.xml
edu.stanford.smi.protege.storage.clips
edu.stanford.smi.protege.resource
edu.stanford.smi.protege.model

Classes:

BrowserLauncher: BrowserLauncher is a class that provides one static method, openURL, which opens the default web browser for the current user of the system to the given URL. It may support other protocols depending on the system -- mailto, ftp, etc. -- but that has not been rigorously tested and is not guaranteed to work. Yes, this is platform-specific code, and yes, it may rely on classes on certain platforms that are not part of the standard JDK. What we're trying to do, though, is to take something that's frequently desirable but inherently platform-specific -- opening a default browser -- and allow programmers ...
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 ...
ConfigNode: Defines an interface for storage of key-value pairs. Essentially all the configuration information for Java TreeView is stored using this interface. You will encounter two implementing classes. The first, most common one is an inner class of XmlConfig, which simply presents an interface to edit an xml document. Thus, when you mess with that inner class through this interface, you're actually writing XML. The second is the DummyConfigNode, which you can use for prototyping stuff or if you just want to use this interface to store key-value pairs in a non-persistant fashion. The easiest way to make ...
TreeViewApp: This class defines the treeview application. The actual Gui handling of a given window is done by TreeViewFrame, which represents a single document. Because multiple documents can be open at a given time, there can be multiple TVFrame objects. however, there can be only one TreeView object. what this really means is that TreeView itself just manages two resources, the window list and the global config. Anything that effects these resources should bottleneck through TreeView. 1/16/2003 by popular demand (with the exception of my advisor) I have decided to try and make an applet version. as a first ...
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 ...
QSortAlgorithm: 19 Feb 1996: Fixed to avoid infinite loop discoved by Paul Haeberli. Misbehaviour expressed when the pivot element was not unique. -Jason Harrison 21 Jun 1996: Modified code based on comments from Paul Haeberli, and Peter Schweizer (Peter.Schweizer@mni.fh-giessen.de). Used Daeron Meyer's (daeron@geom.umn.edu) code for the new pivoting code. - Jason Harrison 09 Jan 1998: Another set of bug fixes by Thomas Everth (everth@wave.co.nz) and John Brzustowski (jbrzusto@gpu.srv.ualberta.ca). 05 Jan 2003: Commented calls to pause(), Added static sort(double) commented refs to stopRequested (camel@alum.mit ...
ClipsImportExportPlugin: Import and Export plugins for the CLIPS file format. Note that this is not a good example of a plugin. An import plugin for clips should be able to read any clips file. This plugin can only read a subset of clips files, in particular those generated by Protege. An export plugin for clips should write out "clean" clips. This output should have none of the "comments" and other Protege encoded information in it. This plugin does neither of these jobs well because it just delegates the calls to the CLIPS backend which has entirely different constraints. Nevertheless this plugin does illustrate how ...
TreeViewAppX: This class defines the treeview application. The actual Gui handling of a given window is done by TreeViewFrame, which represents a single document. Because multiple documents can be open at a given time, there can be multiple TVFrame objects. however, there can be only one TreeView object. what this really means is that TreeView itself just manages two resources, the window list and the global config. Anything that effects these resources should bottleneck through TreeView. 1/16/2003 by popular demand (with the exception of my advisor) I have decided to try and make an applet version. as a first ...
ContainerFocusTracker: Note: I, Alok, didn't write this class. Class for Containers which won't take the keyboard focus. Because of what appears to be a bug in Java 1.1, when you move the focus on to a Frame, or other Container, it keeps the focus, rather than handing it on to an appropriate tabstop inside it. This class collects all focus events for the Container and its contents, and will correct the problem. It also monitors the Container, and keeps track if the focussed component is removed from the container. To use, just create a tracker, passing it the Container you want to deal with.
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.
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.
FrameRenderer: Renderer for frames. This class has logic to render all type of frames: classes, slots, facet, simple instances. There isn't a separate renderer for each frame type because Protege's metaclass architecture is such that any list of "instances" could contain any of the above types. Since all elements of a list use the same renderer is just makes sense to stuff the code for a frame types into a single place. This class is big an clumsy though. It should probably instead delegate the rendering of each of the frame types to another instance.
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.
Daemon: A daemon is a thread that waits for request and forward to a RequestHandler in this case, the TreeViewApp The intention of this : If an instance of the program is running, it shall starts a daemon which waits for requests. When another instance of the program is started, the new program will first try to contact the daemons. If any exists, the new program will ask the daemon to do the task. daemon will delegate the task to the RequestHandler.
ConfigureProjectPanel: The global configuration panel. This panel consists of a set of tabs that each handles a specific part of the configuration. Class has been expanded to allow user defined configuration tabs in the project configuration panel. To add a new tab to the configuration panel, call: ConfigureProjectPanel.registerConfigureTab(String tabTitle, String clsName) To remove a tab from the configuration panel, call: ConfigureProjectPanel.unregisterConfigureTab(String configTabName)
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.
FileSet: Encapsulates a set of files corresponding to a typical hieararichal cluster analysis. Such things are always based upon a cdt or pcl file. The following attributes are meaningful to the FileSet: dir: The directory of the fileset root: The root of the fileset cdt: The extension for the generalized cdt file atr: The extension for the atr jtv: The extension for the jtv
ProgressTrackable: The idea here is that objects which implement this interface can have their progress depicted by a progress bar. You could define a specialized timer class which kept pointers to a ProgressTrackable and a JProgressBar, and every few hundred milliseconds made sure that the JProgressBar reflected the ProgressTrackable. Asynchronously, you could have another thread change the values in the ProgressTrackable.
SwingWorker: This is the 3rd version of SwingWorker (also known as SwingWorker 3), an abstract class that you subclass to perform GUI-related work in a dedicated thread. For instructions on using this class, see: http://java.sun.com/docs/books/tutorial/uiswing/misc/threads.html Note that the API changed slightly in the 3rd version: You must now invoke start() on the SwingWorker after creating it.
UrlScanner: Scan a resource to find the number of tabs and newlines in it. This class implements a scanner which calculates how many lines are in a url resource the number of tabs in the first non-whitespace line It will throw an exception if there are not the same number of tabs in every line As with the FileScanner, it does the scan when it is constructed.
ColorSetI: This is a general interface to color sets. This should be subclassed for particular color sets. Other classes, such as presets, which want to configure or get colors can do it through this interface in a general way. They can also down-cast if they need to. In general, the types should be constants within the subclass. See an existing example to get the idea.
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.
FlatFileStreamTokenizer: implements the "lexical structure" of flat files basically, calling nextToken returns a series of words, nulls and newlines, and finally an EOF. Note that numbers are not parsed by the tokenizer. Also, there is no enforcement of the correct number of tokens per line. it will, however, filter out blank lines.
DragGridPanel: A Panel which is divided into a rectangular grid which the user can change. Components may be added to the grid, and may take up any rectangular set of cells within the grid. The user may drag the borders between the components to change the relative sizes of the cells, and thus the sizes of the components.
XmlConfig: This is a generic class for maintaining a configuration registry for documents. The root element is managed by this class, and configuration should be stored in children of the root. The class is actually implemented as wrapper around XMLElement that is associated with a file, and knows how to store itself.

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