The Sun Java Desktop


A typical desktop

JDS is a window manager, a program that governs the display of windows on your screen. The example shown above illustrates some of the items that might typically be found on the desktop.

As many copies of a program or window can be present on the desktop as you wish.

The Unix Mouse

TThe Mouse in Unix uses 3-buttons. The left button is the Select button. Essentialy everything you do is done with the left button. The right button is the Menu button. Holding down the right button over any window or part of a window, or even the desktop background, will give you a context-dependent menu. The Center button is the paste button. If you select a block of text in one place, you can move the cursor to another place, press the center button, and the selected text will be copied into the new location. This is sometimes a DANGEROUS button, because it is very easy to accidentally select and past a large block of text! On some mice, the center button is also a wheel that can be used for scrolling.

Customizing your desktop

There are two ways to change desktop properties:

Suggested desktop properties
To help you get started, here are suggestions for making JDS easiest to use. As you get more proficient with JDS, you can experiment with different settings until you are satisfied with how your desktop looks and functions.

Window focus

Choose Launch --> Preferences --> Desktop Preferences --> Display --> Window Behavior.
The Window Preferences menu governs the 'focus' of the screen, ie. where the keyboard and mouse take effect. By default, the 'active' window is chosen by clicking on a window. This will also bring that window to the front. However, the extra clicking required with these default settings can get tedious.

The best starting choices are to choose "Select windows when the mouse moves over them" and DE-select "Raise Window after an interval".  The combination of these two settings is usually the most convenient, and certainly the least frustrating for new user

Window List Preferences

To make it easier to have a large number of windows open simultaneously, go to the vertical bar next to the window list on the control panel. Hold down the right mouse button to bring up the menu for the window list:

Choose Preferences, which will bring up the Window List Preferences. Select "Group windows when space is limited"


Create a launcher for the Nautilus file manager

To start, we first need to make some room for a new launcher on the Panel. Hold down the right mouse button on the  vertical bar to the left of the Window List. Choose "Move" and then slid the bar to the right a bit so that you create some extra space.

Next, open the menu for the panel by right clicking on the blank area of the panel.

Choose Add to Panel --> Launcher (do NOT choose Launcher from menu). Now, fill in the Basic tab window as shown at right. To get the folder icon, click on the icon button, and  choose the icon named 'blueprint-gnome-fs-directory-accept.png'.

NOTE: In the Command box, type

nautilus --browser .

 This will launch nautilus in the browser mode, which is a bit more convenient. Remember to include a blank space, between 'nautilus' and '--browser'. The period at the end of the command stands for the current working directory, which for programs launched from the launcher, will always be your $HOME directory.

Tell Nautilus to display details of files and directories

File managers such as Nautilus or Windows Explorer show an Icon view of files. That, is each file is represented only by an icon and a name.

However, other information about files is often very useful. For example, if a program shoud be generating several megabytes of output, but the output file is only 150 bytes, that is a good hint that something is wrong. Therefore, the List view is more informative.

Launch Nautilus by double-clicking on the file folder icon  on the task bar. In Nautilus, choose Edit --> Preferences and make sure the Views tab is displayed. Set View new folders using: List View.

Tell Nautilus which columns to display in list view

Click on the 'List Columns' tab and check the boxes shown at right. These tell Nautilus what information should be displayed for each file or directory.

Choose Nedit as the default text editor

Choose Launch --> Preferences  --> Desktop Preferences -->  File Associations. Open Documents --> Plain Text. Choose Plain text document, and press the Edit button.

Fill in the Edit file type box as shown at right. Check very carefully to make sure that things are typed in precisely as shown.

If Nedit is not the Default action, either choose Nedit from the list, or type  'nedit' (without the quotes) in the Program to run box.

Under Filename extensions, 'txt' and 'TXT' and 'asc' will probably already be present. If not, add them to the list. Also, we will be working with GenBank files, so also add the following extensions: 'gb', 'gen', and 'GEN'.  That way, all of these types of files will be recognized as text fiiles, and will open up in the text editor when you double click on them in Nautilus.

For the icon at the top, choose an icon with a pencil and paper, such as blueprint-gnome-mime-text.png.

Q: Why don't we just use the default editor, gedit?

A: First Nedit is far more powerful than gedit. Secondly, gedit is threaded, and when you have several files open at the same time, it is impossible to get them to appear in separate windows. Gedit will force multiple files into tabs within a single window. Nedit lets you view several files in independent windows: a very important capability when working with data.

Add a Terminal Launcher

Go to the control panel and hold down the right button. Choose Add to Panel --> Launcher from menu --> Utilities --> Terminal. A terminal icon should appear on the control panel:

Start a terminal by clicking on the icon. In the terminal window, choose Edit --> Current profile. Open the 'Compatibility' tab pane, and make sure that both the backspace and delete buttons generate 'ASCII DEL'.

This means that either the backspace key or the delete key can be used for correcting text as you type.


Add a Printer Manager to the Panel

The printer manager lets you monitor print jobs, cancel print jobs, choose a favorite set of printers to display, and even drag and drop files directly from the Nautilus file manager.

Note: Only text and PostScript (.ps) files can be dragged and dropped. For specialized file types (eg. .pdf, .jpg, .gif) you need to open the application and print from the application.

To add the printer manager to the panel, choose Launch --> Preferences  and right click on Printer Preferences. Choose Add this launcher to panel.

Click on the printer icon and the Print Manager will be launched. Choose View --> Select Printers to Show to add the printers that you are most likely to use to your printer list.


Making Nautilus open GenBank files in a text editor

The .gen file extension is commonly used for GenBank flatfiles. Unfortunately, the MIME types used by Nautilus use the .gen extension for Sega Genesis ROM files. To disable this feature, and make it possible to get Nautilus to open GenBank files in a text editor, we need to do several steps.

Choose Launch --> Preferences --> Desktop Preferences --> File Associations. Open Software Development --> ROM Images. Click on "Genesis ROM" and then click on Remove. Do the Same for "Game Boy (some people use .gb, so we might as well get rid of it.

Under the heading 'Misc',  Remove any item with a .gen extension.

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