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Peksystray is a small system tray (also called notification tray) designed for all lightweight window managers that support docking. As more and more applications use a small icon in the system tray to provide some additional functionality and information, it becomes useful for everyone to have common access to them. While "heavy" window managers (Gnome, KDE...) come with a system tray embedded in the rest of the desktop, lighter window managers (Window Maker, Fluxbox ...) do not have this feature. Peksystray is a very simple and light implementation of a system tray for any window manager supporting docking, conforming to the System Tray freedesktop.org standard. Peksystray provides a window where icons will automatically add up depending on the requests from the applications. Both the size of the window and the size of the icons can be selected by the user. If the window is full, it can automatically display another window in order to display more icons. Peksystray has been named after PekWM.

Version 2 of the FASTA packages contains many programs for performing sequence comparisons, producing local alignments, and other related tasks for analysing DNA and proteins. Currently, the FASTA2 suite is in maintenance mode. This package provides the analysis tools from FASTA2. The searching programs are available in version 3 of the FASTA packages, which may be found in the port biology/fasta3. FASTA is described in: W. R. Pearson and D. J. Lipman (1988), "Improved Tools for Biological Sequence Analysis", PNAS 85:2444- 2448, and W. R. Pearson (1990) "Rapid and Sensitive Sequence Comparison with FASTP and FASTA" Methods in Enzymology 183:63- 98). The FASTA2 suite is distributed freely subject to the condition that it may not be sold or incorporated into a commercial product.

From the man page: The mimencode program simply converts a byte stream into (or out of) one of the standard mail encoding formats defined by MIME, the proposed standard for internet multimedia mail formats. Such an encoding is necessary because binary data cannot be sent through the mail. The encodings under- stood by mimencode are preferable to the use of the uuencode/uudecode pro- grams, for use in mail, in several respects that were important to the authors of MIME. Mmencode is part of metamail, and can be installed as part of that package. It is provided here as an independent package since some programs require mmencode only and hence you can avoid having to install the entire metalmail package when not required.

JLine is a Java library for handling console input. It is similar in functionality to BSD editline and GNU readline. People familiar with the readline/editline capabilities for modern shells (such as bash and tcsh) will find most of the command editing features of JLine to be familiar. JLine is distributed under the BSD license, meaning that you are completely free to redistribute, modify, or sell it with almost no restrictions. API documentation can be found in the apidocs directory. You can use the jline.ConsoleRunner application to set up the system input stream and continue on the launch another program. For example, to use JLine as the input handler for the popular BeanShell console application, you can run: java jline.ConsoleRunner bsh.Interpreter

pty is a tool to help debug console programs which take the terminal out of canonical mode, by allowing the program being debugged and the debugger to run on separate terminal devices. To use pty, the programmer changes to the terminal device where he or she wishes to interact with the program to be debugged, and at the shell prompt, runs pty with no arguments. Pty will print out the filename of the slave side of the pseudo-terminal it has opened. Inside the debugger, running in another terminal device, one then redirects the program to be debugged's IO to the slave (tty command of gdb). When you are finished using pty, you must manually kill it. When pty starts it prints out its pid.

tt is an implementation of the well-known game tetris. Quadominoes (groups of four squares joined orthogonally together) slowly fall down the screen, accumulating at the bottom, and when the pile reaches the top of the screen the game is over. The pieces may be moved to the left or right, and rotated as they fall, with the aim of making them tessellate with the pieces already at the bottom of the game area. The height of the stack of pieces can be reduced by filling a complete row of ten squares, at which point that row will disappear, and those above will fall down into its place. It is possible (and desirable) to destroy multiple rows at once.

JGraphT is a free Java graph library that provides mathematical graph-theory objects and algorithms. JGraphT supports various types of graphs including: * directed and undirected graphs. * graphs with weighted / unweighted / labeled or any user-defined edges. * various edge multiplicity options, including: simple-graphs, multigraphs, pseudographs. * unmodifiable graphs - allow modules to provide "read-only" access to internal graphs. * listenable graphs - allow external listeners to track modification events. * subgraphs graphs that are auto-updating subgraph views on other graphs. * all compositions of above graphs. Although powerful, JGraphT is designed to be simple. For example, graph vertices can be of any objects. You can create graphs based on: Strings, URLs, XML documents, etc; you can even create graphs of graphs!

kcd allows user to change directory by using various methods: - By using cursor keys to navigate through the directory tree screen - By searching in directory tree screen - By typing part of the directory name directly at the command line. Other features include: - Can be configured to filter out to some subdirectories, useful for cdrom and msdos partition mounting points - Can be configured to scan directory tree starting from some specified directory inwards, for example, home directory. - If the number directories that matches to the name given in the command line exceeds a specified number, kcd displays the whole list. - Faster directory rescan if old data file exists. Only directories with newer modified/changed time are scanned. - Sorted directory tree listing.

Netatalk is an OpenSource software package, that can be used to turn an inexpensive *NIX machine into an extremely high-performance and reliable file server for Macintosh computers. Using Netatalk's AFP 3.2 compliant file-server leads to significantly higher transmission speeds compared with Macs accessing a server via SaMBa/NFS while providing clients with the best possible user experience (full support for Macintosh metadata, flawlessly supporting mixed environments of classic MacOS and MacOS X clients) Due to Netatalk speaking AppleTalk, the print-server task can provide printing clients with full AppleTalk support as well as the server itself with printing capabilities for AppleTalk-only printers. Starting with version 2.0, Netatalk seamlessly interacts with CUPS on the server. After all, Netatalk can be used to act as an AppleTalk router, providing both segmentation and zone names in Macintosh networks.

The YAZ Proxy is highly configurable and can be used in a number of different applications, ranging from debugging Z39.50-based applications and protecting overworked servers, to improving the performance of stateless WWW/Z39.50 gateways. Among other features, it includes: * SRW/SRU server function, to allow any Z39.50 server to also support the ZiNG protocols * Load balancing across multiple backend servers * Session-sharing and pre-initialization to improve performance in servers with expensive session initialization * Configurable request filtering, to keep bad requests from reaching the server * XML support -- MARC records can be converted to MARCXML, and XSLT-transformations allow the proxy to support arbitrary retrieval schemas in XML * Load governor function limits requests from aggressive batch-mode clients * Configurable logging * Efficient multiplexing software enables small memory footprint and very high performance