FlyNapp is an application for viewing and searching Drosophila data through FlyBase services. This is a preliminary version. This document lacks many details of the application functions. FlyNapp is available at
Are there functions that can be added that would aid flybase's editors and curators?
Which current application bugs are most annoying?
There are system-specific bugs, e.g., parts editor on Xwindows. Let me know which functions you would use that are failing now, and on what platform -- though at this stage it will be hard for you to tell if something just hasn't been written in yet, or if it is supposed to work but is failing due to technical flaws.
The app name may well change -- what is a better one? 'Fly Nap' is a commercial fly knock-out chemical; will that confuse anyone? I hope the nap part won't prove a forecast; one of the reasons behind this app is to provide faster data access by splitting local and network functions smartly. The idea is to store frequently used, primary bits of data locally that are a drag to fetch repeatedly over networks, and to update this data from the network host as needed to keep it current.
This program is built on an application framework written in Java that I am using for various other programs as well (SeqPup, Phylodendron, loopDloop, others planned). It shares about 60% or more common code w/ other apps. I think the framework is a useful one for rapid application development, and would be happy to help any others in flybase (or out) use it for developing other tools.
FlyNapp is available over the Internet at
Macintosh users will find these files in the archive file flynapp.hqx. MSWindows users will find program files in the archive file flynapp.zip. Unix and others will find just the program files in the archive file flynapp.tar.gz. You likely will need to fetch (see below) and install the Java runtime for your system. Newer operating systems (MacOS 8, Warp, Solaris 2.6) include java runtime systems; though you may want to update them to current versions.
As I've learned with other multi-platform applications that I make available to the bioscience community, there are difficulties involved in the time it takes me to update multiple archives for different computer systesm. The simplest way for me to distribute and update this software is to provide it as separate files, e.g., the pictures and documents and p-code files, and to update each one individually as needed. For example, I update this document after I've already produced some of the archive files. So I will also provide the most current version of this software in its un-archived form. You may find the most current versions by looking in the all systems/ folder. Within that, the folder called local/ has those items specific to each computer system. With a bit more programming effort, I hope to have the application do some of its own updating as needed (see below Updates).
This current release is based on the Java Developer Kit 1.0.2. To run it, you should
have installed the runtime compatible with JKD1.0.2. This can be found through
Javasoft, and at various mirror sites around the world.
For Java runtimes for various operating systems, see
A newer Java version, 1.1, became available in 1997. I will provide an update to this program with this new Java version, perhaps by the start of 1998. For now, Java version 1.0.2/1.0.3 runtimes are needed to run the application.
1. Keep in the same folder whereever you prefer, the application flyNapp, the flyNapp.jcode Java class archive, and the fb folder.
2. Use the MRJ installer from Apple Computer to install this Java runtime software. If you have MacOS 8, this is included as part of the OS. However, at the first release of MacOS 8, the MRJ included is an early, slower version. You should upgrade to the MRJ 1.5 release.
3. Put the contents of "->System/Extensions" into System Folder:Extensions:
4.Install the Internet Config application, if you don't have it. MacOS 8 includes this program. This free, widely used program enables links among Internet aware applications. This application uses it to call others like Netscape to open network links and the help document.
1. Keep in the same folder whereever you prefer, the program batch file FLYNAPP.BAT, the flyNapp.jcode Java class archive, and the fb folder.
2. Install a Java Runtime system for MS Windows. Install it in a standard location,
which will be entered in the SEQPUP.BAT file. A recommended Java runtime is
found at http://www.javasoft.com/products/jdk/1.0.2/installation-win32-x86.html
You may want to install this in the same folder as you store SeqPup (and other java
applications). Or you may want to install this in a general MSWindows folder,
perhaps C:\WINDOWS\JAVA. I don't know of a prefered location yet on MS
Window systems for Java runtime files. You will need to edit the batch file (step 3)
to account for this location.
3. Edit the FLYNAPP.BAT file to make the path names match the file locations on your computer.
set base=\temp\java set appclass=%BASE%\flynapp\flyNapp.jcode set java=%BASE%\java
The distribution zip archive containes application files in the path \TEMP\JAVA\flynapp\ and Java runtime files in the path \TEMP\JAVA\java\. If you unzip it with those names preserved, then you shoud be able to run the program from the batch file FLYNAPP.BAT.
For the application to link properly to Netscape or other Internet browser, you may
need to edit the preferences file. You can do this from within the application; see the
Options/Edit Framework ... Menu. Or you can edit the file dclap.ini which will be
created in the \java\ folder. In either case, you want to enter the variable name
user.openurl= then the full path to your browser to be sure that it works properly.
This path may well be the same on your system as mine, which is as follows. Note the
quote marks (due to space in name) and the double backslashes \\ which are required
to insert one \.
If you use the Edit prefs menu, after editing close the window. You should be prompted to save changes; do so.
For Sun Solaris computers (SPARC and Intel):
For IBM Warp on Intel, IBM AIX, and MS Windows 3.1 computers:
For DEC Digital Unix computers:
For various Linux on Intel systems:
For Silicon Graphics IRIX computers:
SGI has hidden their Java runtime version 1.0.2. Sorry.
contact SGI for more details at http://www.sgi.com/
Whatever runtime system you install, it must be called with the SeqPup.zip file. See the file flynapp which is a small shell script to do this on Unix. Edit that to suit your system needs.
You need to define the user.openurl= variable to find your Netscape or equivalent. You can do this from within the application; see the Options/Edit basic prefs... Menu. Or edit the file ~/.dclaprc directly to enter such a line. The variable line for my unix system is
Also, you might instead use a shell script (like the "netscape.sh" included). If you rename that to netscape, edit it to suit, and put in the folder with SeqPup.zip file, it may take the place of editing the preference file.
Currently Java 1.0.3 does not understand printing (a slight oversight due to the Xwindow history of Java). The current Print command just sends postscript of a drawing to the user.print file.
Both of these options, and the help command, link through an accessory program for opening URLs (Internet universal resource locators). Typically this accessory will be Netscape or the like software. In order to use this accessory program properly, it must be configured on your computer.
For Macintosh users, this involves installing Internet Config, a small free program used by
many other Internet applications. Internet Config must be installed on your system, and
you need to configure it to specify Helpers for at least the following protocols: ftp, file, http,
These helpers may all be Netscape.
For Unix users, this involves setting the preference called "user.openurl" to the proper path to reach Netscape or other Internet applications. See also the small shell script that can be used to customize this function.
For MsWindows users, this also involves setting the preference called "user.openurl" to the proper path to reach Netscape or other Internet applications.
If you click on the Help button, the help document (this) will be displayed (if configured properly). If you click on the source or version buttons, those Internet links will be opened (see below).
The current vocabulary list does have hierarchical drop-down tabs, but is a bit baulky/awkward still. You can however, select a cv term and drag/drop it onto a body part image selection to name that part.
I've recreated the images for flynapp from the Bryant group. These are now jpeg format, and I think they look better (less broken) than the gif format you saw a while back. I made them what I think is a good size for using this as a body part lookup (small enough to be quick to display, large enough to see parts), but feel free to substitute other pictures or sizes. The way the body image part of flynapp works now is that one primary image is known by name to the program (fb/body/partsmap.jgp). Any and all added images are linked to it using the parts editor of flynapp. That editor creates data files (e.g., fb/body/partsmap.jpg.map) that tell where to find new images, and what marked regions and names exist on an image.
As of 12Feb97 release, the XWindow version of parts map editor does not work, though the body parts browser does.