About the Software Author: K. James Durbin © 1997-1999 K. James Durbin and Baylor College of Medicine Human Genome Sequencing Center. All rights reserved. Disclaimer The BCM TraceViewer is software provided AS-IS. It has not been tested in multiple environments nor extensively in any environment. Usage Experimenting with the various buttons and slide bars should make the function of each fairly obvious. It is worth noting that clicking on the arrows in slider bars moves/scales by fine increments whereas clicking inside the bar itself moves/scales by large increments. Clicking on the handle inside a slider bar and dragging allows continuous movement/scaling. To use as an applet in a web page you need to include a tag in the page source like the following: The width and height parameters specify the dimensions of the applet. The "trace-name" parameter specifies the name of the .SCF file to read. The "exp-name" parameter specifies the name of the corresponding .EXP file that contains quality data for that trace. Currently, the TraceViewer only reads .scf files for trace data and .exp files (Staden) for quality. This is a reflection of the files used in our internal data pipeline. It is, however, easy to construct an .exp file from a .qual file. Simply add "AV" in front of each line of quality, like this: AV 20 30 40 40 40 40 40 40 40 40 40 40 40 40 60 70 80 40 50 60 40 AV 20 20 20 20 30 20 30 40 40 30 40 40 40 40 60 70 80 40 50 60 40 If you do not specify a quality file, the TraceViewer should still run normally. The current implementation of the TraceViewer reads files by opening up a URL to the file (see source fragment). Effectively this means that the trace files must be in the same directory as the .class files making up the applet, or in a subdirectory of that directory (symbolic links can work, depending on the details of the local setup). All of the files must be accessable (permissions, etc.) to the local web server. To use as an application on a Unix system, type: java TraceViewerApplication This assumes, of course, that the Java runtime is installed somewhere in your current path. On other systems (Mac/PC), you can launch the Java runtime and open up the file "TraceViewerApplication.class." Customization Many people wish to customize the applet for their particular application. In order to facilitate this, I am now bundling the source code with the download. Hopefully, this will encourage useful customizations and bug fixes which I can merge back into this distribution for the rest of the world to benefit from. In particular, it would be nice to support more input file types, but I simply don't have the time myself. Please send me a copy of any customizations you may make. Random Notes Q: In the application version, why is there a special FastFileDialog class? It doesn't work very well, and there is a built-in FileDialog. A: Because the built-in FileDialog class checks each file to see if it is a directory or file, and the system call that does this takes time. Also, the built-in FileDialog re-reads the directory contents each time it is invoked. Some of our directories contain > 4000 files, which is just more than FileDialog can handle in a reasonable time. FastFileDialog doesn't test for file/directory and it buffers the list once it's been read so you don't take the hit each time you open the dialog. Newer versions of Java may have better FileDialogs that make this obsolete. BCM Traceviewer was originally written under Java 1.02.