JavaStudioTM Design for BlastView_IO

This component is responsible for retrieving BLAST data from a URL (e.g. a local file or a remote Web/CGI server) and parsing it into bioWidget data structures. The ShowFileDialog input at the far left sends the signal to read a file. In response the FileDialog component produces a window that allows the user to choose a BLAST file residing on his/her computer. The name of this file is transmitted to the URLReader, a JavaBean responsible for retrieving a stream of data from a URL (local file, CGI script, ftp site, etc.) The data stream is then passed to the BlastParser , a specialized component that reads BLAST output into the generic objects used by bioWidgets to represent local alignment search results. Both BlastParser and URLReader output status messages to a ParserStatus component, which displays progress messages in a separate window. Finally, the BlastParser sends the data it has read to the rest of the application through a NewAnnotation message, and the TimeStamper produces a logical timestamp that is used to synchronize the BLAST data with any follow-up analyses.

Note the modular nature of the design: for example, in order to use BlastView to display the results of a FASTA or Smith Waterman-based search, one would simply replace the BlastParser component with a new parser for the type of data desired. And to use a different method to obtain search data, such as CORBA, RMI, or direct SQL/JDBC access to a database, one would also replace the URLReader.