Hi all, Yesterday I used our blast parsing code for the 1st time. I'm impressed by how painlessly it all works. Thanks to CAT and KeithJ and everyone else for making my life easier.
In return, I have tickled it aground the edges. I've added some convenience search handlers for implementing filters and listeners to the org.biojava.bio.search directory. Also, there are a whole new set of demos in biojava-live/demos/ssbind that I'm quite pleased with. The main one is ProcessBlastReport. Here is a bit of documentation to give you a feel for it. Matthew ps My laptop at home is "stealing" all e-mail from my pop account, so if you want a timely response, it's best to contact me via the chat room today - irc.openprojects.net in #biojava /** * <p> * Driver script that parses a blast report and pumps the result through a * configurable chain of filters and handlers. * </p> * * <p> * This command expects to be given a blast report as the first argument, a * SearchContentHanlder with a no-args constructor as the last argument and * any number of SearchContentFilters inbetween. It assumes that all classes * can be configured using beany accessors (get/setFoo methods). If you supply * the class name as-is, the class will be instantiated. If you give the class * name followed by brackets, you can put any number of property names and their * values within the brackets. * </p> * * <h2>Example</h2> * <pre> * # echo parsing events to stdout * java ProcessBlastReport blast.out ssbind.Echoer * * # echo events that are left after all hits with expectedValue greater * # than 0.1 have been removed * java ProcessBlastReport \ * "ssbind.FilterByValue(maxVal=0.1 keyName=expectedValue)" \ * ssbind.Echoer * * # echo the percentageIdentity of all alignments between 100 and 200 in length * java ProcessBlastReport \ * "ssbind.FilterByValue(minVal=100 maxVal=200 keyName=alignmentSize)" \ * "ssbind.PropertyEchoer(keyName=percentageIdentity)" * </pre> * * @author Matthew Pocock */ __________________________________________________ Do You Yahoo!? Everything you'll ever need on one web page from News and Sport to Email and Music Charts http://uk.my.yahoo.com _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
