[Biojava-l] blast command-line utilities

[Matthew Pocock]

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
 */

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