ssbind
Class ProcessBlastReport

java.lang.Object
  extended by ssbind.ProcessBlastReport

public class ProcessBlastReport
extends Object

Driver script that parses a blast report and pumps the result through a configurable chain of filters and handlers.

This command expects to be given a blast report as the first argument, a SearchContentHandler 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.

Example

 # 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 ssbind.ProcessBlastReport blastFile.out \
    "ssbind.FilterByValue(maxVal=0.1 keyName=expectedValue)" \
    ssbind.Echoer

 # echo the percentageIdentity of all alignments between 100 and 200 in length
 java ssbind.ProcessBlastReport blastFile.out \
   "ssbind.FilterByValue(minVal=100 maxVal=200 keyName=alignmentSize)" \
   "ssbind.PropertyEchoer(keyName=percentageIdentity)"
 

Author:
Matthew Pocock

Constructor Summary
ProcessBlastReport()
           
 
Method Summary
static void main(String[] args)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

ProcessBlastReport

public ProcessBlastReport()
Method Detail

main

public static void main(String[] args)
                 throws Exception
Throws:
Exception