ssbind
Class ProcessBlastReport
java.lang.Object
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
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
ProcessBlastReport
public ProcessBlastReport()
main
public static void main(String[] args)
throws Exception
- Throws:
Exception