util.bio.wrappers
Class Primer3Wrapper

java.lang.Object
  util.bio.wrappers.Primer3Wrapper

public class Primer3Wrapper

extends java.lang.Object

This app wraps the command line primer3 app to make it useful for picking qPCR primers.

Constructor Summary

Primer3Wrapper(java.lang.String[] args)
Uses a shell script file to execute the primer3 app due to a problem feeding to STDIN from java.

Method Summary

java.lang.String	buildExecuteDoc(Primer3Pick[] pp)
static void	main(java.lang.String[] args)
void	parsePrimer3Results(java.lang.String[] results) Takes the output of the primer3 app and breaks by record loading appriopriate Primer3Pick.
static void	printDocs()
void	processArgs(java.lang.String[] args) This method will process each argument and assign any new varibles

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Primer3Wrapper

public Primer3Wrapper(java.lang.String[] args)

Uses a shell script file to execute the primer3 app due to a problem feeding to STDIN from java.

Method Detail

parsePrimer3Results

public void parsePrimer3Results(java.lang.String[] results)

Takes the output of the primer3 app and breaks by record loading appriopriate Primer3Pick.

buildExecuteDoc

public java.lang.String buildExecuteDoc(Primer3Pick[] pp)

main

public static void main(java.lang.String[] args)

processArgs

public void processArgs(java.lang.String[] args)

This method will process each argument and assign any new varibles

printDocs

public static void printDocs()