org.strbio.local
Class Primer3

java.lang.Object
  org.strbio.local.Program
      org.strbio.local.Primer3

public class Primer3
extends Program

Class to run Primer3

   Version 1.0, 6/13/06, based on Modeller
   

Version:

1.0, 6/13/06

Author:

JMC

Field Summary

Fields inherited from class org.strbio.local.Program

processError, processInput, processOutput, PROGRAM_NAME

Constructor Summary

Primer3()

Method Summary

PrimerSet	designPrimers(java.lang.String dna, int coord1, int coord2) Design primers to clone a region of dna between 2 coordinates
PrimerSet	designPrimers(java.lang.String dna, int coord1, int coord2, PrimerSet fixed) Design primers to clone a region of dna between 2 coordinates.
java.lang.String	programName() What's the name of this program?

Methods inherited from class org.strbio.local.Program

clean, exists, run, runBackground, runSilent, setError, setInput, setOutput, setProgramName

Methods inherited from class java.lang.Object

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

Constructor Detail

Primer3

public Primer3()

Method Detail

programName

public final java.lang.String programName()

Description copied from class: Program

What's the name of this program?

Overrides:

programName in class Program

designPrimers

public final PrimerSet designPrimers(java.lang.String dna,
                                     int coord1,
                                     int coord2,
                                     PrimerSet fixed)

Design primers to clone a region of dna between 2 coordinates. If either of the primers it specified by the user, it will design any that are missing. If both are specified by the user, it just returns a copy of that pair. Flexibility is currently hard-coded at 300 bases.

designPrimers

public final PrimerSet designPrimers(java.lang.String dna,
                                     int coord1,
                                     int coord2)

Design primers to clone a region of dna between 2 coordinates