org.strbio.local
Class Mfold

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

public class Mfold
extends Program

Class to run Mfold

   Version 1.0, 6/22/06, based on Primer3
   

Version:

1.0, 6/22/06

Author:

JMC

Field Summary

Fields inherited from class org.strbio.local.Program

processError, processInput, processOutput, PROGRAM_NAME

Constructor Summary

Mfold()

Method Summary

double	getDG(java.lang.String output) get dG from raw output, or Double.NaN if not found
java.lang.String	getOutput(java.lang.String dna) get output for sequence, or null if it doesn't run
double	getTm(java.lang.String output) get tm from raw output, or Double.NaN if not found
boolean	hasHairpin(java.lang.String dna) "hairpin" defined as any secondary structure with Tm of at least 55 degrees.
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

Mfold

public Mfold()

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

getTm

public final double getTm(java.lang.String output)

get tm from raw output, or Double.NaN if not found

getDG

public final double getDG(java.lang.String output)

get dG from raw output, or Double.NaN if not found

hasHairpin

public final boolean hasHairpin(java.lang.String dna)

"hairpin" defined as any secondary structure with Tm of at least 55 degrees.

getOutput

public final java.lang.String getOutput(java.lang.String dna)

get output for sequence, or null if it doesn't run