public ThermoResult correctMeltingResults(Environment environment) {
double Tm = correctTemperature(environment);
environment.setResult(Tm);
return environment.getResult();
}
/**
* corrects the computed melting temperature depending on the environment.
*
* @param environment
* @return double corrected melting temperature
*/
protected double correctTemperature(Environment environment) {
OptionManagement.logMessage("\n The magnesium correction is");
OptionManagement.logMethodName(methodName);
OptionManagement.logMessage(temperatureCorrection);
OptionManagement.logMessage("where : ");
OptionManagement.logMessage("b = " + this.b);
OptionManagement.logMessage("c = " + this.c);
OptionManagement.logMessage("e = " + this.e);
OptionManagement.logMessage("f = " + this.f);
displayVariable();
double Mg = environment.getMg() - environment.getDNTP();
double square = Math.log(Mg) * Math.log(Mg);
double Fgc = environment.getSequences().computesPercentGC() / 100.0;
double TmInverse =
1.0 / (environment.getResult().getTm() + 273.15)
+ this.a
+ this.b * Math.log(Mg)
+ Fgc * (this.c + this.d * Math.log(Mg))
+ 1.0
/ (2.0 * ((double) environment.getSequences().getDuplexLength() - 1.0))
* (this.e + this.f * Math.log(Mg) + this.g * square);
return (1.0 / TmInverse) - 273.15;
}
public ThermoResult correctMeltingResults(Environment environment) {
OptionManagement.logMessage("\n The sodium correction is");
OptionManagement.logMethodName(methodName);
OptionManagement.logMessage(temperatureCorrection);
double NaEq = Helper.computesNaEquivalent(environment);
double Fgc = environment.getSequences().computesPercentGC() / 100.0;
double TmInverse =
1.0 / (environment.getResult().getTm() + 273.15)
+ (3.85 * Fgc - 6.18) * 1 / 100000 * Math.log(NaEq);
environment.setResult((1.0 / TmInverse) - 273.15);
return environment.getResult();
}
public boolean isApplicable(Environment environment) {
boolean isApplicable = true;
if (environment.getMg() == 0) {
OptionManagement.logWarning(
"\n The magnesium concentration must be a positive numeric value.");
isApplicable = false;
} else if (environment.getMg() < 0.0005 || environment.getMg() > 0.6) {
OptionManagement.logWarning(
"\n The magnesium correction of Owczarzy et al. "
+ "(2008) is accurate in the magnesium concentration range of 0.5mM to 600mM.");
}
if (environment.getHybridization().equals("dnadna") == false) {
OptionManagement.logWarning(
"\n The magnesium correction of Owczarzy et al. "
+ "(2008) is originally established for DNA duplexes.");
}
return isApplicable;
}
public boolean isApplicable(Environment environment) {
boolean isApplicable = true;
double NaEq = Helper.computesNaEquivalent(environment);
if (NaEq == 0) {
OptionManagement.logWarning("\n The sodium concentration must be strictly positive.");
isApplicable = false;
}
if (environment.getHybridization().equals("dnadna") == false) {
OptionManagement.logWarning(
"\n The sodium correction of Owczarzy et al. (2004) 20 is originally established for "
+ "DNA duplexes.");
}
return isApplicable;
}
