public class Environment
extends java.lang.Object
Constructor and Description |
---|
Environment(java.util.HashMap<java.lang.String,java.lang.String> options)
creates an Environment object from the different options (default options and options entered by the user).
|
Modifier and Type | Method and Description |
---|---|
void |
addResult(double enthalpy,
double entropy)
increments the ThermoResult enthalpy and ThermoResult entropy of Environment.
|
java.util.HashMap<java.lang.String,java.lang.Double> |
getConcentrations()
This method is called to get the concentrations of Environment.
|
double |
getDMSO()
This method is called to get the DMSO concentration.
|
double |
getDNTP()
This method is called to get the dNTP concentration.
|
int |
getFactor()
This method is called to get the factor of Environment.
|
double |
getFormamide()
This method is called to get the formamide concentration.
|
java.lang.String |
getHybridization()
This method is called to get the hybridization of Environment.
|
double |
getK()
This method is called to get the potassium concentration.
|
double |
getMg()
This method is called to get the magnesium concentration.
|
double |
getNa()
This method is called to get the sodium concentration.
|
double |
getNucleotides()
This method is called to get the oligomerConcentration of Environment.
|
java.util.HashMap<java.lang.String,java.lang.String> |
getOptions()
This method is called to get the HashMap options of Environment.
|
ThermoResult |
getResult()
This method is called to get the ThermoResult of Environment.
|
NucleotidSequences |
getSequences()
This method is called to get the sequences NucleotidSequences of Environment.
|
double |
getTris()
This method is called to get the Tris buffer concentration.
|
boolean |
isSelfComplementarity()
To check if the sequences are self complementary.
|
void |
setFactor(int factor)
changes the factor value of Environment.
|
void |
setMg(double Mg)
changes the magnesium concentration in the environment
|
void |
setNa(double na)
changes the sodium concentration in the environment
|
void |
setResult(double temperature)
changes the melting temperature of ThermoResult.
|
void |
setResult(ThermoResult result)
changes the result ThermoResult of Environment.
|
void |
setSelfComplementarity(boolean b)
changes the boolean value of the isSelfComplementarity boolean.
|
void |
sortSquences(java.lang.String hybridization,
java.lang.String firstSequence,
java.lang.String secondSequence)
sorts the sequences in function of the type of hybridization : In case of DNA/RNA type of hybridization, the sequence (5'3') must be a DNA sequence
and the complementary sequence (3'5') a RNA sequence.
|
public Environment(java.util.HashMap<java.lang.String,java.lang.String> options)
options
- : contains the options (default options and options entered by the user)public void sortSquences(java.lang.String hybridization, java.lang.String firstSequence, java.lang.String secondSequence)
hybridization
- : type of hybridization. Precise the nature of each sequence (DNA, RNA or mRNA)firstSequence
- : sequence (5'3')secondSequence
- : complementary sequence (3'5')public int getFactor()
public void setFactor(int factor)
factor
- : new factor valuepublic ThermoResult getResult()
public NucleotidSequences getSequences()
public double getNucleotides()
public boolean isSelfComplementarity()
public void setSelfComplementarity(boolean b)
b
- public java.lang.String getHybridization()
public java.util.HashMap<java.lang.String,java.lang.String> getOptions()
public double getNa()
public double getMg()
public void setMg(double Mg)
Mg
- : new magnesium concentrationpublic double getTris()
public double getK()
public java.util.HashMap<java.lang.String,java.lang.Double> getConcentrations()
public double getDMSO()
public double getFormamide()
public void setNa(double na)
Na
- : new sodium concentrationpublic void addResult(double enthalpy, double entropy)
enthalpy
- : enthalpy incrementation valueentropy
- : entropy incrementation valuepublic void setResult(double temperature)
temperature
- : new melting temperaturepublic void setResult(ThermoResult result)
result
- : new ThermoResult object.public double getDNTP()