public class Santalucia04LongBulgeLoop extends PatternComputation implements NamedMethod
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
defaultFileName
String defaultFileName : default name for the xml file containing the thermodynamic parameters for long bulge loop
|
protected static java.lang.String |
formulaEnthalpy
String formulaEnthalpy : enthalpy formula
|
protected static java.lang.String |
formulaEntropy
String formulaEntropy : entropy formula
|
collector, fileName| Constructor and Description |
|---|
Santalucia04LongBulgeLoop() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
protected int[] |
correctPositions(int pos1,
int pos2,
int duplexLength)
corrects the pattern positions in the duplex to have the adjacent
base pair of the pattern included in the subsequence between the positions pos1 and pos2
|
java.lang.String |
getName()
Gets the full name of the method.
|
void |
initialiseFileName(java.lang.String methodName)
If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
otherwise the default file name of the model is used.
|
boolean |
isApplicable(Environment environment,
int pos1,
int pos2) |
boolean |
isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
getCollector, getData, getDataFileName, loadData, loadFilepublic static java.lang.String defaultFileName
protected static java.lang.String formulaEnthalpy
protected static java.lang.String formulaEntropy
public boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodisApplicable in class PatternComputationpublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class PatternComputationsequences - which contains the sequences entered by the user.result - which contains the computed enthalpy, entropy and melting temperature.public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
PatternComputationMethodisMissingParameters in interface PatternComputationMethodisMissingParameters in class PatternComputationsequences - which contains the sequences entered by the user.public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodinitialiseFileName in class PatternComputationmethodName - : method or model name entered by the user.protected int[] correctPositions(int pos1,
int pos2,
int duplexLength)
pos1 - : starting position of the internal looppos2 - : ending position of the internal loopduplexLength - : total length of the duplexpublic java.lang.String getName()
getName in interface NamedMethod