public class Turner99_06SingleBulgeLoop extends Turner99_06LongBulgeLoop implements NamedMethod
defaultFileName, formulaEnthalpy
collector, fileName
Constructor and Description |
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Turner99_06SingleBulgeLoop() |
Modifier and Type | Method and Description |
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ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
java.lang.String |
getName()
Gets the full name of the method.
|
protected boolean |
isClosingPenaltyNecessary()
to check if a penalty for the closing base pairs is necessary.
|
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.
|
void |
loadData(java.util.HashMap<java.lang.String,java.lang.String> options)
To load the necessary thermodynamic parameters of the implemented class.
|
correctPositions, initialiseFileName, isApplicable
getCollector, getData, getDataFileName, loadFile
public ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics
in interface PatternComputationMethod
computeThermodynamics
in class Turner99_06LongBulgeLoop
sequences
- 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)
PatternComputationMethod
isMissingParameters
in interface PatternComputationMethod
isMissingParameters
in class Turner99_06LongBulgeLoop
sequences
- which contains the sequences entered by the user.public void loadData(java.util.HashMap<java.lang.String,java.lang.String> options)
PatternComputationMethod
loadData
in interface PatternComputationMethod
loadData
in class PatternComputation
options
- which contains the current options. (default options and options entered by the user)protected boolean isClosingPenaltyNecessary()
Turner99_06LongBulgeLoop
isClosingPenaltyNecessary
in class Turner99_06LongBulgeLoop
public java.lang.String getName()
getName
in interface NamedMethod
getName
in class Turner99_06LongBulgeLoop