public abstract class ZnoskoMethod extends PatternComputation
Modifier and Type | Field and Description |
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protected static java.lang.String |
formulaEnthalpy
String formulaEnthalpy : enthalpy formula
|
collector, fileName
Constructor and Description |
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ZnoskoMethod() |
Modifier and Type | Method and Description |
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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
|
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, initialiseFileName, loadData, loadFile
protected static java.lang.String formulaEnthalpy
public boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable
in interface PatternComputationMethod
isApplicable
in class PatternComputation
public ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics
in interface PatternComputationMethod
computeThermodynamics
in class PatternComputation
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 PatternComputation
sequences
- which contains the sequences 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 duplex