public class Sugimoto02DNADanglingEnd extends SugimotoLongDanglingEndMethod 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 dangling end
(just long poly A)
|
collector, fileName| Constructor and Description |
|---|
Sugimoto02DNADanglingEnd() |
| Modifier and Type | Method and Description |
|---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
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.
|
correctPositionsgetCollector, getData, getDataFileName, loadData, loadFilepublic static java.lang.String defaultFileName
public boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodisApplicable in class SugimotoLongDanglingEndMethodpublic ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodcomputeThermodynamics in class SugimotoLongDanglingEndMethodsequences - 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 SugimotoLongDanglingEndMethodsequences - 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.public java.lang.String getName()
getName in interface NamedMethod