public interface PatternComputationMethod
Modifier and Type | Method and Description |
---|---|
ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
DataCollect |
getCollector()
This method is called to get the DataCollect of the implemented class.
|
java.lang.String |
getDataFileName(java.lang.String methodName) |
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.
|
void |
loadData(java.util.HashMap<java.lang.String,java.lang.String> options)
To load the necessary thermodynamic parameters of the implemented class.
|
void |
loadFile(java.lang.String name,
DataCollect collector)
To load the thermodynamic parameters from the file "name" and stock them in the map of a DataCollect object.
|
boolean isApplicable(Environment environment, int pos1, int pos2)
environment
- pos1.
- Start position of the pattern in the sequence.pos2.
- End position of the pattern in the sequence.ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
sequences
- which contains the sequences entered by the user.pos1.
- Start position of the pattern in the sequence.pos2.
- End position of the pattern in the sequence.result
- which contains the computed enthalpy, entropy and melting temperature.boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2)
sequences
- which contains the sequences entered by the user.pos1.
- Start position of the pattern in the sequence.pos2.
- End position of the pattern in the sequence.DataCollect getCollector()
void loadData(java.util.HashMap<java.lang.String,java.lang.String> options)
options
- which contains the current options. (default options and options entered by the user)void loadFile(java.lang.String name, DataCollect collector)
name
- : the file name where to find the thermodynamic parameterscollector
- : The object which stocks the different thermodynamic parameters in a map.java.lang.String getDataFileName(java.lang.String methodName)
methodName
- : method or model name entered by the user.void initialiseFileName(java.lang.String methodName)
methodName
- : method or model name entered by the user.