public abstract class PatternComputation extends java.lang.Object implements PatternComputationMethod
| Modifier and Type | Field and Description |
|---|---|
protected DataCollect |
collector
DataCollect collector : contains the data HasMap with the thermodynamic parameters for the pattern computation.
|
protected java.lang.String |
fileName
String fileName : name of the xml file containing the thermodynamic parameters.
|
| Constructor and Description |
|---|
PatternComputation() |
| Modifier and Type | Method and Description |
|---|---|
abstract ThermoResult |
computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
DataCollect |
getCollector()
This method is called to get the DataCollect of the implemented class.
|
static java.lang.String |
getData()
This method is called to get the HasMap of DataCollect containing the thermodynamic parameters
|
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.
|
protected DataCollect collector
protected java.lang.String fileName
public boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable in interface PatternComputationMethodpublic abstract ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics in interface PatternComputationMethodsequences - 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 PatternComputationMethodsequences - which contains the sequences entered by the user.public DataCollect getCollector()
PatternComputationMethodgetCollector in interface PatternComputationMethodpublic void loadData(java.util.HashMap<java.lang.String,java.lang.String> options)
PatternComputationMethodloadData in interface PatternComputationMethodoptions - which contains the current options. (default options and options entered by the user)public void loadFile(java.lang.String name,
DataCollect collector)
PatternComputationMethodloadFile in interface PatternComputationMethodname - : the file name where to find the thermodynamic parameterscollector - : The object which stocks the different thermodynamic parameters in a map.public java.lang.String getDataFileName(java.lang.String methodName)
getDataFileName in interface PatternComputationMethodmethodName - : method or model name entered by the user.public void initialiseFileName(java.lang.String methodName)
PatternComputationMethodinitialiseFileName in interface PatternComputationMethodmethodName - : method or model name entered by the user.public static java.lang.String getData()