public abstract class PatternComputation extends java.lang.Object implements PatternComputationMethod
Modifier and Type | Field and Description |
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protected DataCollect |
collector
DataCollect collector : contains the data HasMap with the thermodynamic parameters for the pattern computation.
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protected java.lang.String |
fileName
String fileName : name of the xml file containing the thermodynamic parameters.
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Constructor and Description |
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PatternComputation() |
Modifier and Type | Method and Description |
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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.
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static java.lang.String |
getData()
This method is called to get the HasMap of DataCollect containing the thermodynamic parameters
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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.
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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.
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void |
loadData(java.util.HashMap<java.lang.String,java.lang.String> options)
To load the necessary thermodynamic parameters of the implemented class.
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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.
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protected DataCollect collector
protected java.lang.String fileName
public boolean isApplicable(Environment environment, int pos1, int pos2)
isApplicable
in interface PatternComputationMethod
public abstract ThermoResult computeThermodynamics(NucleotidSequences sequences, int pos1, int pos2, ThermoResult result)
computeThermodynamics
in interface PatternComputationMethod
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
sequences
- which contains the sequences entered by the user.public DataCollect getCollector()
PatternComputationMethod
getCollector
in interface PatternComputationMethod
public void loadData(java.util.HashMap<java.lang.String,java.lang.String> options)
PatternComputationMethod
loadData
in interface PatternComputationMethod
options
- which contains the current options. (default options and options entered by the user)public void loadFile(java.lang.String name, DataCollect collector)
PatternComputationMethod
loadFile
in interface PatternComputationMethod
name
- : 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 PatternComputationMethod
methodName
- : method or model name entered by the user.public void initialiseFileName(java.lang.String methodName)
PatternComputationMethod
initialiseFileName
in interface PatternComputationMethod
methodName
- : method or model name entered by the user.public static java.lang.String getData()