public class MainTest extends Object
Constructor and Description |
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MainTest() |
Modifier and Type | Method and Description |
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static void |
displayResults(Properties properties,
ArrayList<String> methodNames,
String hybridization,
String solution,
String nucleotides,
String option)
displays the computed and experimental melting temperature for each method or model to test.
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static void |
displayResultsDanglingEndMeltingC(Properties properties,
ArrayList<String> methodNames,
String hybridization,
String ion,
String nucleotides)
displays the computed and experimental melting temperature for single dangling ends.
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static void |
displayResultsDNA_RNAMelting4_3(Properties properties,
ArrayList<String> methodNames,
String hybridization,
String ion,
String nucleotides)
displays the computed and experimental melting temperature for DNA/RNA duplexes.
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static void |
displayResultsDNA_RNAMeltingC(Properties properties,
ArrayList<String> methodNames,
String hybridization,
String ion,
String nucleotides)
displays the computed and experimental melting temperature for DNA/RNA duplexes.
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static void |
displayResultsInosineMelting4_3WithComplementarySequence(Properties properties,
ArrayList<String> methodNames,
String hybridization,
String solution,
String nucleotides)
displays the computed and experimental melting temperature for each method or model to test.
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static void |
displayResultsLongDanglingEnd(Properties properties,
ArrayList<String> methodNames,
String hybridization,
String solution,
String nucleotides,
String option)
displays the computed and experimental melting temperature for each dangling end method or model.
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static void |
displayResultsMagnesium(Properties properties,
ArrayList<String> methodNames,
String hybridization,
String nucleotides,
String option)
displays the computed and experimental melting temperature for each method or model to test with different magnesium concentrations.
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static void |
displayResultsMeltingC(Properties properties,
ArrayList<String> methodNames,
String hybridization,
String ion,
String nucleotides)
displays the computed and experimental melting temperature for each method or model to test.
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static void |
displayResultsMeltingC4_3(Properties properties,
ArrayList<String> methodNames,
String hybridization,
String ion,
String nucleotides)
displays the computed and experimental melting temperature for each method or model to test.
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static void |
displayResultsMeltingC4_3SelfComplementary(Properties properties,
ArrayList<String> methodNames,
String hybridization,
String ion,
String nucleotides)
displays the computed and experimental melting temperature for each method or model to test.
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static void |
displayResultsMeltingCSelfComplementary(Properties properties,
ArrayList<String> methodNames,
String hybridization,
String ion,
String nucleotides)
displays the computed and experimental melting temperature for each method or model to test.
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static void |
displayResultsMismatchMeltingCWithComplementarySequence(Properties properties,
ArrayList<String> methodNames,
String hybridization,
String ion,
String nucleotides)
displays the computed and experimental melting temperature for single mismatches.
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static void |
displayResultsNaEq(Properties properties,
ArrayList<String> methodNames,
String hybridization,
String nucleotides,
String option)
displays the computed and experimental melting temperature for each NaEq method or model to test with different magnesium concentrations.
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static void |
displayResultsNaEq(Properties properties,
String hybridization)
displays the computed and experimental melting temperature with MELTING 4.2 approximative formula and with different magnesium concentrations.
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static void |
displayResultsSelf(Properties properties,
ArrayList<String> methodNames,
String hybridization,
String solution,
String nucleotides,
String option)
displays the computed and experimental melting temperature for each method or model to test.
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static void |
displayResultsSodium(Properties properties,
ArrayList<String> methodNames,
String hybridization,
String nucleotides,
String option)
displays the computed and experimental melting temperature for each method or model to test with different sodium concentrations.
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static void |
displayResultsWithComplementarySequence(Properties properties,
ArrayList<String> methodNames,
String hybridization,
String solution,
String nucleotides,
String option)
displays the computed and experimental melting temperature for each method or model to test.
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static double |
getC4_3MeltingResult(String args)
to run melting 4.3 and get the results
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static double |
getCMeltingResult(String args)
to run melting 4.2 and get the results
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static double |
getMeltingTest(String[] args)
computes the enthalpy, entropy and melting temperature with the options in String [] args.
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static Properties |
loadSequencesTest(String fileName)
loads the data from the file and stocks them in a Properties object.
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public static Properties loadSequencesTest(String fileName)
fileName
- : name or pathway of the file containing the experimental data.public static double getMeltingTest(String[] args)
args
- : contains the test optionspublic static void displayResults(Properties properties, ArrayList<String> methodNames, String hybridization, String solution, String nucleotides, String option)
properties
- : contains the experimental data.methodNames
- : contains all the method or model to test with the experimental data.hybridization
- : type of hybridizationsolution
- : contains the different ion and agent concentrationsnucleotides
- : oligomer concentrationoption
- : option name for the pattern computation method.public static void displayResultsSodium(Properties properties, ArrayList<String> methodNames, String hybridization, String nucleotides, String option)
properties
- : contains the experimental data.methodNames
- : contains all the method or model to test with the experimental data.hybridization
- : type of hybridizationnucleotides
- : oligomer concentrationoption
- : option name for the pattern computation method.public static void displayResultsMagnesium(Properties properties, ArrayList<String> methodNames, String hybridization, String nucleotides, String option)
properties
- : contains the experimental data.methodNames
- : contains all the method or model to test with the experimental data.hybridization
- : type of hybridizationnucleotides
- : oligomer concentrationoption
- : option name for the pattern computation method.public static void displayResultsNaEq(Properties properties, ArrayList<String> methodNames, String hybridization, String nucleotides, String option)
properties
- : contains the experimental data.methodNames
- : contains all the method or model to test with the experimental data.hybridization
- : type of hybridizationnucleotides
- : oligomer concentrationoption
- : option name for the pattern computation method.public static void displayResultsNaEq(Properties properties, String hybridization)
properties
- : contains the experimental data.methodNames
- : contains all the method or model to test with the experimental data.hybridization
- : type of hybridizationnucleotides
- : oligomer concentrationoption
- : option name for the pattern computation method.public static void displayResultsLongDanglingEnd(Properties properties, ArrayList<String> methodNames, String hybridization, String solution, String nucleotides, String option)
properties
- : contains the experimental data.methodNames
- : contains all the method or model to test with the experimental data.hybridization
- : type of hybridizationsolution
- : contains the different ion and agent concentrationsnucleotides
- : oligomer concentrationoption
- : option name for the pattern computation method.public static void displayResultsWithComplementarySequence(Properties properties, ArrayList<String> methodNames, String hybridization, String solution, String nucleotides, String option)
properties
- : contains the experimental data.methodNames
- : contains all the method or model to test with the experimental data.hybridization
- : type of hybridizationsolution
- : contains the different ion and agent concentrationsnucleotides
- : oligomer concentrationoption
- : option name for the pattern computation method.public static void displayResultsInosineMelting4_3WithComplementarySequence(Properties properties, ArrayList<String> methodNames, String hybridization, String solution, String nucleotides)
properties
- : contains the experimental data.methodNames
- : contains all the method or model to test with the experimental data.hybridization
- : type of hybridizationsolution
- : contains the different ion and agent concentrationsnucleotides
- : oligomer concentrationoption
- : option name for the pattern computation method.public static void displayResultsMismatchMeltingCWithComplementarySequence(Properties properties, ArrayList<String> methodNames, String hybridization, String ion, String nucleotides)
properties
- : contains the experimental data.methodNames
- : contains all the method or model to test with the experimental data.hybridization
- : type of hybridizationion
- : contains the different ion concentrationsnucleotides
- : oligomer concentrationpublic static void displayResultsDanglingEndMeltingC(Properties properties, ArrayList<String> methodNames, String hybridization, String ion, String nucleotides)
properties
- : contains the experimental data.methodNames
- : contains all the method or model to test with the experimental data.hybridization
- : type of hybridizationion
- : contains the different ion concentrationsnucleotides
- : oligomer concentrationpublic static void displayResultsSelf(Properties properties, ArrayList<String> methodNames, String hybridization, String solution, String nucleotides, String option)
properties
- : contains the experimental data.methodNames
- : contains all the method or model to test with the experimental data.hybridization
- : type of hybridizationsolution
- : contains the different ion and agent concentrationsnucleotides
- : oligomer concentrationoption
- : option name for the pattern computation method.public static double getCMeltingResult(String args)
args
- : contains test optionspublic static double getC4_3MeltingResult(String args)
args
- : contains test optionspublic static void displayResultsMeltingC(Properties properties, ArrayList<String> methodNames, String hybridization, String ion, String nucleotides)
properties
- : contains the experimental data.methodNames
- : contains all the method or model to test with the experimental data.hybridization
- : type of hybridizationion
- : contains the different ion concentrationsnucleotides
- : oligomer concentrationpublic static void displayResultsDNA_RNAMeltingC(Properties properties, ArrayList<String> methodNames, String hybridization, String ion, String nucleotides)
properties
- : contains the experimental data.methodNames
- : contains all the method or model to test with the experimental data.hybridization
- : type of hybridizationion
- : contains the different ion concentrationsnucleotides
- : oligomer concentrationpublic static void displayResultsDNA_RNAMelting4_3(Properties properties, ArrayList<String> methodNames, String hybridization, String ion, String nucleotides)
properties
- : contains the experimental data.methodNames
- : contains all the method or model to test with the experimental data.hybridization
- : type of hybridizationion
- : contains the different ion concentrationsnucleotides
- : oligomer concentrationpublic static void displayResultsMeltingC4_3(Properties properties, ArrayList<String> methodNames, String hybridization, String ion, String nucleotides)
properties
- : contains the experimental data.methodNames
- : contains all the method or model to test with the experimental data.hybridization
- : type of hybridizationion
- : contains the different ion concentrationsnucleotides
- : oligomer concentrationpublic static void displayResultsMeltingCSelfComplementary(Properties properties, ArrayList<String> methodNames, String hybridization, String ion, String nucleotides)
properties
- : contains the experimental data.methodNames
- : contains all the method or model to test with the experimental data.hybridization
- : type of hybridizationsolution
- : contains the different ion and agent concentrationsnucleotides
- : oligomer concentrationoption
- : option name for the pattern computation method.public static void displayResultsMeltingC4_3SelfComplementary(Properties properties, ArrayList<String> methodNames, String hybridization, String ion, String nucleotides)
properties
- : contains the experimental data.methodNames
- : contains all the method or model to test with the experimental data.hybridization
- : type of hybridizationsolution
- : contains the different ion and agent concentrationsnucleotides
- : oligomer concentrationoption
- : option name for the pattern computation method.