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