- d - Variable in class melting.ionCorrection.magnesiumCorrections.Owczarzy08MagnesiumCorrection
-
- DataCollect - Class in melting
-
This class is useful to extract the different thermodynamic parameters from the HashMap which contains them.
- DataCollect() - Constructor for class melting.DataCollect
-
- DataHandler - Class in melting.handlers
-
This class represents a Handler to parse the Data nodes in the xml files.
- DataHandler() - Constructor for class melting.handlers.DataHandler
-
- dataPathway - Static variable in class melting.configuration.OptionManagement
-
Option name for the default melting data files pathway.
- dataPathwayValue - Static variable in class melting.configuration.OptionManagement
-
String dataPathwayValue : default Melting data file pathway.
- decodeSequences(String, String) - Static method in class melting.sequences.NucleotidSequences
-
decodes the String sequence and complementary of NucleotidSequences.
- DecomposedInitiation - Class in melting.patternModels.cricksPair
-
This class represents one model to compute the initiation enthalpy and entropy.
- DecomposedInitiation() - Constructor for class melting.patternModels.cricksPair.DecomposedInitiation
-
- defaultFileName - Static variable in class melting.patternModels.cngPatterns.Broda05CNGRepeats
-
String defaultFileName : default name for the xml file containing the thermodynamic parameters for CNG repeats
- defaultFileName - Static variable in class melting.patternModels.cricksPair.AllawiSantalucia97
-
String defaultFileName : default name for the xml file containing the thermodynamic parameters for each Crick's pair
- defaultFileName - Static variable in class melting.patternModels.cricksPair.Breslauer86
-
String defaultFileName : default name for the xml file containing the thermodynamic parameters for each Crick's pair
- defaultFileName - Static variable in class melting.patternModels.cricksPair.Freier86
-
String defaultFileName : default name for the xml file containing the thermodynamic parameters for each Crick's pair
- defaultFileName - Static variable in class melting.patternModels.cricksPair.Santalucia04
-
String defaultFileName : default name for the xml file containing the thermodynamic parameters for each Crick's pair
- defaultFileName - Static variable in class melting.patternModels.cricksPair.Santalucia96
-
String defaultFileName : default name for the xml file containing the thermodynamic parameters for each Crick's pair
- defaultFileName - Static variable in class melting.patternModels.cricksPair.Sugimoto95
-
String defaultFileName : default name for the xml file containing the thermodynamic parameters for each Crick's pair
- defaultFileName - Static variable in class melting.patternModels.cricksPair.Sugimoto96
-
String defaultFileName : default name for the xml file containing the thermodynamic parameters for each Crick's pair
- defaultFileName - Static variable in class melting.patternModels.cricksPair.Tanaka04
-
String defaultFileName : default name for the xml file containing the thermodynamic parameters for each Crick's pair
- defaultFileName - Static variable in class melting.patternModels.cricksPair.Turner06
-
String defaultFileName : default name for the xml file containing the thermodynamic parameters for each Crick's pair
- defaultFileName - Static variable in class melting.patternModels.cricksPair.Xia98
-
String defaultFileName : default name for the xml file containing the thermodynamic parameters for each Crick's pair
- defaultFileName - Static variable in class melting.patternModels.InternalLoops.Santalucia04InternalLoop
-
String defaultFileName : default name for the xml file containing the thermodynamic parameters for internal loop
- defaultFileName - Static variable in class melting.patternModels.InternalLoops.Turner06InternalLoop
-
String defaultFileName : default name for the xml file containing the thermodynamic parameters for internal loop
- defaultFileName - Static variable in class melting.patternModels.InternalLoops.Znosko071x2Loop
-
String defaultFileName : default name for the xml file containing the thermodynamic parameters for internal loop
- defaultFileName - Static variable in class melting.patternModels.longBulge.Santalucia04LongBulgeLoop
-
String defaultFileName : default name for the xml file containing the thermodynamic parameters for long bulge loop
- defaultFileName - Static variable in class melting.patternModels.longBulge.Turner99_06LongBulgeLoop
-
String defaultFileName : default name for the xml file containing the thermodynamic parameters for long bulge loop
- defaultFileName - Static variable in class melting.patternModels.longDanglingEnds.Sugimoto02DNADanglingEnd
-
String defaultFileName : default name for the xml file containing the thermodynamic parameters for long dangling end
(just long poly A)
- defaultFileName - Static variable in class melting.patternModels.longDanglingEnds.Sugimoto02RNADanglingEnd
-
String defaultFileName : default name for the xml file containing the thermodynamic parameters for long dangling end
(just long poly A)
- defaultFileName - Static variable in class melting.patternModels.secondDanglingEnds.Serra05DoubleDanglingEnd
-
String defaultFileName : default name for the xml file containing the thermodynamic parameters for second dangling end
- defaultFileName - Static variable in class melting.patternModels.secondDanglingEnds.Serra06DoubleDanglingEnd
-
String defaultFileName : default name for the xml file containing the thermodynamic parameters for second dangling end
- defaultFileName - Static variable in class melting.patternModels.singleBulge.Serra07SingleBulgeLoop
-
String defaultFileName : default name for the xml file containing the thermodynamic parameters for single bulge loop
- defaultFileName - Static variable in class melting.patternModels.singleBulge.Tanaka04SingleBulgeLoop
-
String defaultFileName : default name for the xml file containing the thermodynamic parameters for single bulge loop
- defaultFileName - Static variable in class melting.patternModels.singleDanglingEnds.Bommarito00SingleDanglingEnd
-
String defaultFileName : default name for the xml file containing the thermodynamic parameters for single dangling end
- defaultFileName - Static variable in class melting.patternModels.singleDanglingEnds.Serra06_08SingleDanglingEnd
-
String defaultFileName : default name for the xml file containing the thermodynamic parameters for single dangling end
- defaultFileName - Static variable in class melting.patternModels.singleMismatch.AllawiSantaluciaPeyret97_98_99mm
-
String defaultFileName : default name for the xml file containing the thermodynamic parameters for single mismatch
- defaultFileName - Static variable in class melting.patternModels.singleMismatch.Turner06mm
-
String defaultFileName : default name for the xml file containing the thermodynamic parameters for single mismatch
- defaultFileName - Static variable in class melting.patternModels.singleMismatch.Watkins11mm
-
Default name for the xml file containing the thermodynamic parameters for
a single mismatch in a DNA/RNA duplex.
- defaultFileName - Static variable in class melting.patternModels.singleMismatch.Znosko07mm
-
String defaultFileName : default name for the xml file containing the thermodynamic parameters for single mismatch
- defaultFileName - Static variable in class melting.patternModels.singleMismatch.Znosko08mm
-
String defaultFileName : default name for the xml file containing the thermodynamic parameters for single mismatch
- defaultFileName - Static variable in class melting.patternModels.specificAcids.Asanuma05Azobenzene
-
- defaultFileName - Static variable in class melting.patternModels.specificAcids.McTigue04LockedAcid
-
String defaultFileName : default name for the xml file containing the thermodynamic parameters for locked nucleic acid
- defaultFileName - Static variable in class melting.patternModels.specificAcids.Owczarzy11LockedAcid
-
String defaultFileName : default name for the xml file containing the thermodynamic parameters for locked nucleic acid
- defaultFileName - Static variable in class melting.patternModels.specificAcids.Owczarzy11SingleMismatchLockedAcid
-
String defaultFileName : default name for the xml file containing the thermodynamic parameters for locked nucleic acid
- defaultFileName - Static variable in class melting.patternModels.specificAcids.Owczarzy11TandemLockedAcid
-
String defaultFileName : default name for the xml file containing the thermodynamic parameters for locked nucleic acid
- defaultFileName - Static variable in class melting.patternModels.specificAcids.Sugimoto01Hydroxyadenine
-
String defaultFileName : default name for the xml file containing the thermodynamic parameters for hydroxyadenine mismatch
- defaultFileName - Static variable in class melting.patternModels.tandemMismatches.AllawiSantaluciaPeyret97_98_99tanmm
-
String defaultFileName : default name for the xml file containing the thermodynamic parameters for tandem mismatches
- defaultFileName - Static variable in class melting.patternModels.tandemMismatches.Turner99_06tanmm
-
String defaultFileName : default name for the xml file containing the thermodynamic parameters for tandem mismatches
- defaultFileName - Static variable in class melting.patternModels.wobble.Santalucia05Inosine
-
String defaultFileName : default name for the xml file containing the thermodynamic parameters for inosine
- defaultFileName - Static variable in class melting.patternModels.wobble.Serra12Wobble
-
String defaultFileName : default name for the xml file containing the thermodynamic parameters for GU base pairs
- defaultFileName - Static variable in class melting.patternModels.wobble.Turner99Wobble
-
String defaultFileName : default name for the xml file containing the thermodynamic parameters for GU base pairs
- defaultFileName - Static variable in class melting.patternModels.wobble.Znosko07Inosine
-
String defaultFileName : default name for the xml file containing the thermodynamic parameters for inosine
- DialogInterface - Interface in meltinggui.dialogs
-
An interface that represents a dialog on the GUI.
- disable(int) - Method in class meltinggui.widgets.InputFieldArray
-
Disables a widget.
- disableAll() - Method in class meltinggui.widgets.InputFieldArray
-
Disables all widgets.
- disableEnthalpyEntropy() - Method in class meltinggui.dialogs.ResultsPanel
-
Disables the enthalpy and entropy output fields.
- displayMeltingResults(ThermoResult) - Method in class meltinggui.dialogs.ResultsPanel
-
Displays the results from the MELTING program.
- displayMeltingResults(ThermoResult) - Method in class meltinggui.frames.MeltingFrame
-
Displays the MELTING results.
- displayMeltingResults(ThermoResult) - Method in class meltinggui.frames.OuterFrame
-
Displays MELTING results on the MELTING frame.
- displayResults(Properties, ArrayList<String>, String, String, String, String) - Static method in class examples.MainTest
-
displays the computed and experimental melting temperature for each method or model to test.
- displayResultsDanglingEndMeltingC(Properties, ArrayList<String>, String, String, String) - Static method in class examples.MainTest
-
displays the computed and experimental melting temperature for single dangling ends.
- displayResultsDNA_RNAMelting4_3(Properties, ArrayList<String>, String, String, String) - Static method in class examples.MainTest
-
displays the computed and experimental melting temperature for DNA/RNA duplexes.
- displayResultsDNA_RNAMeltingC(Properties, ArrayList<String>, String, String, String) - Static method in class examples.MainTest
-
displays the computed and experimental melting temperature for DNA/RNA duplexes.
- displayResultsInosineMelting4_3WithComplementarySequence(Properties, ArrayList<String>, String, String, String) - Static method in class examples.MainTest
-
displays the computed and experimental melting temperature for each method or model to test.
- displayResultsLongDanglingEnd(Properties, ArrayList<String>, String, String, String, String) - Static method in class examples.MainTest
-
displays the computed and experimental melting temperature for each dangling end method or model.
- displayResultsMagnesium(Properties, ArrayList<String>, String, String, String) - Static method in class examples.MainTest
-
displays the computed and experimental melting temperature for each method or model to test with different magnesium concentrations.
- displayResultsMeltingC(Properties, ArrayList<String>, String, String, String) - Static method in class examples.MainTest
-
displays the computed and experimental melting temperature for each method or model to test.
- displayResultsMeltingC4_3(Properties, ArrayList<String>, String, String, String) - Static method in class examples.MainTest
-
displays the computed and experimental melting temperature for each method or model to test.
- displayResultsMeltingC4_3SelfComplementary(Properties, ArrayList<String>, String, String, String) - Static method in class examples.MainTest
-
displays the computed and experimental melting temperature for each method or model to test.
- displayResultsMeltingCSelfComplementary(Properties, ArrayList<String>, String, String, String) - Static method in class examples.MainTest
-
displays the computed and experimental melting temperature for each method or model to test.
- displayResultsMismatchMeltingCWithComplementarySequence(Properties, ArrayList<String>, String, String, String) - Static method in class examples.MainTest
-
displays the computed and experimental melting temperature for single mismatches.
- displayResultsNaEq(Properties, ArrayList<String>, String, String, String) - Static method in class examples.MainTest
-
displays the computed and experimental melting temperature for each NaEq method or model to test with different magnesium concentrations.
- displayResultsNaEq(Properties, String) - Static method in class examples.MainTest
-
displays the computed and experimental melting temperature with MELTING 4.2 approximative formula and with different magnesium concentrations.
- displayResultsSelf(Properties, ArrayList<String>, String, String, String, String) - Static method in class examples.MainTest
-
displays the computed and experimental melting temperature for each method or model to test.
- displayResultsSodium(Properties, ArrayList<String>, String, String, String) - Static method in class examples.MainTest
-
displays the computed and experimental melting temperature for each method or model to test with different sodium concentrations.
- displayResultsWithComplementarySequence(Properties, ArrayList<String>, String, String, String, String) - Static method in class examples.MainTest
-
displays the computed and experimental melting temperature for each method or model to test.
- displayVariable() - Method in class melting.ionCorrection.magnesiumCorrections.Owczarzy08MagnesiumCorrection
-
logs the a, d and g variables.
- displayVariable() - Method in class melting.ionCorrection.mixedNaMgCorrections.Owczarzy08MixedNaMgCorrection
-
- DMSOCorrection - Static variable in class melting.configuration.OptionManagement
-
Option name for the choice of DMSO correction computation method.
- DNADMSOCorrections - Class in melting.correctionMethods
-
This class represents the DMSO correction.
- DNADMSOCorrections() - Constructor for class melting.correctionMethods.DNADMSOCorrections
-
- doubleDanglingEndMethod - Static variable in class melting.configuration.OptionManagement
-
Option name for the choice of double dangling end computation method.