D-Index
Date: 2014-08-08

A B C D E F G H I L M N O P R S T U V W X Z

## D

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.

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