- Santalucia04 - Class in melting.patternModels.cricksPair
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This class represents the nearest neighbor model san04.
- Santalucia04() - Constructor for class melting.patternModels.cricksPair.Santalucia04
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- Santalucia04InternalLoop - Class in melting.patternModels.InternalLoops
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This class represents the internal loop model san04.
- Santalucia04InternalLoop() - Constructor for class melting.patternModels.InternalLoops.Santalucia04InternalLoop
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- Santalucia04LongBulgeLoop - Class in melting.patternModels.longBulge
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This class represents the long bulge loop model san04.
- Santalucia04LongBulgeLoop() - Constructor for class melting.patternModels.longBulge.Santalucia04LongBulgeLoop
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- Santalucia04SingleBulgeLoop - Class in melting.patternModels.singleBulge
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This class represents the single bulge loop model san04.
- Santalucia04SingleBulgeLoop() - Constructor for class melting.patternModels.singleBulge.Santalucia04SingleBulgeLoop
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- Santalucia05Inosine - Class in melting.patternModels.wobble
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This class represents the inosine model san05.
- Santalucia05Inosine() - Constructor for class melting.patternModels.wobble.Santalucia05Inosine
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- Santalucia96 - Class in melting.patternModels.cricksPair
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This class represents the nearest neighbor model san96.
- Santalucia96() - Constructor for class melting.patternModels.cricksPair.Santalucia96
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- Santalucia96SodiumCorrection - Class in melting.ionCorrection.sodiumCorrections
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This class represents the sodium correction model san96.
- Santalucia96SodiumCorrection() - Constructor for class melting.ionCorrection.sodiumCorrections.Santalucia96SodiumCorrection
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- Santalucia98 - Class in melting.approximativeMethods
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This class represents the model san98.
- Santalucia98() - Constructor for class melting.approximativeMethods.Santalucia98
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- Santalucia98_04SodiumCorrection - Class in melting.ionCorrection.sodiumCorrections
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This class represents the sodium correction model san04.
- Santalucia98_04SodiumCorrection() - Constructor for class melting.ionCorrection.sodiumCorrections.Santalucia98_04SodiumCorrection
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- SchildkrautLifson65SodiumCorrection - Class in melting.ionCorrection.sodiumCorrections
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This class represents the sodium correction model schlif.
- SchildkrautLifson65SodiumCorrection() - Constructor for class melting.ionCorrection.sodiumCorrections.SchildkrautLifson65SodiumCorrection
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- SecondDanglingEndMethod - Class in melting.patternModels.secondDanglingEnds
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This class represents the second dangling end model.
- SecondDanglingEndMethod() - Constructor for class melting.patternModels.secondDanglingEnds.SecondDanglingEndMethod
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- selectAll() - Method in class meltinggui.widgets.InputField
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Selects all the text in the widget.
- selectAll(int) - Method in class meltinggui.widgets.InputFieldArray
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Selects all the text in a particular widget.
- selectAll() - Method in interface meltinggui.widgets.InputWidgetInterface
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Selects all the text in a widget.
- selectAll() - Method in class meltinggui.widgets.MeltingComboBox
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Does nothing.
- selectAll() - Method in class meltinggui.widgets.MeltingTextArea
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Selects all the text in the area.
- selectAll() - Method in class meltinggui.widgets.MeltingTextField
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Selects all the text in the field.
- selectAllSequence() - Method in class meltinggui.dialogs.SequenceDialog
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Selects all the text in the "Sequence" text box.
- selfComplementarity - Static variable in class melting.configuration.OptionManagement
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Option name to precise the self complementarity of the sequences.
- sendMeltingArgs() - Method in class meltinggui.frames.MeltingFrame
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Calculates and displays the MELTING results.
- sequence - Static variable in class melting.configuration.OptionManagement
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Option name for the sequence (5'3').
- SequenceDialog - Class in meltinggui.dialogs
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Dialog for specifying the sequence and complementary sequence.
- SequenceDialog() - Constructor for class meltinggui.dialogs.SequenceDialog
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Creates the dialog.
- SequenceException - Exception in melting.exceptions
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This class represents a problem within the sequences.
- SequenceException() - Constructor for exception melting.exceptions.SequenceException
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- SequenceException(String, Throwable) - Constructor for exception melting.exceptions.SequenceException
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- SequenceException(Throwable) - Constructor for exception melting.exceptions.SequenceException
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- SequenceException(String) - Constructor for exception melting.exceptions.SequenceException
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- Serra05DoubleDanglingEnd - Class in melting.patternModels.secondDanglingEnds
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This class represents the second dangling end model ser05.
- Serra05DoubleDanglingEnd() - Constructor for class melting.patternModels.secondDanglingEnds.Serra05DoubleDanglingEnd
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- Serra06_08SingleDanglingEnd - Class in melting.patternModels.singleDanglingEnds
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This class represents the single dangling end model ser08.
- Serra06_08SingleDanglingEnd() - Constructor for class melting.patternModels.singleDanglingEnds.Serra06_08SingleDanglingEnd
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- Serra06DoubleDanglingEnd - Class in melting.patternModels.secondDanglingEnds
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This class represents the second dangling end model ser06.
- Serra06DoubleDanglingEnd() - Constructor for class melting.patternModels.secondDanglingEnds.Serra06DoubleDanglingEnd
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- Serra07SingleBulgeLoop - Class in melting.patternModels.singleBulge
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This class represents the single bulge loop model ser07.
- Serra07SingleBulgeLoop() - Constructor for class melting.patternModels.singleBulge.Serra07SingleBulgeLoop
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- Serra12Wobble - Class in melting.patternModels.wobble
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This class represents the GU base pair model ser12.
- Serra12Wobble() - Constructor for class melting.patternModels.wobble.Serra12Wobble
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- setArgsOption(String[]) - Method in class meltinggui.MeltingCalculator
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Sets the command-line arguments.
- setBottomAcid(String) - Method in class melting.sequences.BasePair
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To change the BottomAcid Value of BasePair.
- setCalculMethod(MeltingComputationMethod) - Method in class melting.ThermoResult
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Changes the calculation method in the ThermoResult
.
- setChanged() - Method in class meltinggui.MeltingObservable
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Notifies the program that the observable has changed.
- setCommandLineText(String) - Method in class meltinggui.widgets.ComboBoxOption
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Sets the command-line text.
- setDisabled() - Method in class meltinggui.widgets.InputField
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Disables the widget.
- setEnabled() - Method in class meltinggui.widgets.InputField
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Enables the widget.
- setEnthalpy(double) - Method in class melting.Thermodynamics
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This method is called to change the enthalpy of Thermodynamics.
- setEntropy(double) - Method in class melting.Thermodynamics
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This method is called to change the entropy of Thermodynamics.
- setFactor(int) - Method in class melting.Environment
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changes the factor value of Environment.
- setMg(double) - Method in class melting.Environment
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changes the magnesium concentration in the environment
- setNa(double) - Method in class melting.Environment
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changes the sodium concentration in the environment
- setOptionText(String) - Method in class meltinggui.widgets.ComboBoxOption
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Sets the option text.
- setResult(double) - Method in class melting.Environment
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changes the melting temperature of ThermoResult.
- setResult(ThermoResult) - Method in class melting.Environment
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changes the result ThermoResult of Environment.
- setSaltIndependentEntropy(double) - Method in class melting.ThermoResult
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This method is called to change the SaltIndependentEntropy of ThermoResult.
- setScreenPosition(Frame) - Method in class meltinggui.frames.FrameScreenPosition
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Sets up a Frame
object using the stored fields.
- setScreenPosition(JInternalFrame) - Method in class meltinggui.frames.FrameScreenPosition
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Sets up a JInternalFrame
object using the stored fields.
- setScreenPositions(OuterFrame, MeltingFrame, ErrorFrame) - Method in class meltinggui.frames.GuiScreenPositions
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Sets the screen positions of the frames from the stored fields.
- setSelfComplementarity(boolean) - Method in class melting.Environment
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changes the boolean value of the isSelfComplementarity boolean.
- setTm(double) - Method in class melting.ThermoResult
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This method is called to change the Tm of ThermoResult.
- setTopAcid(String) - Method in class melting.sequences.BasePair
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To change the TopAcid Value of BasePair..
- setUpVariables(HashMap<String, String>) - Method in class melting.approximativeMethods.ApproximativeMode
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- setUpVariables(HashMap<String, String>) - Method in class melting.approximativeMethods.MarmurChester62_93
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- setUpVariables(HashMap<String, String>) - Method in interface melting.methodInterfaces.MeltingComputationMethod
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Creates the Environment object and set up the variables of the chosen model.
- setUpVariables(HashMap<String, String>) - Method in class melting.nearestNeighborModel.NearestNeighborMode
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- setValue(String) - Method in class meltinggui.widgets.InputField
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Sets the value in the widget.
- setValue(int, String) - Method in class meltinggui.widgets.InputFieldArray
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Sets the value in a particular widget.
- setValue(String) - Method in interface meltinggui.widgets.InputWidgetInterface
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Sets the value in the widget.
- setValue(String) - Method in class meltinggui.widgets.MeltingComboBox
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Does nothing.
- setValue(String) - Method in class meltinggui.widgets.MeltingTextArea
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Sets the text in the area.
- setValue(String) - Method in class meltinggui.widgets.MeltingTextField
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Sets the text in the field.
- singleBulgeLoopMethod - Static variable in class melting.configuration.OptionManagement
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Option name for the choice of single bulge loop computation method.
- singleDanglingEndMethod - Static variable in class melting.configuration.OptionManagement
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Option name for the choice of single dangling end computation method.
- SingleDanglingEndMethod - Class in melting.patternModels.singleDanglingEnds
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This class represents the single dangling end model.
- SingleDanglingEndMethod() - Constructor for class melting.patternModels.singleDanglingEnds.SingleDanglingEndMethod
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- singleMismatchMethod - Static variable in class melting.configuration.OptionManagement
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Option name for the choice of single mismatch computation method.
- SodiumEquivalent - Class in melting.ionCorrection.sodiumEquivalence
-
This class represents the methods to compute a sodium equivalence.
- SodiumEquivalent() - Constructor for class melting.ionCorrection.sodiumEquivalence.SodiumEquivalent
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- SodiumEquivalentMethod - Interface in melting.methodInterfaces
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This interface is implemented by classes which contain a method to compute an equivalent sodium concentration when
other ions are present.
- solutioncomposition - Static variable in class melting.configuration.OptionManagement
-
Option name for the different ion and agent concentrations (mol/L).
- sortSquences(String, String, String) - Method in class melting.Environment
-
sorts the sequences in function of the type of hybridization : In case of DNA/RNA type of hybridization, the sequence (5'3') must be a DNA sequence
and the complementary sequence (3'5') a RNA sequence.
- SpecificAcidNames - Enum in melting.sequences
-
This enum represents the name of the specific or modified nucleic acid, which can be inosine, locked nucleic acid, hydroxyadenine and azobenzene
- startElement(String, String, String, Attributes) - Method in class melting.handlers.DataHandler
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- startElement(String, String, String, Attributes) - Method in class melting.handlers.EnergyHandler
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- startElement(String, String, String, Attributes) - Method in class melting.handlers.ThermoHandler
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- subHandler - Variable in class melting.handlers.NodeHandler
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NodeHandler subHandler : the Handler for the subnode.
- Sugimoto01Hydroxyadenine - Class in melting.patternModels.specificAcids
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This class represents the hydroxyadenine (A*) model sug01.
- Sugimoto01Hydroxyadenine() - Constructor for class melting.patternModels.specificAcids.Sugimoto01Hydroxyadenine
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- Sugimoto02DNADanglingEnd - Class in melting.patternModels.longDanglingEnds
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This class represents the long dangling end model sugdna02 (for long poly A only).
- Sugimoto02DNADanglingEnd() - Constructor for class melting.patternModels.longDanglingEnds.Sugimoto02DNADanglingEnd
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- Sugimoto02RNADanglingEnd - Class in melting.patternModels.longDanglingEnds
-
This class represents the long dangling end model sugrna02 (for long poly A only).
- Sugimoto02RNADanglingEnd() - Constructor for class melting.patternModels.longDanglingEnds.Sugimoto02RNADanglingEnd
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- Sugimoto95 - Class in melting.patternModels.cricksPair
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This class represents the nearest neighbor model sug95.
- Sugimoto95() - Constructor for class melting.patternModels.cricksPair.Sugimoto95
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- Sugimoto96 - Class in melting.patternModels.cricksPair
-
This class represents the nearest neighbor model sug96.
- Sugimoto96() - Constructor for class melting.patternModels.cricksPair.Sugimoto96
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- SugimotoLongDanglingEndMethod - Class in melting.patternModels.longDanglingEnds
-
This class represents the long dangling end model (for long poly A only)from Sugimoto et al.
- SugimotoLongDanglingEndMethod() - Constructor for class melting.patternModels.longDanglingEnds.SugimotoLongDanglingEndMethod
-