S-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

## S

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

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