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M

main(String[]) - Static method in class examples.MainTestApproximativeMode
 
main(String[]) - Static method in class examples.MainTestApproximativeModeMeltingC
 
main(String[]) - Static method in class examples.MainTestAzobenzene
 
main(String[]) - Static method in class examples.MainTestCNGSequences
 
main(String[]) - Static method in class examples.MainTestDNADanglingEndMeltingC
 
main(String[]) - Static method in class examples.MainTestDNAMagnesiumCorrections
 
main(String[]) - Static method in class examples.MainTestDNAMismatchesMeltingC
 
main(String[]) - Static method in class examples.MainTestDNASodiumCorrections
 
main(String[]) - Static method in class examples.MainTestGUBasePairs
 
main(String[]) - Static method in class examples.MainTestHydroxyadenine
 
main(String[]) - Static method in class examples.MainTestInosineBasePairs
 
main(String[]) - Static method in class examples.MainTestInosineMelting4_3
 
main(String[]) - Static method in class examples.MainTestInternalLoop
 
main(String[]) - Static method in class examples.MainTestLockedAcidNucleic
 
main(String[]) - Static method in class examples.MainTestLongDanglingEnd
 
main(String[]) - Static method in class examples.MainTestMeltingC4_3PerfectMatching
 
main(String[]) - Static method in class examples.MainTestMeltingCPerfectMatching
 
main(String[]) - Static method in class examples.MainTestNaEqMethods
 
main(String[]) - Static method in class examples.MainTestPerfectMatching
 
main(String[]) - Static method in class examples.MainTestSecondDanglingEnd
 
main(String[]) - Static method in class examples.MainTestSingleBulgeLoops
 
main(String[]) - Static method in class examples.MainTestSingleDanglingEnd
 
main(String[]) - Static method in class examples.MainTestSingleMismatches
 
main(String[]) - Static method in class examples.MainTestSingleMismatchLockedAcidNucleic
 
main(String[]) - Static method in class examples.MainTestTandemLockedAcidNucleic
 
main(String[]) - Static method in class examples.MainTestTandemMismatches
 
main(String[]) - Static method in class melting.BatchMain
 
main(String[]) - Static method in class melting.CompatibleMain
 
Main - Class in melting
The Melting main class which contains the public static void main(String[] args) method.
Main() - Constructor for class melting.Main
 
main(String[]) - Static method in class melting.Main
 
main(String[]) - Static method in class meltinggui.MeltingGui
Starts up the new frame, and creates an instance of MELTING on it.
MainTest - Class in examples
This class contains the different method tests.
MainTest() - Constructor for class examples.MainTest
 
MainTestApproximativeMode - Class in examples
This class exists to test the different approximative methods.
MainTestApproximativeMode() - Constructor for class examples.MainTestApproximativeMode
 
MainTestApproximativeModeMeltingC - Class in examples
This class exists to test the formulas approximations of MELTING 4.2 with DNA sequences.
MainTestApproximativeModeMeltingC() - Constructor for class examples.MainTestApproximativeModeMeltingC
 
MainTestAzobenzene - Class in examples
This class exists to test the different azobenzene methods.
MainTestAzobenzene() - Constructor for class examples.MainTestAzobenzene
 
MainTestCNGSequences - Class in examples
This class exists to test the different CNG repeats methods.
MainTestCNGSequences() - Constructor for class examples.MainTestCNGSequences
 
MainTestDNADanglingEndMeltingC - Class in examples
 
MainTestDNADanglingEndMeltingC() - Constructor for class examples.MainTestDNADanglingEndMeltingC
 
MainTestDNAMagnesiumCorrections - Class in examples
This class exists to test the different magnesium corrections with DNA sequences.
MainTestDNAMagnesiumCorrections() - Constructor for class examples.MainTestDNAMagnesiumCorrections
 
MainTestDNAMismatchesMeltingC - Class in examples
 
MainTestDNAMismatchesMeltingC() - Constructor for class examples.MainTestDNAMismatchesMeltingC
 
MainTestDNASodiumCorrections - Class in examples
This class exists to test the different sodium corrections with DNA sequences.
MainTestDNASodiumCorrections() - Constructor for class examples.MainTestDNASodiumCorrections
 
MainTestGUBasePairs - Class in examples
This class exists to test the different GU base pair methods.
MainTestGUBasePairs() - Constructor for class examples.MainTestGUBasePairs
 
MainTestHydroxyadenine - Class in examples
This class exists to test the different hydroxyadenine methods.
MainTestHydroxyadenine() - Constructor for class examples.MainTestHydroxyadenine
 
MainTestInosineBasePairs - Class in examples
This class exists to test the different inosine methods.
MainTestInosineBasePairs() - Constructor for class examples.MainTestInosineBasePairs
 
MainTestInosineMelting4_3 - Class in examples
 
MainTestInosineMelting4_3() - Constructor for class examples.MainTestInosineMelting4_3
 
MainTestInternalLoop - Class in examples
This class exists to test the different internal loop methods.
MainTestInternalLoop() - Constructor for class examples.MainTestInternalLoop
 
MainTestLockedAcidNucleic - Class in examples
This class exists to test the different locked nucleic acid methods.
MainTestLockedAcidNucleic() - Constructor for class examples.MainTestLockedAcidNucleic
 
MainTestLongDanglingEnd - Class in examples
This class exists to test the different long dangling end methods.
MainTestLongDanglingEnd() - Constructor for class examples.MainTestLongDanglingEnd
 
MainTestMeltingC4_3PerfectMatching - Class in examples
This class exists to test the different nearest neighbor parameters with Melting 4.3.
MainTestMeltingC4_3PerfectMatching() - Constructor for class examples.MainTestMeltingC4_3PerfectMatching
 
MainTestMeltingCPerfectMatching - Class in examples
This class exists to test the different nearest neighbor parameters with Melting 4.2.
MainTestMeltingCPerfectMatching() - Constructor for class examples.MainTestMeltingCPerfectMatching
 
MainTestNaEqMethods - Class in examples
This class exists to test the sodium equivalent formulas with DNA sequences.
MainTestNaEqMethods() - Constructor for class examples.MainTestNaEqMethods
 
MainTestPerfectMatching - Class in examples
This class exists to test the different nearest neighbor methods.
MainTestPerfectMatching() - Constructor for class examples.MainTestPerfectMatching
 
MainTestSecondDanglingEnd - Class in examples
This class exists to test the different second dangling end methods.
MainTestSecondDanglingEnd() - Constructor for class examples.MainTestSecondDanglingEnd
 
MainTestSingleBulgeLoops - Class in examples
This class exists to test the different single bulge loop methods.
MainTestSingleBulgeLoops() - Constructor for class examples.MainTestSingleBulgeLoops
 
MainTestSingleDanglingEnd - Class in examples
This class exists to test the different single dangling end methods.
MainTestSingleDanglingEnd() - Constructor for class examples.MainTestSingleDanglingEnd
 
MainTestSingleMismatches - Class in examples
This class exists to test the different single mismatch methods.
MainTestSingleMismatches() - Constructor for class examples.MainTestSingleMismatches
 
MainTestSingleMismatchLockedAcidNucleic - Class in examples
This class exists to test the different tandem locked nucleic acid methods.
MainTestSingleMismatchLockedAcidNucleic() - Constructor for class examples.MainTestSingleMismatchLockedAcidNucleic
 
MainTestTandemLockedAcidNucleic - Class in examples
This class exists to test the different tandem locked nucleic acid methods.
MainTestTandemLockedAcidNucleic() - Constructor for class examples.MainTestTandemLockedAcidNucleic
 
MainTestTandemMismatches - Class in examples
This class exists to test the different tandem mimsatches methods.
MainTestTandemMismatches() - Constructor for class examples.MainTestTandemMismatches
 
makeMethodList() - Static method in class melting.configuration.RegisterMethods
Creates an instance of the MethodType enum, initialized with all the (non-final) methods from the RegisterMethods class.
MarmurChester62_93 - Class in melting.approximativeMethods
This class represents the model che93.
MarmurChester62_93(double, String) - Constructor for class melting.approximativeMethods.MarmurChester62_93
Sets up the private variables: parameter and methodName.
MarmurChester62_93() - Constructor for class melting.approximativeMethods.MarmurChester62_93
Sets up the private variables for the uncorrected version.
MarmurChester62_93_corr - Class in melting.approximativeMethods
This class represents the model che93corr.
MarmurChester62_93_corr() - Constructor for class melting.approximativeMethods.MarmurChester62_93_corr
Sets up the private variables for the corrected method.
MarmurSchildkrautDoty - Class in melting.approximativeMethods
This class represents the model schdot.
MarmurSchildkrautDoty() - Constructor for class melting.approximativeMethods.MarmurSchildkrautDoty
 
MarmurSchildkrautDoty98_62SodiumCorrection - Class in melting.ionCorrection.sodiumCorrections
This class represents the sodium correction model marschdot.
MarmurSchildkrautDoty98_62SodiumCorrection() - Constructor for class melting.ionCorrection.sodiumCorrections.MarmurSchildkrautDoty98_62SodiumCorrection
 
maximumLayoutSize(Container) - Method in class meltinggui.MeltingLayout
Returns the maximum size for the specified container.
McTigue04LockedAcid - Class in melting.patternModels.specificAcids
This class represents the locked nucleic acid (AL, GL, CL or TL) model mct04.
McTigue04LockedAcid() - Constructor for class melting.patternModels.specificAcids.McTigue04LockedAcid
 
melting - package melting
 
melting.approximativeMethods - package melting.approximativeMethods
 
melting.configuration - package melting.configuration
 
melting.correctionMethods - package melting.correctionMethods
 
melting.exceptions - package melting.exceptions
 
melting.handlers - package melting.handlers
 
melting.ionCorrection.magnesiumCorrections - package melting.ionCorrection.magnesiumCorrections
 
melting.ionCorrection.mixedNaMgCorrections - package melting.ionCorrection.mixedNaMgCorrections
 
melting.ionCorrection.sodiumCorrections - package melting.ionCorrection.sodiumCorrections
 
melting.ionCorrection.sodiumEquivalence - package melting.ionCorrection.sodiumEquivalence
 
melting.methodInterfaces - package melting.methodInterfaces
 
melting.nearestNeighborModel - package melting.nearestNeighborModel
 
melting.otherCorrections.dmsoCorrections - package melting.otherCorrections.dmsoCorrections
 
melting.otherCorrections.formamideCorrections - package melting.otherCorrections.formamideCorrections
 
melting.patternModels - package melting.patternModels
 
melting.patternModels.cngPatterns - package melting.patternModels.cngPatterns
 
melting.patternModels.cricksPair - package melting.patternModels.cricksPair
 
melting.patternModels.InternalLoops - package melting.patternModels.InternalLoops
 
melting.patternModels.longBulge - package melting.patternModels.longBulge
 
melting.patternModels.longDanglingEnds - package melting.patternModels.longDanglingEnds
 
melting.patternModels.secondDanglingEnds - package melting.patternModels.secondDanglingEnds
 
melting.patternModels.singleBulge - package melting.patternModels.singleBulge
 
melting.patternModels.singleDanglingEnds - package melting.patternModels.singleDanglingEnds
 
melting.patternModels.singleMismatch - package melting.patternModels.singleMismatch
 
melting.patternModels.specificAcids - package melting.patternModels.specificAcids
 
melting.patternModels.tandemMismatches - package melting.patternModels.tandemMismatches
 
melting.patternModels.wobble - package melting.patternModels.wobble
 
melting.sequences - package melting.sequences
 
MeltingCalculator - Class in meltinggui
Class intended to provide an interface between the GUI and the MELTING program itself.
MeltingCalculator(String[]) - Constructor for class meltinggui.MeltingCalculator
Creates the calculator.
MeltingComboBox - Class in meltinggui.widgets
A combo box where the user can specify a particular option.
MeltingComboBox(ComboBoxOption[]) - Constructor for class meltinggui.widgets.MeltingComboBox
Fills in the combo box options, and sets up the combo box model.
MeltingComputationMethod - Interface in melting.methodInterfaces
This interface is implemented by classes which contain methods to compute the melting temperature.
MeltingFormatter - Class in melting
This class extends Formatter.
MeltingFormatter() - Constructor for class melting.MeltingFormatter
 
MeltingFrame - Class in meltinggui.frames
The frame that opens when the user runs the GUI.
MeltingFrame() - Constructor for class meltinggui.frames.MeltingFrame
Creates the new frame.
meltinggui - package meltinggui
 
MeltingGui - Class in meltinggui
The Main class for the Melting GUI.
MeltingGui() - Constructor for class meltinggui.MeltingGui
Sets up the GUI and displays the main MELTING frame.
meltinggui.dialogs - package meltinggui.dialogs
 
meltinggui.frames - package meltinggui.frames
 
meltinggui.widgets - package meltinggui.widgets
 
meltingHelp - Static variable in class melting.configuration.OptionManagement
Option name for the melting help documentation.
meltingHelpAlt - Static variable in class melting.configuration.OptionManagement
Alternative option name for the melting help documentation.
MeltingLayout - Class in meltinggui
A layout manager designed for use with label/text pairs.
MeltingLayout(Container) - Constructor for class meltinggui.MeltingLayout
Constructs a new MELTING layout with no gaps between components.
MeltingLayout(Container, int, int) - Constructor for class meltinggui.MeltingLayout
Constructs a MELTING layout with the specified gaps between components.
MeltingLayout.ComponentGroupType - Enum in meltinggui
The two possible component groups: Label group and Input group.
MeltingLayout.Size - Enum in meltinggui
Different types of sizes that we might want to find: maximum size, preferred size and minimum size.
MeltingObservable - Class in meltinggui
Class created with the sole intention of extending the {@link java.util.Observable Observable class and overriding its setChanged method so it is no longer protected.
MeltingObservable() - Constructor for class meltinggui.MeltingObservable
 
MeltingTextArea - Class in meltinggui.widgets
A text area for use with the MELTING program.
MeltingTextArea() - Constructor for class meltinggui.widgets.MeltingTextArea
Creates a new MELTING text area with the default number of 4 rows and 32 columns.
MeltingTextArea(int, int) - Constructor for class meltinggui.widgets.MeltingTextArea
Creates a new MELTING text area with a given number of columns.
MeltingTextField - Class in meltinggui.widgets
A text box for use with the MELTING program.
MeltingTextField() - Constructor for class meltinggui.widgets.MeltingTextField
Creates a new MELTING text field with the default number of 16 columns.
MeltingTextField(int) - Constructor for class meltinggui.widgets.MeltingTextField
Creates a new MELTING text field with a given number of columns.
MethodNotApplicableException - Exception in melting.exceptions
This class represents an exception for a method or model which is not applicable.
MethodNotApplicableException(String) - Constructor for exception melting.exceptions.MethodNotApplicableException
 
MethodNotApplicableException() - Constructor for exception melting.exceptions.MethodNotApplicableException
 
MethodNotApplicableException(String, Throwable) - Constructor for exception melting.exceptions.MethodNotApplicableException
 
MethodNotApplicableException(Throwable) - Constructor for exception melting.exceptions.MethodNotApplicableException
 
MethodText - Class in melting.configuration
The text representations corresponding to a method used in melting temperature computation.
MethodText(String, String) - Constructor for class melting.configuration.MethodText
Sets up the method name and command line flag.
minimumLayoutSize(Container) - Method in class meltinggui.MeltingLayout
Returns the minimum size for the specified container.
Mitsuhashi96NaEquivalent - Class in melting.ionCorrection.sodiumEquivalence
This class represents the model for a sodium equivalence mit96.
Mitsuhashi96NaEquivalent() - Constructor for class melting.ionCorrection.sodiumEquivalence.Mitsuhashi96NaEquivalent
 
Musielski81DMSOCorrection - Class in melting.otherCorrections.dmsoCorrections
This class represents the DMSO correction model mus81.
Musielski81DMSOCorrection() - Constructor for class melting.otherCorrections.dmsoCorrections.Musielski81DMSOCorrection
 
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