M-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

## 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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