- 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
-