Class Hierarchy
Date: 2014-08-08

# Hierarchy For All Packages

Package Hierarchies:

- examples,
- melting,
- melting.approximativeMethods,
- melting.configuration,
- melting.correctionMethods,
- melting.exceptions,
- melting.handlers,
- melting.ionCorrection.magnesiumCorrections,
- melting.ionCorrection.mixedNaMgCorrections,
- melting.ionCorrection.sodiumCorrections,
- melting.ionCorrection.sodiumEquivalence,
- melting.methodInterfaces,
- melting.nearestNeighborModel,
- melting.otherCorrections.dmsoCorrections,
- melting.otherCorrections.formamideCorrections,
- melting.patternModels,
- melting.patternModels.cngPatterns,
- melting.patternModels.cricksPair,
- melting.patternModels.InternalLoops,
- melting.patternModels.longBulge,
- melting.patternModels.longDanglingEnds,
- melting.patternModels.secondDanglingEnds,
- melting.patternModels.singleBulge,
- melting.patternModels.singleDanglingEnds,
- melting.patternModels.singleMismatch,
- melting.patternModels.specificAcids,
- melting.patternModels.tandemMismatches,
- melting.patternModels.wobble,
- melting.sequences,
- meltinggui,
- meltinggui.dialogs,
- meltinggui.frames,
- meltinggui.widgets

## Class Hierarchy

- java.lang.Object
  - melting.approximativeMethods.ApproximativeMode (implements melting.methodInterfaces.MeltingComputationMethod)
    - melting.approximativeMethods.Ahsen01 (implements melting.methodInterfaces.NamedMethod)
    - melting.approximativeMethods.MarmurChester62_93 (implements melting.methodInterfaces.NamedMethod)
      - melting.approximativeMethods.MarmurChester62_93_corr
    - melting.approximativeMethods.MarmurSchildkrautDoty (implements melting.methodInterfaces.NamedMethod)
    - melting.approximativeMethods.Owen69 (implements melting.methodInterfaces.NamedMethod)
    - melting.approximativeMethods.Santalucia98 (implements melting.methodInterfaces.NamedMethod)
    - melting.approximativeMethods.Wetmur91
      - melting.approximativeMethods.WetmurDNA91 (implements melting.methodInterfaces.NamedMethod)
      - melting.approximativeMethods.WetmurDNARNA91 (implements melting.methodInterfaces.NamedMethod)
      - melting.approximativeMethods.WetmurRNA91 (implements melting.methodInterfaces.NamedMethod)
  - meltinggui.ArgsMessage
  - melting.sequences.BasePair
  - melting.BatchMain
  - melting.otherCorrections.formamideCorrections.Blake96FormamideCorrection (implements melting.methodInterfaces.CorrectionMethod, melting.methodInterfaces.NamedMethod)
  - meltinggui.widgets.ComboBoxOption
  - melting.CompatibleMain
  - java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
    - java.awt.Container
      - javax.swing.JComponent (implements java.io.Serializable)
        - javax.swing.JComboBox<E> (implements javax.accessibility.Accessible, java.awt.event.ActionListener, java.awt.ItemSelectable, javax.swing.event.ListDataListener)
          - meltinggui.dialogs.IonConcentrationDialog (implements meltinggui.dialogs.DialogInterface)
          - meltinggui.widgets.MeltingComboBox (implements meltinggui.widgets.InputWidgetInterface)
            - meltinggui.widgets.HybridizationWidget
        - javax.swing.JInternalFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
          - meltinggui.frames.ErrorFrame
          - meltinggui.frames.MeltingFrame
        - javax.swing.JPanel (implements javax.accessibility.Accessible)
          - meltinggui.dialogs.ComboBoxDialog (implements meltinggui.dialogs.DialogInterface)
          - meltinggui.widgets.InputFieldArray<W>
            - meltinggui.widgets.InputField<W> (implements meltinggui.widgets.InputWidgetInterface)
              - meltinggui.dialogs.HybridizationDialog (implements meltinggui.dialogs.DialogInterface)
              - meltinggui.dialogs.OligomerConcentrationDialog (implements meltinggui.dialogs.DialogInterface)
              - meltinggui.widgets.OutputField (implements meltinggui.widgets.InputWidgetInterface)
            - meltinggui.dialogs.SequenceDialog (implements meltinggui.dialogs.DialogInterface)
          - meltinggui.dialogs.ResultsPanel
        - javax.swing.text.JTextComponent (implements javax.accessibility.Accessible, javax.swing.Scrollable)
          - javax.swing.JTextArea
            - meltinggui.widgets.MeltingTextArea (implements meltinggui.widgets.InputWidgetInterface)
          - javax.swing.JTextField (implements javax.swing.SwingConstants)
            - meltinggui.widgets.MeltingTextField (implements meltinggui.widgets.InputWidgetInterface)
      - java.awt.Window (implements javax.accessibility.Accessible)
        - java.awt.Frame (implements java.awt.MenuContainer)
          - javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            - meltinggui.MeltingGui (implements java.util.Observer)
            - meltinggui.frames.OuterFrame
  - melting.DataCollect
  - org.xml.sax.helpers.DefaultHandler (implements org.xml.sax.ContentHandler, org.xml.sax.DTDHandler, org.xml.sax.EntityResolver, org.xml.sax.ErrorHandler)
    - melting.handlers.NodeHandler
      - melting.handlers.DataHandler
      - melting.handlers.EnergyHandler
      - melting.handlers.ThermoHandler
  - melting.correctionMethods.DNADMSOCorrections (implements melting.methodInterfaces.CorrectionMethod)
    - melting.otherCorrections.dmsoCorrections.Ahsen01DMSOCorrection (implements melting.methodInterfaces.NamedMethod)
    - melting.otherCorrections.dmsoCorrections.Cullen76DMSOCorrection (implements melting.methodInterfaces.NamedMethod)
    - melting.otherCorrections.dmsoCorrections.Escara80DMSOCorrection (implements melting.methodInterfaces.NamedMethod)
    - melting.otherCorrections.dmsoCorrections.Musielski81DMSOCorrection (implements melting.methodInterfaces.NamedMethod)
  - melting.correctionMethods.EntropyCorrection (implements melting.methodInterfaces.CorrectionMethod)
    - melting.ionCorrection.sodiumCorrections.Ahsen01SodiumCorrection (implements melting.methodInterfaces.NamedMethod)
    - melting.ionCorrection.sodiumCorrections.Santalucia98_04SodiumCorrection (implements melting.methodInterfaces.NamedMethod)
    - melting.ionCorrection.magnesiumCorrections.Tan06MagnesiumCorrection (implements melting.methodInterfaces.NamedMethod)
    - melting.ionCorrection.sodiumCorrections.Tan06SodiumCorrection (implements melting.methodInterfaces.NamedMethod)
    - melting.ionCorrection.magnesiumCorrections.Tan07MagnesiumCorrection (implements melting.methodInterfaces.NamedMethod)
    - melting.ionCorrection.mixedNaMgCorrections.Tan07MixedNaMgCorrection (implements melting.methodInterfaces.NamedMethod)
    - melting.ionCorrection.sodiumCorrections.Tan07SodiumCorrection (implements melting.methodInterfaces.NamedMethod)
  - melting.Environment
  - melting.FileReader
  - melting.otherCorrections.formamideCorrections.FormamideLinearMethod (implements melting.methodInterfaces.CorrectionMethod, melting.methodInterfaces.NamedMethod)
  - java.util.logging.Formatter
    - melting.MeltingFormatter
  - meltinggui.frames.FrameScreenPosition (implements java.io.Serializable)
  - melting.ionCorrection.sodiumCorrections.FrankKamenetskii71SodiumCorrection (implements melting.methodInterfaces.CorrectionMethod, melting.methodInterfaces.NamedMethod)
  - meltinggui.frames.GuiScreenPositions (implements java.io.Serializable)
  - melting.Helper
  - melting.Main
  - examples.MainTest
  - examples.MainTestApproximativeMode
  - examples.MainTestApproximativeModeMeltingC
  - examples.MainTestAzobenzene
  - examples.MainTestCNGSequences
  - examples.MainTestDNADanglingEndMeltingC
  - examples.MainTestDNAMagnesiumCorrections
  - examples.MainTestDNAMismatchesMeltingC
  - examples.MainTestDNASodiumCorrections
  - examples.MainTestGUBasePairs
  - examples.MainTestHydroxyadenine
  - examples.MainTestInosineBasePairs
  - examples.MainTestInosineMelting4_3
  - examples.MainTestInternalLoop
  - examples.MainTestLockedAcidNucleic
  - examples.MainTestLongDanglingEnd
  - examples.MainTestMeltingC4_3PerfectMatching
  - examples.MainTestMeltingCPerfectMatching
  - examples.MainTestNaEqMethods
  - examples.MainTestPerfectMatching
  - examples.MainTestSecondDanglingEnd
  - examples.MainTestSingleBulgeLoops
  - examples.MainTestSingleDanglingEnd
  - examples.MainTestSingleMismatches
  - examples.MainTestSingleMismatchLockedAcidNucleic
  - examples.MainTestTandemLockedAcidNucleic
  - examples.MainTestTandemMismatches
  - melting.ionCorrection.sodiumCorrections.MarmurSchildkrautDoty98_62SodiumCorrection (implements melting.methodInterfaces.CorrectionMethod, melting.methodInterfaces.NamedMethod)
  - meltinggui.MeltingCalculator
  - meltinggui.MeltingLayout (implements java.awt.LayoutManager2, java.io.Serializable)
  - melting.configuration.MethodText
  - melting.nearestNeighborModel.NearestNeighborMode (implements melting.methodInterfaces.MeltingComputationMethod)
  - melting.sequences.NucleotidSequences
  - java.util.Observable
    - meltinggui.MeltingObservable
  - melting.configuration.OptionManagement
  - melting.ionCorrection.sodiumCorrections.Owczarzy04SodiumCorrection19 (implements melting.methodInterfaces.CorrectionMethod, melting.methodInterfaces.NamedMethod)
  - melting.ionCorrection.sodiumCorrections.Owczarzy04SodiumCorrection20 (implements melting.methodInterfaces.CorrectionMethod, melting.methodInterfaces.NamedMethod)
  - melting.ionCorrection.sodiumCorrections.Owczarzy04SodiumCorrection21 (implements melting.methodInterfaces.CorrectionMethod, melting.methodInterfaces.NamedMethod)
  - melting.ionCorrection.sodiumCorrections.Owczarzy04SodiumCorrection22 (implements melting.methodInterfaces.CorrectionMethod, melting.methodInterfaces.NamedMethod)
  - melting.ionCorrection.magnesiumCorrections.Owczarzy08MagnesiumCorrection (implements melting.methodInterfaces.CorrectionMethod, melting.methodInterfaces.NamedMethod)
    - melting.ionCorrection.mixedNaMgCorrections.Owczarzy08MixedNaMgCorrection (implements melting.methodInterfaces.NamedMethod)
  - melting.patternModels.PatternComputation (implements melting.methodInterfaces.PatternComputationMethod)
    - melting.patternModels.singleMismatch.AllawiSantaluciaPeyret97_98_99mm (implements melting.methodInterfaces.NamedMethod)
    - melting.patternModels.tandemMismatches.AllawiSantaluciaPeyret97_98_99tanmm (implements melting.methodInterfaces.NamedMethod)
    - melting.patternModels.specificAcids.Asanuma05Azobenzene (implements melting.methodInterfaces.NamedMethod)
    - melting.patternModels.cngPatterns.Broda05CNGRepeats (implements melting.methodInterfaces.NamedMethod)
    - melting.patternModels.cricksPair.CricksNNMethod
      - melting.patternModels.cricksPair.DecomposedInitiation
        - melting.patternModels.cricksPair.AllawiSantalucia97 (implements melting.methodInterfaces.NamedMethod)
        - melting.patternModels.cricksPair.Tanaka04 (implements melting.methodInterfaces.NamedMethod)
      - melting.patternModels.cricksPair.Freier86 (implements melting.methodInterfaces.NamedMethod)
      - melting.patternModels.cricksPair.GlobalInitiation
        - melting.patternModels.cricksPair.Breslauer86 (implements melting.methodInterfaces.NamedMethod)
        - melting.patternModels.cricksPair.Santalucia96 (implements melting.methodInterfaces.NamedMethod)
      - melting.patternModels.cricksPair.Santalucia04 (implements melting.methodInterfaces.NamedMethod)
      - melting.patternModels.cricksPair.Sugimoto95 (implements melting.methodInterfaces.NamedMethod)
      - melting.patternModels.cricksPair.Sugimoto96 (implements melting.methodInterfaces.NamedMethod)
      - melting.patternModels.cricksPair.Turner06 (implements melting.methodInterfaces.NamedMethod)
      - melting.patternModels.cricksPair.Xia98 (implements melting.methodInterfaces.NamedMethod)
    - melting.patternModels.singleBulge.GlobalSingleBulgeLoopMethod
      - melting.patternModels.singleBulge.Serra07SingleBulgeLoop (implements melting.methodInterfaces.NamedMethod)
      - melting.patternModels.singleBulge.Tanaka04SingleBulgeLoop (implements melting.methodInterfaces.NamedMethod)
    - melting.patternModels.wobble.InosineNNMethod
      - melting.patternModels.wobble.Santalucia05Inosine (implements melting.methodInterfaces.NamedMethod)
      - melting.patternModels.wobble.Znosko07Inosine (implements melting.methodInterfaces.NamedMethod)
    - melting.patternModels.specificAcids.LockedAcidNNMethod (implements melting.methodInterfaces.NamedMethod)
      - melting.patternModels.specificAcids.Owczarzy11SingleMismatchLockedAcid (implements melting.methodInterfaces.NamedMethod)
      - melting.patternModels.specificAcids.Owczarzy11TandemLockedAcid (implements melting.methodInterfaces.NamedMethod)
    - melting.patternModels.specificAcids.McTigue04LockedAcid (implements melting.methodInterfaces.NamedMethod)
    - melting.patternModels.specificAcids.Owczarzy11LockedAcid (implements melting.methodInterfaces.NamedMethod)
    - melting.patternModels.InternalLoops.Santalucia04InternalLoop (implements melting.methodInterfaces.NamedMethod)
    - melting.patternModels.longBulge.Santalucia04LongBulgeLoop (implements melting.methodInterfaces.NamedMethod)
      - melting.patternModels.singleBulge.Santalucia04SingleBulgeLoop (implements melting.methodInterfaces.NamedMethod)
    - melting.patternModels.secondDanglingEnds.SecondDanglingEndMethod
      - melting.patternModels.secondDanglingEnds.Serra05DoubleDanglingEnd (implements melting.methodInterfaces.NamedMethod)
      - melting.patternModels.secondDanglingEnds.Serra06DoubleDanglingEnd (implements melting.methodInterfaces.NamedMethod)
    - melting.patternModels.wobble.Serra12Wobble (implements melting.methodInterfaces.NamedMethod)
    - melting.patternModels.singleDanglingEnds.SingleDanglingEndMethod
      - melting.patternModels.singleDanglingEnds.Bommarito00SingleDanglingEnd (implements melting.methodInterfaces.NamedMethod)
      - melting.patternModels.singleDanglingEnds.Serra06_08SingleDanglingEnd (implements melting.methodInterfaces.NamedMethod)
    - melting.patternModels.specificAcids.Sugimoto01Hydroxyadenine (implements melting.methodInterfaces.NamedMethod)
    - melting.patternModels.longDanglingEnds.SugimotoLongDanglingEndMethod
      - melting.patternModels.longDanglingEnds.Sugimoto02DNADanglingEnd (implements melting.methodInterfaces.NamedMethod)
      - melting.patternModels.longDanglingEnds.Sugimoto02RNADanglingEnd (implements melting.methodInterfaces.NamedMethod)
    - melting.patternModels.InternalLoops.Turner06InternalLoop (implements melting.methodInterfaces.NamedMethod)
    - melting.patternModels.singleMismatch.Turner06mm (implements melting.methodInterfaces.NamedMethod)
    - melting.patternModels.longBulge.Turner99_06LongBulgeLoop (implements melting.methodInterfaces.NamedMethod)
      - melting.patternModels.singleBulge.Turner99_06SingleBulgeLoop (implements melting.methodInterfaces.NamedMethod)
    - melting.patternModels.tandemMismatches.Turner99_06tanmm (implements melting.methodInterfaces.NamedMethod)
    - melting.patternModels.wobble.Turner99Wobble (implements melting.methodInterfaces.NamedMethod)
    - melting.patternModels.singleMismatch.Watkins11mm (implements melting.methodInterfaces.NamedMethod)
    - melting.patternModels.InternalLoops.Znosko071x2Loop (implements melting.methodInterfaces.NamedMethod)
    - melting.patternModels.singleMismatch.ZnoskoMethod
      - melting.patternModels.singleMismatch.Znosko07mm (implements melting.methodInterfaces.NamedMethod)
      - melting.patternModels.singleMismatch.Znosko08mm (implements melting.methodInterfaces.NamedMethod)
  - melting.configuration.RegisterMethods
  - melting.ionCorrection.sodiumCorrections.Santalucia96SodiumCorrection (implements melting.methodInterfaces.CorrectionMethod, melting.methodInterfaces.NamedMethod)
  - melting.ionCorrection.sodiumCorrections.SchildkrautLifson65SodiumCorrection (implements melting.methodInterfaces.CorrectionMethod, melting.methodInterfaces.NamedMethod)
  - melting.ionCorrection.sodiumEquivalence.SodiumEquivalent (implements melting.methodInterfaces.SodiumEquivalentMethod)
    - melting.ionCorrection.sodiumEquivalence.Ahsen01_NaEquivalent (implements melting.methodInterfaces.NamedMethod)
    - melting.ionCorrection.sodiumEquivalence.Mitsuhashi96NaEquivalent (implements melting.methodInterfaces.NamedMethod)
    - melting.ionCorrection.sodiumEquivalence.Peyret00_NaEquivalent (implements melting.methodInterfaces.NamedMethod)
  - melting.Thermodynamics
    - melting.ThermoResult
  - java.lang.Throwable (implements java.io.Serializable)
    - java.lang.Exception
      - java.lang.RuntimeException
        - melting.exceptions.FileException
        - melting.exceptions.MethodNotApplicableException
        - melting.exceptions.NoExistingMethodException
        - melting.exceptions.NoExistingOutputFileException
        - melting.exceptions.NucleicAcidNotKnownException
        - melting.exceptions.OptionSyntaxError
        - melting.exceptions.SequenceException
        - melting.exceptions.ThermodynamicParameterError
  - melting.ionCorrection.sodiumCorrections.Wetmur91SodiumCorrection (implements melting.methodInterfaces.CorrectionMethod, melting.methodInterfaces.NamedMethod)

## Interface Hierarchy

- melting.methodInterfaces.CorrectionMethod
- meltinggui.dialogs.DialogInterface
- meltinggui.widgets.InputWidgetInterface
- melting.methodInterfaces.MeltingComputationMethod
- melting.methodInterfaces.NamedMethod
- melting.methodInterfaces.PatternComputationMethod
- melting.methodInterfaces.SodiumEquivalentMethod

## Enum Hierarchy

- java.lang.Object
  - java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    - melting.configuration.RegisterMethods.MethodType
    - meltinggui.ArgsMessage.ArgumentType
    - meltinggui.MeltingLayout.ComponentGroupType
    - meltinggui.MeltingLayout.Size
    - melting.sequences.SpecificAcidNames