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<div class="contentContainer"><a href="index-1.html">A</a> <a href="index-2.html">B</a> <a href="index-3.html">C</a> <a href="index-4.html">D</a> <a href="index-5.html">E</a> <a href="index-6.html">F</a> <a href="index-7.html">G</a> <a href="index-8.html">H</a> <a href="index-9.html">I</a> <a href="index-10.html">L</a> <a href="index-11.html">M</a> <a href="index-12.html">N</a> <a href="index-13.html">O</a> <a href="index-14.html">P</a> <a href="index-15.html">R</a> <a href="index-16.html">S</a> <a href="index-17.html">T</a> <a href="index-18.html">U</a> <a href="index-19.html">V</a> <a href="index-20.html">W</a> <a href="index-21.html">X</a> <a href="index-22.html">Z</a> <a name="_G_">
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<h2 class="title">G</h2>
<dl>
<dt><span class="strong"><a href="../melting/ionCorrection/magnesiumCorrections/Owczarzy08MagnesiumCorrection.html#g">g</a></span> - Variable in class melting.ionCorrection.magnesiumCorrections.<a href="../melting/ionCorrection/magnesiumCorrections/Owczarzy08MagnesiumCorrection.html" title="class in melting.ionCorrection.magnesiumCorrections">Owczarzy08MagnesiumCorrection</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="../meltinggui/ArgsMessage.html#getArgumentType()">getArgumentType()</a></span> - Method in class meltinggui.<a href="../meltinggui/ArgsMessage.html" title="class in meltinggui">ArgsMessage</a></dt>
<dd>
<div class="block">Gets the type of the message.</div>
</dd>
<dt><span class="strong"><a href="../melting/DataCollect.html#getAsymmetry()">getAsymmetry()</a></span> - Method in class melting.<a href="../melting/DataCollect.html" title="class in melting">DataCollect</a></dt>
<dd>
<div class="block">to get the Thermodynamics object containing the parameters for the internal loop asymmetry.</div>
</dd>
<dt><span class="strong"><a href="../melting/handlers/ThermoHandler.html#getAttribut()">getAttribut()</a></span> - Method in class melting.handlers.<a href="../melting/handlers/ThermoHandler.html" title="class in melting.handlers">ThermoHandler</a></dt>
<dd>
<div class="block">This method is called to get the attribut HashMap of the ThermoHandler object.</div>
</dd>
<dt><span class="strong"><a href="../melting/DataCollect.html#getAzobenzeneValue(java.lang.String, java.lang.String)">getAzobenzeneValue(String, String)</a></span> - Method in class melting.<a href="../melting/DataCollect.html" title="class in melting">DataCollect</a></dt>
<dd>
<div class="block">to get the Thermodynamics object containing the parameters for the String seq1 and the String seq2 with one of the sequences containing an
azobenzene ("X_C" or "X_T").</div>
</dd>
<dt><span class="strong"><a href="../melting/DataCollect.html#getBonus(java.lang.String, java.lang.String, java.lang.String, java.lang.String)">getBonus(String, String, String, String)</a></span> - Method in class melting.<a href="../melting/DataCollect.html" title="class in melting">DataCollect</a></dt>
<dd>
<div class="block">to get the Thermodynamics object containing the parameters for a Hairpin loop 'seqLoop' preceded
by the base 'base1' and followed by the base 'lastBase'.</div>
</dd>
<dt><span class="strong"><a href="../melting/sequences/BasePair.html#getBottomAcid()">getBottomAcid()</a></span> - Method in class melting.sequences.<a href="../melting/sequences/BasePair.html" title="class in melting.sequences">BasePair</a></dt>
<dd>
<div class="block">This method is called to get the nucleic acid "BottomAcid" of BasePair..</div>
</dd>
<dt><span class="strong"><a href="../melting/DataCollect.html#getBulgeLoopvalue(java.lang.String)">getBulgeLoopvalue(String)</a></span> - Method in class melting.<a href="../melting/DataCollect.html" title="class in melting">DataCollect</a></dt>
<dd>
<div class="block">to get the Thermodynamics object containing the parameters for a bulge loop of size 'size'.</div>
</dd>
<dt><span class="strong"><a href="../examples/MainTest.html#getC4_3MeltingResult(java.lang.String)">getC4_3MeltingResult(String)</a></span> - Static method in class examples.<a href="../examples/MainTest.html" title="class in examples">MainTest</a></dt>
<dd>
<div class="block">to run melting 4.3 and get the results</div>
</dd>
<dt><span class="strong"><a href="../melting/ThermoResult.html#getCalculMethod()">getCalculMethod()</a></span> - Method in class melting.<a href="../melting/ThermoResult.html" title="class in melting">ThermoResult</a></dt>
<dd>
<div class="block">Gets the calculation method of the <code>ThermoResult</code>.</div>
</dd>
<dt><span class="strong"><a href="../melting/DataCollect.html#getClosureValue(java.lang.String, java.lang.String)">getClosureValue(String, String)</a></span> - Method in class melting.<a href="../melting/DataCollect.html" title="class in melting">DataCollect</a></dt>
<dd>
<div class="block">to get the Thermodynamics object containing the parameters for the base pair (base1, base2) next to the mismatching base pair.</div>
</dd>
<dt><span class="strong"><a href="../examples/MainTest.html#getCMeltingResult(java.lang.String)">getCMeltingResult(String)</a></span> - Static method in class examples.<a href="../examples/MainTest.html" title="class in examples">MainTest</a></dt>
<dd>
<div class="block">to run melting 4.2 and get the results</div>
</dd>
<dt><span class="strong"><a href="../melting/DataCollect.html#getCNGvalue(java.lang.String, java.lang.String)">getCNGvalue(String, String)</a></span> - Method in class melting.<a href="../melting/DataCollect.html" title="class in melting">DataCollect</a></dt>
<dd>
<div class="block">to get the Thermodynamics object containing the parameters for the CNG pattern 'seq1'.</div>
</dd>
<dt><span class="strong"><a href="../melting/methodInterfaces/PatternComputationMethod.html#getCollector()">getCollector()</a></span> - Method in interface melting.methodInterfaces.<a href="../melting/methodInterfaces/PatternComputationMethod.html" title="interface in melting.methodInterfaces">PatternComputationMethod</a></dt>
<dd>
<div class="block">This method is called to get the DataCollect of the implemented class.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/PatternComputation.html#getCollector()">getCollector()</a></span> - Method in class melting.patternModels.<a href="../melting/patternModels/PatternComputation.html" title="class in melting.patternModels">PatternComputation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="../meltinggui/dialogs/ComboBoxDialog.html#getCommandLineFlags()">getCommandLineFlags()</a></span> - Method in class meltinggui.dialogs.<a href="../meltinggui/dialogs/ComboBoxDialog.html" title="class in meltinggui.dialogs">ComboBoxDialog</a></dt>
<dd>
<div class="block">Returns the command-line flags corresponding to the user's choice on the
combo box.</div>
</dd>
<dt><span class="strong"><a href="../meltinggui/dialogs/DialogInterface.html#getCommandLineFlags()">getCommandLineFlags()</a></span> - Method in interface meltinggui.dialogs.<a href="../meltinggui/dialogs/DialogInterface.html" title="interface in meltinggui.dialogs">DialogInterface</a></dt>
<dd>
<div class="block">Gets the command-line flags from the dialog.</div>
</dd>
<dt><span class="strong"><a href="../meltinggui/dialogs/HybridizationDialog.html#getCommandLineFlags()">getCommandLineFlags()</a></span> - Method in class meltinggui.dialogs.<a href="../meltinggui/dialogs/HybridizationDialog.html" title="class in meltinggui.dialogs">HybridizationDialog</a></dt>
<dd>
<div class="block">Returns the command-line flags corresponding to the user's choice of
hybridization type.</div>
</dd>
<dt><span class="strong"><a href="../meltinggui/dialogs/IonConcentrationDialog.html#getCommandLineFlags()">getCommandLineFlags()</a></span> - Method in class meltinggui.dialogs.<a href="../meltinggui/dialogs/IonConcentrationDialog.html" title="class in meltinggui.dialogs">IonConcentrationDialog</a></dt>
<dd>
<div class="block">Gets the command line flags the user would have typed in were they using
the command line.</div>
</dd>
<dt><span class="strong"><a href="../meltinggui/dialogs/OligomerConcentrationDialog.html#getCommandLineFlags()">getCommandLineFlags()</a></span> - Method in class meltinggui.dialogs.<a href="../meltinggui/dialogs/OligomerConcentrationDialog.html" title="class in meltinggui.dialogs">OligomerConcentrationDialog</a></dt>
<dd>
<div class="block">Gets the command-line flags.</div>
</dd>
<dt><span class="strong"><a href="../meltinggui/dialogs/SequenceDialog.html#getCommandLineFlags()">getCommandLineFlags()</a></span> - Method in class meltinggui.dialogs.<a href="../meltinggui/dialogs/SequenceDialog.html" title="class in meltinggui.dialogs">SequenceDialog</a></dt>
<dd>
<div class="block">Gets the command-line flags corresponding to the chosen sequence and
complementary sequence.</div>
</dd>
<dt><span class="strong"><a href="../meltinggui/ArgsMessage.html#getCommandLineText()">getCommandLineText()</a></span> - Method in class meltinggui.<a href="../meltinggui/ArgsMessage.html" title="class in meltinggui">ArgsMessage</a></dt>
<dd>
<div class="block">Gets the command-line arguments.</div>
</dd>
<dt><span class="strong"><a href="../meltinggui/widgets/ComboBoxOption.html#getCommandLineText()">getCommandLineText()</a></span> - Method in class meltinggui.widgets.<a href="../meltinggui/widgets/ComboBoxOption.html" title="class in meltinggui.widgets">ComboBoxOption</a></dt>
<dd>
<div class="block">Gets the command-line text.</div>
</dd>
<dt><span class="strong"><a href="../melting/sequences/NucleotidSequences.html#getComplementary(int, int, java.lang.String)">getComplementary(int, int, String)</a></span> - Method in class melting.sequences.<a href="../melting/sequences/NucleotidSequences.html" title="class in melting.sequences">NucleotidSequences</a></dt>
<dd>
<div class="block">This method is called to get a substring of the complementary String between the positions pos1 and pos2 in the duplex.</div>
</dd>
<dt><span class="strong"><a href="../melting/sequences/NucleotidSequences.html#getComplementary()">getComplementary()</a></span> - Method in class melting.sequences.<a href="../melting/sequences/NucleotidSequences.html" title="class in melting.sequences">NucleotidSequences</a></dt>
<dd>
<div class="block">This method is called to get the encoded complementary String of NucleotidSequences.</div>
</dd>
<dt><span class="strong"><a href="../melting/sequences/NucleotidSequences.html#getComplementary(int, int)">getComplementary(int, int)</a></span> - Method in class melting.sequences.<a href="../melting/sequences/NucleotidSequences.html" title="class in melting.sequences">NucleotidSequences</a></dt>
<dd>
<div class="block">This method is called to get a substring between two positions of the complementary String.</div>
</dd>
<dt><span class="strong"><a href="../melting/sequences/NucleotidSequences.html#getComplementaryNNPair(int)">getComplementaryNNPair(int)</a></span> - Method in class melting.sequences.<a href="../melting/sequences/NucleotidSequences.html" title="class in melting.sequences">NucleotidSequences</a></dt>
<dd>
<div class="block">to get the two nucleic acids which are from the complementary sequence (3'5') in the Crick's pair at the position "pos" in the duplex.</div>
</dd>
<dt><span class="strong"><a href="../melting/sequences/NucleotidSequences.html#getComplementaryNNPairUnlocked(int)">getComplementaryNNPairUnlocked(int)</a></span> - Method in class melting.sequences.<a href="../melting/sequences/NucleotidSequences.html" title="class in melting.sequences">NucleotidSequences</a></dt>
<dd>
<div class="block">to get the two unlocked nucleic acids which are from the complementary sequence (3'5') in the Crick's pair at the position "pos" in the duplex.</div>
</dd>
<dt><span class="strong"><a href="../melting/sequences/NucleotidSequences.html#getComplementarySequence(java.lang.String, java.lang.String)">getComplementarySequence(String, String)</a></span> - Static method in class melting.sequences.<a href="../melting/sequences/NucleotidSequences.html" title="class in melting.sequences">NucleotidSequences</a></dt>
<dd>
<div class="block">This method is called when we want to get the complementary of NucleotidSequences with the
type of hybridization "hybridization".</div>
</dd>
<dt><span class="strong"><a href="../meltinggui/dialogs/SequenceDialog.html#getComplementaryText()">getComplementaryText()</a></span> - Method in class meltinggui.dialogs.<a href="../meltinggui/dialogs/SequenceDialog.html" title="class in meltinggui.dialogs">SequenceDialog</a></dt>
<dd>
<div class="block">Gets the complementary sequence text.</div>
</dd>
<dt><span class="strong"><a href="../melting/sequences/NucleotidSequences.html#getComplementaryTo(java.lang.String, int, int)">getComplementaryTo(String, int, int)</a></span> - Method in class melting.sequences.<a href="../melting/sequences/NucleotidSequences.html" title="class in melting.sequences">NucleotidSequences</a></dt>
<dd>
<div class="block">This method is called to get the complementary sequence to the sequence String between the positions pos1 and pos2.</div>
</dd>
<dt><span class="strong"><a href="../melting/Environment.html#getConcentrations()">getConcentrations()</a></span> - Method in class melting.<a href="../melting/Environment.html" title="class in melting">Environment</a></dt>
<dd>
<div class="block">This method is called to get the concentrations of Environment.</div>
</dd>
<dt><span class="strong"><a href="../melting/configuration/RegisterMethods.html#getCorrectionMethod(java.lang.String, java.lang.String)">getCorrectionMethod(String, String)</a></span> - Method in class melting.configuration.<a href="../melting/configuration/RegisterMethods.html" title="class in melting.configuration">RegisterMethods</a></dt>
<dd>
<div class="block">This method is called to get the CorrectionMethod which represents the method 'methodName'
entered with the option 'optionName'.</div>
</dd>
<dt><span class="strong"><a href="../melting/sequences/NucleotidSequences.html#getDanglingSens(java.lang.String, java.lang.String)">getDanglingSens(String, String)</a></span> - Static method in class melting.sequences.<a href="../melting/sequences/NucleotidSequences.html" title="class in melting.sequences">NucleotidSequences</a></dt>
<dd>
<div class="block">this method is called to get the sens of the dangling end for the sequences seq1 and seq2</div>
</dd>
<dt><span class="strong"><a href="../melting/DataCollect.html#getDanglingValue(java.lang.String, java.lang.String)">getDanglingValue(String, String)</a></span> - Method in class melting.<a href="../melting/DataCollect.html" title="class in melting">DataCollect</a></dt>
<dd>
<div class="block">to get the Thermodynamics object containing the parameters for the dangling end present in the duplex
composed of seq1 and seq2.</div>
</dd>
<dt><span class="strong"><a href="../melting/DataCollect.html#getData()">getData()</a></span> - Method in class melting.<a href="../melting/DataCollect.html" title="class in melting">DataCollect</a></dt>
<dd>
<div class="block">This method is called to get the data of DataCollect.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/PatternComputation.html#getData()">getData()</a></span> - Static method in class melting.patternModels.<a href="../melting/patternModels/PatternComputation.html" title="class in melting.patternModels">PatternComputation</a></dt>
<dd>
<div class="block">This method is called to get the HasMap of DataCollect containing the thermodynamic parameters</div>
</dd>
<dt><span class="strong"><a href="../melting/methodInterfaces/PatternComputationMethod.html#getDataFileName(java.lang.String)">getDataFileName(String)</a></span> - Method in interface melting.methodInterfaces.<a href="../melting/methodInterfaces/PatternComputationMethod.html" title="interface in melting.methodInterfaces">PatternComputationMethod</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="../melting/patternModels/PatternComputation.html#getDataFileName(java.lang.String)">getDataFileName(String)</a></span> - Method in class melting.patternModels.<a href="../melting/patternModels/PatternComputation.html" title="class in melting.patternModels">PatternComputation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="../melting/Environment.html#getDMSO()">getDMSO()</a></span> - Method in class melting.<a href="../melting/Environment.html" title="class in melting">Environment</a></dt>
<dd>
<div class="block">This method is called to get the DMSO concentration.</div>
</dd>
<dt><span class="strong"><a href="../melting/configuration/OptionManagement.html#getDNADefaultOptions()">getDNADefaultOptions()</a></span> - Method in class melting.configuration.<a href="../melting/configuration/OptionManagement.html" title="class in melting.configuration">OptionManagement</a></dt>
<dd>
<div class="block">This method is called to get the DNADefaultOptions of OptionManagement.</div>
</dd>
<dt><span class="strong"><a href="../melting/Environment.html#getDNTP()">getDNTP()</a></span> - Method in class melting.<a href="../melting/Environment.html" title="class in melting">Environment</a></dt>
<dd>
<div class="block">This method is called to get the dNTP concentration.</div>
</dd>
<dt><span class="strong"><a href="../melting/sequences/NucleotidSequences.html#getDuplex()">getDuplex()</a></span> - Method in class melting.sequences.<a href="../melting/sequences/NucleotidSequences.html" title="class in melting.sequences">NucleotidSequences</a></dt>
<dd>
<div class="block">This method is called to get the duplex of NucleotidSequences.</div>
</dd>
<dt><span class="strong"><a href="../melting/sequences/NucleotidSequences.html#getDuplexFrom(java.lang.String, java.lang.String)">getDuplexFrom(String, String)</a></span> - Static method in class melting.sequences.<a href="../melting/sequences/NucleotidSequences.html" title="class in melting.sequences">NucleotidSequences</a></dt>
<dd>
<div class="block">This method is called to get the duplex of NucleotidSequences.</div>
</dd>
<dt><span class="strong"><a href="../melting/sequences/NucleotidSequences.html#getDuplexLength()">getDuplexLength()</a></span> - Method in class melting.sequences.<a href="../melting/sequences/NucleotidSequences.html" title="class in melting.sequences">NucleotidSequences</a></dt>
<dd>
<div class="block">This method is called to get the length of the ArrayList duplex of NucleotidSequences.</div>
</dd>
<dt><span class="strong"><a href="../melting/handlers/EnergyHandler.html#getEnergy()">getEnergy()</a></span> - Method in class melting.handlers.<a href="../melting/handlers/EnergyHandler.html" title="class in melting.handlers">EnergyHandler</a></dt>
<dd>
<div class="block">This method is called to get the energy of EnergyHandler.</div>
</dd>
<dt><span class="strong"><a href="../melting/ThermoResult.html#getEnergyValueInJ(double)">getEnergyValueInJ(double)</a></span> - Method in class melting.<a href="../melting/ThermoResult.html" title="class in melting">ThermoResult</a></dt>
<dd>
<div class="block">converts the energyValy double in cal/mol into an energy value in J/mol.</div>
</dd>
<dt><span class="strong"><a href="../melting/handlers/ThermoHandler.html#getEnthalpy()">getEnthalpy()</a></span> - Method in class melting.handlers.<a href="../melting/handlers/ThermoHandler.html" title="class in melting.handlers">ThermoHandler</a></dt>
<dd>
<div class="block">This method is called to get the enthalpy double value of the ThermoHandler object.</div>
</dd>
<dt><span class="strong"><a href="../melting/Thermodynamics.html#getEnthalpy()">getEnthalpy()</a></span> - Method in class melting.<a href="../melting/Thermodynamics.html" title="class in melting">Thermodynamics</a></dt>
<dd>
<div class="block">This method is called to get the enthalpy of Thermodynamics.</div>
</dd>
<dt><span class="strong"><a href="../melting/handlers/ThermoHandler.html#getEntropy()">getEntropy()</a></span> - Method in class melting.handlers.<a href="../melting/handlers/ThermoHandler.html" title="class in melting.handlers">ThermoHandler</a></dt>
<dd>
<div class="block">This method is called to get the entropy double value of the ThermoHandler object.</div>
</dd>
<dt><span class="strong"><a href="../melting/Thermodynamics.html#getEntropy()">getEntropy()</a></span> - Method in class melting.<a href="../melting/Thermodynamics.html" title="class in melting">Thermodynamics</a></dt>
<dd>
<div class="block">This method is called to get the entropy of Thermodynamics.</div>
</dd>
<dt><span class="strong"><a href="../melting/sequences/NucleotidSequences.html#getEquivalentSequences(java.lang.String)">getEquivalentSequences(String)</a></span> - Method in class melting.sequences.<a href="../melting/sequences/NucleotidSequences.html" title="class in melting.sequences">NucleotidSequences</a></dt>
<dd>
<div class="block">This method is called when the same NucleotidSequences is required but with the sequences converted in the new
hybridization type "hybridizationType"</div>
</dd>
<dt><span class="strong"><a href="../melting/sequences/BasePair.html#getExistingNucleicAcids()">getExistingNucleicAcids()</a></span> - Static method in class melting.sequences.<a href="../melting/sequences/BasePair.html" title="class in melting.sequences">BasePair</a></dt>
<dd>
<div class="block">This method is called to get the existingNucleicAcids of BasePair.</div>
</dd>
<dt><span class="strong"><a href="../melting/Environment.html#getFactor()">getFactor()</a></span> - Method in class melting.<a href="../melting/Environment.html" title="class in melting">Environment</a></dt>
<dd>
<div class="block">This method is called to get the factor of Environment.</div>
</dd>
<dt><span class="strong"><a href="../melting/DataCollect.html#getFirstMismatch(java.lang.String, java.lang.String, java.lang.String)">getFirstMismatch(String, String, String)</a></span> - Method in class melting.<a href="../melting/DataCollect.html" title="class in melting">DataCollect</a></dt>
<dd>
<div class="block">to get the Thermodynamics object containing the parameters for the first non canonical pair in the internal loop.</div>
</dd>
<dt><span class="strong"><a href="../melting/Environment.html#getFormamide()">getFormamide()</a></span> - Method in class melting.<a href="../melting/Environment.html" title="class in melting">Environment</a></dt>
<dd>
<div class="block">This method is called to get the formamide concentration.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/wobble/Serra12Wobble.html#getGUThermoResult(melting.sequences.NucleotidSequences, int, int, melting.ThermoResult)">getGUThermoResult(NucleotidSequences, int, int, ThermoResult)</a></span> - Method in class melting.patternModels.wobble.<a href="../melting/patternModels/wobble/Serra12Wobble.html" title="class in melting.patternModels.wobble">Serra12Wobble</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="../melting/patternModels/wobble/Turner99Wobble.html#getGUThermoResult(melting.sequences.NucleotidSequences, int, int, melting.ThermoResult)">getGUThermoResult(NucleotidSequences, int, int, ThermoResult)</a></span> - Method in class melting.patternModels.wobble.<a href="../melting/patternModels/wobble/Turner99Wobble.html" title="class in melting.patternModels.wobble">Turner99Wobble</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="../melting/DataCollect.html#getHairpinLoopvalue(java.lang.String)">getHairpinLoopvalue(String)</a></span> - Method in class melting.<a href="../melting/DataCollect.html" title="class in melting">DataCollect</a></dt>
<dd>
<div class="block">to get the Thermodynamics object containing the parameters for a Hairpin loop of size 'size'.</div>
</dd>
<dt><span class="strong"><a href="../melting/handlers/EnergyHandler.html#getHasEnergy()">getHasEnergy()</a></span> - Method in class melting.handlers.<a href="../melting/handlers/EnergyHandler.html" title="class in melting.handlers">EnergyHandler</a></dt>
<dd>
<div class="block">This method is called to get the hasEnergy of EnergyHandler.</div>
</dd>
<dt><span class="strong"><a href="../melting/configuration/OptionManagement.html#getHybridDefaultOptions()">getHybridDefaultOptions()</a></span> - Method in class melting.configuration.<a href="../melting/configuration/OptionManagement.html" title="class in melting.configuration">OptionManagement</a></dt>
<dd>
<div class="block">This method is called to get the hybridDefaultOptions of OptionManagement.</div>
</dd>
<dt><span class="strong"><a href="../melting/Environment.html#getHybridization()">getHybridization()</a></span> - Method in class melting.<a href="../melting/Environment.html" title="class in melting">Environment</a></dt>
<dd>
<div class="block">This method is called to get the hybridization of Environment.</div>
</dd>
<dt><span class="strong"><a href="../melting/DataCollect.html#getHydroxyadenosineValue(java.lang.String, java.lang.String)">getHydroxyadenosineValue(String, String)</a></span> - Method in class melting.<a href="../melting/DataCollect.html" title="class in melting">DataCollect</a></dt>
<dd>
<div class="block">to get the Thermodynamics object containing the parameters for the String seq1 and the String seq2 with one of the sequences containing a
hydroxyadenine ("A*").</div>
</dd>
<dt><span class="strong"><a href="../melting/DataCollect.html#getInitiation()">getInitiation()</a></span> - Method in class melting.<a href="../melting/DataCollect.html" title="class in melting">DataCollect</a></dt>
<dd>
<div class="block">to get the Thermodynamics object containing the parameters for the hybridization initiation.</div>
</dd>
<dt><span class="strong"><a href="../melting/DataCollect.html#getInitiation(java.lang.String)">getInitiation(String)</a></span> - Method in class melting.<a href="../melting/DataCollect.html" title="class in melting">DataCollect</a></dt>
<dd>
<div class="block">to get the Thermodynamics object containing the parameters for the initiation with the specified type of initiation.</div>
</dd>
<dt><span class="strong"><a href="../melting/DataCollect.html#getInitiationBulgevalue(java.lang.String)">getInitiationBulgevalue(String)</a></span> - Method in class melting.<a href="../melting/DataCollect.html" title="class in melting">DataCollect</a></dt>
<dd>
<div class="block">to get the Thermodynamics object containing the parameters for the initiation of a bulge loop of size 'size'.</div>
</dd>
<dt><span class="strong"><a href="../melting/DataCollect.html#getInitiationLoopValue(java.lang.String)">getInitiationLoopValue(String)</a></span> - Method in class melting.<a href="../melting/DataCollect.html" title="class in melting">DataCollect</a></dt>
<dd>
<div class="block">to get the Thermodynamics object containing the parameters for the initiation of an internal loop with a specified size.</div>
</dd>
<dt><span class="strong"><a href="../melting/DataCollect.html#getInitiationLoopValue()">getInitiationLoopValue()</a></span> - Method in class melting.<a href="../melting/DataCollect.html" title="class in melting">DataCollect</a></dt>
<dd>
<div class="block">to get the Thermodynamics object containing the parameters for the initiation of an internal loop.</div>
</dd>
<dt><span class="strong"><a href="../melting/sequences/NucleotidSequences.html#getInternalLoopType(int, int)">getInternalLoopType(int, int)</a></span> - Method in class melting.sequences.<a href="../melting/sequences/NucleotidSequences.html" title="class in melting.sequences">NucleotidSequences</a></dt>
<dd>
<div class="block">gives the type of the internal loop at the positions pos1 + 1 and pos2 - 1 in the duplex ArrayList of the NucleotidSequences object.</div>
</dd>
<dt><span class="strong"><a href="../melting/DataCollect.html#getInternalLoopValue(java.lang.String)">getInternalLoopValue(String)</a></span> - Method in class melting.<a href="../melting/DataCollect.html" title="class in melting">DataCollect</a></dt>
<dd>
<div class="block">to get the Thermodynamics object containing the parameters for an internal loop with a specified size.</div>
</dd>
<dt><span class="strong"><a href="../melting/sequences/NucleotidSequences.html#getInversedSequence(java.lang.String)">getInversedSequence(String)</a></span> - Static method in class melting.sequences.<a href="../melting/sequences/NucleotidSequences.html" title="class in melting.sequences">NucleotidSequences</a></dt>
<dd>
<div class="block">creates the inverse String of the sequence</div>
</dd>
<dt><span class="strong"><a href="../melting/configuration/RegisterMethods.html#getIonCorrectionMethod(melting.Environment)">getIonCorrectionMethod(Environment)</a></span> - Method in class melting.configuration.<a href="../melting/configuration/RegisterMethods.html" title="class in melting.configuration">RegisterMethods</a></dt>
<dd>
<div class="block">This method is called to get the CorrectionMethod which represents the method or model
used for the ion correction in the environment 'environment'.</div>
</dd>
<dt><span class="strong"><a href="../melting/Environment.html#getK()">getK()</a></span> - Method in class melting.<a href="../melting/Environment.html" title="class in melting">Environment</a></dt>
<dd>
<div class="block">This method is called to get the potassium concentration.</div>
</dd>
<dt><span class="strong"><a href="../meltinggui/MeltingLayout.html#getLayoutAlignmentX(java.awt.Container)">getLayoutAlignmentX(Container)</a></span> - Method in class meltinggui.<a href="../meltinggui/MeltingLayout.html" title="class in meltinggui">MeltingLayout</a></dt>
<dd>
<div class="block">Returns the alignment along the x axis.</div>
</dd>
<dt><span class="strong"><a href="../meltinggui/MeltingLayout.html#getLayoutAlignmentY(java.awt.Container)">getLayoutAlignmentY(Container)</a></span> - Method in class meltinggui.<a href="../meltinggui/MeltingLayout.html" title="class in meltinggui">MeltingLayout</a></dt>
<dd>
<div class="block">Returns the alignment along the y axis.</div>
</dd>
<dt><span class="strong"><a href="../melting/sequences/BasePair.html#getLengthAcid()">getLengthAcid()</a></span> - Method in class melting.sequences.<a href="../melting/sequences/BasePair.html" title="class in melting.sequences">BasePair</a></dt>
<dd>
<div class="block">This method is called to get the length of the nucleic acid.</div>
</dd>
<dt><span class="strong"><a href="../melting/FileReader.html#getLoadedData()">getLoadedData()</a></span> - Static method in class melting.<a href="../melting/FileReader.html" title="class in melting">FileReader</a></dt>
<dd>
<div class="block">This method is called to get the loadedData of FileReader.</div>
</dd>
<dt><span class="strong"><a href="../melting/DataCollect.html#getLockedAcidValue(java.lang.String, java.lang.String)">getLockedAcidValue(String, String)</a></span> - Method in class melting.<a href="../melting/DataCollect.html" title="class in melting">DataCollect</a></dt>
<dd>
<div class="block">to get the Thermodynamics object containing the parameters for the String seq1 and the String seq2 with one of the sequences containing a
locked nucleic acid ("AL", "TL", "GL" or "CL").</div>
</dd>
<dt><span class="strong"><a href="../melting/sequences/NucleotidSequences.html#getLoopFistMismatch(int)">getLoopFistMismatch(int)</a></span> - Method in class melting.sequences.<a href="../melting/sequences/NucleotidSequences.html" title="class in melting.sequences">NucleotidSequences</a></dt>
<dd>
<div class="block">This method is called to get the first mismatch of the internal loop at the positions pos1 + 1 and pos2 - 1
in the duplex ArrayList of the NucleotidSequences object.</div>
</dd>
<dt><span class="strong"><a href="../melting/handlers/DataHandler.html#getMap()">getMap()</a></span> - Method in class melting.handlers.<a href="../melting/handlers/DataHandler.html" title="class in melting.handlers">DataHandler</a></dt>
<dd>
<div class="block">This method is called to get the map of DataHandler.</div>
</dd>
<dt><span class="strong"><a href="../melting/configuration/RegisterMethods.html#getMeltingComputationMethod(java.util.HashMap)">getMeltingComputationMethod(HashMap<String, String>)</a></span> - Method in class melting.configuration.<a href="../melting/configuration/RegisterMethods.html" title="class in melting.configuration">RegisterMethods</a></dt>
<dd>
<div class="block">This method is called to get the MeltingComputationMethod which represents the method or model
for the enthalpy, entropy and melting temperature computation in the HashMap 'optionSet'.</div>
</dd>
<dt><span class="strong"><a href="../melting/Main.html#getMeltingResults(java.lang.String[], melting.configuration.OptionManagement)">getMeltingResults(String[], OptionManagement)</a></span> - Static method in class melting.<a href="../melting/Main.html" title="class in melting">Main</a></dt>
<dd>
<div class="block">Compute the entropy, enthalpy and melting temperature, and return
these results.</div>
</dd>
<dt><span class="strong"><a href="../examples/MainTest.html#getMeltingTest(java.lang.String[])">getMeltingTest(String[])</a></span> - Static method in class examples.<a href="../examples/MainTest.html" title="class in examples">MainTest</a></dt>
<dd>
<div class="block">computes the enthalpy, entropy and melting temperature with the options in String [] args.</div>
</dd>
<dt><span class="strong"><a href="../melting/configuration/MethodText.html#getMethodCommandLineFlag()">getMethodCommandLineFlag()</a></span> - Method in class melting.configuration.<a href="../melting/configuration/MethodText.html" title="class in melting.configuration">MethodText</a></dt>
<dd>
<div class="block">Gets the method command line flag.</div>
</dd>
<dt><span class="strong"><a href="../melting/configuration/MethodText.html#getMethodName()">getMethodName()</a></span> - Method in class melting.configuration.<a href="../melting/configuration/MethodText.html" title="class in melting.configuration">MethodText</a></dt>
<dd>
<div class="block">Gets the method name.</div>
</dd>
<dt><span class="strong"><a href="../melting/configuration/RegisterMethods.MethodType.html#getMethodTextList()">getMethodTextList()</a></span> - Method in enum melting.configuration.<a href="../melting/configuration/RegisterMethods.MethodType.html" title="enum in melting.configuration">RegisterMethods.MethodType</a></dt>
<dd>
<div class="block">Gets a list of the text representations of methods of this type.</div>
</dd>
<dt><span class="strong"><a href="../melting/configuration/RegisterMethods.html#getMethodType()">getMethodType()</a></span> - Method in class melting.configuration.<a href="../melting/configuration/RegisterMethods.html" title="class in melting.configuration">RegisterMethods</a></dt>
<dd>
<div class="block">Gets an instance of the <code>MethodType</code> enum from the current
instance of <code>RegisterMethods</code>.</div>
</dd>
<dt><span class="strong"><a href="../melting/Environment.html#getMg()">getMg()</a></span> - Method in class melting.<a href="../melting/Environment.html" title="class in melting">Environment</a></dt>
<dd>
<div class="block">This method is called to get the magnesium concentration.</div>
</dd>
<dt><span class="strong"><a href="../meltinggui/widgets/MeltingTextArea.html#getMinimumSize()">getMinimumSize()</a></span> - Method in class meltinggui.widgets.<a href="../meltinggui/widgets/MeltingTextArea.html" title="class in meltinggui.widgets">MeltingTextArea</a></dt>
<dd>
<div class="block">Override the <code>getMinimumSize</code> method to return the preferred
size - these text areas should never be any smaller than their preferred
size.</div>
</dd>
<dt><span class="strong"><a href="../melting/DataCollect.html#getMismatchParameterValue(java.lang.String, java.lang.String)">getMismatchParameterValue(String, String)</a></span> - Method in class melting.<a href="../melting/DataCollect.html" title="class in melting">DataCollect</a></dt>
<dd>
<div class="block">to get the Thermodynamics object containing the parameters for the mismatching base pair (base1, base2).</div>
</dd>
<dt><span class="strong"><a href="../melting/DataCollect.html#getMismatchValue(java.lang.String, java.lang.String)">getMismatchValue(String, String)</a></span> - Method in class melting.<a href="../melting/DataCollect.html" title="class in melting">DataCollect</a></dt>
<dd>
<div class="block">to get the Thermodynamics object containing the parameters for the mismatch(es) present in the duplex
composed of seq1 and seq2.</div>
</dd>
<dt><span class="strong"><a href="../melting/DataCollect.html#getMismatchValue(java.lang.String, java.lang.String, java.lang.String)">getMismatchValue(String, String, String)</a></span> - Method in class melting.<a href="../melting/DataCollect.html" title="class in melting">DataCollect</a></dt>
<dd>
<div class="block">to get the Thermodynamics object containing the parameters for the the duplex composed of seq1 and seq2 with the
specified type of closing base pairs.</div>
</dd>
<dt><span class="strong"><a href="../melting/sequences/NucleotidSequences.html#getModifiedAcidName(melting.sequences.BasePair)">getModifiedAcidName(BasePair)</a></span> - Method in class melting.sequences.<a href="../melting/sequences/NucleotidSequences.html" title="class in melting.sequences">NucleotidSequences</a></dt>
<dd>
<div class="block">This method is called to get the name of a specific nucleic acid in the base pair (BasePair object).</div>
</dd>
<dt><span class="strong"><a href="../melting/sequences/NucleotidSequences.html#getModifiedAcidNames()">getModifiedAcidNames()</a></span> - Static method in class melting.sequences.<a href="../melting/sequences/NucleotidSequences.html" title="class in melting.sequences">NucleotidSequences</a></dt>
<dd>
<div class="block">This method is called to get the modifiedAcidNames of NucleotidSequences.</div>
</dd>
<dt><span class="strong"><a href="../melting/DataCollect.html#getModifiedvalue(java.lang.String, java.lang.String)">getModifiedvalue(String, String)</a></span> - Method in class melting.<a href="../melting/DataCollect.html" title="class in melting">DataCollect</a></dt>
<dd>
<div class="block">to get the Thermodynamics object containing the parameters for the crick's pair composed of the String seq1 and the String seq2 with
one of the sequences containing a specific nucleic acid.</div>
</dd>
<dt><span class="strong"><a href="../melting/DataCollect.html#getModifiedvalue(java.lang.String, java.lang.String, java.lang.String)">getModifiedvalue(String, String, String)</a></span> - Method in class melting.<a href="../melting/DataCollect.html" title="class in melting">DataCollect</a></dt>
<dd>
<div class="block">to get the Thermodynamics object containing the parameters for the String seq1 and the String seq2 with one of the sequences containing a specific
nucleic acid and a dangling end.</div>
</dd>
<dt><span class="strong"><a href="../melting/configuration/OptionManagement.html#getMRNADefaultOptions()">getMRNADefaultOptions()</a></span> - Method in class melting.configuration.<a href="../melting/configuration/OptionManagement.html" title="class in melting.configuration">OptionManagement</a></dt>
<dd>
<div class="block">This method is called to get the mRNADefaultOptions of OptionManagement.</div>
</dd>
<dt><span class="strong"><a href="../melting/Environment.html#getNa()">getNa()</a></span> - Method in class melting.<a href="../melting/Environment.html" title="class in melting">Environment</a></dt>
<dd>
<div class="block">This method is called to get the sodium concentration.</div>
</dd>
<dt><span class="strong"><a href="../melting/configuration/RegisterMethods.html#getNaEqMethod(java.util.HashMap)">getNaEqMethod(HashMap<String, String>)</a></span> - Method in class melting.configuration.<a href="../melting/configuration/RegisterMethods.html" title="class in melting.configuration">RegisterMethods</a></dt>
<dd>
<div class="block">This method is called to get the SodiumEquivalentMethod which represents the method or model
for the sodium equivalence in the HashMap 'optionSet'.</div>
</dd>
<dt><span class="strong"><a href="../melting/approximativeMethods/Ahsen01.html#getName()">getName()</a></span> - Method in class melting.approximativeMethods.<a href="../melting/approximativeMethods/Ahsen01.html" title="class in melting.approximativeMethods">Ahsen01</a></dt>
<dd>
<div class="block">Gets the name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/approximativeMethods/MarmurChester62_93.html#getName()">getName()</a></span> - Method in class melting.approximativeMethods.<a href="../melting/approximativeMethods/MarmurChester62_93.html" title="class in melting.approximativeMethods">MarmurChester62_93</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/approximativeMethods/MarmurSchildkrautDoty.html#getName()">getName()</a></span> - Method in class melting.approximativeMethods.<a href="../melting/approximativeMethods/MarmurSchildkrautDoty.html" title="class in melting.approximativeMethods">MarmurSchildkrautDoty</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/approximativeMethods/Owen69.html#getName()">getName()</a></span> - Method in class melting.approximativeMethods.<a href="../melting/approximativeMethods/Owen69.html" title="class in melting.approximativeMethods">Owen69</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/approximativeMethods/Santalucia98.html#getName()">getName()</a></span> - Method in class melting.approximativeMethods.<a href="../melting/approximativeMethods/Santalucia98.html" title="class in melting.approximativeMethods">Santalucia98</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/approximativeMethods/WetmurDNA91.html#getName()">getName()</a></span> - Method in class melting.approximativeMethods.<a href="../melting/approximativeMethods/WetmurDNA91.html" title="class in melting.approximativeMethods">WetmurDNA91</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/approximativeMethods/WetmurDNARNA91.html#getName()">getName()</a></span> - Method in class melting.approximativeMethods.<a href="../melting/approximativeMethods/WetmurDNARNA91.html" title="class in melting.approximativeMethods">WetmurDNARNA91</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/approximativeMethods/WetmurRNA91.html#getName()">getName()</a></span> - Method in class melting.approximativeMethods.<a href="../melting/approximativeMethods/WetmurRNA91.html" title="class in melting.approximativeMethods">WetmurRNA91</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/handlers/ThermoHandler.html#getName()">getName()</a></span> - Method in class melting.handlers.<a href="../melting/handlers/ThermoHandler.html" title="class in melting.handlers">ThermoHandler</a></dt>
<dd>
<div class="block">This method is called to get the name String of the ThermoHandler object.</div>
</dd>
<dt><span class="strong"><a href="../melting/ionCorrection/magnesiumCorrections/Owczarzy08MagnesiumCorrection.html#getName()">getName()</a></span> - Method in class melting.ionCorrection.magnesiumCorrections.<a href="../melting/ionCorrection/magnesiumCorrections/Owczarzy08MagnesiumCorrection.html" title="class in melting.ionCorrection.magnesiumCorrections">Owczarzy08MagnesiumCorrection</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/ionCorrection/magnesiumCorrections/Tan06MagnesiumCorrection.html#getName()">getName()</a></span> - Method in class melting.ionCorrection.magnesiumCorrections.<a href="../melting/ionCorrection/magnesiumCorrections/Tan06MagnesiumCorrection.html" title="class in melting.ionCorrection.magnesiumCorrections">Tan06MagnesiumCorrection</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/ionCorrection/magnesiumCorrections/Tan07MagnesiumCorrection.html#getName()">getName()</a></span> - Method in class melting.ionCorrection.magnesiumCorrections.<a href="../melting/ionCorrection/magnesiumCorrections/Tan07MagnesiumCorrection.html" title="class in melting.ionCorrection.magnesiumCorrections">Tan07MagnesiumCorrection</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/ionCorrection/mixedNaMgCorrections/Owczarzy08MixedNaMgCorrection.html#getName()">getName()</a></span> - Method in class melting.ionCorrection.mixedNaMgCorrections.<a href="../melting/ionCorrection/mixedNaMgCorrections/Owczarzy08MixedNaMgCorrection.html" title="class in melting.ionCorrection.mixedNaMgCorrections">Owczarzy08MixedNaMgCorrection</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/ionCorrection/mixedNaMgCorrections/Tan07MixedNaMgCorrection.html#getName()">getName()</a></span> - Method in class melting.ionCorrection.mixedNaMgCorrections.<a href="../melting/ionCorrection/mixedNaMgCorrections/Tan07MixedNaMgCorrection.html" title="class in melting.ionCorrection.mixedNaMgCorrections">Tan07MixedNaMgCorrection</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/ionCorrection/sodiumCorrections/Ahsen01SodiumCorrection.html#getName()">getName()</a></span> - Method in class melting.ionCorrection.sodiumCorrections.<a href="../melting/ionCorrection/sodiumCorrections/Ahsen01SodiumCorrection.html" title="class in melting.ionCorrection.sodiumCorrections">Ahsen01SodiumCorrection</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/ionCorrection/sodiumCorrections/FrankKamenetskii71SodiumCorrection.html#getName()">getName()</a></span> - Method in class melting.ionCorrection.sodiumCorrections.<a href="../melting/ionCorrection/sodiumCorrections/FrankKamenetskii71SodiumCorrection.html" title="class in melting.ionCorrection.sodiumCorrections">FrankKamenetskii71SodiumCorrection</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/ionCorrection/sodiumCorrections/MarmurSchildkrautDoty98_62SodiumCorrection.html#getName()">getName()</a></span> - Method in class melting.ionCorrection.sodiumCorrections.<a href="../melting/ionCorrection/sodiumCorrections/MarmurSchildkrautDoty98_62SodiumCorrection.html" title="class in melting.ionCorrection.sodiumCorrections">MarmurSchildkrautDoty98_62SodiumCorrection</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/ionCorrection/sodiumCorrections/Owczarzy04SodiumCorrection19.html#getName()">getName()</a></span> - Method in class melting.ionCorrection.sodiumCorrections.<a href="../melting/ionCorrection/sodiumCorrections/Owczarzy04SodiumCorrection19.html" title="class in melting.ionCorrection.sodiumCorrections">Owczarzy04SodiumCorrection19</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/ionCorrection/sodiumCorrections/Owczarzy04SodiumCorrection20.html#getName()">getName()</a></span> - Method in class melting.ionCorrection.sodiumCorrections.<a href="../melting/ionCorrection/sodiumCorrections/Owczarzy04SodiumCorrection20.html" title="class in melting.ionCorrection.sodiumCorrections">Owczarzy04SodiumCorrection20</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/ionCorrection/sodiumCorrections/Owczarzy04SodiumCorrection21.html#getName()">getName()</a></span> - Method in class melting.ionCorrection.sodiumCorrections.<a href="../melting/ionCorrection/sodiumCorrections/Owczarzy04SodiumCorrection21.html" title="class in melting.ionCorrection.sodiumCorrections">Owczarzy04SodiumCorrection21</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/ionCorrection/sodiumCorrections/Owczarzy04SodiumCorrection22.html#getName()">getName()</a></span> - Method in class melting.ionCorrection.sodiumCorrections.<a href="../melting/ionCorrection/sodiumCorrections/Owczarzy04SodiumCorrection22.html" title="class in melting.ionCorrection.sodiumCorrections">Owczarzy04SodiumCorrection22</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/ionCorrection/sodiumCorrections/Santalucia96SodiumCorrection.html#getName()">getName()</a></span> - Method in class melting.ionCorrection.sodiumCorrections.<a href="../melting/ionCorrection/sodiumCorrections/Santalucia96SodiumCorrection.html" title="class in melting.ionCorrection.sodiumCorrections">Santalucia96SodiumCorrection</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/ionCorrection/sodiumCorrections/Santalucia98_04SodiumCorrection.html#getName()">getName()</a></span> - Method in class melting.ionCorrection.sodiumCorrections.<a href="../melting/ionCorrection/sodiumCorrections/Santalucia98_04SodiumCorrection.html" title="class in melting.ionCorrection.sodiumCorrections">Santalucia98_04SodiumCorrection</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/ionCorrection/sodiumCorrections/SchildkrautLifson65SodiumCorrection.html#getName()">getName()</a></span> - Method in class melting.ionCorrection.sodiumCorrections.<a href="../melting/ionCorrection/sodiumCorrections/SchildkrautLifson65SodiumCorrection.html" title="class in melting.ionCorrection.sodiumCorrections">SchildkrautLifson65SodiumCorrection</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/ionCorrection/sodiumCorrections/Tan06SodiumCorrection.html#getName()">getName()</a></span> - Method in class melting.ionCorrection.sodiumCorrections.<a href="../melting/ionCorrection/sodiumCorrections/Tan06SodiumCorrection.html" title="class in melting.ionCorrection.sodiumCorrections">Tan06SodiumCorrection</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/ionCorrection/sodiumCorrections/Tan07SodiumCorrection.html#getName()">getName()</a></span> - Method in class melting.ionCorrection.sodiumCorrections.<a href="../melting/ionCorrection/sodiumCorrections/Tan07SodiumCorrection.html" title="class in melting.ionCorrection.sodiumCorrections">Tan07SodiumCorrection</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/ionCorrection/sodiumCorrections/Wetmur91SodiumCorrection.html#getName()">getName()</a></span> - Method in class melting.ionCorrection.sodiumCorrections.<a href="../melting/ionCorrection/sodiumCorrections/Wetmur91SodiumCorrection.html" title="class in melting.ionCorrection.sodiumCorrections">Wetmur91SodiumCorrection</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/ionCorrection/sodiumEquivalence/Ahsen01_NaEquivalent.html#getName()">getName()</a></span> - Method in class melting.ionCorrection.sodiumEquivalence.<a href="../melting/ionCorrection/sodiumEquivalence/Ahsen01_NaEquivalent.html" title="class in melting.ionCorrection.sodiumEquivalence">Ahsen01_NaEquivalent</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/ionCorrection/sodiumEquivalence/Mitsuhashi96NaEquivalent.html#getName()">getName()</a></span> - Method in class melting.ionCorrection.sodiumEquivalence.<a href="../melting/ionCorrection/sodiumEquivalence/Mitsuhashi96NaEquivalent.html" title="class in melting.ionCorrection.sodiumEquivalence">Mitsuhashi96NaEquivalent</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/ionCorrection/sodiumEquivalence/Peyret00_NaEquivalent.html#getName()">getName()</a></span> - Method in class melting.ionCorrection.sodiumEquivalence.<a href="../melting/ionCorrection/sodiumEquivalence/Peyret00_NaEquivalent.html" title="class in melting.ionCorrection.sodiumEquivalence">Peyret00_NaEquivalent</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/methodInterfaces/NamedMethod.html#getName()">getName()</a></span> - Method in interface melting.methodInterfaces.<a href="../melting/methodInterfaces/NamedMethod.html" title="interface in melting.methodInterfaces">NamedMethod</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="../melting/otherCorrections/dmsoCorrections/Ahsen01DMSOCorrection.html#getName()">getName()</a></span> - Method in class melting.otherCorrections.dmsoCorrections.<a href="../melting/otherCorrections/dmsoCorrections/Ahsen01DMSOCorrection.html" title="class in melting.otherCorrections.dmsoCorrections">Ahsen01DMSOCorrection</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/otherCorrections/dmsoCorrections/Cullen76DMSOCorrection.html#getName()">getName()</a></span> - Method in class melting.otherCorrections.dmsoCorrections.<a href="../melting/otherCorrections/dmsoCorrections/Cullen76DMSOCorrection.html" title="class in melting.otherCorrections.dmsoCorrections">Cullen76DMSOCorrection</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/otherCorrections/dmsoCorrections/Escara80DMSOCorrection.html#getName()">getName()</a></span> - Method in class melting.otherCorrections.dmsoCorrections.<a href="../melting/otherCorrections/dmsoCorrections/Escara80DMSOCorrection.html" title="class in melting.otherCorrections.dmsoCorrections">Escara80DMSOCorrection</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/otherCorrections/dmsoCorrections/Musielski81DMSOCorrection.html#getName()">getName()</a></span> - Method in class melting.otherCorrections.dmsoCorrections.<a href="../melting/otherCorrections/dmsoCorrections/Musielski81DMSOCorrection.html" title="class in melting.otherCorrections.dmsoCorrections">Musielski81DMSOCorrection</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/otherCorrections/formamideCorrections/Blake96FormamideCorrection.html#getName()">getName()</a></span> - Method in class melting.otherCorrections.formamideCorrections.<a href="../melting/otherCorrections/formamideCorrections/Blake96FormamideCorrection.html" title="class in melting.otherCorrections.formamideCorrections">Blake96FormamideCorrection</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/otherCorrections/formamideCorrections/FormamideLinearMethod.html#getName()">getName()</a></span> - Method in class melting.otherCorrections.formamideCorrections.<a href="../melting/otherCorrections/formamideCorrections/FormamideLinearMethod.html" title="class in melting.otherCorrections.formamideCorrections">FormamideLinearMethod</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/cngPatterns/Broda05CNGRepeats.html#getName()">getName()</a></span> - Method in class melting.patternModels.cngPatterns.<a href="../melting/patternModels/cngPatterns/Broda05CNGRepeats.html" title="class in melting.patternModels.cngPatterns">Broda05CNGRepeats</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/cricksPair/AllawiSantalucia97.html#getName()">getName()</a></span> - Method in class melting.patternModels.cricksPair.<a href="../melting/patternModels/cricksPair/AllawiSantalucia97.html" title="class in melting.patternModels.cricksPair">AllawiSantalucia97</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/cricksPair/Breslauer86.html#getName()">getName()</a></span> - Method in class melting.patternModels.cricksPair.<a href="../melting/patternModels/cricksPair/Breslauer86.html" title="class in melting.patternModels.cricksPair">Breslauer86</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/cricksPair/Freier86.html#getName()">getName()</a></span> - Method in class melting.patternModels.cricksPair.<a href="../melting/patternModels/cricksPair/Freier86.html" title="class in melting.patternModels.cricksPair">Freier86</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/cricksPair/Santalucia04.html#getName()">getName()</a></span> - Method in class melting.patternModels.cricksPair.<a href="../melting/patternModels/cricksPair/Santalucia04.html" title="class in melting.patternModels.cricksPair">Santalucia04</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/cricksPair/Santalucia96.html#getName()">getName()</a></span> - Method in class melting.patternModels.cricksPair.<a href="../melting/patternModels/cricksPair/Santalucia96.html" title="class in melting.patternModels.cricksPair">Santalucia96</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/cricksPair/Sugimoto95.html#getName()">getName()</a></span> - Method in class melting.patternModels.cricksPair.<a href="../melting/patternModels/cricksPair/Sugimoto95.html" title="class in melting.patternModels.cricksPair">Sugimoto95</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/cricksPair/Sugimoto96.html#getName()">getName()</a></span> - Method in class melting.patternModels.cricksPair.<a href="../melting/patternModels/cricksPair/Sugimoto96.html" title="class in melting.patternModels.cricksPair">Sugimoto96</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/cricksPair/Tanaka04.html#getName()">getName()</a></span> - Method in class melting.patternModels.cricksPair.<a href="../melting/patternModels/cricksPair/Tanaka04.html" title="class in melting.patternModels.cricksPair">Tanaka04</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/cricksPair/Turner06.html#getName()">getName()</a></span> - Method in class melting.patternModels.cricksPair.<a href="../melting/patternModels/cricksPair/Turner06.html" title="class in melting.patternModels.cricksPair">Turner06</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/cricksPair/Xia98.html#getName()">getName()</a></span> - Method in class melting.patternModels.cricksPair.<a href="../melting/patternModels/cricksPair/Xia98.html" title="class in melting.patternModels.cricksPair">Xia98</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/InternalLoops/Santalucia04InternalLoop.html#getName()">getName()</a></span> - Method in class melting.patternModels.InternalLoops.<a href="../melting/patternModels/InternalLoops/Santalucia04InternalLoop.html" title="class in melting.patternModels.InternalLoops">Santalucia04InternalLoop</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/InternalLoops/Turner06InternalLoop.html#getName()">getName()</a></span> - Method in class melting.patternModels.InternalLoops.<a href="../melting/patternModels/InternalLoops/Turner06InternalLoop.html" title="class in melting.patternModels.InternalLoops">Turner06InternalLoop</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/InternalLoops/Znosko071x2Loop.html#getName()">getName()</a></span> - Method in class melting.patternModels.InternalLoops.<a href="../melting/patternModels/InternalLoops/Znosko071x2Loop.html" title="class in melting.patternModels.InternalLoops">Znosko071x2Loop</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/longBulge/Santalucia04LongBulgeLoop.html#getName()">getName()</a></span> - Method in class melting.patternModels.longBulge.<a href="../melting/patternModels/longBulge/Santalucia04LongBulgeLoop.html" title="class in melting.patternModels.longBulge">Santalucia04LongBulgeLoop</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/longBulge/Turner99_06LongBulgeLoop.html#getName()">getName()</a></span> - Method in class melting.patternModels.longBulge.<a href="../melting/patternModels/longBulge/Turner99_06LongBulgeLoop.html" title="class in melting.patternModels.longBulge">Turner99_06LongBulgeLoop</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/longDanglingEnds/Sugimoto02DNADanglingEnd.html#getName()">getName()</a></span> - Method in class melting.patternModels.longDanglingEnds.<a href="../melting/patternModels/longDanglingEnds/Sugimoto02DNADanglingEnd.html" title="class in melting.patternModels.longDanglingEnds">Sugimoto02DNADanglingEnd</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/longDanglingEnds/Sugimoto02RNADanglingEnd.html#getName()">getName()</a></span> - Method in class melting.patternModels.longDanglingEnds.<a href="../melting/patternModels/longDanglingEnds/Sugimoto02RNADanglingEnd.html" title="class in melting.patternModels.longDanglingEnds">Sugimoto02RNADanglingEnd</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/secondDanglingEnds/Serra05DoubleDanglingEnd.html#getName()">getName()</a></span> - Method in class melting.patternModels.secondDanglingEnds.<a href="../melting/patternModels/secondDanglingEnds/Serra05DoubleDanglingEnd.html" title="class in melting.patternModels.secondDanglingEnds">Serra05DoubleDanglingEnd</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/secondDanglingEnds/Serra06DoubleDanglingEnd.html#getName()">getName()</a></span> - Method in class melting.patternModels.secondDanglingEnds.<a href="../melting/patternModels/secondDanglingEnds/Serra06DoubleDanglingEnd.html" title="class in melting.patternModels.secondDanglingEnds">Serra06DoubleDanglingEnd</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/singleBulge/Santalucia04SingleBulgeLoop.html#getName()">getName()</a></span> - Method in class melting.patternModels.singleBulge.<a href="../melting/patternModels/singleBulge/Santalucia04SingleBulgeLoop.html" title="class in melting.patternModels.singleBulge">Santalucia04SingleBulgeLoop</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/singleBulge/Serra07SingleBulgeLoop.html#getName()">getName()</a></span> - Method in class melting.patternModels.singleBulge.<a href="../melting/patternModels/singleBulge/Serra07SingleBulgeLoop.html" title="class in melting.patternModels.singleBulge">Serra07SingleBulgeLoop</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/singleBulge/Tanaka04SingleBulgeLoop.html#getName()">getName()</a></span> - Method in class melting.patternModels.singleBulge.<a href="../melting/patternModels/singleBulge/Tanaka04SingleBulgeLoop.html" title="class in melting.patternModels.singleBulge">Tanaka04SingleBulgeLoop</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/singleBulge/Turner99_06SingleBulgeLoop.html#getName()">getName()</a></span> - Method in class melting.patternModels.singleBulge.<a href="../melting/patternModels/singleBulge/Turner99_06SingleBulgeLoop.html" title="class in melting.patternModels.singleBulge">Turner99_06SingleBulgeLoop</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/singleDanglingEnds/Bommarito00SingleDanglingEnd.html#getName()">getName()</a></span> - Method in class melting.patternModels.singleDanglingEnds.<a href="../melting/patternModels/singleDanglingEnds/Bommarito00SingleDanglingEnd.html" title="class in melting.patternModels.singleDanglingEnds">Bommarito00SingleDanglingEnd</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/singleDanglingEnds/Serra06_08SingleDanglingEnd.html#getName()">getName()</a></span> - Method in class melting.patternModels.singleDanglingEnds.<a href="../melting/patternModels/singleDanglingEnds/Serra06_08SingleDanglingEnd.html" title="class in melting.patternModels.singleDanglingEnds">Serra06_08SingleDanglingEnd</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/singleMismatch/AllawiSantaluciaPeyret97_98_99mm.html#getName()">getName()</a></span> - Method in class melting.patternModels.singleMismatch.<a href="../melting/patternModels/singleMismatch/AllawiSantaluciaPeyret97_98_99mm.html" title="class in melting.patternModels.singleMismatch">AllawiSantaluciaPeyret97_98_99mm</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/singleMismatch/Turner06mm.html#getName()">getName()</a></span> - Method in class melting.patternModels.singleMismatch.<a href="../melting/patternModels/singleMismatch/Turner06mm.html" title="class in melting.patternModels.singleMismatch">Turner06mm</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/singleMismatch/Watkins11mm.html#getName()">getName()</a></span> - Method in class melting.patternModels.singleMismatch.<a href="../melting/patternModels/singleMismatch/Watkins11mm.html" title="class in melting.patternModels.singleMismatch">Watkins11mm</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/singleMismatch/Znosko07mm.html#getName()">getName()</a></span> - Method in class melting.patternModels.singleMismatch.<a href="../melting/patternModels/singleMismatch/Znosko07mm.html" title="class in melting.patternModels.singleMismatch">Znosko07mm</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/singleMismatch/Znosko08mm.html#getName()">getName()</a></span> - Method in class melting.patternModels.singleMismatch.<a href="../melting/patternModels/singleMismatch/Znosko08mm.html" title="class in melting.patternModels.singleMismatch">Znosko08mm</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/specificAcids/Asanuma05Azobenzene.html#getName()">getName()</a></span> - Method in class melting.patternModels.specificAcids.<a href="../melting/patternModels/specificAcids/Asanuma05Azobenzene.html" title="class in melting.patternModels.specificAcids">Asanuma05Azobenzene</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/specificAcids/LockedAcidNNMethod.html#getName()">getName()</a></span> - Method in class melting.patternModels.specificAcids.<a href="../melting/patternModels/specificAcids/LockedAcidNNMethod.html" title="class in melting.patternModels.specificAcids">LockedAcidNNMethod</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/specificAcids/McTigue04LockedAcid.html#getName()">getName()</a></span> - Method in class melting.patternModels.specificAcids.<a href="../melting/patternModels/specificAcids/McTigue04LockedAcid.html" title="class in melting.patternModels.specificAcids">McTigue04LockedAcid</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/specificAcids/Owczarzy11LockedAcid.html#getName()">getName()</a></span> - Method in class melting.patternModels.specificAcids.<a href="../melting/patternModels/specificAcids/Owczarzy11LockedAcid.html" title="class in melting.patternModels.specificAcids">Owczarzy11LockedAcid</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/specificAcids/Owczarzy11SingleMismatchLockedAcid.html#getName()">getName()</a></span> - Method in class melting.patternModels.specificAcids.<a href="../melting/patternModels/specificAcids/Owczarzy11SingleMismatchLockedAcid.html" title="class in melting.patternModels.specificAcids">Owczarzy11SingleMismatchLockedAcid</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/specificAcids/Owczarzy11TandemLockedAcid.html#getName()">getName()</a></span> - Method in class melting.patternModels.specificAcids.<a href="../melting/patternModels/specificAcids/Owczarzy11TandemLockedAcid.html" title="class in melting.patternModels.specificAcids">Owczarzy11TandemLockedAcid</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/specificAcids/Sugimoto01Hydroxyadenine.html#getName()">getName()</a></span> - Method in class melting.patternModels.specificAcids.<a href="../melting/patternModels/specificAcids/Sugimoto01Hydroxyadenine.html" title="class in melting.patternModels.specificAcids">Sugimoto01Hydroxyadenine</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/tandemMismatches/AllawiSantaluciaPeyret97_98_99tanmm.html#getName()">getName()</a></span> - Method in class melting.patternModels.tandemMismatches.<a href="../melting/patternModels/tandemMismatches/AllawiSantaluciaPeyret97_98_99tanmm.html" title="class in melting.patternModels.tandemMismatches">AllawiSantaluciaPeyret97_98_99tanmm</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/tandemMismatches/Turner99_06tanmm.html#getName()">getName()</a></span> - Method in class melting.patternModels.tandemMismatches.<a href="../melting/patternModels/tandemMismatches/Turner99_06tanmm.html" title="class in melting.patternModels.tandemMismatches">Turner99_06tanmm</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/wobble/Santalucia05Inosine.html#getName()">getName()</a></span> - Method in class melting.patternModels.wobble.<a href="../melting/patternModels/wobble/Santalucia05Inosine.html" title="class in melting.patternModels.wobble">Santalucia05Inosine</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/wobble/Serra12Wobble.html#getName()">getName()</a></span> - Method in class melting.patternModels.wobble.<a href="../melting/patternModels/wobble/Serra12Wobble.html" title="class in melting.patternModels.wobble">Serra12Wobble</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/wobble/Turner99Wobble.html#getName()">getName()</a></span> - Method in class melting.patternModels.wobble.<a href="../melting/patternModels/wobble/Turner99Wobble.html" title="class in melting.patternModels.wobble">Turner99Wobble</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/wobble/Znosko07Inosine.html#getName()">getName()</a></span> - Method in class melting.patternModels.wobble.<a href="../melting/patternModels/wobble/Znosko07Inosine.html" title="class in melting.patternModels.wobble">Znosko07Inosine</a></dt>
<dd>
<div class="block">Gets the full name of the method.</div>
</dd>
<dt><span class="strong"><a href="../melting/sequences/NucleotidSequences.html#getNNPairWithoutHydroxyA(int)">getNNPairWithoutHydroxyA(int)</a></span> - Method in class melting.sequences.<a href="../melting/sequences/NucleotidSequences.html" title="class in melting.sequences">NucleotidSequences</a></dt>
<dd>
<div class="block">to get the two nucleic acids from each sequence in the Crick's pair at the position "pos" in the duplex.</div>
</dd>
<dt><span class="strong"><a href="../melting/DataCollect.html#getNNvalue(java.lang.String, java.lang.String)">getNNvalue(String, String)</a></span> - Method in class melting.<a href="../melting/DataCollect.html" title="class in melting">DataCollect</a></dt>
<dd>
<div class="block">to get the Thermodynamics containing the parameters for the crick's pair composed of the String seq1 and the String seq2.</div>
</dd>
<dt><span class="strong"><a href="../melting/Environment.html#getNucleotides()">getNucleotides()</a></span> - Method in class melting.<a href="../melting/Environment.html" title="class in melting">Environment</a></dt>
<dd>
<div class="block">This method is called to get the oligomerConcentration of Environment.</div>
</dd>
<dt><span class="strong"><a href="../melting/sequences/NucleotidSequences.html#getNumberTerminal5TA(int, int)">getNumberTerminal5TA(int, int)</a></span> - Method in class melting.sequences.<a href="../melting/sequences/NucleotidSequences.html" title="class in melting.sequences">NucleotidSequences</a></dt>
<dd>
<div class="block">calculates the number of terminal 5'T3'A in the subduplex between pos1 and pos2</div>
</dd>
<dt><span class="strong"><a href="../melting/Environment.html#getOptions()">getOptions()</a></span> - Method in class melting.<a href="../melting/Environment.html" title="class in melting">Environment</a></dt>
<dd>
<div class="block">This method is called to get the HashMap options of Environment.</div>
</dd>
<dt><span class="strong"><a href="../meltinggui/widgets/ComboBoxOption.html#getOptionText()">getOptionText()</a></span> - Method in class meltinggui.widgets.<a href="../meltinggui/widgets/ComboBoxOption.html" title="class in meltinggui.widgets">ComboBoxOption</a></dt>
<dd>
<div class="block">Gets the option text.</div>
</dd>
<dt><span class="strong"><a href="../melting/configuration/RegisterMethods.html#getPatternComputationMethod(java.lang.String, java.lang.String)">getPatternComputationMethod(String, String)</a></span> - Method in class melting.configuration.<a href="../melting/configuration/RegisterMethods.html" title="class in melting.configuration">RegisterMethods</a></dt>
<dd>
<div class="block">This method is called to get the PatternComputationMethod which represents the method 'methodName'
entered with the option 'optionName'.</div>
</dd>
<dt><span class="strong"><a href="../melting/DataCollect.html#getPenalty(java.lang.String)">getPenalty(String)</a></span> - Method in class melting.<a href="../melting/DataCollect.html" title="class in melting">DataCollect</a></dt>
<dd>
<div class="block">to get the Thermodynamics object containing the parameters for the penalty of type 'type'.</div>
</dd>
<dt><span class="strong"><a href="../melting/DataCollect.html#getPenalty(java.lang.String, java.lang.String)">getPenalty(String, String)</a></span> - Method in class melting.<a href="../melting/DataCollect.html" title="class in melting">DataCollect</a></dt>
<dd>
<div class="block">to get the Thermodynamics object containing the parameters for a penalty of type 'type'
for the specified parameter.</div>
</dd>
<dt><span class="strong"><a href="../melting/sequences/BasePair.html#getPosition()">getPosition()</a></span> - Method in class melting.sequences.<a href="../melting/sequences/BasePair.html" title="class in melting.sequences">BasePair</a></dt>
<dd>
<div class="block">This method is called to get the position of BasePair in the duplex.</div>
</dd>
<dt><span class="strong"><a href="../meltinggui/widgets/MeltingTextArea.html#getPreferredSize()">getPreferredSize()</a></span> - Method in class meltinggui.widgets.<a href="../meltinggui/widgets/MeltingTextArea.html" title="class in meltinggui.widgets">MeltingTextArea</a></dt>
<dd>
<div class="block">We override the <code>getPreferredSize</code> method in order to produce
better resizing behaviour.</div>
</dd>
<dt><span class="strong"><a href="../melting/approximativeMethods/ApproximativeMode.html#getRegister()">getRegister()</a></span> - Method in class melting.approximativeMethods.<a href="../melting/approximativeMethods/ApproximativeMode.html" title="class in melting.approximativeMethods">ApproximativeMode</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="../melting/methodInterfaces/MeltingComputationMethod.html#getRegister()">getRegister()</a></span> - Method in interface melting.methodInterfaces.<a href="../melting/methodInterfaces/MeltingComputationMethod.html" title="interface in melting.methodInterfaces">MeltingComputationMethod</a></dt>
<dd>
<div class="block">This method is called to get the RegisterMethod of the implemented class.</div>
</dd>
<dt><span class="strong"><a href="../melting/nearestNeighborModel/NearestNeighborMode.html#getRegister()">getRegister()</a></span> - Method in class melting.nearestNeighborModel.<a href="../melting/nearestNeighborModel/NearestNeighborMode.html" title="class in melting.nearestNeighborModel">NearestNeighborMode</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="../melting/Environment.html#getResult()">getResult()</a></span> - Method in class melting.<a href="../melting/Environment.html" title="class in melting">Environment</a></dt>
<dd>
<div class="block">This method is called to get the ThermoResult of Environment.</div>
</dd>
<dt><span class="strong"><a href="../meltinggui/MeltingCalculator.html#getResults()">getResults()</a></span> - Method in class meltinggui.<a href="../meltinggui/MeltingCalculator.html" title="class in meltinggui">MeltingCalculator</a></dt>
<dd>
<div class="block">Returns the results from MELTING.</div>
</dd>
<dt><span class="strong"><a href="../melting/configuration/OptionManagement.html#getRNADefaultOptions()">getRNADefaultOptions()</a></span> - Method in class melting.configuration.<a href="../melting/configuration/OptionManagement.html" title="class in melting.configuration">OptionManagement</a></dt>
<dd>
<div class="block">This method is called to get the RNADefaultOptions of OptionManagement.</div>
</dd>
<dt><span class="strong"><a href="../melting/ThermoResult.html#getSaltIndependentEntropy()">getSaltIndependentEntropy()</a></span> - Method in class melting.<a href="../melting/ThermoResult.html" title="class in melting">ThermoResult</a></dt>
<dd>
<div class="block">This method is called to get the SaltIndependentEntropy of ThermoResult.</div>
</dd>
<dt><span class="strong"><a href="../meltinggui/frames/FrameScreenPosition.html#getScreenPosition(java.awt.Frame)">getScreenPosition(Frame)</a></span> - Method in class meltinggui.frames.<a href="../meltinggui/frames/FrameScreenPosition.html" title="class in meltinggui.frames">FrameScreenPosition</a></dt>
<dd>
<div class="block">Fills in the fields from the current screen position of a
<code>Frame</code> object.</div>
</dd>
<dt><span class="strong"><a href="../meltinggui/frames/FrameScreenPosition.html#getScreenPosition(javax.swing.JInternalFrame)">getScreenPosition(JInternalFrame)</a></span> - Method in class meltinggui.frames.<a href="../meltinggui/frames/FrameScreenPosition.html" title="class in meltinggui.frames">FrameScreenPosition</a></dt>
<dd>
<div class="block">Fills in the fields from the current screen position of a
<code>JInternalFrame</code> object.</div>
</dd>
<dt><span class="strong"><a href="../melting/DataCollect.html#getSecondDanglingValue(java.lang.String, java.lang.String, java.lang.String)">getSecondDanglingValue(String, String, String)</a></span> - Method in class melting.<a href="../melting/DataCollect.html" title="class in melting">DataCollect</a></dt>
<dd>
<div class="block">to get the Thermodynamics object containing the parameters for the dangling end present in the duplex
composed of seq1 and seq2 with the specified sens.</div>
</dd>
<dt><span class="strong"><a href="../melting/sequences/NucleotidSequences.html#getSequence(int, int, java.lang.String)">getSequence(int, int, String)</a></span> - Method in class melting.sequences.<a href="../melting/sequences/NucleotidSequences.html" title="class in melting.sequences">NucleotidSequences</a></dt>
<dd>
<div class="block">This method is called to get a substring of the sequence String between the positions pos1 and pos2 in the duplex.</div>
</dd>
<dt><span class="strong"><a href="../melting/sequences/NucleotidSequences.html#getSequence()">getSequence()</a></span> - Method in class melting.sequences.<a href="../melting/sequences/NucleotidSequences.html" title="class in melting.sequences">NucleotidSequences</a></dt>
<dd>
<div class="block">This method is called to get the encoded sequence String of NucleotidSequences.</div>
</dd>
<dt><span class="strong"><a href="../melting/sequences/NucleotidSequences.html#getSequence(int, int)">getSequence(int, int)</a></span> - Method in class melting.sequences.<a href="../melting/sequences/NucleotidSequences.html" title="class in melting.sequences">NucleotidSequences</a></dt>
<dd>
<div class="block">This method is called to get a substring between two positions of the sequence String.</div>
</dd>
<dt><span class="strong"><a href="../melting/sequences/NucleotidSequences.html#getSequenceContaining(java.lang.String, int, int)">getSequenceContaining(String, int, int)</a></span> - Method in class melting.sequences.<a href="../melting/sequences/NucleotidSequences.html" title="class in melting.sequences">NucleotidSequences</a></dt>
<dd>
<div class="block">this method is called to get the String sequence or complementary of NucleotidSequences.</div>
</dd>
<dt><span class="strong"><a href="../melting/sequences/NucleotidSequences.html#getSequenceNNPair(int)">getSequenceNNPair(int)</a></span> - Method in class melting.sequences.<a href="../melting/sequences/NucleotidSequences.html" title="class in melting.sequences">NucleotidSequences</a></dt>
<dd>
<div class="block">to get the two nucleic acids which are from the sequence (5'3') in the Crick's pair at the position "pos" in the duplex.</div>
</dd>
<dt><span class="strong"><a href="../melting/sequences/NucleotidSequences.html#getSequenceNNPairUnlocked(int)">getSequenceNNPairUnlocked(int)</a></span> - Method in class melting.sequences.<a href="../melting/sequences/NucleotidSequences.html" title="class in melting.sequences">NucleotidSequences</a></dt>
<dd>
<div class="block">to get the two unlocked nucleic acids which are from the sequence (5'3') in the Crick's pair at the position "pos" in the duplex.</div>
</dd>
<dt><span class="strong"><a href="../melting/Environment.html#getSequences()">getSequences()</a></span> - Method in class melting.<a href="../melting/Environment.html" title="class in melting">Environment</a></dt>
<dd>
<div class="block">This method is called to get the sequences NucleotidSequences of Environment.</div>
</dd>
<dt><span class="strong"><a href="../melting/sequences/NucleotidSequences.html#getSequenceSens(java.lang.String, int, int)">getSequenceSens(String, int, int)</a></span> - Method in class melting.sequences.<a href="../melting/sequences/NucleotidSequences.html" title="class in melting.sequences">NucleotidSequences</a></dt>
<dd>
<div class="block">To get the orientation of the subsequence sequence.</div>
</dd>
<dt><span class="strong"><a href="../meltinggui/dialogs/SequenceDialog.html#getSequenceText()">getSequenceText()</a></span> - Method in class meltinggui.dialogs.<a href="../meltinggui/dialogs/SequenceDialog.html" title="class in meltinggui.dialogs">SequenceDialog</a></dt>
<dd>
<div class="block">Gets the sequence text.</div>
</dd>
<dt><span class="strong"><a href="../melting/DataCollect.html#getSingleBulgeLoopvalue(java.lang.String, java.lang.String)">getSingleBulgeLoopvalue(String, String)</a></span> - Method in class melting.<a href="../melting/DataCollect.html" title="class in melting">DataCollect</a></dt>
<dd>
<div class="block">to get the Thermodynamics object containing the parameters for the single bulge (seq1, seq2).</div>
</dd>
<dt><span class="strong"><a href="../melting/sequences/NucleotidSequences.html#getSingleBulgeNeighbors(int)">getSingleBulgeNeighbors(int)</a></span> - Method in class melting.sequences.<a href="../melting/sequences/NucleotidSequences.html" title="class in melting.sequences">NucleotidSequences</a></dt>
<dd>
<div class="block">This method is called to get the base pairs adjacent to the single bulge loop (unpaired nucleic acid) at the position pos1 in the duplex ArrayList</div>
</dd>
<dt><span class="strong"><a href="../melting/ionCorrection/sodiumEquivalence/SodiumEquivalent.html#getSodiumEquivalent(double, double, double, double, double, double)">getSodiumEquivalent(double, double, double, double, double, double)</a></span> - Method in class melting.ionCorrection.sodiumEquivalence.<a href="../melting/ionCorrection/sodiumEquivalence/SodiumEquivalent.html" title="class in melting.ionCorrection.sodiumEquivalence">SodiumEquivalent</a></dt>
<dd>
<div class="block">This method is called to get a sodium equivalent concentration when other cations are present.</div>
</dd>
<dt><span class="strong"><a href="../melting/DataCollect.html#getsymmetry()">getsymmetry()</a></span> - Method in class melting.<a href="../melting/DataCollect.html" title="class in melting">DataCollect</a></dt>
<dd>
<div class="block">to get the Thermodynamics object containing the parameters for the symmetry correction.</div>
</dd>
<dt><span class="strong"><a href="../melting/DataCollect.html#getTerminal(java.lang.String)">getTerminal(String)</a></span> - Method in class melting.<a href="../melting/DataCollect.html" title="class in melting">DataCollect</a></dt>
<dd>
<div class="block">to get the Thermodynamics containing the parameters for the specified type of terminal base pair.</div>
</dd>
<dt><span class="strong"><a href="../melting/DataCollect.html#getTerminalMismatchvalue(java.lang.String, java.lang.String)">getTerminalMismatchvalue(String, String)</a></span> - Method in class melting.<a href="../melting/DataCollect.html" title="class in melting">DataCollect</a></dt>
<dd>
<div class="block">to get the Thermodynamics object containing the parameters for the terminal mismatching base pair (seq1, seq2)
of a hairpin loop.</div>
</dd>
<dt><span class="strong"><a href="../melting/handlers/ThermoHandler.html#getThermo()">getThermo()</a></span> - Method in class melting.handlers.<a href="../melting/handlers/ThermoHandler.html" title="class in melting.handlers">ThermoHandler</a></dt>
<dd>
<div class="block">This method is called to get the Thermodynamics of the ThermoHandler object.</div>
</dd>
<dt><span class="strong"><a href="../melting/ThermoResult.html#getTm()">getTm()</a></span> - Method in class melting.<a href="../melting/ThermoResult.html" title="class in melting">ThermoResult</a></dt>
<dd>
<div class="block">This method is called to get the Tm of ThermoResult.</div>
</dd>
<dt><span class="strong"><a href="../melting/sequences/BasePair.html#getTopAcid()">getTopAcid()</a></span> - Method in class melting.sequences.<a href="../melting/sequences/BasePair.html" title="class in melting.sequences">BasePair</a></dt>
<dd>
<div class="block">This method is called to get the nucleic acid "TopAcid" of BasePair.</div>
</dd>
<dt><span class="strong"><a href="../melting/Environment.html#getTris()">getTris()</a></span> - Method in class melting.<a href="../melting/Environment.html" title="class in melting">Environment</a></dt>
<dd>
<div class="block">This method is called to get the Tris buffer concentration.</div>
</dd>
<dt><span class="strong"><a href="../melting/handlers/DataHandler.html#getType()">getType()</a></span> - Method in class melting.handlers.<a href="../melting/handlers/DataHandler.html" title="class in melting.handlers">DataHandler</a></dt>
<dd>
<div class="block">This method is called to get the type String of DataHandler.</div>
</dd>
<dt><span class="strong"><a href="../meltinggui/widgets/InputField.html#getValue()">getValue()</a></span> - Method in class meltinggui.widgets.<a href="../meltinggui/widgets/InputField.html" title="class in meltinggui.widgets">InputField</a></dt>
<dd>
<div class="block">Gets the value from the widget.</div>
</dd>
<dt><span class="strong"><a href="../meltinggui/widgets/InputFieldArray.html#getValue(int)">getValue(int)</a></span> - Method in class meltinggui.widgets.<a href="../meltinggui/widgets/InputFieldArray.html" title="class in meltinggui.widgets">InputFieldArray</a></dt>
<dd>
<div class="block">Get the value from a particular widget.</div>
</dd>
<dt><span class="strong"><a href="../meltinggui/widgets/InputWidgetInterface.html#getValue()">getValue()</a></span> - Method in interface meltinggui.widgets.<a href="../meltinggui/widgets/InputWidgetInterface.html" title="interface in meltinggui.widgets">InputWidgetInterface</a></dt>
<dd>
<div class="block">Gets the value given by the user.</div>
</dd>
<dt><span class="strong"><a href="../meltinggui/widgets/MeltingComboBox.html#getValue()">getValue()</a></span> - Method in class meltinggui.widgets.<a href="../meltinggui/widgets/MeltingComboBox.html" title="class in meltinggui.widgets">MeltingComboBox</a></dt>
<dd>
<div class="block">Gets the command-line text corrseponding to the selected option.</div>
</dd>
<dt><span class="strong"><a href="../meltinggui/widgets/MeltingTextArea.html#getValue()">getValue()</a></span> - Method in class meltinggui.widgets.<a href="../meltinggui/widgets/MeltingTextArea.html" title="class in meltinggui.widgets">MeltingTextArea</a></dt>
<dd>
<div class="block">Returns the text from the area.</div>
</dd>
<dt><span class="strong"><a href="../meltinggui/widgets/MeltingTextField.html#getValue()">getValue()</a></span> - Method in class meltinggui.widgets.<a href="../meltinggui/widgets/MeltingTextField.html" title="class in meltinggui.widgets">MeltingTextField</a></dt>
<dd>
<div class="block">Returns the text from the field.</div>
</dd>
<dt><span class="strong"><a href="../melting/ionCorrection/magnesiumCorrections/Tan06MagnesiumCorrection.html#gFormula">gFormula</a></span> - Static variable in class melting.ionCorrection.magnesiumCorrections.<a href="../melting/ionCorrection/magnesiumCorrections/Tan06MagnesiumCorrection.html" title="class in melting.ionCorrection.magnesiumCorrections">Tan06MagnesiumCorrection</a></dt>
<dd>
<div class="block">String gFormula : function associated with the electrostatic folding free energy per base stack.</div>
</dd>
<dt><span class="strong"><a href="../melting/ionCorrection/magnesiumCorrections/Tan07MagnesiumCorrection.html#gFormula">gFormula</a></span> - Static variable in class melting.ionCorrection.magnesiumCorrections.<a href="../melting/ionCorrection/magnesiumCorrections/Tan07MagnesiumCorrection.html" title="class in melting.ionCorrection.magnesiumCorrections">Tan07MagnesiumCorrection</a></dt>
<dd>
<div class="block">String gFormula : function associated with the electrostatic folding free energy per base stack.</div>
</dd>
<dt><span class="strong"><a href="../melting/ionCorrection/mixedNaMgCorrections/Tan07MixedNaMgCorrection.html#gFormula">gFormula</a></span> - Static variable in class melting.ionCorrection.mixedNaMgCorrections.<a href="../melting/ionCorrection/mixedNaMgCorrections/Tan07MixedNaMgCorrection.html" title="class in melting.ionCorrection.mixedNaMgCorrections">Tan07MixedNaMgCorrection</a></dt>
<dd>
<div class="block">String gFormula : function associated with the electrostatic folding free energy per base stack.</div>
</dd>
<dt><a href="../melting/patternModels/cricksPair/GlobalInitiation.html" title="class in melting.patternModels.cricksPair"><span class="strong">GlobalInitiation</span></a> - Class in <a href="../melting/patternModels/cricksPair/package-summary.html">melting.patternModels.cricksPair</a></dt>
<dd>
<div class="block">This class represents one model to compute the initiation enthalpy and entropy.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/cricksPair/GlobalInitiation.html#GlobalInitiation()">GlobalInitiation()</a></span> - Constructor for class melting.patternModels.cricksPair.<a href="../melting/patternModels/cricksPair/GlobalInitiation.html" title="class in melting.patternModels.cricksPair">GlobalInitiation</a></dt>
<dd> </dd>
<dt><span class="strong"><a href="../melting/configuration/OptionManagement.html#globalMethod">globalMethod</a></span> - Static variable in class melting.configuration.<a href="../melting/configuration/OptionManagement.html" title="class in melting.configuration">OptionManagement</a></dt>
<dd>
<div class="block">Option name for the choice of computation method (approximative "-A" or nearest neighbor "-NN").</div>
</dd>
<dt><a href="../melting/patternModels/singleBulge/GlobalSingleBulgeLoopMethod.html" title="class in melting.patternModels.singleBulge"><span class="strong">GlobalSingleBulgeLoopMethod</span></a> - Class in <a href="../melting/patternModels/singleBulge/package-summary.html">melting.patternModels.singleBulge</a></dt>
<dd>
<div class="block">This class represents one single bulge loop model.</div>
</dd>
<dt><span class="strong"><a href="../melting/patternModels/singleBulge/GlobalSingleBulgeLoopMethod.html#GlobalSingleBulgeLoopMethod()">GlobalSingleBulgeLoopMethod()</a></span> - Constructor for class melting.patternModels.singleBulge.<a href="../melting/patternModels/singleBulge/GlobalSingleBulgeLoopMethod.html" title="class in melting.patternModels.singleBulge">GlobalSingleBulgeLoopMethod</a></dt>
<dd> </dd>
<dt><a href="../meltinggui/frames/GuiScreenPositions.html" title="class in meltinggui.frames"><span class="strong">GuiScreenPositions</span></a> - Class in <a href="../meltinggui/frames/package-summary.html">meltinggui.frames</a></dt>
<dd>
<div class="block">The locations on the screen of the GUI and all the components it contains.</div>
</dd>
<dt><span class="strong"><a href="../meltinggui/frames/GuiScreenPositions.html#GuiScreenPositions(meltinggui.frames.OuterFrame, meltinggui.frames.MeltingFrame, meltinggui.frames.ErrorFrame)">GuiScreenPositions(OuterFrame, MeltingFrame, ErrorFrame)</a></span> - Constructor for class meltinggui.frames.<a href="../meltinggui/frames/GuiScreenPositions.html" title="class in meltinggui.frames">GuiScreenPositions</a></dt>
<dd>
<div class="block">Fills in the fields from the frames themselves.</div>
</dd>
</dl>
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