MarmurSchildkrautDoty
Date: 2014-08-08

melting.approximativeMethods

## Class MarmurSchildkrautDoty

- java.lang.Object
- - melting.approximativeMethods.ApproximativeMode
  - - melting.approximativeMethods.MarmurSchildkrautDoty

- All Implemented Interfaces:
    MeltingComputationMethod, NamedMethod

      public class MarmurSchildkrautDoty
      extends ApproximativeMode
      implements NamedMethod

  This class represents the model schdot. It extends ApproximativeMode. James G. Wetmur, "DNA Probes : applications of the principles of nucleic acid hybridization", 1991, Critical reviews in biochemistry and molecular biology, 26, 227-259 Marmur J, Doty P, "Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature", 1962, Journal of molecular biology, 5, 109-118. Chester N, Marshak DR, "dimethyl sulfoxide-mediated primer Tm reduction : a method for analyzing the role of renaturation temperature in the polymerase chain reaction", 1993, Analytical Biochemistry, 209, 284-290. Schildkraut C, Lifson S, "Dependance of the melting temperature of DNA on salt concentration", 1965, Biopolymers, 3, 95-110. Wahl GM, Berger SL, Kimmel AR. Molecular hybridization of immobilized nucleic acids: theoretical concepts and practical considerations. Methods Enzymol 1987;152:399 – 407. Britten RJ, Graham DE, Neufeld BR. Analysis of repeating DNA sequences by reassociation. Methods Enzymol 1974;29:363–418. Hall TJ, Grula JW, Davidson EH, Britten RJ. Evolution of sea urchin non-repetitive DNA. J Mol Evol 1980;16:95–110.

- - ### Field Summary

    - ### Fields inherited from class melting.approximativeMethods.ApproximativeMode

      `environment, register`

  - ### Constructor Summary

    Constructors
    Constructor and Description
    `MarmurSchildkrautDoty()`

  - ### Method Summary

    Methods
    Modifier and Type | Method and Description
    --- | ---
    `ThermoResult` | `computesThermodynamics()` This method is called to compute the melting temperature.
    `java.lang.String` | `getName()` Gets the full name of the method.
    `boolean` | `isApplicable()` This method is called to check that the options entered by the users are applicable with the used model (class).

    - ### Methods inherited from class melting.approximativeMethods.ApproximativeMode

      `getRegister, isNaEqPossible, setUpVariables`

    - ### Methods inherited from class java.lang.Object

      `clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`

- - ### Constructor Detail

    - #### MarmurSchildkrautDoty

          public MarmurSchildkrautDoty()

  - ### Method Detail

    - #### computesThermodynamics

          public ThermoResult computesThermodynamics()

      Description copied from interface: `MeltingComputationMethod`
      This method is called to compute the melting temperature.
      Specified by:
        `computesThermodynamics` in interface `MeltingComputationMethod`
      Overrides:
        `computesThermodynamics` in class `ApproximativeMode`
      Returns:
        ThermoResult containing the computed enthalpy, entropy and melting temperature.

    - #### isApplicable

          public boolean isApplicable()

      Description copied from interface: `MeltingComputationMethod`
      This method is called to check that the options entered by the users are applicable with the used model (class).
      Specified by:
        `isApplicable` in interface `MeltingComputationMethod`
      Overrides:
        `isApplicable` in class `ApproximativeMode`
      Returns:
        false if at least one chosen option makes the model completely false. If one chosen option may lead to less reliable results, a warning message will appear. (ex : wrong hybridization type)

    - #### getName

          public java.lang.String getName()

      Gets the full name of the method.
      Specified by:
        `getName` in interface `NamedMethod`
      Returns:
        The full name of the method.