Uses of Class melting.Thermodynamics (MELTING Java 5 API)
Date: 2013-10-04

## Uses of Class
melting.Thermodynamics

- Packages that use Thermodynamics
  Package | Description
  --- | ---
  melting |
  melting.handlers |

- - ### Uses of Thermodynamics in melting

    Subclasses of Thermodynamics in melting
    Modifier and Type | Class and Description
    --- | ---
    `class` | `ThermoResult` This class extends Thermodynamics.

    Methods in melting that return Thermodynamics
    Modifier and Type | Method and Description
    --- | ---
    `Thermodynamics` | DataCollect.`getAsymmetry()` to get the Thermodynamics object containing the parameters for the internal loop asymmetry.
    `Thermodynamics` | DataCollect.`getAzobenzeneValue(String seq1, String seq2)` 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").
    `Thermodynamics` | DataCollect.`getBonus(String base1, String lastBase, String seqLoop, String type)` to get the Thermodynamics object containing the parameters for a Hairpin loop 'seqLoop' preceded by the base 'base1' and followed by the base 'lastBase'.
    `Thermodynamics` | DataCollect.`getBulgeLoopvalue(String size)` to get the Thermodynamics object containing the parameters for a bulge loop of size 'size'.
    `Thermodynamics` | DataCollect.`getClosureValue(String base1, String base2)` to get the Thermodynamics object containing the parameters for the base pair (base1, base2) next to the mismatching base pair.
    `Thermodynamics` | DataCollect.`getCNGvalue(String repeats, String seq1)` to get the Thermodynamics object containing the parameters for the CNG pattern 'seq1'.
    `Thermodynamics` | DataCollect.`getDanglingValue(String seq1, String seq2)` to get the Thermodynamics object containing the parameters for the dangling end present in the duplex composed of seq1 and seq2.
    `Thermodynamics` | DataCollect.`getFirstMismatch(String seq1, String seq2, String loop)` to get the Thermodynamics object containing the parameters for the first non canonical pair in the internal loop.
    `Thermodynamics` | DataCollect.`getHairpinLoopvalue(String size)` to get the Thermodynamics object containing the parameters for a Hairpin loop of size 'size'.
    `Thermodynamics` | DataCollect.`getHydroxyadenosineValue(String seq1, String seq2)` 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*").
    `Thermodynamics` | DataCollect.`getInitiation()` to get the Thermodynamics object containing the parameters for the hybridization initiation.
    `Thermodynamics` | DataCollect.`getInitiation(String type)` to get the Thermodynamics object containing the parameters for the initiation with the specified type of initiation.
    `Thermodynamics` | DataCollect.`getInitiationBulgevalue(String size)` to get the Thermodynamics object containing the parameters for the initiation of a bulge loop of size 'size'.
    `Thermodynamics` | DataCollect.`getInitiationLoopValue()` to get the Thermodynamics object containing the parameters for the initiation of an internal loop.
    `Thermodynamics` | DataCollect.`getInitiationLoopValue(String size)` to get the Thermodynamics object containing the parameters for the initiation of an internal loop with a specified size.
    `Thermodynamics` | DataCollect.`getInternalLoopValue(String size)` to get the Thermodynamics object containing the parameters for an internal loop with a specified size.
    `Thermodynamics` | DataCollect.`getLockedAcidValue(String seq1, String seq2)` 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").
    `Thermodynamics` | DataCollect.`getMismatchParameterValue(String base1, String base2)` to get the Thermodynamics object containing the parameters for the mismatching base pair (base1, base2).
    `Thermodynamics` | DataCollect.`getMismatchValue(String seq1, String seq2)` to get the Thermodynamics object containing the parameters for the mismatch(es) present in the duplex composed of seq1 and seq2.
    `Thermodynamics` | DataCollect.`getMismatchValue(String seq1, String seq2, String closing)` 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.
    `Thermodynamics` | DataCollect.`getModifiedvalue(String seq1, String seq2)` 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.
    `Thermodynamics` | DataCollect.`getModifiedvalue(String seq1, String seq2, String sens)` 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.
    `Thermodynamics` | DataCollect.`getNNvalue(String seq1, String seq2)` to get the Thermodynamics containing the parameters for the crick's pair composed of the String seq1 and the String seq2.
    `Thermodynamics` | DataCollect.`getPenalty(String type)` to get the Thermodynamics object containing the parameters for the penalty of type 'type'.
    `Thermodynamics` | DataCollect.`getPenalty(String type, String parameter)` to get the Thermodynamics object containing the parameters for a penalty of type 'type' for the specified parameter.
    `Thermodynamics` | DataCollect.`getSecondDanglingValue(String seq1, String seq2, String sens)` 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.
    `Thermodynamics` | DataCollect.`getSingleBulgeLoopvalue(String seq1, String seq2)` to get the Thermodynamics object containing the parameters for the single bulge (seq1, seq2).
    `Thermodynamics` | DataCollect.`getsymmetry()` to get the Thermodynamics object containing the parameters for the symmetry correction.
    `Thermodynamics` | DataCollect.`getTerminal(String type)` to get the Thermodynamics containing the parameters for the specified type of terminal base pair.
    `Thermodynamics` | DataCollect.`getTerminalMismatchvalue(String seq1, String seq2)` to get the Thermodynamics object containing the parameters for the terminal mismatching base pair (seq1, seq2) of a hairpin loop.

    Methods in melting that return types with arguments of type Thermodynamics
    Modifier and Type | Method and Description
    --- | ---
    `HashMap<String,Thermodynamics>` | DataCollect.`getData()` This method is called to get the data of DataCollect.
    `static HashMap<String,HashMap<String,Thermodynamics>>` | FileReader.`getLoadedData()` This method is called to get the loadedData of FileReader.
    `static HashMap<String,Thermodynamics>` | FileReader.`readFile(File file)` stocks the thermodynamic parameters from the file in a HashMap.

    Method parameters in melting with type arguments of type Thermodynamics
    Modifier and Type | Method and Description
    --- | ---
    `void` | DataCollect.`addData(HashMap<String,Thermodynamics> parameters)` add all of the mappings from the specified HashMap to the data of DataCollect.

  - ### Uses of Thermodynamics in melting.handlers

    Methods in melting.handlers that return Thermodynamics
    Modifier and Type | Method and Description
    --- | ---
    `Thermodynamics` | ThermoHandler.`getThermo()` This method is called to get the Thermodynamics of the ThermoHandler object.

    Methods in melting.handlers that return types with arguments of type Thermodynamics
    Modifier and Type | Method and Description
    --- | ---
    `HashMap<String,Thermodynamics>` | DataHandler.`getMap()` This method is called to get the map of DataHandler.