Package org.biojava.nbio.structure.align.multiple.mc

Class MultipleMcParameters

java.lang.Object
org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters
All Implemented Interfaces:
ConfigStrucAligParams
public class MultipleMcParameters extends Object implements ConfigStrucAligParams
Contains the parameters to be sent to the MC optimization.
Since:
4.1.0
Author:
Aleix Lafita

  • Constructor Details

    • MultipleMcParameters

      public MultipleMcParameters()
      Constructor with DEFAULT values of the parameters.

  • Method Details

    • getUserConfigParameters

      public List<String> getUserConfigParameters()
      Description copied from interface: ConfigStrucAligParams
      get the list of parameters that the user can change through the user interface. Parameter names are the same names as the corresponding Get/Set methods.
      Specified by:
      getUserConfigParameters in interface ConfigStrucAligParams
      Returns:
      list of parameters

    • getUserConfigParameterNames

      public List<String> getUserConfigParameterNames()
      Description copied from interface: ConfigStrucAligParams
      The labels to be displayed to the user for each parameter
      Specified by:
      getUserConfigParameterNames in interface ConfigStrucAligParams
      Returns:
      list of parameter names

    • getUserConfigTypes

      public List<Class> getUserConfigTypes()
      Description copied from interface: ConfigStrucAligParams
      Get the data types of the parameters
      Specified by:
      getUserConfigTypes in interface ConfigStrucAligParams
      Returns:
      list of parameter classes

    • getUserConfigHelp

      public List<String> getUserConfigHelp()
      Description copied from interface: ConfigStrucAligParams
      The help text for each of these parameters.
      Specified by:
      getUserConfigHelp in interface ConfigStrucAligParams
      Returns:
      help strings

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • reset

      public void reset()
      Description copied from interface: ConfigStrucAligParams
      Set the parameters to the default.
      Specified by:
      reset in interface ConfigStrucAligParams

    • getRandomSeed

      public int getRandomSeed()

    • setRandomSeed

      public void setRandomSeed(Integer randomSeed)

    • getMinBlockLen

      public int getMinBlockLen()

    • setMinBlockLen

      public void setMinBlockLen(Integer minBlockLen)

    • getMinAlignedStructures

      public int getMinAlignedStructures()

    • setMinAlignedStructures

      public void setMinAlignedStructures(Integer minAlignedStructures)

    • getGapOpen

      public double getGapOpen()

    • setGapOpen

      public void setGapOpen(Double gapOpen)

    • getGapExtension

      public double getGapExtension()

    • setGapExtension

      public void setGapExtension(Double gapExtension)

    • getConvergenceSteps

      public int getConvergenceSteps()

    • setConvergenceSteps

      public void setConvergenceSteps(Integer convergenceSteps)

    • getNrThreads

      public int getNrThreads()

    • setNrThreads

      public void setNrThreads(Integer nrThreads)

    • getDistanceCutoff

      public double getDistanceCutoff()

    • setDistanceCutoff

      public void setDistanceCutoff(Double distanceCutoff)