Class SmithWaterman3DParameters

Method Details

• 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

• 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

• 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

• 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

• reset

  public void reset()

  Description copied from interface: ConfigStrucAligParams

  Set the parameters to the default.

  Specified by:

  reset in interface ConfigStrucAligParams

• getGapExtend

  public Short getGapExtend()

• setGapExtend

  public void setGapExtend(Short gapExtend)

• getGapOpen

  public Short getGapOpen()

• setGapOpen

  public void setGapOpen(Short gapOpen)