org.biojava.bio.structure.align.seq
Class SmithWaterman3DParameters

java.lang.Object
  extended by org.biojava.bio.structure.align.seq.SmithWaterman3DParameters
All Implemented Interfaces:
ConfigStrucAligParams

public class SmithWaterman3DParameters
extends Object
implements ConfigStrucAligParams


Constructor Summary
SmithWaterman3DParameters()
           
 
Method Summary
 Short getGapExtend()
           
 Short getGapOpen()
           
 List<String> getUserConfigHelp()
          The help text for each of these parameters.
 List<String> getUserConfigParameterNames()
          The labels to be displayed to the user for each parameter
 List<String> getUserConfigParameters()
          get the list of parameters that the user can change through the user interface.
 List<Class> getUserConfigTypes()
          Get the data types of the parameters
 void reset()
          Set the parameters to the default.
 void setGapExtend(Short gapExtend)
           
 void setGapOpen(Short gapOpen)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

SmithWaterman3DParameters

public SmithWaterman3DParameters()
Method Detail

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)