SmithWaterman3DParameters

java.lang.Object
- org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters

All Implemented Interfaces:: ConfigStrucAligParams

public class SmithWaterman3DParameters
extends java.lang.Object
implements ConfigStrucAligParams

Constructor Summary

Constructors
Constructor Description

SmithWaterman3DParameters()

Constructors
Constructor	Description
`SmithWaterman3DParameters()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`java.lang.Short`	`getGapExtend()`
`java.lang.Short`	`getGapOpen()`
`java.util.List<java.lang.String>`	`getUserConfigHelp()`	The help text for each of these parameters.
`java.util.List<java.lang.String>`	`getUserConfigParameterNames()`	The labels to be displayed to the user for each parameter
`java.util.List<java.lang.String>`	`getUserConfigParameters()`	get the list of parameters that the user can change through the user interface.
`java.util.List<java.lang.Class>`	`getUserConfigTypes()`	Get the data types of the parameters
`void`	`reset()`	Set the parameters to the default.
`void`	`setGapExtend(java.lang.Short gapExtend)`
`void`	`setGapOpen(java.lang.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 java.util.List<java.lang.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 java.util.List<java.lang.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 java.util.List<java.lang.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 java.util.List<java.lang.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 java.lang.Short getGapExtend()
```
  - setGapExtend
```
public void setGapExtend(java.lang.Short gapExtend)
```
  - getGapOpen
```
public java.lang.Short getGapOpen()
```
  - setGapOpen
```
public void setGapOpen(java.lang.Short gapOpen)
```

Class SmithWaterman3DParameters

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

SmithWaterman3DParameters

Method Detail

getUserConfigHelp

getUserConfigParameterNames

getUserConfigParameters

getUserConfigTypes

reset

getGapExtend

setGapExtend

getGapOpen

setGapOpen