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 Summary

Constructors
Constructor Description

MultipleMcParameters()
Constructor with DEFAULT values of the parameters.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`int`	`getConvergenceSteps()`
`double`	`getDistanceCutoff()`
`double`	`getGapExtension()`
`double`	`getGapOpen()`
`int`	`getMinAlignedStructures()`
`int`	`getMinBlockLen()`
`int`	`getNrThreads()`
`int`	`getRandomSeed()`
`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`	`setConvergenceSteps(Integer convergenceSteps)`
`void`	`setDistanceCutoff(Double distanceCutoff)`
`void`	`setGapExtension(Double gapExtension)`
`void`	`setGapOpen(Double gapOpen)`
`void`	`setMinAlignedStructures(Integer minAlignedStructures)`
`void`	`setMinBlockLen(Integer minBlockLen)`
`void`	`setNrThreads(Integer nrThreads)`
`void`	`setRandomSeed(Integer randomSeed)`
`String`	`toString()`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Constructor Detail
  - MultipleMcParameters
```
public MultipleMcParameters()
```
    Constructor with DEFAULT values of the parameters.
- Method Detail
  - 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)
```

Class MultipleMcParameters

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

MultipleMcParameters

Method Detail

getUserConfigParameters

getUserConfigParameterNames

getUserConfigTypes

getUserConfigHelp

toString

reset

getRandomSeed

setRandomSeed

getMinBlockLen

setMinBlockLen

getMinAlignedStructures

setMinAlignedStructures

getGapOpen

setGapOpen

getGapExtension

setGapExtension

getConvergenceSteps

setConvergenceSteps

getNrThreads

setNrThreads

getDistanceCutoff

setDistanceCutoff