SmithWatermanUserArgumentProcessor

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java.lang.Object
- org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
- - org.biojava.nbio.structure.align.seq.SmithWatermanUserArgumentProcessor

All Implemented Interfaces:: UserArgumentProcessor

public class SmithWatermanUserArgumentProcessor
extends AbstractUserArgumentProcessor

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

protected static class SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams

Field Summary
- Fields inherited from class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
  mandatoryArgs, newline, params

Constructor Summary

Constructors
Constructor and Description

SmithWatermanUserArgumentProcessor()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`StructureAlignment`	`getAlgorithm()`
`java.lang.String`	`getDbSearchLegend()`
`java.lang.Object`	`getParameters()`
`protected StartupParameters`	`getStartupParametersInstance()` StartupParameters is a bean to store all the possible command line parameters.

Methods inherited from class org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor
getDbSearchResult, printAboutMe, printHelp, process

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

- Constructor Detail
  - SmithWatermanUserArgumentProcessor
```
public SmithWatermanUserArgumentProcessor()
```
- Method Detail
  - getAlgorithm
```
public StructureAlignment getAlgorithm()
```
    Specified by:
    
    getAlgorithm in class AbstractUserArgumentProcessor
  - getParameters
```
public java.lang.Object getParameters()
```
    Specified by:
    
    getParameters in class AbstractUserArgumentProcessor
  - getDbSearchLegend
```
public java.lang.String getDbSearchLegend()
```
    Specified by:
    
    getDbSearchLegend in class AbstractUserArgumentProcessor
  - getStartupParametersInstance
```
protected StartupParameters getStartupParametersInstance()
```
    Description copied from class: AbstractUserArgumentProcessor
    
    StartupParameters is a bean to store all the possible command line parameters. The `StartupParameter` class contains the basic set of CLI parameters common to all `StructureAligmnent`s. This method should return a subclass of StartupParameters which has been extended to store values for all additional parameters.
    
    Specified by:
    
    getStartupParametersInstance in class AbstractUserArgumentProcessor
    
    Returns:
    
    A new instance of the correct StartupParameters subclass

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