SmithWatermanLinearSpace (JEBL2 lib API)

java.lang.Object
- jebl.evolution.align.Align
- - jebl.evolution.align.SmithWatermanLinearSpace

public class SmithWatermanLinearSpace
extends Align

Constructor Summary

Constructors
Constructor Description

SmithWatermanLinearSpace(Scores sub, float d)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`doAlignment(java.lang.String sq1, java.lang.String sq2)`	Performs the alignment.
`java.lang.String[]`	`getMatch()`
`float`	`getScore()`
`Traceback`	`next(Traceback tb)`	Get the next state in the traceback
`void`	`prepareAlignment(java.lang.String sq1, java.lang.String sq2)`	Initialises the matrices for the alignment.
`void`	`printf(Output out)`	Print matrix used to calculate this alignment.
`void`	`traceback(TracebackPlotter plotter)`

Methods inherited from class jebl.evolution.align.Align
doMatch, doMatch, formatScore, setGapOpen, setScores

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

- Constructor Detail
  - SmithWatermanLinearSpace
```
public SmithWatermanLinearSpace(Scores sub,
                                float d)
```
- Method Detail
  - doAlignment
```
public void doAlignment(java.lang.String sq1,
                        java.lang.String sq2)
```
    Performs the alignment. Abstract.
    
    Parameters:
    
    sq1 -
    
    sq2 -
  - getScore
```
public float getScore()
```
    Returns:
    
    the score of the best alignment
  - getMatch
```
public java.lang.String[] getMatch()
```
    Overrides:
    
    getMatch in class Align
    
    Returns:
    
    two-element array containing an alignment with maximal score
  - traceback
```
public void traceback(TracebackPlotter plotter)
```
    Overrides:
    
    traceback in class Align
  - prepareAlignment
```
public void prepareAlignment(java.lang.String sq1,
                             java.lang.String sq2)
```
    Description copied from class: Align
    
    Initialises the matrices for the alignment.
  - printf
```
public void printf(Output out)
```
    Print matrix used to calculate this alignment.
    
    Parameters:
    
    out - Output to print to.
  - next
```
public Traceback next(Traceback tb)
```
    Get the next state in the traceback
    
    Overrides:
    
    next in class Align
    
    Parameters:
    
    tb - current Traceback
    
    Returns:
    
    next Traceback