OldNeedlemanWunschAffine (JEBL2 lib API)

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

public class OldNeedlemanWunschAffine
extends Align

Constructor Summary

Constructors
Constructor Description

OldNeedlemanWunschAffine(Scores sub, float d, float e)

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.
`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`	`setGapExtend(float e)`

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

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

- Constructor Detail
  - OldNeedlemanWunschAffine
```
public OldNeedlemanWunschAffine(Scores sub,
                                float d,
                                float e)
```
- Method Detail
  - doAlignment
```
public void doAlignment(java.lang.String sq1,
                        java.lang.String sq2)
```
    Performs the alignment. Abstract.
    
    Parameters:
    
    sq1 -
    
    sq2 -
  - prepareAlignment
```
public void prepareAlignment(java.lang.String sq1,
                             java.lang.String sq2)
```
    Description copied from class: Align
    
    Initialises the matrices for the alignment.
    
    Specified by:
    
    prepareAlignment in class Align
  - setGapExtend
```
public void setGapExtend(float e)
```
  - 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
  - getScore
```
public float getScore()
```
    Specified by:
    
    getScore in class Align
    
    Returns:
    
    score for this alignment
  - printf
```
public void printf(Output out)
```
    Print matrix used to calculate this alignment.
    
    Specified by:
    
    printf in class Align
    
    Parameters:
    
    out - Output to print to.