OverlapAlign (JEBL2 lib API)

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

```
public class OverlapAlign
extends Align
```

Constructor Summary

Constructors
Constructor Description

OverlapAlign(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.
`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.

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
  - OverlapAlign
```
public OverlapAlign(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 -
  - 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
  - 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:
    
    the score of the best 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.