Align (JEBL2 lib API)

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

Direct Known Subclasses:

MaximalSegmentPair, NeedlemanWunsch, NeedlemanWunschAffine, NeedlemanWunschLinearSpace, NeedlemanWunschLinearSpaceAffine, NonOverlapMultipleLocalAffine, OldNeedlemanWunschAffine, OverlapAlign, SmithWaterman, SmithWatermanLinearSpace, SmithWatermanLinearSpaceAffine
```
public abstract class Align
extends java.lang.Object
```

Constructor Summary

Constructors
Constructor Description

Align(Scores sub, float d)

Constructors
Constructor	Description
`Align(Scores sub, float d)`

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method	Description
`abstract void`	`doAlignment(java.lang.String sq1, java.lang.String sq2)`	Performs the alignment, abstract.
`void`	`doMatch(Output out, java.lang.String msg)`	Print the score and the alignment
`void`	`doMatch(Output out, java.lang.String msg, boolean outputFMatrix)`	Print the score, the F matrix, and the alignment
`java.lang.String`	`formatScore(float val)`
`java.lang.String[]`	`getMatch()`
`abstract float`	`getScore()`
`Traceback`	`next(Traceback tb)`	Get the next state in the traceback
`abstract void`	`prepareAlignment(java.lang.String seq1, java.lang.String seq2)`	Initialises the matrices for the alignment.
`abstract void`	`printf(Output out)`	Print the matrix (matrices) used to compute the alignment
`void`	`setGapOpen(float d)`
`void`	`setScores(Scores sub)`
`void`	`traceback(TracebackPlotter plotter)`

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

Constructor Detail

Align

public Align(Scores sub,
             float d)

Method Detail
- doAlignment
```
public abstract void doAlignment(java.lang.String sq1,
                                 java.lang.String sq2)
```
  Performs the alignment, abstract.
  
  Parameters:
  
  sq1 -
  
  sq2 -
- prepareAlignment
```
public abstract void prepareAlignment(java.lang.String seq1,
                                      java.lang.String seq2)
```
  Initialises the matrices for the alignment.
  
  Parameters:
  
  seq1 -
  
  seq2 -
- setGapOpen
```
public void setGapOpen(float d)
```
- setScores
```
public void setScores(Scores sub)
```
- getMatch
```
public java.lang.String[] getMatch()
```
  Returns:
  
  two-element array containing an alignment with maximal score
- formatScore
```
public java.lang.String formatScore(float val)
```
  Parameters:
  
  val -
  
  Returns:
  
  float value of string val
- doMatch
```
public void doMatch(Output out,
                    java.lang.String msg,
                    boolean outputFMatrix)
```
  Print the score, the F matrix, and the alignment
  
  Parameters:
  
  out - output to print to
  
  msg - message printed at start
  
  outputFMatrix - print the score matrix
- traceback
```
public void traceback(TracebackPlotter plotter)
```
- doMatch
```
public void doMatch(Output out,
                    java.lang.String msg)
```
  Print the score and the alignment
  
  Parameters:
  
  out - output to print to
  
  msg - msg printed at the start
- next
```
public Traceback next(Traceback tb)
```
  Get the next state in the traceback
  
  Parameters:
  
  tb - current Traceback
  
  Returns:
  
  next Traceback
- getScore
```
public abstract float getScore()
```
  Returns:
  
  the score of the best alignment
- printf
```
public abstract void printf(Output out)
```
  Print the matrix (matrices) used to compute the alignment
  
  Parameters:
  
  out - output to print to

Class Align

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

Align

Method Detail

doAlignment

prepareAlignment

setGapOpen

setScores

getMatch

formatScore

doMatch

traceback

doMatch

next

getScore

printf