AlignmentAlgorithm (biojava-legacy 1.9.5 API)

AlignmentAlgorithm (biojava-legacy 1.9.5 API)

java.lang.Object
- org.biojava.bio.alignment.AlignmentAlgorithm

Direct Known Subclasses:

NeedlemanWunsch, SmithWaterman
```
public abstract class AlignmentAlgorithm
extends Object
```
This Interface provides methods for the alignment of bio-sequences.

Author:

Andreas Dräger , Mark Schreiber

Constructor Summary

Constructors
Constructor Description

AlignmentAlgorithm()

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method	Description
`List<AlignmentPair>`	`alignAll(SequenceIterator source, SequenceDB subjectDB)`
`abstract AlignmentPair`	`pairwiseAlignment(SymbolList query, SymbolList subject)`	Performs a pairwise sequence alignment of the two given sequences.

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

- Constructor Detail
  - AlignmentAlgorithm
```
public AlignmentAlgorithm()
```
- Method Detail
  - alignAll
```
public List<AlignmentPair> alignAll(SequenceIterator source,
                                    SequenceDB subjectDB)
                             throws Exception
```
    Parameters:
    
    source - a SequenceIterator containing a set of sequences to be aligned with
    
    subjectDB - the SequenceDB containing another set of sequences.
    
    Returns:
    
    a list containing the results of all single alignments performed by this method.
    
    Throws:
    
    NoSuchElementException
    
    Exception
  - pairwiseAlignment
```
public abstract AlignmentPair pairwiseAlignment(SymbolList query,
                                                SymbolList subject)
                                         throws Exception
```
    Performs a pairwise sequence alignment of the two given sequences.
    
    Parameters:
    
    query -
    
    subject -
    
    Returns:
    
    score of the alignment or the distance.
    
    Throws:
    
    Exception