Package org.biojava.bio.alignment
Class AlignmentAlgorithm
java.lang.Object
org.biojava.bio.alignment.AlignmentAlgorithm
- Direct Known Subclasses:
NeedlemanWunsch
,SmithWaterman
This Interface provides methods for the alignment of bio-sequences.
- Author:
- Andreas Dräger invalid input: '<'andreas.draeger@uni-tuebingen.de>, Mark Schreiber
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionalignAll
(SequenceIterator source, SequenceDB subjectDB) abstract AlignmentPair
pairwiseAlignment
(SymbolList query, SymbolList subject) Performs a pairwise sequence alignment of the two given sequences.
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Constructor Details
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AlignmentAlgorithm
public AlignmentAlgorithm()
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Method Details
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alignAll
- Parameters:
source
- a SequenceIterator containing a set of sequences to be aligned withsubjectDB
- the SequenceDB containing another set of sequences.- Returns:
- a list containing the results of all single alignments performed by this method.
- Throws:
NoSuchElementException
Exception
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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
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