Package | Description |
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org.biojava.bio.alignment |
Classes to generate and describe sequence alignments.
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org.biojava.bio.structure.io |
Input and Output of Structures
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Class and Description |
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AbstractULAlignment |
AlignmentElement
AlignmentElement is a class which represents a SymbolList and its
location within an Alignment This is for use in
UnequalLengthAlignments and ARAlignments.
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ARAlignment
ARAlignment is an interface that defines methods for adding and
removing seqeunces from an Alignment.
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EditableAlignment
EditableAlignment is an interface that defines methods for
shifting bases within an Alignment.
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IllegalAlignmentEditException
The usual reason for throwing an IllegalAlignmentEditException is that you are
trying to shift a group of bases in such a way that it would require deleting bases.
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NeedlemanWunsch
Needleman and Wunsch defined the problem of global sequence alignments, from
the first till the last symbol of a sequence.
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SequenceAlignment
This Interface provides methods for the alignment of bio-sequences.
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SubstitutionMatrix
This object is able to read a substitution matrix file and constructs a short
matrix in memory.
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UnequalLengthAlignment
UnequalLengthAlignment has the following behavior.
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Class and Description |
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SubstitutionMatrix
This object is able to read a substitution matrix file and constructs a short
matrix in memory.
|