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Packages that use org.biojava.bio.alignment | |
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org.biojava.bio.alignment | Classes to generate and describe sequence alignments. |
org.biojava.bio.structure.io | Input and Output of Structures |
Classes in org.biojava.bio.alignment used by org.biojava.bio.alignment | |
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AbstractULAlignment
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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. |
Classes in org.biojava.bio.alignment used by org.biojava.bio.structure.io | |
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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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