Name | Description | Type | Package | Framework |
AlignmentBlock | This class is used by the CrochemoreLandauZivUkelson algorithm to store the information of an alignment block. | Class | org.jscience.biology.alignment | JScience |
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BasicScoringScheme | This class implements a basic scoring scheme. | Class | org.jscience.biology.alignment | JScience |
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CharSequence | This class implements a sequence of characters stored as an array that provides random access to any position in constant time. | Class | org.jscience.biology.alignment | JScience |
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CrochemoreLandauZivUkelson | This abstract class is the superclass of both global and local sequence alignment algorithms (with linear gap penalty function) due to Maxime Crochemore, Gad Landau and | Class | org.jscience.biology.alignment | JScience |
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CrochemoreLandauZivUkelsonGlobalAlignment | This class implements the global pairwise sequence alignment algorithm (with linear gap penalty function) due to Maxime Crochemore, Gad Landau and Michal | Class | org.jscience.biology.alignment | JScience |
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CrochemoreLandauZivUkelsonLocalAlignment | This class implements the local pairwise sequence alignment algorithm (with linear gap penalty function) due to Maxime Crochemore, Gad Landau and Michal | Class | org.jscience.biology.alignment | JScience |
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Factor | This class is used by FactorSequence to create a linked list of factors of a text as induced by its Lempel-Ziv (LZ78) factorisation. | Class | org.jscience.biology.alignment | JScience |
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FactorSequence | This class builds a list of factors of a character sequence as induced by its Lempel-Ziv (LZ78) factorisation. | Class | org.jscience.biology.alignment | JScience |
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IncompatibleScoringSchemeException | Signals that an scoring scheme is not compatible with the sequencesSee Also:ScoringScheme, | Class | org.jscience.biology.alignment | JScience |
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InvalidScoringMatrixException | Signals that the substitution matrix does not comply with the specification (see for details). | Class | org.jscience.biology.alignment | JScience |
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InvalidSequenceException | Signals that the sequence does not comply with the specification (seeSee Also:CharSequence, | Class | org.jscience.biology.alignment | JScience |
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LocalAlignmentBlock | This class is used by the CrochemoreLandauZivUkelsonLocalAlignment algorithm to store the information of an alignment block. | Class | org.jscience.biology.alignment | JScience |
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Matrix | This interface defines a minimal set of operations that a matrix must implement. | Interface | org.jscience.biology.alignment | JScience |
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NeedlemanWunsch | This class implements the classic global alignment algorithm (with linear gap penalty function) due to S. | Class | org.jscience.biology.alignment | JScience |
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OutMatrix | CrochemoreLandauZivUkelson and subclasses to enconde the OUT matrix from the input border and DIST matrix of an AlignmentBlock. | Class | org.jscience.biology.alignment | JScience |
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PairwiseAlignment | This class is the product of a pairwise alignment, generated by one subclasses of PairwiseAlignmentAlgorithm. | Class | org.jscience.biology.alignment | JScience |
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PairwiseAlignmentAlgorithm | This abstract class is the superclass of all classes implementing pairwise sequence alignment algorithms. | Class | org.jscience.biology.alignment | JScience |
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ScoringMatrix | This class implements a scoring scheme based on a substitution matrix. | Class | org.jscience.biology.alignment | JScience |
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ScoringScheme | This abstract class is the superclass of all scoring schemes. | Class | org.jscience.biology.alignment | JScience |
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Smawk | This class implement the SMAWK algorithm to compute column maxima on a totally monotone matrix as described. | Class | org.jscience.biology.alignment | JScience |
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SmithWaterman | This class implement the classic local alignment algorithm (with linear gap penalty function) due to T. | Class | org.jscience.biology.alignment | JScience |
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Trie | This class implements a trie, or a digital search tree. | Class | org.jscience.biology.alignment | JScience |