Search Java Classes and Packages
#Org.jscience.biology.alignment Classes and Interfaces - 22 results found.
| 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 |
| BasicScoringScheme | This class implements a basic scoring scheme. | Class | org.jscience.biology.alignment | JScience |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| IncompatibleScoringSchemeException | Signals that an scoring scheme is not compatible with the sequencesSee Also:ScoringScheme, | Class | org.jscience.biology.alignment | JScience |
| InvalidScoringMatrixException | Signals that the substitution matrix does not comply with the specification (see for details). | Class | org.jscience.biology.alignment | JScience |
| InvalidSequenceException | Signals that the sequence does not comply with the specification (seeSee Also:CharSequence, | Class | org.jscience.biology.alignment | JScience |
| LocalAlignmentBlock | This class is used by the CrochemoreLandauZivUkelsonLocalAlignment algorithm to store the information of an alignment block. | Class | org.jscience.biology.alignment | JScience |
| Matrix | This interface defines a minimal set of operations that a matrix must implement. | Interface | org.jscience.biology.alignment | JScience |
| NeedlemanWunsch | This class implements the classic global alignment algorithm (with linear gap penalty function) due to S. | Class | org.jscience.biology.alignment | JScience |
| 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 |
| PairwiseAlignment | This class is the product of a pairwise alignment, generated by one subclasses of PairwiseAlignmentAlgorithm. | Class | org.jscience.biology.alignment | JScience |
| PairwiseAlignmentAlgorithm | This abstract class is the superclass of all classes implementing pairwise sequence alignment algorithms. | Class | org.jscience.biology.alignment | JScience |
| ScoringMatrix | This class implements a scoring scheme based on a substitution matrix. | Class | org.jscience.biology.alignment | JScience |
| ScoringScheme | This abstract class is the superclass of all scoring schemes. | Class | org.jscience.biology.alignment | JScience |
| Smawk | This class implement the SMAWK algorithm to compute column maxima on a totally monotone matrix as described. | Class | org.jscience.biology.alignment | JScience |
| SmithWaterman | This class implement the classic local alignment algorithm (with linear gap penalty function) due to T. | Class | org.jscience.biology.alignment | JScience |
| Trie | This class implements a trie, or a digital search tree. | Class | org.jscience.biology.alignment | JScience |