Search Java Classes and Packages
#Org.biojava.nbio.alignment Classes and Interfaces - 51 results found.
| Name | Description | Type | Package | Framework |
| AbstractMatrixAligner | Class | org.biojava.nbio.alignment.template | BioJava | |
| AbstractPairwiseSequenceAligner | Class | org.biojava.nbio.alignment.template | BioJava | |
| AbstractProfileProfileAligner | Class | org.biojava.nbio.alignment.template | BioJava | |
| AbstractScorer | Class | org.biojava.nbio.alignment.template | BioJava | |
| Aligner | Defines an algorithm which computes an alignment Profile from a list of Sequences. | Interface | org.biojava.nbio.alignment.template | BioJava |
| AlignerHelper | Static utility to construct alignment routines from a common library of methods. | Class | org.biojava.nbio.alignment.routines | BioJava |
| AlignerHelper .Anchor | Compounds in query and target sequences that must alignAuthor:Daniel Cameron | Class | org.biojava.nbio.alignment.routines | BioJava |
| AlignerHelper .Anchor .QueryIndexComparator | Class | org.biojava.nbio.alignment.routines | BioJava | |
| AlignerHelper .Cut | Defines a 'cut' row for divide-and-conquer alignment in which a new anchor is found. | Class | org.biojava.nbio.alignment.routines | BioJava |
| AlignerHelper .Last | Define a traceback pointer for the three edit operations: substitution (match/replacement of a query compound with a target compound), deletion (removal of a query compound leaving a gap in the target sequence), and | Class | org.biojava.nbio.alignment.routines | BioJava |
| AlignerHelper .Subproblem | Alignment subproblem. | Class | org.biojava.nbio.alignment.routines | BioJava |
| Alignments | Static utility to easily run alignment routines. | Class | org.biojava.nbio.alignment | BioJava |
| Alignments .PairInProfileScorerType | List of implemented sequence pair in a profile scoring routines. | Class | org.biojava.nbio.alignment | BioJava |
| Alignments .PairwiseSequenceAlignerType | List of implemented pairwise sequence alignment routines. | Class | org.biojava.nbio.alignment | BioJava |
| Alignments .PairwiseSequenceScorerType | List of implemented pairwise sequence scoring routines. | Class | org.biojava.nbio.alignment | BioJava |
| Alignments .ProfileProfileAlignerType | List of implemented profile-profile alignment routines. | Class | org.biojava.nbio.alignment | BioJava |
| Alignments .RefinerType | List of implemented profile refinement routines. | Class | org.biojava.nbio.alignment | BioJava |
| AnchoredPairwiseSequenceAligner | This algorithm uses a divide-and-conquer approach to find optimal pairwise global sequence alignments (from the first until the last Compound of each Sequence) with the restriction that any alignment produced | Class | org.biojava.nbio.alignment.routines | BioJava |
| CallablePairwiseSequenceAligner | Class | org.biojava.nbio.alignment.template | BioJava | |
| CallablePairwiseSequenceScorer | Class | org.biojava.nbio.alignment.template | BioJava | |
| CallableProfileProfileAligner | Class | org.biojava.nbio.alignment.template | BioJava | |
| FractionalIdentityInProfileScorer | Profile. | Class | org.biojava.nbio.alignment | BioJava |
| FractionalIdentityScorer | alignment columns which have identical Compounds. | Class | org.biojava.nbio.alignment | BioJava |
| FractionalSimilarityInProfileScorer | Profile. | Class | org.biojava.nbio.alignment | BioJava |
| FractionalSimilarityScorer | alignment columns which have similar Compounds. | Class | org.biojava.nbio.alignment | BioJava |
| GapPenalty | Defines a data structure for the gap penalties used during a sequence alignment routine. | Interface | org.biojava.nbio.alignment.template | BioJava |
| GapPenalty .Type | Defines the possible types of gap penalties. | Class | org.biojava.nbio.alignment.template | BioJava |
| GuanUberbacher | Guan and Uberbacher defined an algorithm for pairwise global sequence alignments (from the first until the last Compound of each Sequence). | Class | org.biojava.nbio.alignment.routines | BioJava |
| GuideTree | GuideTree. | Class | org.biojava.nbio.alignment | BioJava |
| GuideTreeNode | Defines a data structure for the node in a guide tree used during progressive multiple sequence alignment. | Interface | org.biojava.nbio.alignment.template | BioJava |
| HierarchicalClusterer | Defines a clustering algorithm that converts a distance matrix into a tree. | Interface | org.biojava.nbio.alignment.template | BioJava |
| MatrixAligner | Defines an Aligner which builds a score matrix during computation. | Interface | org.biojava.nbio.alignment.template | BioJava |
| NeedlemanWunsch | Needleman and Wunsch defined an algorithm for pairwise global sequence alignments (from the first until the last Compound of each Sequence). | Class | org.biojava.nbio.alignment | BioJava |
| PairInProfileScorer | Defines an algorithm which computes a score for a sequence alignment pair picked from an alignment Profile. | Interface | org.biojava.nbio.alignment.template | BioJava |
| PairwiseSequenceAligner | Defines an Aligner for a pair of Sequences. | Interface | org.biojava.nbio.alignment.template | BioJava |
| PairwiseSequenceScorer | Defines an algorithm which computes a score for a pair of sequences. | Interface | org.biojava.nbio.alignment.template | BioJava |
| PartitionRefiner | Defines an algorithm which computes a new alignment Profile by splitting a current alignment and realigning. | Interface | org.biojava.nbio.alignment.template | BioJava |
| ProfileProfileAligner | Defines an Aligner for a pair of Profiles. | Interface | org.biojava.nbio.alignment.template | BioJava |
| ProfileProfileScorer | Defines an algorithm which computes a score for a pairing of alignment profiles. | Interface | org.biojava.nbio.alignment.template | BioJava |
| RescoreRefiner | Interface | org.biojava.nbio.alignment.template | BioJava | |
| Scorer | Defines an algorithm which computes a score. | Interface | org.biojava.nbio.alignment.template | BioJava |
| SimpleGapPenalty | Class | org.biojava.nbio.alignment | BioJava | |
| SimpleProfileProfileAligner | NeedlemanWunsch pairwise sequence aligner to pairwise profile alignment using a sum-of-pairs score. | Class | org.biojava.nbio.alignment | BioJava |
| SmithWaterman | Smith and Waterman defined an algorithm for pairwise local sequence alignments (best match of sections from each Sequence). | Class | org.biojava.nbio.alignment | BioJava |
| StandardRescoreRefiner | Class | org.biojava.nbio.alignment | BioJava | |
| StockholmFileAnnotation | Stores all the content parsed from the #=GF linesSince:3. | Class | org.biojava.nbio.alignment.io | BioJava |
| StockholmFileAnnotation .StockholmFileAnnotationReference | Class | org.biojava.nbio.alignment.io | BioJava | |
| StockholmFileParser | Stockholm file parser. | Class | org.biojava.nbio.alignment.io | BioJava |
| StockholmStructure | Stores all the content of a Stockholm file. | Class | org.biojava.nbio.alignment.io | BioJava |
| StockholmStructure .DatabaseReference | Class | org.biojava.nbio.alignment.io | BioJava | |
| SubstitutionMatrixScorer | Scores using a substitution matrix. | Class | org.biojava.nbio.alignment | BioJava |