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#Org.biojava.nbio.core.sequence Classes and Interfaces - 148 results found.
| Name | Description | Type | Package | Framework |
| AbstractCompound | Class | org.biojava.nbio.core.sequence.template | BioJava | |
| AbstractCompoundSet | Class | org.biojava.nbio.core.sequence.template | BioJava | |
| AbstractCompoundTranslator | Class | org.biojava.nbio.core.sequence.template | BioJava | |
| AbstractFeature | A feature is currently any descriptive item that can be associated with a sequence position(s) A feature has a type and a source which is currently a string to allow flexibility for the user | Class | org.biojava.nbio.core.sequence.features | BioJava |
| AbstractLocation | Base abstraction of a location which encodes for the majority of important features about a location such as the start, end and strand | Class | org.biojava.nbio.core.sequence.location.template | BioJava |
| AbstractNucleotideCompoundSet | Class | org.biojava.nbio.core.sequence.template | BioJava | |
| AbstractSequence | The base class for DNA, RNA and Protein sequences. | Class | org.biojava.nbio.core.sequence.template | BioJava |
| AbstractSequence .AnnotationType | Class | org.biojava.nbio.core.sequence.template | BioJava | |
| AccesionedLocation | A location which is bound to an AccessionID. | Interface | org.biojava.nbio.core.sequence.location.template | BioJava |
| Accessioned | Interface | org.biojava.nbio.core.sequence.template | BioJava | |
| AccessionID | Used in Sequences as the unique indentifier. | Class | org.biojava.nbio.core.sequence | BioJava |
| AmbiguityDNACompoundSet | Class | org.biojava.nbio.core.sequence.compound | BioJava | |
| AmbiguityDNARNAHybridCompoundSet | Ambiguity set for hybrid DNA/RNA sequences. | Class | org.biojava.nbio.core.sequence.compound | BioJava |
| AmbiguityRNACompoundSet | Class | org.biojava.nbio.core.sequence.compound | BioJava | |
| AminoAcidCompound | Used to describe an Amino Acid. | Class | org.biojava.nbio.core.sequence.compound | BioJava |
| AminoAcidCompoundSet | Set of proteinogenic amino acids. | Class | org.biojava.nbio.core.sequence.compound | BioJava |
| ArrayListProxySequenceReader | Class | org.biojava.nbio.core.sequence.loader | BioJava | |
| ArrayListSequenceReader | Class | org.biojava.nbio.core.sequence.storage | BioJava | |
| BasicSequence | Bare bones version of the Sequence object to be used sparingly. | Class | org.biojava.nbio.core.sequence | BioJava |
| BitSequenceReader | An implementation of the popular bit encodings. | Class | org.biojava.nbio.core.sequence.storage | BioJava |
| BitSequenceReader .BitArrayWorker | The logic of working with a bit has been separated out into this class to help developers create the bit data structures without having to | Class | org.biojava.nbio.core.sequence.storage | BioJava |
| BufferedReaderBytesRead | Need to keep track of actual bytes read and take advantage of buffered reader performance. | Class | org.biojava.nbio.core.sequence.io | BioJava |
| CaseInsensitiveCompound | Attempts to wrap compounds so it is possible to view them in a case insensitive manner | Class | org.biojava.nbio.core.sequence.transcription | BioJava |
| CasePreservingProteinSequenceCreator | A sequence creator which preserves the case of its input string in the user collection of the returned ProteinSequence. | Class | org.biojava.nbio.core.sequence.io | BioJava |
| CDSComparator | Class | org.biojava.nbio.core.sequence | BioJava | |
| CDSSequence | Represents a exon or coding sequence in a gene. | Class | org.biojava.nbio.core.sequence | BioJava |
| ChromosomeSequence | A ChromosomeSequence is a DNASequence but keeps track of geneSequencesAuthor:Scooter Willis | Class | org.biojava.nbio.core.sequence | BioJava |
| ClasspathResource | This object represents a classpath resource on the local system. | Class | org.biojava.nbio.core.sequence.io.util | BioJava |
| CodonCompound | Class | org.biojava.nbio.core.sequence.compound | BioJava | |
| ComplementCompound | Interface | org.biojava.nbio.core.sequence.template | BioJava | |
| ComplementSequenceView | For a given sequence this class will create a view over the top of it and for every request the code will return the complement of the underlying | Class | org.biojava.nbio.core.sequence.views | BioJava |
| Compound | Interface | org.biojava.nbio.core.sequence.template | BioJava | |
| CompoundSet | Interface | org.biojava.nbio.core.sequence.template | BioJava | |
| CompoundTranslator | Interface | org.biojava.nbio.core.sequence.template | BioJava | |
| DatabaseReferenceInterface | If a SequenceProxyReader implements this interface then that external source has a list of cross reference id(s) | Interface | org.biojava.nbio.core.sequence.features | BioJava |
| DataSource | GenBank gi | Class | org.biojava.nbio.core.sequence | BioJava |
| DBReferenceInfo | If you have a uniprot ID then it is possible to get a collection of other id(s) that the protein is known by. | Class | org.biojava.nbio.core.sequence.features | BioJava |
| DNACompoundSet | Class | org.biojava.nbio.core.sequence.compound | BioJava | |
| DNASequence | This is class should model the attributes associated with a DNA sequenceAuthor:Scooter Willis | Class | org.biojava.nbio.core.sequence | BioJava |
| DNASequence .DNAType | Class | org.biojava.nbio.core.sequence | BioJava | |
| DNASequenceCreator | A helper class that allows different ways to read a string and create a DNA sequence. | Class | org.biojava.nbio.core.sequence.io | BioJava |
| DNAToRNATranslator | Performs the first stage of transcription by going from DNA to RNA. | Class | org.biojava.nbio.core.sequence.transcription | BioJava |
| Edit | Interface for carrying out edit operations on a Sequence. | Interface | org.biojava.nbio.core.sequence.edits | BioJava |
| Edit .AbstractEdit | Abstract class which defines all edit operations as a call to discover what 5' and 3' ends of an editing Sequence should be joined together | Class | org.biojava.nbio.core.sequence.edits | BioJava |
| Edit .Delete | Class | org.biojava.nbio.core.sequence.edits | BioJava | |
| Edit .Insert | Edit implementation which allows us to insert a base at any position in a Sequence. | Class | org.biojava.nbio.core.sequence.edits | BioJava |
| Edit .Substitute | Allows for the substitution of bases into an existing Sequence. | Class | org.biojava.nbio.core.sequence.edits | BioJava |
| ExonComparator | Sort Exon where it is a little confusing if exons shoud always be ordered left to right where a negative stranded gene should go the other direction. | Class | org.biojava.nbio.core.sequence | BioJava |
| ExonSequence | A gene contains a collection of Exon sequencesAuthor:Scooter Willis | Class | org.biojava.nbio.core.sequence | BioJava |
| FastaGeneWriter | A Gene sequence has a Positive or Negative Strand where we want to write out to a stream the 5 to 3 prime version. | Class | org.biojava.nbio.core.sequence.io | BioJava |
| FastaHeaderFormatInterface | Interface | org.biojava.nbio.core.sequence.io.template | BioJava | |
| FastaReader | Use FastaReaderHelper as an example of how to use this class where FastaReaderHelper should be the primary class used to read Fasta files | Class | org.biojava.nbio.core.sequence.io | BioJava |
| FastaReaderHelper | Class | org.biojava.nbio.core.sequence.io | BioJava | |
| FastaSequenceParser | Used to parse a stream of a fasta file to get the sequenceAuthor:Scooter Willis | Class | org.biojava.nbio.core.sequence.io | BioJava |
| FastaWriter | The FastaWriter writes a collection of sequences to an outputStream. | Class | org.biojava.nbio.core.sequence.io | BioJava |
| FastaWriterHelper | The class that should be used to write out fasta file of a sequence collectionAuthor:Scooter Willis | Class | org.biojava.nbio.core.sequence.io | BioJava |
| FeatureDbReferenceInfo | It is DBReferenceInfo which implements FeatureInterface. | Class | org.biojava.nbio.core.sequence.features | BioJava |
| FeatureInterface | Interface class to handle describing arbitrary features. | Interface | org.biojava.nbio.core.sequence.features | BioJava |
| FeatureRetriever | If a SequenceProxyReader implements this interface then that external source has a list features | Interface | org.biojava.nbio.core.sequence.features | BioJava |
| FeaturesKeyWordInterface | Models the keywords that are annotated for a protein sequence at Uniprot. | Interface | org.biojava.nbio.core.sequence.features | BioJava |
| FileProxyDNASequenceCreator | This class is a good example of using the SequenceCreatorInterface where during parsing of the stream the sequence and the offset index are passed to create a Protein sequence that will be loaded in lazily. | Class | org.biojava.nbio.core.sequence.io | BioJava |
| FileProxyProteinSequenceCreator | This class is a good example of using the SequenceCreatorInterface where during parsing of the stream the sequence and the offset index are passed to create a Protein sequence that will be loaded in lazily. | Class | org.biojava.nbio.core.sequence.io | BioJava |
| FourBitSequenceReader | Four bit encoding of the bit formats. | Class | org.biojava.nbio.core.sequence.storage | BioJava |
| FourBitSequenceReader .FourBitArrayWorker | A four bit per compound implementation of the bit array worker code. | Class | org.biojava.nbio.core.sequence.storage | BioJava |
| Frame | Indicates a way of translating a sequence. | Class | org.biojava.nbio.core.sequence.transcription | BioJava |
| FuzzyPoint | Class | org.biojava.nbio.core.sequence.location | BioJava | |
| GenbankHeaderFormatInterface | Interface | org.biojava.nbio.core.sequence.io.template | BioJava | |
| GenbankProxySequenceReader | Class | org.biojava.nbio.core.sequence.loader | BioJava | |
| GenbankReader | Use GenbankReaderHelper as an example of how to use this class where GenbankReaderHelper should be the primary class used to read Genbank files | Class | org.biojava.nbio.core.sequence.io | BioJava |
| GenbankReaderHelper | Class | org.biojava.nbio.core.sequence.io | BioJava | |
| GenbankSequenceParser | Class | org.biojava.nbio.core.sequence.io | BioJava | |
| GenbankWriter | Class | org.biojava.nbio.core.sequence.io | BioJava | |
| GenbankWriterHelper | Class | org.biojava.nbio.core.sequence.io | BioJava | |
| GenericFastaHeaderFormat | We store the original header if the sequence is parsed from a fasta file and will use that exact sequence if we write out the sequences to a fasta file. | Class | org.biojava.nbio.core.sequence.io | BioJava |
| GenericFastaHeaderParser | The default fasta header parser where some headers are well defined based on the source database which allows us to set the source of the protein sequence and the identifier | Class | org.biojava.nbio.core.sequence.io | BioJava |
| GenericGenbankHeaderFormat | Class | org.biojava.nbio.core.sequence.io | BioJava | |
| GenericGenbankHeaderParser | Class | org.biojava.nbio.core.sequence.io | BioJava | |
| GenericInsdcHeaderFormat | Class | org.biojava.nbio.core.sequence.io | BioJava | |
| GeneSequence | Class | org.biojava.nbio.core.sequence | BioJava | |
| InsdcLocations | A collection of locations which are used whenever we work with INSDC; some of which could be deprecated (from INSDC's point of view) yet appear | Class | org.biojava.nbio.core.sequence.location | BioJava |
| InsdcLocations .BondLocation | Used to represent bond locations equivalent to bond(7,8) or bond(7). | Class | org.biojava.nbio.core.sequence.location | BioJava |
| InsdcLocations .GroupLocation | Deprecated in INSDC yet still appears; equivalent to the order() directive except no 5' to 3' ordering is defined. | Class | org.biojava.nbio.core.sequence.location | BioJava |
| InsdcLocations .OneOfLocation | Deprecated in INSDC; refers to a set of locations of which one location could be valid e. | Class | org.biojava.nbio.core.sequence.location | BioJava |
| InsdcLocations .OrderLocation | Used to describe a 5' to 3' ordering but no firm assurance it is correctSee Also:Serialized Form | Class | org.biojava.nbio.core.sequence.location | BioJava |
| InsdcParser | Parser for working with INSDC style locations. | Class | org.biojava.nbio.core.sequence.location | BioJava |
| IntronSequence | Class | org.biojava.nbio.core.sequence | BioJava | |
| IOUtils | Class | org.biojava.nbio.core.sequence.io.util | BioJava | |
| IOUtils .ReaderProcessor | Closure interface used when working with IOUtils#processReader(String). | Interface | org.biojava.nbio.core.sequence.io.util | BioJava |
| IUPACParser | Available translations 1 - UNIVERSAL2 - VERTEBRATE_MITOCHONDRIAL3 - YEAST_MITOCHONDRIAL4 - MOLD_MITOCHONDRIAL5 - INVERTEBRATE_MITOCHONDRIAL6 - CILIATE_NUCLEAR9 - ECHINODERM_MITOCHONDRIAL10 - EUPLOTID_NUCLEAR11 - BACTERIAL12 - ALTERNATIVE_YEAST_NUCLEAR13 - ASCIDIAN_MITOCHONDRIAL14 - FLATWORM_MITOCHONDRIAL15 - BLEPHARISMA_MACRONUCLEAR16 - 2CHLOROPHYCEAN_MITOCHONDRIAL21 - TREMATODE_MITOCHONDRIAL23 - SCENEDESMUS_MITOCHONDRIAL | Class | org.biojava.nbio.core.sequence.io | BioJava |
| IUPACParser .IUPACTable | Class | org.biojava.nbio.core.sequence.io | BioJava | |
| JoiningSequenceReader | This reader actually proxies onto multiple types of sequence in order to allow a number of sequence objects to act as if they are one sequence. | Class | org.biojava.nbio.core.sequence.storage | BioJava |
| LightweightProfile | Defines a minimal data structure for reading and writing a sequence alignment. | Interface | org.biojava.nbio.core.sequence.template | BioJava |
| LightweightProfile .StringFormat | List of output formats. | Class | org.biojava.nbio.core.sequence.template | BioJava |
| Location | Sets of integers used to represent the location of features on sequence. | Interface | org.biojava.nbio.core.sequence.location.template | BioJava |
| Location .Tools | Helper methods for use with the Location classes. | Class | org.biojava.nbio.core.sequence.location.template | BioJava |
| LocationHelper | Helper methods for use with the Location classes. | Class | org.biojava.nbio.core.sequence.location | BioJava |
| MultipleSequenceAlignment | structure in the alignment module provides additional functionality. | Class | org.biojava.nbio.core.sequence | BioJava |
| NucleotideCompound | Class | org.biojava.nbio.core.sequence.compound | BioJava | |
| PlainFastaHeaderParser | The plain fasta header takes everything in the header as a single entity. | Class | org.biojava.nbio.core.sequence.io | BioJava |
| Point | Interface | org.biojava.nbio.core.sequence.location.template | BioJava | |
| Point .Resolver | Interface | org.biojava.nbio.core.sequence.location.template | BioJava | |
| ProteinSequence | The representation of a ProteinSequenceAuthor:Scooter Willis, Paolo Pavan | Class | org.biojava.nbio.core.sequence | BioJava |
| ProteinSequenceCreator | Used to create a ProteinSequence from a String to allow for details about the location of the sequence etc. | Class | org.biojava.nbio.core.sequence.io | BioJava |
| ProxySequenceReader | Interface | org.biojava.nbio.core.sequence.template | BioJava | |
| Qualifier | Class | org.biojava.nbio.core.sequence.features | BioJava | |
| QualityFeature | DNA Sequences produced by modern sequencers usually have quality informaion attached to them. | Class | org.biojava.nbio.core.sequence.features | BioJava |
| QuantityFeature | It is common to have a numerical value or values associated with a feature. | Class | org.biojava.nbio.core.sequence.features | BioJava |
| ReversedSequenceView | For a given sequence this class will return the base at the reversed position i. | Class | org.biojava.nbio.core.sequence.views | BioJava |
| RNACompoundSet | Class | org.biojava.nbio.core.sequence.compound | BioJava | |
| RNASequence | RNASequence where RNACompoundSet are the allowed valuesAuthor:Scooter Willis | Class | org.biojava.nbio.core.sequence | BioJava |
| RNASequenceCreator | Used to create a RNA sequenceAuthor:Scooter Willis | Class | org.biojava.nbio.core.sequence.io | BioJava |
| RnaSequenceView | Class | org.biojava.nbio.core.sequence.views | BioJava | |
| RNAToAminoAcidTranslator | Takes a Sequence of NucleotideCompound which should represent an RNA sequence (RNASequence is good for this) and returns a list of | Class | org.biojava.nbio.core.sequence.transcription | BioJava |
| Sequence | Main interface for defining a collection of Compounds and accessing them using biological indexes | Interface | org.biojava.nbio.core.sequence.template | BioJava |
| SequenceAsStringHelper | This is a common method that can be used across multiple storage/proxy implementations to handle Negative strand and other interesting elements of sequence data. | Class | org.biojava.nbio.core.sequence.storage | BioJava |
| SequenceComparator | Used to sort sequencesAuthor:Scooter Willis | Class | org.biojava.nbio.core.sequence | BioJava |
| SequenceCreatorInterface | Interface | org.biojava.nbio.core.sequence.io.template | BioJava | |
| SequenceFileProxyLoader | This class represents the storage container of a sequence stored in a fasta file where the initial parsing of the file we store the offset and length of the sequence. | Class | org.biojava.nbio.core.sequence.loader | BioJava |
| SequenceHeaderParserInterface | Interface | org.biojava.nbio.core.sequence.io.template | BioJava | |
| SequenceLocation | A location in a sequence that keeps a reference to its parent sequenceAuthor:Scooter Willis , Paolo PavanSee Also:Serialized Form | Class | org.biojava.nbio.core.sequence.location | BioJava |
| SequenceMixin | Provides a set of static methods to be used as static imports when needed across multiple Sequence implementations but inheritance gets in the way. | Class | org.biojava.nbio.core.sequence.template | BioJava |
| SequenceMixin .SequenceIterator | A basic sequence iterator which iterates over the given Sequence by biological index. | Class | org.biojava.nbio.core.sequence.template | BioJava |
| SequenceOptimizationHints | A static class that provides optimization hints for memory or performance handling of sequence data. | Class | org.biojava.nbio.core.sequence | BioJava |
| SequenceOptimizationHints .SequenceCollection | Class | org.biojava.nbio.core.sequence | BioJava | |
| SequenceOptimizationHints .SequenceUsage | Class | org.biojava.nbio.core.sequence | BioJava | |
| SequenceParserInterface | Interface | org.biojava.nbio.core.sequence.io.template | BioJava | |
| SequenceProxyView | Class | org.biojava.nbio.core.sequence.template | BioJava | |
| SequenceReader | Interface | org.biojava.nbio.core.sequence.template | BioJava | |
| SequenceView | Interface | org.biojava.nbio.core.sequence.template | BioJava | |
| SimpleLocation | Very basic implementation of the Location interface which defines a series of simple constructors. | Class | org.biojava.nbio.core.sequence.location | BioJava |
| SimplePoint | Basic implementation of the Point interface. | Class | org.biojava.nbio.core.sequence.location | BioJava |
| SingleCompoundSequenceReader | An implementation of the SequenceReader interface which for every call will return only 1 compound (given to it during construction; a String | Class | org.biojava.nbio.core.sequence.storage | BioJava |
| StartCodonSequence | Used to map the start codon feature on a geneAuthor:Scooter Willis | Class | org.biojava.nbio.core.sequence | BioJava |
| StopCodonSequence | Used to map the stop codon sequence on a geneAuthor:Scooter Willis | Class | org.biojava.nbio.core.sequence | BioJava |
| Strand | Provides a way of representing the strand of a sequence, locationEnum Constant Summary | Class | org.biojava.nbio.core.sequence | BioJava |
| StringProxySequenceReader | An example of a ProxySequenceReader that is created from a String. | Class | org.biojava.nbio.core.sequence.loader | BioJava |
| Table | Provides a way of separating us from the specific IUPACParser. | Interface | org.biojava.nbio.core.sequence.transcription | BioJava |
| Table .CaseInsensitiveTriplet | to be assessed in a case insensitive manner. | Class | org.biojava.nbio.core.sequence.transcription | BioJava |
| Table .Codon | Instance of a Codon which is 3 NucleotideCompounds, its corresponding AminoAcidCompound and if it is a start or stop codon. | Class | org.biojava.nbio.core.sequence.transcription | BioJava |
| TaxonomyID | A sequence can be associated with a species or Taxonomy IDAuthor:Scooter Willis | Class | org.biojava.nbio.core.sequence | BioJava |
| TextFeature | A implmentation of AbstractFeatureAuthor:Scooter Willis | Class | org.biojava.nbio.core.sequence.features | BioJava |
| TranscriptionEngine | Used as a way of encapsulating the data structures required to parse DNA to a In order to build one look at @ TranscriptionEngine. | Class | org.biojava.nbio.core.sequence.transcription | BioJava |
| TranscriptionEngine .Builder | This class is the way to create a TranslationEngine. | Class | org.biojava.nbio.core.sequence.transcription | BioJava |
| TranscriptSequence | This is the sequence if you want to go from a gene sequence to a protein sequence. | Class | org.biojava.nbio.core.sequence | BioJava |
| TwoBitSequenceReader | 0 - T1 - C2 - A3 - G We also do not support case sensitive encodings therefore if you pass a | Class | org.biojava.nbio.core.sequence.storage | BioJava |
| TwoBitSequenceReader .TwoBitArrayWorker | Extension of the BitArrayWorker which provides the 2bit implementation code. | Class | org.biojava.nbio.core.sequence.storage | BioJava |
| UniprotProxySequenceReader | Pass in a Uniprot ID and this ProxySequenceReader when passed to a ProteinSequence will get the sequence data and other data elements associated with the ProteinSequence by Uniprot. | Class | org.biojava.nbio.core.sequence.loader | BioJava |
| WindowedSequence | A sliding window view of a sequence which does not implement any interfaces like Sequence because they do not fit how this works. | Class | org.biojava.nbio.core.sequence.views | BioJava |