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#Org.biojava.nbio.core.sequence.io Classes and Interfaces - 34 results found.
| Name | Description | Type | Package | Framework |
| BufferedReaderBytesRead | Need to keep track of actual bytes read and take advantage of buffered reader performance. | Class | org.biojava.nbio.core.sequence.io | 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 |
| ClasspathResource | This object represents a classpath resource on the local system. | Class | org.biojava.nbio.core.sequence.io.util | 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 |
| 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 |
| 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 |
| GenbankHeaderFormatInterface | Interface | org.biojava.nbio.core.sequence.io.template | 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 | |
| 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 | |
| PlainFastaHeaderParser | The plain fasta header takes everything in the header as a single entity. | Class | org.biojava.nbio.core.sequence.io | 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 |
| RNASequenceCreator | Used to create a RNA sequenceAuthor:Scooter Willis | Class | org.biojava.nbio.core.sequence.io | BioJava |
| SequenceCreatorInterface | Interface | org.biojava.nbio.core.sequence.io.template | BioJava | |
| SequenceHeaderParserInterface | Interface | org.biojava.nbio.core.sequence.io.template | BioJava | |
| SequenceParserInterface | Interface | org.biojava.nbio.core.sequence.io.template | BioJava | |