Package org.biojava.nbio.core.sequence.io
package org.biojava.nbio.core.sequence.io
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ClassesClassDescriptionNeed to keep track of actual bytes read and take advantage of buffered reader performance.A sequence creator which preserves the case of its input string in the user collection of the returned ProteinSequence.A helper class that allows different ways to read a string and create a DNA sequence.A Gene sequence has a Positive or Negative Strand where we want to write out to a stream the 5 to 3 prime version.Use FastaReaderHelper as an example of how to use this class where FastaReaderHelper should be the primary class used to read Fasta filesUsed to parse a stream of a fasta file to get the sequenceThe FastaWriter writes a collection of sequences to an outputStream.The class that should be used to write out fasta file of a sequence collectionThis 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.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.Use GenbankReaderHelper as an example of how to use this class where GenbankReaderHelper should be the primary class used to read Genbank filesThe class that should be used to write out genbank file of a sequence collectionWe 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.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 that can be used in future implementations to load features from external sources If the user has a custom header with local data then they can create their own implementation of a FastaHeaderParserInterfaceAvailable translations 1 - UNIVERSAL 2 - VERTEBRATE_MITOCHONDRIAL 3 - YEAST_MITOCHONDRIAL 4 - MOLD_MITOCHONDRIAL 5 - INVERTEBRATE_MITOCHONDRIAL 6 - CILIATE_NUCLEAR 9 - ECHINODERM_MITOCHONDRIAL 10 - EUPLOTID_NUCLEAR 11 - BACTERIAL 12 - ALTERNATIVE_YEAST_NUCLEAR 13 - ASCIDIAN_MITOCHONDRIAL 14 - FLATWORM_MITOCHONDRIAL 15 - BLEPHARISMA_MACRONUCLEAR 16 - 2CHLOROPHYCEAN_MITOCHONDRIAL 21 - TREMATODE_MITOCHONDRIAL 23 - SCENEDESMUS_MITOCHONDRIAL Taken from NCBI with slight modification and put into the classpath resource.Holds the concept of a codon table from the IUPAC formatThe plain fasta header takes everything in the header as a single entity.Used to create a ProteinSequence from a String to allow for details about the location of the sequence etc.Used to create a RNA sequence