Package | Description |
---|---|
org.biojava.nbio.core.sequence.io | |
org.biojava.nbio.core.sequence.template | |
org.biojava.nbio.core.sequence.transcription | |
org.biojava.nbio.structure.io |
Input and Output of Structures
|
Modifier and Type | Class and Description |
---|---|
class |
CasePreservingProteinSequenceCreator
A sequence creator which preserves the case of its input string in
the user collection of the returned ProteinSequence.
|
class |
DNASequenceCreator
A helper class that allows different ways to read a string and create a DNA sequence.
|
class |
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 |
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 |
ProteinSequenceCreator
Used to create a ProteinSequence from a String to allow for details
about the location of the sequence etc.
|
class |
RNASequenceCreator
Used to create a RNA sequence
|
Constructor and Description |
---|
FastaReader(File file,
SequenceHeaderParserInterface<S,C> headerParser,
SequenceCreatorInterface<C> sequenceCreator)
If you are going to use the FileProxyProteinSequenceCreator then you
need to use this constructor because we need details about
the location of the file.
|
FastaReader(InputStream is,
SequenceHeaderParserInterface<S,C> headerParser,
SequenceCreatorInterface<C> sequenceCreator)
If you are going to use FileProxyProteinSequenceCreator then do not use this constructor because we need details about
local file offsets for quick reads.
|
GenbankReader(File file,
SequenceHeaderParserInterface<S,C> headerParser,
SequenceCreatorInterface<C> sequenceCreator)
If you are going to use the FileProxyProteinSequenceCreator then you
need to use this constructor because we need details about
the location of the file.
|
GenbankReader(InputStream is,
SequenceHeaderParserInterface<S,C> headerParser,
SequenceCreatorInterface<C> sequenceCreator)
If you are going to use FileProxyProteinSequenceCreator then do not use this constructor because we need details about
local file offsets for quick reads.
|
Modifier and Type | Method and Description |
---|---|
SequenceCreatorInterface<T> |
AbstractCompoundTranslator.getCreator() |
Constructor and Description |
---|
AbstractCompoundTranslator(SequenceCreatorInterface<T> creator,
CompoundSet<F> fromCompoundSet,
CompoundSet<T> toCompoundSet) |
Modifier and Type | Method and Description |
---|---|
SequenceCreatorInterface<AminoAcidCompound> |
TranscriptionEngine.getProteinSequenceCreator() |
SequenceCreatorInterface<NucleotideCompound> |
TranscriptionEngine.getRnaSequenceCreator() |
Modifier and Type | Method and Description |
---|---|
TranscriptionEngine.Builder |
TranscriptionEngine.Builder.proteinCreator(SequenceCreatorInterface<AminoAcidCompound> creator) |
TranscriptionEngine.Builder |
TranscriptionEngine.Builder.rnaCreator(SequenceCreatorInterface<NucleotideCompound> creator) |
Constructor and Description |
---|
DNAToRNATranslator(SequenceCreatorInterface<NucleotideCompound> rnaCreator,
CompoundSet<NucleotideCompound> dna,
CompoundSet<NucleotideCompound> rna,
boolean shortCutTranslation) |
RNAToAminoAcidTranslator(SequenceCreatorInterface<AminoAcidCompound> creator,
CompoundSet<NucleotideCompound> nucleotides,
CompoundSet<Table.Codon> codons,
CompoundSet<AminoAcidCompound> aminoAcids,
Table table,
boolean trimStops,
boolean initMetOnly,
boolean translateNCodons)
Deprecated.
Retained for backwards compatability, setting
RNAToAminoAcidTranslator.stopAtStopCodons to false |
RNAToAminoAcidTranslator(SequenceCreatorInterface<AminoAcidCompound> creator,
CompoundSet<NucleotideCompound> nucleotides,
CompoundSet<Table.Codon> codons,
CompoundSet<AminoAcidCompound> aminoAcids,
Table table,
boolean trimStops,
boolean initMetOnly,
boolean translateNCodons,
boolean stopAtStopCodons)
Deprecated.
|
RNAToAminoAcidTranslator(SequenceCreatorInterface<AminoAcidCompound> creator,
CompoundSet<NucleotideCompound> nucleotides,
CompoundSet<Table.Codon> codons,
CompoundSet<AminoAcidCompound> aminoAcids,
Table table,
boolean trimStops,
boolean initMetOnly,
boolean translateNCodons,
boolean stopAtStopCodons,
boolean waitForStartCodon) |
Constructor and Description |
---|
FastaStructureParser(File file,
SequenceHeaderParserInterface<ProteinSequence,AminoAcidCompound> headerParser,
SequenceCreatorInterface<AminoAcidCompound> sequenceCreator,
AtomCache cache) |
FastaStructureParser(InputStream is,
SequenceHeaderParserInterface<ProteinSequence,AminoAcidCompound> headerParser,
SequenceCreatorInterface<AminoAcidCompound> sequenceCreator,
AtomCache cache) |
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