| Package | Description |
|---|---|
| demo | |
| org.biojava.nbio.core.sequence | |
| org.biojava.nbio.core.sequence.io | |
| org.biojava.nbio.core.sequence.io.template | |
| org.biojava.nbio.core.sequence.loader | |
| org.biojava.nbio.core.sequence.storage | |
| org.biojava.nbio.core.sequence.template | |
| org.biojava.nbio.core.sequence.views | |
| org.biojava.nbio.core.util | |
| org.biojava.nbio.sequencing.io.fastq |
FASTQ and variants sequence format I/O.
|
| org.biojava.nbio.structure.align.multiple.util | |
| org.biojava.nbio.structure.io |
Input and Output of Structures
|
| Modifier and Type | Method and Description |
|---|---|
static void |
BioJavaAADemo.main(String[] args) |
| Constructor and Description |
|---|
BasicSequence(String sequence,
CompoundSet<C> compoundSet) |
ChromosomeSequence(String seqString)
String is king and assume DNA
|
ChromosomeSequence(String seqString,
CompoundSet<NucleotideCompound> compoundSet)
Allows the creation of a ChromosomeSequence using String for the sequence with a custom CompoundSet
|
DNASequence(String seqString)
String is king and create a sequence from DNA with default DNA compound set
|
DNASequence(String seqString,
CompoundSet<NucleotideCompound> compoundSet)
Create a sequence from a string with user defined compound set
|
ProteinSequence(String seqString)
Create a protein from a string
|
ProteinSequence(String seqString,
CompoundSet<AminoAcidCompound> compoundSet)
Create a protein from a string with a user defined set of amino acids
|
RNASequence(String seqString)
Create a RNA sequence from a String
|
RNASequence(String seqString,
CompoundSet<NucleotideCompound> compoundSet)
Create a RNA sequence from a string with a user defined RNA compound set
|
| Modifier and Type | Method and Description |
|---|---|
AbstractSequence<AminoAcidCompound> |
ProteinSequenceCreator.getSequence(String sequence,
long index) |
AbstractSequence<AminoAcidCompound> |
CasePreservingProteinSequenceCreator.getSequence(String sequence,
long index) |
AbstractSequence<NucleotideCompound> |
DNASequenceCreator.getSequence(String sequence,
long index) |
AbstractSequence<NucleotideCompound> |
RNASequenceCreator.getSequence(String sequence,
long index) |
AbstractSequence<NucleotideCompound> |
FileProxyDNASequenceCreator.getSequence(String sequence,
long index)
Even though we are passing in the sequence we really only care about the length of the sequence and the offset
index in the fasta file.
|
AbstractSequence<AminoAcidCompound> |
FileProxyProteinSequenceCreator.getSequence(String sequence,
long index)
Even though we are passing in the sequence we really only care about the length of the sequence and the offset
index in the fasta file.
|
LinkedHashMap<String,S> |
GenbankReader.process()
The parsing is done in this method.
This method tries to process all the available Genbank records in the File or InputStream, closes the underlying resource, and return the results in LinkedHashMap.You don't need to call GenbankReader.close() after calling this method. |
LinkedHashMap<String,S> |
GenbankReader.process(int max)
This method tries to parse maximum
max records from
the open File or InputStream, and leaves the underlying resource open.Subsequent calls to the same method continue parsing the rest of the file. This is particularly useful when dealing with very big data files, (e.g. |
| Modifier and Type | Method and Description |
|---|---|
AbstractSequence<C> |
SequenceCreatorInterface.getSequence(String sequence,
long index) |
| Modifier and Type | Method and Description |
|---|---|
void |
UniprotProxySequenceReader.setContents(String sequence)
Once the sequence is retrieved set the contents and make sure everything this is valid
|
void |
StringProxySequenceReader.setContents(String sequence) |
void |
SequenceFileProxyLoader.setContents(String sequence) |
void |
StringProxySequenceReader.setContents(String sequence,
ArrayList features) |
| Constructor and Description |
|---|
GenbankProxySequenceReader(String genbankDirectoryCache,
String accessionID,
CompoundSet<C> compoundSet) |
SequenceFileProxyLoader(File file,
SequenceParserInterface sequenceParser,
long sequenceStartIndex,
int sequenceLength,
CompoundSet<C> compoundSet) |
StringProxySequenceReader(String sequence,
CompoundSet<C> compoundSet) |
UniprotProxySequenceReader(Document document,
CompoundSet<C> compoundSet)
The xml is passed in as a DOM object so we know everything about the protein.
|
UniprotProxySequenceReader(String accession,
CompoundSet<C> compoundSet)
The UniProt id is used to retrieve the UniProt XML which is then parsed as a DOM object
so we know everything about the protein.
|
| Modifier and Type | Method and Description |
|---|---|
void |
SingleCompoundSequenceReader.setContents(String sequence)
Unsupported
|
void |
JoiningSequenceReader.setContents(String sequence) |
void |
ArrayListSequenceReader.setContents(String sequence) |
void |
BitSequenceReader.setContents(String sequence)
Class is immutable & so this is unsupported
|
| Constructor and Description |
|---|
ArrayListSequenceReader(String sequence,
CompoundSet<C> compoundSet) |
| Modifier and Type | Method and Description |
|---|---|
void |
SequenceReader.setContents(String sequence) |
| Constructor and Description |
|---|
AbstractSequence(String seqString,
CompoundSet<C> compoundSet)
Create a Sequence from a simple string where the values should be found in compoundSet
|
| Modifier and Type | Method and Description |
|---|---|
void |
RnaSequenceView.setContents(String sequence) |
| Modifier and Type | Method and Description |
|---|---|
Sequence<?> |
SequenceTools.getSequenceFromString(String sequence) |
| Modifier and Type | Method and Description |
|---|---|
static DNASequence |
FastqTools.createDNASequence(Fastq fastq)
Create and return a new
DNASequence from the specified FASTQ formatted sequence. |
static DNASequence |
FastqTools.createDNASequenceWithErrorProbabilities(Fastq fastq)
Create and return a new
DNASequence with error probabilities from the specified
FASTQ formatted sequence. |
static DNASequence |
FastqTools.createDNASequenceWithQualityScores(Fastq fastq)
Create and return a new
DNASequence with quality scores from the specified
FASTQ formatted sequence. |
static DNASequence |
FastqTools.createDNASequenceWithQualityScoresAndErrorProbabilities(Fastq fastq)
Create and return a new
DNASequence with quality scores and error probabilities from the
specified FASTQ formatted sequence. |
| Modifier and Type | Method and Description |
|---|---|
static org.forester.phylogeny.Phylogeny |
MultipleAlignmentTools.getHSDMTree(MultipleAlignment msta)
Calculate a phylogenetic tree of the MultipleAlignment using
dissimilarity scores (DS), based in SDM Substitution Matrix (ideal for
distantly related proteins, structure-derived) and the Neighbor Joining
algorithm from forester.
|
static org.forester.phylogeny.Phylogeny |
MultipleAlignmentTools.getKimuraTree(MultipleAlignment msta)
Calculate a phylogenetic tree of the MultipleAlignment using Kimura
distances and the Neighbor Joining algorithm from forester.
|
static MultipleSequenceAlignment<ProteinSequence,AminoAcidCompound> |
MultipleAlignmentTools.toProteinMSA(MultipleAlignment msta)
Convert a MultipleAlignment into a MultipleSequenceAlignment of AminoAcid
residues.
|
| Modifier and Type | Method and Description |
|---|---|
static AFPChain |
FastaAFPChainConverter.cpFastaToAfpChain(String first,
String second,
Structure structure,
int cpSite) |
static AFPChain |
FastaAFPChainConverter.fastaStringToAfpChain(String sequence1,
String sequence2,
Structure structure1,
Structure structure2)
Returns an AFPChain corresponding to the alignment between
structure1 and structure2, which is given by the gapped protein sequences sequence1 and sequence2. |
static AFPChain |
FastaAFPChainConverter.fastaToAfpChain(String sequence1,
String sequence2,
Structure structure1,
Structure structure2)
TODO Write comment
|
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