Uses of Class
org.biojava.nbio.data.sequence.FastaSequence

Packages that use FastaSequence

Package	Description
org.biojava.nbio.data.sequence	Set of classes that responsible for data handling.
org.biojava.nbio.ronn	BioJava provide a module biojava-protein-disorder for prediction disordered regions from a protein sequence.

Uses of FastaSequence in org.biojava.nbio.data.sequence

Methods in org.biojava.nbio.data.sequence that return types with arguments of type FastaSequence

Modifier and Type	Method and Description
static List<FastaSequence>	SequenceUtil.readFasta(InputStream inStream) Reads fasta sequences from inStream into the list of FastaSequence objects

Methods in org.biojava.nbio.data.sequence with parameters of type FastaSequence

Modifier and Type	Method and Description
int	FastaSequence.compareTo(FastaSequence o)
static boolean	SequenceUtil.isNucleotideSequence(FastaSequence s)

Method parameters in org.biojava.nbio.data.sequence with type arguments of type FastaSequence

Modifier and Type	Method and Description
static void	SequenceUtil.writeFasta(OutputStream os, List<FastaSequence> sequences) Writes FastaSequence in the file, each sequence will take one line only
static void	SequenceUtil.writeFasta(OutputStream outstream, List<FastaSequence> sequences, int width) Writes list of FastaSequeces into the outstream formatting the sequence so that it contains width chars on each line

Uses of FastaSequence in org.biojava.nbio.ronn

Methods in org.biojava.nbio.ronn that return FastaSequence

Modifier and Type	Method and Description
static FastaSequence	Jronn.convertProteinSequencetoFasta(ProteinSequence sequence) Utility method to convert a BioJava ProteinSequence object to the FastaSequence object used internally in JRonn.

Methods in org.biojava.nbio.ronn that return types with arguments of type FastaSequence

Modifier and Type	Method and Description
static Map<FastaSequence,Jronn.Range[]>	Jronn.getDisorder(List<FastaSequence> sequences) Calculates the disordered regions of the sequence for many sequences in the input.
static Map<FastaSequence,Jronn.Range[]>	Jronn.getDisorder(String fastaFile) Calculates the disordered regions of the protein sequence.
static Map<FastaSequence,float[]>	Jronn.getDisorderScores(List<FastaSequence> sequences) Calculates the probability of disorder scores for each residue in the sequence for many sequences in the input.

Methods in org.biojava.nbio.ronn with parameters of type FastaSequence

Modifier and Type	Method and Description
static Jronn.Range[]	Jronn.getDisorder(FastaSequence sequence) Calculates the disordered regions of the sequence.
static float[]	Jronn.getDisorderScores(FastaSequence sequence) Calculates the probability value for each residue in the protein sequence, telling the probability that the residue belongs to disordered region.

Method parameters in org.biojava.nbio.ronn with type arguments of type FastaSequence

Modifier and Type	Method and Description
static Map<FastaSequence,Jronn.Range[]>	Jronn.getDisorder(List<FastaSequence> sequences) Calculates the disordered regions of the sequence for many sequences in the input.
static Map<FastaSequence,float[]>	Jronn.getDisorderScores(List<FastaSequence> sequences) Calculates the probability of disorder scores for each residue in the sequence for many sequences in the input.