A B C D E F G H I J M N O P R S T V W

A

AA - Static variable in class org.biojava.nbio.data.sequence.SequenceUtil

Valid Amino acids

AMBIGUOUS_AA - Static variable in class org.biojava.nbio.data.sequence.SequenceUtil

Same as AA pattern but with two additional letters - XU

AMBIGUOUS_NUCLEOTIDE - Static variable in class org.biojava.nbio.data.sequence.SequenceUtil

Ambiguous nucleotide

B

Blosum62 - Static variable in class org.biojava.nbio.ronn.RonnConstraint

C

call() - Method in class org.biojava.nbio.ronn.ORonn

checkPoint() - Method in class org.biojava.nbio.ronn.Timer

cleanSequence(String) - Static method in class org.biojava.nbio.data.sequence.SequenceUtil

Removes all whitespace chars in the sequence string

compareTo(FastaSequence) - Method in class org.biojava.nbio.data.sequence.FastaSequence

convertProteinSequencetoFasta(ProteinSequence) - Static method in class org.biojava.nbio.ronn.Jronn

Utility method to convert a BioJava ProteinSequence object to the FastaSequence object used internally in JRonn.

countMatchesInSequence(String, String) - Static method in class org.biojava.nbio.data.sequence.FastaSequence

D

deepCleanSequence(String) - Static method in class org.biojava.nbio.data.sequence.SequenceUtil

Removes all special characters and digits as well as whitespace chars from the sequence

DEFAULT_DISORDER - Static variable in class org.biojava.nbio.ronn.RonnConstraint

DEFAULT_ORDER - Static variable in class org.biojava.nbio.ronn.RonnConstraint

DEFAULT_RANGE_PROBABILITY_THRESHOLD - Static variable in class org.biojava.nbio.ronn.RonnConstraint

demo - package demo

DIGIT - Static variable in class org.biojava.nbio.data.sequence.SequenceUtil

A digit

E

equals(Object) - Method in class org.biojava.nbio.data.sequence.FastaSequence

equals(Object) - Method in class org.biojava.nbio.ronn.Jronn.Range

equals(Object) - Method in class org.biojava.nbio.ronn.ModelLoader.Model

F

FastaSequence - Class in org.biojava.nbio.data.sequence

A FASTA formatted sequence.

FastaSequence(String, String) - Constructor for class org.biojava.nbio.data.sequence.FastaSequence

Upon construction the any whitespace characters are removed from the sequence

from - Variable in class org.biojava.nbio.ronn.Jronn.Range

Range starting position counts from 1 (the first position on the sequence is 1)

G

getDisorder(FastaSequence) - Static method in class org.biojava.nbio.ronn.Jronn

Calculates the disordered regions of the sequence.

getDisorder(List<FastaSequence>) - Static method in class org.biojava.nbio.ronn.Jronn

Calculates the disordered regions of the sequence for many sequences in the input.

getDisorder(String) - Static method in class org.biojava.nbio.ronn.Jronn

Calculates the disordered regions of the protein sequence.

getDisorderScores(FastaSequence) - Static method in class org.biojava.nbio.ronn.Jronn

Calculates the probability value for each residue in the protein sequence, telling the probability that the residue belongs to disordered region.

getDisorderScores(ProteinSequence) - Static method in class org.biojava.nbio.ronn.Jronn

Calculates the probability value for each residue in the protein sequence, telling the probability that the residue belongs to disordered region.

getDisorderScores(List<FastaSequence>) - Static method in class org.biojava.nbio.ronn.Jronn

Calculates the probability of disorder scores for each residue in the sequence for many sequences in the input.

getFormatedSequence(int) - Method in class org.biojava.nbio.data.sequence.FastaSequence

Format sequence per width letter in one string.

getFormattedFasta() - Method in class org.biojava.nbio.data.sequence.FastaSequence

getId() - Method in class org.biojava.nbio.data.sequence.FastaSequence

Gets the value of id

getLength() - Method in class org.biojava.nbio.data.sequence.FastaSequence

getModel(int) - Method in class org.biojava.nbio.ronn.ModelLoader

getOnelineFasta() - Method in class org.biojava.nbio.data.sequence.FastaSequence

getScores(File) - Method in class org.biojava.nbio.ronn.ORonnModel

getSequence() - Method in class org.biojava.nbio.data.sequence.FastaSequence

Gets the value of sequence

getTreshold(int) - Static method in enum org.biojava.nbio.ronn.RonnConstraint.Threshold

getValues() - Method in enum org.biojava.nbio.ronn.RonnConstraint.Threshold

H

hashCode() - Method in class org.biojava.nbio.data.sequence.FastaSequence

hashCode() - Method in class org.biojava.nbio.ronn.Jronn.Range

hashCode() - Method in class org.biojava.nbio.ronn.ModelLoader.Model

I

INDEX - Static variable in class org.biojava.nbio.ronn.RonnConstraint

isAmbiguosProtein(String) - Static method in class org.biojava.nbio.data.sequence.SequenceUtil

Check whether the sequence confirms to amboguous protein sequence

isNonAmbNucleotideSequence(String) - Static method in class org.biojava.nbio.data.sequence.SequenceUtil

Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one (!) - B char

isNucleotideSequence(FastaSequence) - Static method in class org.biojava.nbio.data.sequence.SequenceUtil

isProteinSequence(String) - Static method in class org.biojava.nbio.data.sequence.SequenceUtil

J

Jronn - Class in org.biojava.nbio.ronn

This class gives public API to RONN functions.

Jronn() - Constructor for class org.biojava.nbio.ronn.Jronn

Jronn.Range - Class in org.biojava.nbio.ronn

Holder for the ranges, contain pointers to starting and ending position on the sequence which comprises a disordered region.

M

main(String[]) - Static method in class demo.PredictDisorder

main(String[]) - Static method in class org.biojava.nbio.ronn.ModelLoader

main(String[]) - Static method in class org.biojava.nbio.ronn.ORonn

Model(int, int) - Constructor for class org.biojava.nbio.ronn.ModelLoader.Model

ModelLoader - Class in org.biojava.nbio.ronn

Class that loads data from the model files into ModelLoader.Model objects

ModelLoader() - Constructor for class org.biojava.nbio.ronn.ModelLoader

ModelLoader.Model - Class in org.biojava.nbio.ronn

Represent a RONN model

ModelLoader.Threshold - Class in org.biojava.nbio.ronn

Represents a Threshold

N

NON_AA - Static variable in class org.biojava.nbio.data.sequence.SequenceUtil

inversion of AA pattern

NON_NUCLEOTIDE - Static variable in class org.biojava.nbio.data.sequence.SequenceUtil

Non nucleotide

NONWORD - Static variable in class org.biojava.nbio.data.sequence.SequenceUtil

Non word

NUCLEOTIDE - Static variable in class org.biojava.nbio.data.sequence.SequenceUtil

Nucleotides a, t, g, c, u

NullOutputStream - Class in org.biojava.nbio.ronn

The stream that void its input

NullOutputStream() - Constructor for class org.biojava.nbio.ronn.NullOutputStream

O

org.biojava.nbio.data.sequence - package org.biojava.nbio.data.sequence

Set of classes that responsible for data handling.

org.biojava.nbio.ronn - package org.biojava.nbio.ronn

BioJava provide a module biojava-protein-disorder for prediction disordered regions from a protein sequence.

ORonn - Class in org.biojava.nbio.ronn

Fully re-factored and enhanced version of RONN.

ORonnModel - Class in org.biojava.nbio.ronn

Fully re-factored version of RONN model.

ORonnModel(String, ModelLoader.Model, float) - Constructor for class org.biojava.nbio.ronn.ORonnModel

P

PredictDisorder - Class in demo

PredictDisorder() - Constructor for class demo.PredictDisorder

R

Range(int, int, float) - Constructor for class org.biojava.nbio.ronn.Jronn.Range

readFasta(InputStream) - Static method in class org.biojava.nbio.data.sequence.SequenceUtil

Reads fasta sequences from inStream into the list of FastaSequence objects

RonnConstraint - Class in org.biojava.nbio.ronn

A collection of various constrain values used by RONN

RonnConstraint() - Constructor for class org.biojava.nbio.ronn.RonnConstraint

RonnConstraint.Threshold - Enum in org.biojava.nbio.ronn

S

score - Variable in class org.biojava.nbio.ronn.Jronn.Range

scoresToRanges(float[], float) - Static method in class org.biojava.nbio.ronn.Jronn

Convert raw scores to ranges.

SequenceUtil - Class in org.biojava.nbio.data.sequence

Utility class for operations on sequences

T

Threshold(int) - Constructor for class org.biojava.nbio.ronn.ModelLoader.Threshold

Timer - Class in org.biojava.nbio.ronn

A simple timer, calculates the time interval between two events.

Timer() - Constructor for class org.biojava.nbio.ronn.Timer

Timer(TimeUnit) - Constructor for class org.biojava.nbio.ronn.Timer

to - Variable in class org.biojava.nbio.ronn.Jronn.Range

The range ending position includes the last residue.

toString() - Method in class org.biojava.nbio.data.sequence.FastaSequence

Same as oneLineFasta

toString() - Method in class org.biojava.nbio.ronn.Jronn.Range

toString() - Method in class org.biojava.nbio.ronn.ModelLoader.Model

V

valueOf(String) - Static method in enum org.biojava.nbio.ronn.RonnConstraint.Threshold

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.biojava.nbio.ronn.RonnConstraint.Threshold

Returns an array containing the constants of this enum type, in the order they are declared.

W

WHITE_SPACE - Static variable in class org.biojava.nbio.data.sequence.SequenceUtil

A whitespace character: [\t\n\x0B\f\r]

write(int) - Method in class org.biojava.nbio.ronn.NullOutputStream

writeFasta(OutputStream, List<FastaSequence>, int) - Static method in class org.biojava.nbio.data.sequence.SequenceUtil

Writes list of FastaSequeces into the outstream formatting the sequence so that it contains width chars on each line

writeFasta(OutputStream, List<FastaSequence>) - Static method in class org.biojava.nbio.data.sequence.SequenceUtil

Writes FastaSequence in the file, each sequence will take one line only

A B C D E F G H I J M N O P R S T V W