org.biojava.nbio.ronn

Class Jronn

java.lang.Object

org.biojava.nbio.ronn.Jronn

public class Jronn
extends Object

This class gives public API to RONN functions. It is build on top of the command line client. Due to this fact a few things could be improved and extended pending the refactoring of the command line client. The input sequence limitations - the input sequence must not contain any ambiguous characters, and have a minimum length of 19 amino acids.

Since:

3.0.2

Version:

1.0

Author:

Peter Troshin

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	Jronn.Range Holder for the ranges, contain pointers to starting and ending position on the sequence which comprises a disordered region.

Constructor Summary

Constructors

Constructor and Description
Jronn()

Method Summary

Modifier and Type	Method and Description
static FastaSequence	convertProteinSequencetoFasta(ProteinSequence sequence) Utility method to convert a BioJava ProteinSequence object to the FastaSequence object used internally in JRonn.
static Jronn.Range[]	getDisorder(FastaSequence sequence) Calculates the disordered regions of the sequence.
static Map<FastaSequence,Jronn.Range[]>	getDisorder(List<FastaSequence> sequences) Calculates the disordered regions of the sequence for many sequences in the input.
static Map<FastaSequence,Jronn.Range[]>	getDisorder(String fastaFile) Calculates the disordered regions of the protein sequence.
static float[]	getDisorderScores(FastaSequence sequence) Calculates the probability value for each residue in the protein sequence, telling the probability that the residue belongs to disordered region.
static Map<FastaSequence,float[]>	getDisorderScores(List<FastaSequence> sequences) Calculates the probability of disorder scores for each residue in the sequence for many sequences in the input.
static float[]	getDisorderScores(ProteinSequence sequence) Calculates the probability value for each residue in the protein sequence, telling the probability that the residue belongs to disordered region.
static Jronn.Range[]	scoresToRanges(float[] scores, float probability) Convert raw scores to ranges.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Jronn

public Jronn()

Method Detail

getDisorderScores

public static float[] getDisorderScores(FastaSequence sequence)

Calculates the probability value for each residue in the protein sequence, telling the probability that the residue belongs to disordered region. In general, values greater than 0.5 considered to be in the disordered regions.

Parameters:

sequence - an instance of FastaSequence object, holding the name and the sequence.

Returns:

the probability scores for each residue in the sequence

getDisorderScores

public static float[] getDisorderScores(ProteinSequence sequence)

Calculates the probability value for each residue in the protein sequence, telling the probability that the residue belongs to disordered region. In general, values greater than 0.5 considered to be in the disordered regions.

Parameters:

sequence - an instance of FastaSequence object, holding the name and the sequence.

Returns:

the probability scores for each residue in the sequence

convertProteinSequencetoFasta

public static FastaSequence convertProteinSequencetoFasta(ProteinSequence sequence)

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

Parameters:

sequence -

Returns:

getDisorder

public static Jronn.Range[] getDisorder(FastaSequence sequence)

Calculates the disordered regions of the sequence. More formally, the regions for which the probability of disorder is greater then 0.50.

Parameters:

sequence - an instance of FastaSequence object, holding the name and the sequence.

Returns:

the array of ranges if there are any residues predicted to have the probability of disorder greater then 0.5, null otherwise.

scoresToRanges

public static Jronn.Range[] scoresToRanges(float[] scores,
                                           float probability)

Convert raw scores to ranges. Gives ranges for given probability of disorder value

Parameters:

scores - the raw probability of disorder scores for each residue in the sequence.

probability - the cut off threshold. Include all residues with the probability of disorder greater then this value

Returns:

the array of ranges if there are any residues predicted to have the probability of disorder greater then probability, null otherwise.

getDisorderScores

public static Map<FastaSequence,float[]> getDisorderScores(List<FastaSequence> sequences)

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

Parameters:

sequences - the list of the FastaSequence objects

Returns:

the Map with key->FastaSequence, value->probability of disorder for each residue

See Also:

getDisorder(FastaSequence)

getDisorder

public static Map<FastaSequence,Jronn.Range[]> getDisorder(List<FastaSequence> sequences)

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

Parameters:

sequences - sequences the list of the FastaSequence objects

Returns:

See Also:

getDisorder(FastaSequence)

getDisorder

public static Map<FastaSequence,Jronn.Range[]> getDisorder(String fastaFile)
                                                    throws FileNotFoundException,
                                                           IOException

Calculates the disordered regions of the protein sequence.

Parameters:

fastaFile - input file name containing the sequence in FASTA

Returns:

the Map with key->FastaSequence, value->the list of disordered regions for each sequence

Throws:

FileNotFoundException - if the input file cannot be found

IOException - of the system cannot access or read from the input file

See Also:

getDisorder(FastaSequence), #Jronn.Range