Package org.biojava.nbio.ronn
Class Jronn
 java.lang.Object

 org.biojava.nbio.ronn.Jronn

 All Implemented Interfaces:
Serializable
public class Jronn extends Object implements Serializable
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
 See Also:
 Serialized Form


Nested Class Summary
Nested Classes Modifier and Type Class 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 Description Jronn()

Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static FastaSequence
convertProteinSequencetoFasta(ProteinSequence sequence)
Utility method to convert a BioJava ProteinSequence object to the FastaSequence object used internally in JRonn.static Map<FastaSequence,Jronn.Range[]>
getDisorder(String fastaFile)
Calculates the disordered regions of the protein sequence.static Map<FastaSequence,Jronn.Range[]>
getDisorder(List<FastaSequence> sequences)
Calculates the disordered regions of the sequence for many sequences in the input.static Jronn.Range[]
getDisorder(FastaSequence sequence)
Calculates the disordered regions of the sequence.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 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 Jronn.Range[]
scoresToRanges(float[] scores, float probability)
Convert raw scores to ranges.



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 foundIOException
 of the system cannot access or read from the input file See Also:
getDisorder(FastaSequence)

