Class Jronn

  • All Implemented Interfaces:
    java.io.Serializable

    public class Jronn
    extends java.lang.Object
    implements java.io.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()  
    • 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 java.util.Map<FastaSequence,​float[]> getDisorderScores​(java.util.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 java.util.Map<FastaSequence,​Jronn.Range[]> getDisorder​(java.util.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 java.util.Map<FastaSequence,​Jronn.Range[]> getDisorder​(java.lang.String fastaFile)
                                                                            throws java.io.FileNotFoundException,
                                                                                   java.io.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:
        java.io.FileNotFoundException - if the input file cannot be found
        java.io.IOException - of the system cannot access or read from the input file
        See Also:
        getDisorder(FastaSequence)