Package 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

  • Constructor Details

    • Jronn

      public Jronn()

  • Method Details

    • 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

      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

      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: