public class Jronn extends Object
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 and Description 

Jronn() 
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.

public Jronn()
public static float[] getDisorderScores(FastaSequence sequence)
sequence
 an instance of FastaSequence object, holding the name and the sequence.public static float[] getDisorderScores(ProteinSequence sequence)
sequence
 an instance of FastaSequence object, holding the name and the sequence.public static FastaSequence convertProteinSequencetoFasta(ProteinSequence sequence)
sequence
 public static Jronn.Range[] getDisorder(FastaSequence sequence)
sequence
 an instance of FastaSequence object, holding the name and the sequence.public static Jronn.Range[] scoresToRanges(float[] scores, float probability)
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 valueprobability
, null otherwise.public static Map<FastaSequence,float[]> getDisorderScores(List<FastaSequence> sequences)
sequences
 the list of the FastaSequence objectsgetDisorder(FastaSequence)
public static Map<FastaSequence,Jronn.Range[]> getDisorder(List<FastaSequence> sequences)
sequences
 sequences the list of the FastaSequence objectsgetDisorder(FastaSequence)
public static Map<FastaSequence,Jronn.Range[]> getDisorder(String fastaFile) throws FileNotFoundException, IOException
fastaFile
 input file name containing the sequence in FASTAFileNotFoundException
 if the input file cannot be foundIOException
 of the system cannot access or read from the input filegetDisorder(FastaSequence)
,
#Jronn.Range
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