public class Jronn
extends java.lang.Object
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 | Description |
---|---|
Jronn() |
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 java.util.Map<FastaSequence,Jronn.Range[]> |
getDisorder(java.lang.String fastaFile) |
Calculates the disordered regions of the protein sequence.
|
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.
|
static Jronn.Range[] |
getDisorder(FastaSequence sequence) |
Calculates the disordered regions of the sequence.
|
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.
|
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.
|
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 java.util.Map<FastaSequence,float[]> getDisorderScores(java.util.List<FastaSequence> sequences)
sequences
- the list of the FastaSequence objectsgetDisorder(FastaSequence)
public static java.util.Map<FastaSequence,Jronn.Range[]> getDisorder(java.util.List<FastaSequence> sequences)
sequences
- sequences the list of the FastaSequence objectsgetDisorder(FastaSequence)
public static java.util.Map<FastaSequence,Jronn.Range[]> getDisorder(java.lang.String fastaFile) throws java.io.FileNotFoundException, java.io.IOException
fastaFile
- input file name containing the sequence in FASTAjava.io.FileNotFoundException
- if the input file cannot be foundjava.io.IOException
- of the system cannot access or read from the input filegetDisorder(FastaSequence)