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java.lang.Objectorg.biojava3.ronn.Jronn
public class Jronn
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.
Nested Class Summary | |
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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 | |
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Jronn()
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Method Summary | |
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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 Jronn.Range[] |
scoresToRanges(float[] scores,
float probability)
Convert raw scores to ranges. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public Jronn()
Method Detail |
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public static float[] getDisorderScores(FastaSequence sequence)
sequence
- an instance of FastaSequence object, holding the name and the 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 value
probability
, null otherwise.public static Map<FastaSequence,float[]> getDisorderScores(List<FastaSequence> sequences)
sequences
- the list of the FastaSequence objects
getDisorder(FastaSequence)
public static Map<FastaSequence,Jronn.Range[]> getDisorder(List<FastaSequence> sequences)
sequences
- sequences the list of the FastaSequence objects
getDisorder(FastaSequence)
public static Map<FastaSequence,Jronn.Range[]> getDisorder(String fastaFile) throws FileNotFoundException, IOException
fastaFile
- input file name containing the sequence in FASTA
FileNotFoundException
- if the input file cannot be found
IOException
- of the system cannot access or read from the input filegetDisorder(FastaSequence)
,
#Jronn.Range
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