jspp
Class SignalPeptidePredictor

java.lang.Object
  |
  +--jspp.SignalPeptidePredictor

public class SignalPeptidePredictor
extends java.lang.Object


Constructor Summary
SignalPeptidePredictor(SearchMatrix positive)
          Constructs a SignalPeptidePredictor
SignalPeptidePredictor(java.lang.String[] positive, java.lang.String[] negative, int clpos)
          Constructs a SignalPeptidePredictor object
 
Method Summary
 double getRawScore()
          Returns the raw score of the analyzed sequence.
 double getScore()
          Returns the normalized score of the analyzed sequence.
 boolean isSignalPeptide()
          True if analyzed sequence contains a predicted signal sequence, otherwise false.
static void main(java.lang.String[] args)
           
 int predictEnhancedPosition(java.lang.String sequence)
          Predicts the most probable cleavage position inside the sequence
 int predictPosition(java.lang.String sequence)
           
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

SignalPeptidePredictor

public SignalPeptidePredictor(java.lang.String[] positive,
                              java.lang.String[] negative,
                              int clpos)
Constructs a SignalPeptidePredictor object

Parameters:
positive - String-array of aligned sequences containing a leader peptide for the sec pathway
negative - String array of negative sequences lacking a leader peptide for the sec pathway
clpos - cleavage position

SignalPeptidePredictor

public SignalPeptidePredictor(SearchMatrix positive)
Constructs a SignalPeptidePredictor

Parameters:
positive - a SearchMatrix
Method Detail

predictEnhancedPosition

public int predictEnhancedPosition(java.lang.String sequence)
Predicts the most probable cleavage position inside the sequence

Parameters:
sequence - the sequence to test
Returns:
the most probable cleavage position

predictPosition

public int predictPosition(java.lang.String sequence)

getRawScore

public double getRawScore()
Returns the raw score of the analyzed sequence. Only call this method after running predictEnhancedPosition !

Returns:
the raw score

getScore

public double getScore()
Returns the normalized score of the analyzed sequence. Only call this method after running predictEnhancedPosition !

Returns:
the normalized score

isSignalPeptide

public boolean isSignalPeptide()
True if analyzed sequence contains a predicted signal sequence, otherwise false. Only call this method after running predictEnhancedPosition !

Returns:
true or false

main

public static void main(java.lang.String[] args)