public class PhosphoRS
extends java.lang.Object
Modifier and Type | Field and Description |
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static int |
maxDepth
The maximal depth to use per window (8 in the original paper).
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Constructor and Description |
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PhosphoRS() |
Modifier and Type | Method and Description |
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static java.util.HashMap<java.util.ArrayList<java.lang.Integer>,java.lang.Double> |
getSequenceProbabilities(Peptide peptide,
java.util.ArrayList<PTM> ptms,
MSnSpectrum spectrum,
java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
NeutralLossesMap neutralLosses,
java.util.ArrayList<java.lang.Integer> charges,
int precursorCharge,
double mzTolerance,
boolean accountNeutralLosses)
Returns the PhosphoRS sequence probabilities for the PTM possible
locations.
|
public static final int maxDepth
public static java.util.HashMap<java.util.ArrayList<java.lang.Integer>,java.lang.Double> getSequenceProbabilities(Peptide peptide, java.util.ArrayList<PTM> ptms, MSnSpectrum spectrum, java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes, NeutralLossesMap neutralLosses, java.util.ArrayList<java.lang.Integer> charges, int precursorCharge, double mzTolerance, boolean accountNeutralLosses) throws java.io.IOException, java.lang.IllegalArgumentException, java.lang.InterruptedException, java.io.FileNotFoundException, java.lang.ClassNotFoundException, java.sql.SQLException
peptide
- The peptide of interestptms
- The PTMs to score, for instance different phosphorylations.
These PTMs are considered as indistinguishable, i.e. of same mass.spectrum
- The corresponding spectrumiontypes
- The fragment ions to look forneutralLosses
- The neutral losses to look forcharges
- The fragment ions charges to look forprecursorCharge
- The precursor chargemzTolerance
- The m/z tolerance to useaccountNeutralLosses
- a boolean indicating whether or not the
calculation shall account for neutral losses.java.io.IOException
- exception thrown whenever an error occurred while
reading a protein sequencejava.lang.IllegalArgumentException
- exception thrown whenever an error
occurred while reading a protein sequencejava.lang.InterruptedException
- exception thrown whenever an error occurred
while reading a protein sequencejava.io.FileNotFoundException
java.lang.ClassNotFoundException
java.sql.SQLException
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