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java.lang.Objectcom.compomics.util.experiment.identification.SpectrumAnnotator
public class SpectrumAnnotator
The spectrum annotator annotates peaks in a spectrum.
Constructor Summary | |
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SpectrumAnnotator()
Constructor. |
Method Summary | |
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boolean |
chargeValidated(Ion theoreticIon,
int charge,
int precursorCharge)
Returns a boolean indicating whether the given charge can be found on the given fragment ion. |
ArrayList<IonMatch> |
getCurrentAnnotation(HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges)
Returns the currently matched ions with the given settings. |
Peptide |
getCurrentlyLoadedPeptide()
Returns the currently inspected peptide. |
String |
getCurrentlyLoadedSpectrumKey()
Returns the spectrum currently inspected. |
static NeutralLossesMap |
getDefaultLosses(Peptide peptide)
Returns the possible neutral losses expected by default for a given peptide. /! |
HashMap<Integer,ArrayList<Ion>> |
getExpectedIons(HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
Peptide peptide)
Returns the expected ions in a map indexed by the possible charges. |
double |
getMassShift()
Returns the m/z shift applied to the fragment ions. |
static Vector<DefaultSpectrumAnnotation> |
getSpectrumAnnotation(ArrayList<IonMatch> ionMatches)
Translates the list of ion matches into a vector of annotations which can be read by the SpectrumPanel. |
ArrayList<IonMatch> |
getSpectrumAnnotation(HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
MSnSpectrum spectrum,
Peptide peptide,
double intensityLimit,
double mzTolerance,
boolean isPpm)
Returns the spectrum annotations of a spectrum in a list of IonMatches. |
boolean |
isAccounted(NeutralLossesMap neutralLosses,
NeutralLoss neutralLoss,
Ion ion,
Peptide peptide)
Returns a boolean indicating whether the neutral loss should be accounted for. |
boolean |
lossesValidated(NeutralLossesMap neutralLosses,
Ion theoreticIon,
Peptide peptide)
Returns a boolean indicating whether the neutral losses of the given fragment ion are fit the requirement of the given neutral losses map. |
ArrayList<IonMatch> |
matchPeak(Peptide peptide,
HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
ArrayList<Integer> charges,
int precursorCharge,
NeutralLossesMap neutralLosses,
Peak peak)
This method matches the potential fragment ions of a given peptide with a given peak. |
void |
setMassShift(double massShift)
Sets an m/z shift on all ions. |
void |
setPeptide(Peptide peptide,
int precursorCharge)
Sets a new peptide to match. |
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 SpectrumAnnotator()
Method Detail |
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public ArrayList<IonMatch> matchPeak(Peptide peptide, HashMap<Ion.IonType,ArrayList<Integer>> iontypes, ArrayList<Integer> charges, int precursorCharge, NeutralLossesMap neutralLosses, Peak peak)
peptide
- The peptideiontypes
- The fragment ions selectedcharges
- The charges of the fragment to search forprecursorCharge
- The precursor charge as deduced by the search
engineneutralLosses
- Map of expected neutral losses: neutral loss ->
maximal position in the sequence (first aa is 1). let null if neutral
losses should not be considered.peak
- The peak to match
public static Vector<DefaultSpectrumAnnotation> getSpectrumAnnotation(ArrayList<IonMatch> ionMatches)
ionMatches
- list of ion matches
public void setPeptide(Peptide peptide, int precursorCharge)
peptide
- the new peptideprecursorCharge
- the new precursor chargepublic static NeutralLossesMap getDefaultLosses(Peptide peptide)
peptide
- the peptide of interest
public boolean isAccounted(NeutralLossesMap neutralLosses, NeutralLoss neutralLoss, Ion ion, Peptide peptide)
neutralLosses
- Map of expected neutral lossesneutralLoss
- the neutral loss of interestion
- the fragment ion of interestpeptide
- the peptide of interest
public boolean lossesValidated(NeutralLossesMap neutralLosses, Ion theoreticIon, Peptide peptide)
neutralLosses
- Map of expected neutral losses: neutral loss.theoreticIon
- the ion of interestpeptide
- the inspected peptide
public boolean chargeValidated(Ion theoreticIon, int charge, int precursorCharge)
theoreticIon
- the ion of interestcharge
- the candidate charge
public ArrayList<IonMatch> getSpectrumAnnotation(HashMap<Ion.IonType,ArrayList<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, MSnSpectrum spectrum, Peptide peptide, double intensityLimit, double mzTolerance, boolean isPpm)
iontypes
- The expected ions to look forneutralLosses
- Map of expected neutral losses: neutral loss ->
first position in the sequence (first aa is 1). let null if neutral
losses should not be considered.charges
- List of expected chargesprecursorCharge
- the precursor chargespectrum
- The spectrum to matchpeptide
- The peptide of interestintensityLimit
- The intensity limit to usemzTolerance
- The m/z tolerance to useisPpm
- a boolean indicating whether the mass tolerance is in ppm or
in Da
public HashMap<Integer,ArrayList<Ion>> getExpectedIons(HashMap<Ion.IonType,ArrayList<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges, int precursorCharge, Peptide peptide)
iontypes
- The expected ions to look forneutralLosses
- Map of expected neutral losses: neutral loss ->
first position in the sequence (first aa is 1). let null if neutral
losses should not be considered.charges
- List of expected chargespeptide
- The peptide of interestprecursorCharge
- The precursor charge
public ArrayList<IonMatch> getCurrentAnnotation(HashMap<Ion.IonType,ArrayList<Integer>> iontypes, NeutralLossesMap neutralLosses, ArrayList<Integer> charges)
iontypes
- The expected fragment ions to look forneutralLosses
- Map of expected neutral losses: neutral loss ->
first position in the sequence (first aa is 1). let null if neutral
losses should not be considered.charges
- List of expected charges
public String getCurrentlyLoadedSpectrumKey()
public Peptide getCurrentlyLoadedPeptide()
public double getMassShift()
public void setMassShift(double massShift)
massShift
- the m/z shift to apply
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