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java.lang.Objectcom.compomics.util.experiment.identification.SpectrumAnnotator
public class SpectrumAnnotator
The spectrum annotator annotates peaks in a spectrum.
Nested Class Summary | |
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class |
SpectrumAnnotator.SpectrumAnnotationMap
A support class for "hiding" the HashMap inside an object for easier use in other methods. |
Constructor Summary | |
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SpectrumAnnotator()
Constructor |
Method Summary | |
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SpectrumAnnotator.SpectrumAnnotationMap |
annotateSpectrum(Peptide peptide,
MSnSpectrum spectrum,
double massTolerance,
double intensityLimit)
Annotates a spectrum and returns a map containing the annotations: ion type -> charge -> Ion match |
Vector<DefaultSpectrumAnnotation> |
getSpectrumAnnotations(Peptide peptide,
MSnSpectrum spectrum,
double massTolerance,
double intensityLimit)
Annotates a spectrum and returns the annotations as a vector of DefaultSpectrumAnnotation that can be added to a SpectrumPanel. |
Vector<DefaultSpectrumAnnotation> |
getSpectrumAnnotations(SpectrumAnnotator.SpectrumAnnotationMap annotations)
Annotates a spectrum and returns the annotations as a vector of DefaultSpectrumAnnotation that can be added to a SpectrumPanel. |
ArrayList<IonMatch> |
matchPeak(Peptide peptide,
Peak peak,
double massTolerance,
Charge charge)
This method matches the potential fragment ions of a given peptide with a given peak. |
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, Peak peak, double massTolerance, Charge charge)
peptide
- The peptidepeak
- The peak to matchmassTolerance
- The mass tolerance to use (in Dalton)charge
- The charge of the fragment to search for
public Vector<DefaultSpectrumAnnotation> getSpectrumAnnotations(Peptide peptide, MSnSpectrum spectrum, double massTolerance, double intensityLimit)
peptide
- The theoretic peptide to matchspectrum
- The spectrummassTolerance
- The mass tolerance to use (in Dalton)intensityLimit
- The minimal intensity to search for
public Vector<DefaultSpectrumAnnotation> getSpectrumAnnotations(SpectrumAnnotator.SpectrumAnnotationMap annotations)
annotations
- the annotations to transform into DefaultSpectrumAnnotations
public SpectrumAnnotator.SpectrumAnnotationMap annotateSpectrum(Peptide peptide, MSnSpectrum spectrum, double massTolerance, double intensityLimit)
peptide
- The theoretic peptide to matchspectrum
- The spectrummassTolerance
- The mass tolerance to use (in Dalton)intensityLimit
- The minimal intensity to search for
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