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Packages that use Peptide | |
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com.compomics.util.experiment.biology | This package contains experiement classes related to biological entities. |
com.compomics.util.experiment.identification | This package contains experiment classes related to identifications. |
com.compomics.util.experiment.identification.matches | This package contains experiment classes releated to matches. |
com.compomics.util.gui.spectrum | This package contains GUI classes related to Spectrum and Chromatogram visualization. |
Uses of Peptide in com.compomics.util.experiment.biology |
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Methods in com.compomics.util.experiment.biology with parameters of type Peptide | |
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ArrayList<PeptideFragmentIon> |
FragmentFactory.getFragmentIons(Peptide peptide)
This method returns the theoretic fragment ions expected from a peptide sequence. |
boolean |
Peptide.isSameAs(Peptide anotherPeptide)
a method which compares to peptides. |
boolean |
Peptide.sameModificationsAs(Peptide anotherPeptide)
Indicates whether another peptide has the same modifications at the same localization as this peptide. |
Uses of Peptide in com.compomics.util.experiment.identification |
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Methods in com.compomics.util.experiment.identification that return Peptide | |
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Peptide |
SpectrumAnnotator.getCurrentlyLoadedPeptide()
Returns the currently inspected peptide |
Peptide |
PeptideAssumption.getPeptide()
get the theoretic peptide |
Methods in com.compomics.util.experiment.identification with parameters of type Peptide | |
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static HashMap<NeutralLoss,Integer> |
SpectrumAnnotator.getDefaultLosses(Peptide peptide)
Returns the possible neutral losses expected by default for a given peptide. |
static HashMap<NeutralLoss,Integer> |
SpectrumAnnotator.getDefaultLosses(Peptide peptide,
ArrayList<NeutralLoss> imposedNeutralLosses)
Returns the neutral losses map by default for a given peptide and a given list of neutral losses. |
ArrayList<IonMatch> |
SpectrumAnnotator.getSpectrumAnnotation(ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons,
HashMap<NeutralLoss,Integer> neutralLosses,
ArrayList<Integer> charges,
MSnSpectrum spectrum,
Peptide peptide,
double intensityLimit,
double mzTolerance)
Returns the spectrum annotations of a spectrum in a list of IonMatches Note that, except for +1 precursors, fragments ions will be expected to have a charge strictly smaller than the precursor ion charge. |
boolean |
SpectrumAnnotator.isAccounted(HashMap<NeutralLoss,Integer> neutralLosses,
NeutralLoss neutralLoss,
PeptideFragmentIon fragmentIon,
Peptide peptide)
Returns a boolean indicating whether the neutral loss should be accounted for |
boolean |
SpectrumAnnotator.lossesValidated(HashMap<NeutralLoss,Integer> neutralLosses,
PeptideFragmentIon fragmentIon,
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> |
SpectrumAnnotator.matchPeak(Peptide peptide,
ArrayList<PeptideFragmentIon.PeptideFragmentIonType> iontypes,
ArrayList<Integer> charges,
HashMap<NeutralLoss,Integer> neutralLosses,
Peak peak,
double massTolerance)
This method matches the potential fragment ions of a given peptide with a given peak. |
Constructors in com.compomics.util.experiment.identification with parameters of type Peptide | |
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PeptideAssumption(Peptide aPeptide,
int rank,
int advocate,
double measuredMass,
double eValue,
String identificationFile)
Constructor for a peptide assumption |
Uses of Peptide in com.compomics.util.experiment.identification.matches |
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Methods in com.compomics.util.experiment.identification.matches that return Peptide | |
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Peptide |
PeptideMatch.getTheoreticPeptide()
getter for the theoretic peptide |
Methods in com.compomics.util.experiment.identification.matches with parameters of type Peptide | |
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static String |
ProteinMatch.getProteinMatchKey(Peptide peptide)
Convenience method which returns the protein key of a peptide |
void |
PeptideMatch.setTheoreticPeptide(Peptide theoreticPeptide)
setter for the theoretic peptide |
Constructors in com.compomics.util.experiment.identification.matches with parameters of type Peptide | |
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PeptideMatch(Peptide peptide)
Constructor for the peptide match |
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PeptideMatch(Peptide peptide,
String spectrumMatchKey)
Constructor for the peptide match |
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ProteinMatch(Peptide peptide)
Constructor for the protein match |
Uses of Peptide in com.compomics.util.gui.spectrum |
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Constructors in com.compomics.util.gui.spectrum with parameters of type Peptide | |
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FragmentIonTable(Peptide currentPeptide,
ArrayList<ArrayList<IonMatch>> allAnnotations,
ArrayList<MSnSpectrum> allSpectra,
ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIonTypes,
boolean singleCharge,
boolean twoCharges)
Creates a novel fragment ion table displaying bar charts with the intensity of each fragment ion type. |
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FragmentIonTable(Peptide currentPeptide,
ArrayList<IonMatch> annotations,
ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIonTypes,
boolean singleCharge,
boolean twoCharges)
Creates a traditional fragment ion table with the theoretical mz values and the detected fragment ions highlighted. |
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