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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.biology.ions | This package contains experiment classes related to ions. |
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. e.g., pepties, proteins, modifications and spectra. |
com.compomics.util.experiment.identification.ptm | |
com.compomics.util.gui.spectrum | This package contains GUI classes related to Spectrum and Chromatogram visualization. |
com.compomics.util.preferences |
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<Ion> |
IonFactory.getFragmentIons(Peptide peptide)
This method returns the theoretic ions expected from a peptide. /! |
static String |
Peptide.getModifiedSequenceAsHtml(HashMap<String,Color> colors,
boolean includeHtmlStartEndTag,
Peptide peptide,
HashMap<Integer,ArrayList<String>> mainModificationSites,
HashMap<Integer,ArrayList<String>> secondaryModificationSites)
Returns the modified sequence as an HTML string with potential modification sites color coding. /! |
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.biology.ions |
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Constructors in com.compomics.util.experiment.biology.ions with parameters of type Peptide | |
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PrecursorIon(Peptide peptide)
Constructor. |
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 NeutralLossesMap |
SpectrumAnnotator.getDefaultLosses(Peptide peptide)
Returns the possible neutral losses expected by default for a given peptide. /! |
HashMap<Integer,ArrayList<Ion>> |
SpectrumAnnotator.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. |
ArrayList<IonMatch> |
SpectrumAnnotator.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 |
SpectrumAnnotator.isAccounted(NeutralLossesMap neutralLosses,
NeutralLoss neutralLoss,
Ion ion,
Peptide peptide)
Returns a boolean indicating whether the neutral loss should be accounted for. |
boolean |
SpectrumAnnotator.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> |
SpectrumAnnotator.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 |
SpectrumAnnotator.setPeptide(Peptide peptide,
int precursorCharge)
Sets a new peptide to match. |
Constructors in com.compomics.util.experiment.identification with parameters of type Peptide | |
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PeptideAssumption(Peptide aPeptide,
int rank,
int advocate,
Charge identificationCharge,
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.experiment.identification.ptm |
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Methods in com.compomics.util.experiment.identification.ptm with parameters of type Peptide | |
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static HashMap<ArrayList<Integer>,Double> |
PTMLocationScores.getAScore(Peptide peptide,
PTM ptm,
int nPTM,
MSnSpectrum spectrum,
HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance)
Returns the A-score for the best PTM location without accounting for neutral losses. |
static HashMap<ArrayList<Integer>,Double> |
PTMLocationScores.getAScore(Peptide peptide,
PTM ptm,
int nPTM,
MSnSpectrum spectrum,
HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance)
Returns the A-score for the best PTM location accounting for neutral losses. |
static HashMap<ArrayList<Integer>,Double> |
PTMLocationScores.getAScore(Peptide peptide,
PTM ptm,
int nPTM,
MSnSpectrum spectrum,
HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
boolean accountNeutralLosses)
Returns the A-score for the best PTM location. |
static HashMap<PeptideFragmentIon,ArrayList<IonMatch>> |
PTMLocationScores.getPTMPlotData(Peptide peptide,
PTM ptm,
int nPTM,
MSnSpectrum spectrum,
HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
double intensityLimit)
Returns the ptm plot series in the jfreechart format for one psm. |
static PtmtableContent |
PTMLocationScores.getPTMTableContent(Peptide peptide,
PTM ptm,
int nPTM,
MSnSpectrum spectrum,
HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
double intensityLimit)
Get the PTM table content. |
Uses of Peptide in com.compomics.util.gui.spectrum |
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Methods in com.compomics.util.gui.spectrum with parameters of type Peptide | |
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void |
SpectrumPanel.addAutomaticDeNovoSequencing(Peptide currentPeptide,
ArrayList<IonMatch> annotations,
int aForwardIon,
int aReverseIon,
int aDeNovoCharge,
boolean showForwardTags,
boolean showReverseTags)
Add reference areas annotating the de novo tags. |
Constructors in com.compomics.util.gui.spectrum with parameters of type Peptide | |
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FragmentIonTable(Peptide currentPeptide,
ArrayList<ArrayList<IonMatch>> allAnnotations,
ArrayList<Integer> currentFragmentIonTypes,
NeutralLossesMap neutralLosses,
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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FragmentIonTable(Peptide currentPeptide,
ArrayList<ArrayList<IonMatch>> allAnnotations,
ArrayList<MSnSpectrum> allSpectra,
ArrayList<Integer> currentFragmentIonTypes,
NeutralLossesMap neutralLosses,
boolean singleCharge,
boolean twoCharges)
Creates a novel fragment ion table displaying bar charts with the intensity of each fragment ion type. |
Uses of Peptide in com.compomics.util.preferences |
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Methods in com.compomics.util.preferences with parameters of type Peptide | |
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void |
AnnotationPreferences.setCurrentSettings(Peptide currentPeptide,
int currentPrecursorCharge,
boolean newSpectrum)
Sets the annotation settings for the current peptide and precursor charge. |
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