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Packages that use MSnSpectrum | |
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com.compomics.util.experiment.filters.massspectrometry | |
com.compomics.util.experiment.filters.massspectrometry.spectrumfilters | |
com.compomics.util.experiment.identification | This package contains experiment classes related to identifications. |
com.compomics.util.experiment.identification.ptm | |
com.compomics.util.experiment.identification.scoring | |
com.compomics.util.experiment.io.massspectrometry | |
com.compomics.util.gui.spectrum | This package contains GUI classes related to Spectrum and Chromatogram visualization. |
Uses of MSnSpectrum in com.compomics.util.experiment.filters.massspectrometry |
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Methods in com.compomics.util.experiment.filters.massspectrometry with parameters of type MSnSpectrum | |
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abstract boolean |
SpectrumFilter.validateSpectrum(MSnSpectrum spectrum)
Indicates whether a spectrum passed the filter. |
Uses of MSnSpectrum in com.compomics.util.experiment.filters.massspectrometry.spectrumfilters |
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Methods in com.compomics.util.experiment.filters.massspectrometry.spectrumfilters with parameters of type MSnSpectrum | |
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boolean |
PeakFilter.validateSpectrum(MSnSpectrum spectrum)
Indicates whether a peak was found in the spectrum at the desired m/z in the given intensity quartile. |
boolean |
Or.validateSpectrum(MSnSpectrum spectrum)
Returns a boolean indicating whether one of the implemented filters validated the spectrum. |
boolean |
MzFilter.validateSpectrum(MSnSpectrum spectrum)
Indicates whether a peak was found in the spectrum at the desired m/z in the given intensity quartile. |
boolean |
FingerprintPattern.validateSpectrum(MSnSpectrum spectrum)
Returns a boolean indicating whether the filter fingerprint was found in the spectrum. |
boolean |
CombFilter.validateSpectrum(MSnSpectrum spectrum)
Returns a boolean indicating whether the filter m/z comb was found in the spectrum. |
boolean |
And.validateSpectrum(MSnSpectrum spectrum)
Returns a boolean indicating whether all implemented filters validated the spectrum. |
Uses of MSnSpectrum in com.compomics.util.experiment.identification |
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Methods in com.compomics.util.experiment.identification with parameters of type MSnSpectrum | |
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java.util.ArrayList<IonMatch> |
SpectrumAnnotator.getSpectrumAnnotation(java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
NeutralLossesMap neutralLosses,
java.util.ArrayList<java.lang.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. |
Uses of MSnSpectrum in com.compomics.util.experiment.identification.ptm |
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Methods in com.compomics.util.experiment.identification.ptm that return types with arguments of type MSnSpectrum | |
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static java.util.HashMap<java.lang.Integer,MSnSpectrum> |
PTMLocationScores.getReducedSpectra(MSnSpectrum baseSpectrum,
double mzTolerance)
Generates a map containing the spectra filtered on intensity with a basis of 20*mz tolerance indexed by the depth used. |
static java.util.HashMap<java.lang.Integer,MSnSpectrum> |
PTMLocationScores.getReducedSpectra(MSnSpectrum baseSpectrum,
double mzTolerance,
int depthMax)
Generates a map containing the spectra filtered on intensity with a basis of 20*mz tolerance indexed by the depth used. |
Methods in com.compomics.util.experiment.identification.ptm with parameters of type MSnSpectrum | |
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static java.util.HashMap<java.util.ArrayList<java.lang.Integer>,java.lang.Double> |
PTMLocationScores.getAScore(Peptide peptide,
java.util.ArrayList<PTM> ptms,
MSnSpectrum spectrum,
java.util.HashMap<Ion.IonType,java.util.ArrayList<java.lang.Integer>> iontypes,
java.util.ArrayList<java.lang.Integer> charges,
int precursorCharge,
double mzTolerance)
Returns the A-score for the best PTM location without accounting for neutral losses. |
static java.util.HashMap<java.util.ArrayList<java.lang.Integer>,java.lang.Double> |
PTMLocationScores.getAScore(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)
Returns the A-score for the best PTM location accounting for neutral losses. |
static java.util.HashMap<java.util.ArrayList<java.lang.Integer>,java.lang.Double> |
PTMLocationScores.getAScore(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 A-score for the best PTM location. |
static java.util.HashMap<PeptideFragmentIon,java.util.ArrayList<IonMatch>> |
PTMLocationScores.getPTMPlotData(Peptide peptide,
PTM ptm,
int nPTM,
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,
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,
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,
double intensityLimit)
Get the PTM table content. |
static java.util.HashMap<java.lang.Integer,MSnSpectrum> |
PTMLocationScores.getReducedSpectra(MSnSpectrum baseSpectrum,
double mzTolerance)
Generates a map containing the spectra filtered on intensity with a basis of 20*mz tolerance indexed by the depth used. |
static java.util.HashMap<java.lang.Integer,MSnSpectrum> |
PTMLocationScores.getReducedSpectra(MSnSpectrum baseSpectrum,
double mzTolerance,
int depthMax)
Generates a map containing the spectra filtered on intensity with a basis of 20*mz tolerance indexed by the depth used. |
Uses of MSnSpectrum in com.compomics.util.experiment.identification.scoring |
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Methods in com.compomics.util.experiment.identification.scoring that return types with arguments of type MSnSpectrum | |
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static java.util.HashMap<java.lang.Integer,MSnSpectrum> |
PsmScores.getReducedSpectra(MSnSpectrum baseSpectrum,
double mzTolerance)
Generates a map containing the spectra filtered on intensity with a basis of 20*mz tolerance indexed by the depth used. |
static java.util.HashMap<java.lang.Integer,MSnSpectrum> |
PsmScores.getReducedSpectra(MSnSpectrum baseSpectrum,
double mzTolerance,
int depthMax)
Generates a map containing the spectra filtered on intensity with a basis of 20*mz tolerance indexed by the depth used. |
Methods in com.compomics.util.experiment.identification.scoring with parameters of type MSnSpectrum | |
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static double |
PsmScores.getAScorePeptideScore(Peptide peptide,
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 a PSM score like the peptide score calculated for the A-score. |
static java.util.HashMap<java.lang.Integer,MSnSpectrum> |
PsmScores.getReducedSpectra(MSnSpectrum baseSpectrum,
double mzTolerance)
Generates a map containing the spectra filtered on intensity with a basis of 20*mz tolerance indexed by the depth used. |
static java.util.HashMap<java.lang.Integer,MSnSpectrum> |
PsmScores.getReducedSpectra(MSnSpectrum baseSpectrum,
double mzTolerance,
int depthMax)
Generates a map containing the spectra filtered on intensity with a basis of 20*mz tolerance indexed by the depth used. |
Uses of MSnSpectrum in com.compomics.util.experiment.io.massspectrometry |
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Methods in com.compomics.util.experiment.io.massspectrometry that return MSnSpectrum | |
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static MSnSpectrum |
MgfReader.getSpectrum(uk.ac.ebi.pride.tools.braf.BufferedRandomAccessFile bufferedRandomAccessFile,
long index,
java.lang.String fileName)
Returns the next spectrum starting from the given index. |
Methods in com.compomics.util.experiment.io.massspectrometry that return types with arguments of type MSnSpectrum | |
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java.util.ArrayList<MSnSpectrum> |
MgfReader.getSpectra(java.io.File aFile)
Reads an MGF file and retrieves a list of spectra. |
Uses of MSnSpectrum in com.compomics.util.gui.spectrum |
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Constructors in com.compomics.util.gui.spectrum with parameters of type MSnSpectrum | |
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IntensityHistogram(java.util.ArrayList<IonMatch> annotations,
java.util.ArrayList<java.lang.Integer> currentFragmentIons,
MSnSpectrum currentSpectrum,
double intensityLevel,
boolean includeSinglyCharge,
boolean includeDoublyCharge,
boolean includeMoreThanTwoCharges)
Creates an IntensityHistogram plot //@TODO improve charge compatibility |
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MassErrorPlot(java.util.ArrayList<IonMatch> annotations,
java.util.ArrayList<java.lang.Integer> currentFragmentIons,
MSnSpectrum currentSpectrum,
double massTolerance,
boolean includeSinglyCharge,
boolean includeDoublyCharge,
boolean includeMoreThanTwoCharges)
Creates a new MassErrorPlot. |
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MassErrorPlot(java.util.ArrayList<IonMatch> annotations,
java.util.ArrayList<java.lang.Integer> currentFragmentIons,
MSnSpectrum currentSpectrum,
double massTolerance,
boolean includeSinglyCharge,
boolean includeDoublyCharge,
boolean includeMoreThanTwoCharges,
boolean useRelativeError)
Creates a new MassErrorPlot. |
Constructor parameters in com.compomics.util.gui.spectrum with type arguments of type MSnSpectrum | |
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FragmentIonTable(Peptide currentPeptide,
java.util.ArrayList<java.util.ArrayList<IonMatch>> allAnnotations,
java.util.ArrayList<MSnSpectrum> allSpectra,
java.util.ArrayList<java.lang.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. |
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MassErrorBubblePlot(java.util.ArrayList<java.lang.String> dataIndexes,
java.util.ArrayList<java.util.ArrayList<IonMatch>> annotations,
java.util.ArrayList<java.lang.Integer> currentFragmentIons,
java.util.ArrayList<MSnSpectrum> currentSpectra,
double massTolerance,
boolean includeSinglyCharge,
boolean includeDoublyCharge,
boolean includeMoreThanTwoCharges,
boolean fragmentIonLabels,
boolean addMarkers)
Creates a new MassErrorBubblePlot. |
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MassErrorBubblePlot(java.util.ArrayList<java.lang.String> dataIndexes,
java.util.ArrayList<java.util.ArrayList<IonMatch>> annotations,
java.util.ArrayList<java.lang.Integer> currentFragmentIons,
java.util.ArrayList<MSnSpectrum> currentSpectra,
double massTolerance,
boolean includeSinglyCharge,
boolean includeDoublyCharge,
boolean includeMoreThanTwoCharges,
boolean fragmentIonLabels,
boolean addMarkers,
boolean useRelativeError)
Creates a new MassErrorBubblePlot. |
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MassErrorBubblePlot(java.util.ArrayList<java.lang.String> dataIndexes,
java.util.ArrayList<java.util.ArrayList<IonMatch>> annotations,
java.util.ArrayList<java.lang.Integer> currentFragmentIons,
java.util.ArrayList<MSnSpectrum> currentSpectra,
double massTolerance,
double bubbleScale,
boolean includeSinglyCharge,
boolean includeDoublyCharge,
boolean includeMoreThanTwoCharges,
boolean fragmentIonLabels,
boolean addMarkers,
boolean useRelativeError)
Creates a new MassErrorBubblePlot. |
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