Package | Description |
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com.compomics.util.experiment.biology |
This package contains experiement classes related to biological entities.
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com.compomics.util.experiment.identification |
This package contains experiment classes related to identifications.
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com.compomics.util.experiment.identification.protein_inference.proteintree | |
com.compomics.util.experiment.identification.spectrum_annotators | |
com.compomics.util.experiment.identification.tags | |
com.compomics.util.gui.spectrum |
This package contains GUI classes related to Spectrum and Chromatogram visualization.
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Modifier and Type | Method and Description |
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ArrayList<Ion> |
IonFactory.getFragmentIons(Tag tag)
This method returns the theoretic ions expected from a tag.
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Modifier and Type | Method and Description |
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Tag |
TagAssumption.getTag()
Returns the tag of this assumption.
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Constructor and Description |
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TagAssumption(int advocate,
int rank,
Tag tag,
Charge identificationCharge,
double score)
Constructor.
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Modifier and Type | Method and Description |
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HashMap<Peptide,HashMap<String,ArrayList<Integer>>> |
ProteinTree.getProteinMapping(Tag tag,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance,
ArrayList<String> fixedModifications,
ArrayList<String> variableModifications,
boolean limitXs,
boolean reportFixedPtms)
Returns the protein mappings for the given peptide sequence.
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Modifier and Type | Method and Description |
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Tag |
TagSpectrumAnnotator.getTag()
Returns the tag to annotate.
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Modifier and Type | Method and Description |
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static NeutralLossesMap |
TagSpectrumAnnotator.getDefaultLosses(Tag tag,
AminoAcidPattern.MatchingType matchingType,
double mzTolerance)
Returns the possible neutral losses expected by default for a given
peptide.
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ArrayList<IonMatch> |
TagSpectrumAnnotator.getSpectrumAnnotation(HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
MSnSpectrum spectrum,
Tag tag,
double intensityLimit,
double mzTolerance,
boolean isPpm,
boolean pickMostAccuratePeak)
Returns the spectrum annotations of a spectrum in a list of IonMatches.
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void |
TagSpectrumAnnotator.setTag(Tag newTag,
int precursorCharge)
Sets a new peptide to match.
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Modifier and Type | Method and Description |
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static String |
Tag.getTaggedModifiedSequence(ModificationProfile modificationProfile,
Tag tag,
boolean useHtmlColorCoding,
boolean includeHtmlStartEndTags,
boolean useShortName,
boolean excludeAllFixedPtms,
boolean includeTerminalGaps)
Returns the modified sequence as an tagged string with potential
modification sites color coded or with PTM tags, e.g, <mox>.
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boolean |
Tag.isSameAs(Tag anotherTag)
Indicates whether this tag is the same as another tag.
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Modifier and Type | Method and Description |
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void |
SpectrumPanel.addAutomaticDeNovoSequencing(Tag tag,
ArrayList<IonMatch> annotations,
int aForwardIon,
int aRewindIon,
int aDeNovoCharge,
boolean showForwardTags,
boolean showRewindTags)
Add reference areas annotating the de novo tags, using default percent
height of 0.9 for the forward ions and 1.0 for the reverse ions default
alpha levels of 0.2.
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void |
SpectrumPanel.addAutomaticDeNovoSequencing(Tag tag,
ArrayList<IonMatch> annotations,
int aForwardIon,
int aRewindIon,
int aDeNovoCharge,
boolean showForwardTags,
boolean showRewindTags,
double forwardIonPercentHeight,
double rewindIonPercentHeight)
Add reference areas annotating the de novo tags, using default alpha
levels of 0.2.
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void |
SpectrumPanel.addAutomaticDeNovoSequencing(Tag tag,
ArrayList<IonMatch> annotations,
int aForwardIon,
int aRewindIon,
int aDeNovoCharge,
boolean showForwardTags,
boolean showRewindTags,
double forwardIonPercentHeight,
double rewindIonPercentHeight,
boolean excludeFixedPtms)
Add reference areas annotating the de novo tags, using default alpha
levels of 0.2.
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void |
SpectrumPanel.addAutomaticDeNovoSequencing(Tag tag,
ArrayList<IonMatch> annotations,
int aForwardIon,
int aRewindIon,
int aDeNovoCharge,
boolean showForwardTags,
boolean showReverseTags,
double forwardIonPercentHeight,
double rewindIonPercentHeight,
float forwardIonAlphaLevel,
float rewindIonAlphaLevel,
boolean excludeFixedPtms)
Add reference areas annotating the de novo tags.
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