Package | Description |
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com.compomics.util.experiment.biology |
Experiment classes related to biological entities.
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com.compomics.util.experiment.identification.amino_acid_tags |
Amino Acid Tag classes.
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com.compomics.util.experiment.identification.amino_acid_tags.matchers |
Tag matching classes.
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com.compomics.util.experiment.identification.protein_inference.proteintree |
Protein sequence database indexing classes.
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com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators |
Spectrum annotation.
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com.compomics.util.experiment.identification.spectrum_assumptions |
Implementations of the SpectrumIdentificationAssumption.
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com.compomics.util.gui.spectrum |
Spectrum and Chromatogram visualization GUI classes.
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Modifier and Type | Method and Description |
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void |
PTMFactory.checkFixedModifications(PtmSettings modificationProfile,
Tag tag,
SequenceMatchingPreferences sequenceMatchingPreferences)
Removes the fixed modifications of the given tag and remaps the one
searched for according to the ModificationProfile.
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HashMap<Integer,HashMap<Integer,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 |
Tag.reverse(boolean yIon)
Returns a new tag instance which is a reversed version of the current
tag.
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Modifier and Type | Method and Description |
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static String |
Tag.getTaggedModifiedSequence(PtmSettings 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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static String |
Tag.getTagModificationsAsString(Tag tag)
Returns the tag modifications as a string.
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boolean |
Tag.isSameAs(Tag anotherTag,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether this tag is the same as another tag.
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boolean |
Tag.isSameSequenceAndModificationStatusAs(Tag anotherTag,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether this tag is the same as another tag without accounting
for modification localization.
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Constructor and Description |
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Tag(Tag tag)
Creates a new tag instance based on the given one.
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Modifier and Type | Method and Description |
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HashMap<Integer,ArrayList<Peptide>> |
TagMatcher.getPeptideMatches(Tag tag,
String accession,
String sequence,
Integer tagIndex,
Integer componentIndex,
double massTolerance)
Returns the possible peptides which can be created on this sequence
indexed by their start index.
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Modifier and Type | Method and Description |
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HashMap<Peptide,HashMap<String,ArrayList<Integer>>> |
ProteinTree.getProteinMapping(Tag tag,
TagMatcher tagMatcher,
SequenceMatchingPreferences sequenceMatchingPreferences,
Double massTolerance)
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,
SequenceMatchingPreferences ptmSequenceMatchingSettings)
Returns the possible neutral losses expected by default for a given tag.
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ArrayList<IonMatch> |
TagSpectrumAnnotator.getSpectrumAnnotation(AnnotationSettings annotationSettings,
SpecificAnnotationSettings specificAnnotationSettings,
MSnSpectrum spectrum,
Tag tag)
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 tag to match.
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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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void |
SpectrumPanel.addAutomaticDeNovoSequencing(Tag tag,
ArrayList<IonMatch> annotations,
int aForwardIon,
int aRewindIon,
int aDeNovoCharge,
boolean showForwardTags,
boolean showRewindTags,
boolean mirrored)
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,
ArrayList<float[]> alphaLevels,
boolean excludeFixedPtms,
boolean mirrored)
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 mirrored)
Add reference areas annotating the de novo tags, using default alpha
levels of 0.2.
|
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,
ArrayList<float[]> alphaLevels,
boolean excludeFixedPtms,
boolean mirrored)
Add reference areas annotating the de novo tags.
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