Package | Description |
---|---|
com.compomics.cli.peptide_mapper |
Command line for PeptideMapper.
|
com.compomics.util.experiment.biology.ions |
Experiment classes related to ions.
|
com.compomics.util.experiment.identification.amino_acid_tags |
Amino Acid Tag classes.
|
com.compomics.util.experiment.identification.protein_inference |
Classes related to protein inference.
|
com.compomics.util.experiment.identification.protein_inference.fm_index |
Protein sequence database indexing classes based on Burrows-Wheeler transform.
|
com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators |
This package contains implementations of the SpectrumAnnotator allowing the annotation of all ions.
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com.compomics.util.experiment.identification.spectrum_assumptions |
Implementations of the SpectrumIdentificationAssumption.
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com.compomics.util.experiment.identification.utils |
This package contains utilities classes to handle identification objects.
|
com.compomics.util.gui.spectrum |
Spectrum and Chromatogram visualization GUI classes.
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Modifier and Type | Method and Description |
---|---|
static String |
PeptideMapperCLI.tagToString(Tag tag) |
Modifier and Type | Method and Description |
---|---|
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> |
IonFactory.getFragmentIons(Tag tag,
ModificationParameters modificationParameters,
SequenceMatchingParameters modificationsSequenceMatchingParameters)
This method returns the theoretic ions expected from a tag.
|
Modifier and Type | Method and Description |
---|---|
Tag |
Tag.reverse(boolean yIon)
Returns a new tag instance which is a reversed version of the current
tag.
|
Modifier and Type | Method and Description |
---|---|
static String |
Tag.getTaggedModifiedSequence(ModificationParameters modificationParameters,
Tag tag,
boolean useHtmlColorCoding,
boolean includeHtmlStartEndTags,
boolean useShortName,
boolean includeTerminalGaps,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
HashSet<String> displayedModifications)
Returns the modified sequence as an tagged string with potential
modification sites color coded or with modification tags, e.g,
<mox>.
|
static String |
Tag.getTagModificationsAsString(Tag tag)
Returns the tag modifications as a string.
|
boolean |
Tag.isSameAs(Tag anotherTag,
SequenceMatchingParameters sequenceMatchingPreferences)
Indicates whether this tag is the same as another tag.
|
boolean |
Tag.isSameSequenceAndModificationStatusAs(Tag anotherTag,
SequenceMatchingParameters sequenceMatchingPreferences)
Indicates whether this tag is the same as another tag without accounting
for modification localization.
|
Constructor and Description |
---|
Tag(Tag tag)
Creates a new tag instance based on the given one.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<PeptideProteinMapping> |
FastaMapper.getProteinMapping(Tag tag,
SequenceMatchingParameters sequenceMatchingPreferences)
Returns the protein mappings for the given peptide sequence.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<PeptideProteinMapping> |
FMIndex.getProteinMapping(Tag tag,
SequenceMatchingParameters sequenceMatchingPreferences) |
ArrayList<PeptideProteinMapping> |
FMIndex.getProteinMappingWithoutVariants(Tag tag,
SequenceMatchingParameters sequenceMatchingPreferences,
int indexPart)
Mapping tags against proteome without variants.
|
ArrayList<PeptideProteinMapping> |
FMIndex.getProteinMappingWithVariants(Tag tag,
SequenceMatchingParameters sequenceMatchingPreferences,
int indexPart)
Mapping tags against proteome with variants.
|
Modifier and Type | Method and Description |
---|---|
Tag |
TagSpectrumAnnotator.getTag()
Returns the tag to annotate.
|
Modifier and Type | Method and Description |
---|---|
static NeutralLossesMap |
TagSpectrumAnnotator.getDefaultLosses(Tag tag,
ModificationParameters modificationParameters,
SequenceMatchingParameters modificationsSequenceMatchingParameters)
Returns the possible neutral losses expected by default for a given tag.
|
IonMatch[] |
TagSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings,
ModificationParameters modificationParameters,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
SpecificAnnotationParameters specificAnnotationSettings,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
Tag tag)
Returns the spectrum annotations of a spectrum in a list of IonMatches
using an intensity filter.
|
IonMatch[] |
TagSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings,
ModificationParameters modificationParameters,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
SpecificAnnotationParameters specificAnnotationSettings,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
Tag tag,
boolean useIntensityFilter)
Returns the spectrum annotations of a spectrum in a list of IonMatches.
|
void |
TagSpectrumAnnotator.setTag(Tag newTag,
ModificationParameters modificationParameters,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
int precursorCharge)
Sets a new tag to match.
|
Modifier and Type | Method and Description |
---|---|
Tag |
TagAssumption.getTag()
Returns the tag of this assumption.
|
Modifier and Type | Method and Description |
---|---|
void |
TagAssumption.setTag(Tag tag) |
Constructor and Description |
---|
TagAssumption(int advocate,
int rank,
Tag tag,
int identificationCharge,
double rawScore,
double score)
Constructor.Note: if PsmScores.scoreRoundingDecimal is not null the
scored will be floored accordingly.
|
Modifier and Type | Method and Description |
---|---|
static HashSet<String> |
ModificationUtils.getAllModifications(Tag tag,
ModificationParameters modificationParameters,
SequenceMatchingParameters sequenceMatchingParameters)
Returns a set of the names of all modifications found on a tag.
|
Modifier and Type | Method and Description |
---|---|
void |
SpectrumPanel.addAutomaticDeNovoSequencing(Tag tag,
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.
|
void |
SpectrumPanel.addAutomaticDeNovoSequencing(Tag tag,
IonMatch[] annotations,
int aForwardIon,
int aRewindIon,
int aDeNovoCharge,
boolean showForwardTags,
boolean showRewindTags,
double forwardIonPercentHeight,
double rewindIonPercentHeight,
ArrayList<float[]> alphaLevels,
boolean excludeFixedModifications,
boolean mirrored)
Add reference areas annotating the de novo tags, using default alpha
levels of 0.2.
|
void |
SpectrumPanel.addAutomaticDeNovoSequencing(Tag tag,
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,
IonMatch[] annotations,
int aForwardIon,
int aRewindIon,
int aDeNovoCharge,
boolean showForwardTags,
boolean showReverseTags,
double forwardIonPercentHeight,
double rewindIonPercentHeight,
float forwardIonAlphaLevel,
float rewindIonAlphaLevel,
ArrayList<float[]> alphaLevels,
boolean excludeFixedModifications,
boolean mirrored)
Add reference areas annotating the de novo tags.
|
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