Package | Description |
---|---|
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.matches |
This package contains experiment classes releated to matches.
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com.compomics.util.experiment.identification.protein_inference.proteintree | |
com.compomics.util.experiment.identification.ptm.ptmscores | |
com.compomics.util.experiment.identification.spectrum_annotators | |
com.compomics.util.experiment.identification.tags | |
com.compomics.util.preferences |
Modifier and Type | Method and Description |
---|---|
static AminoAcidPattern.MatchingType |
AminoAcidPattern.MatchingType.valueOf(String name)
Returns the enum constant of this type with the specified name.
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static AminoAcidPattern.MatchingType[] |
AminoAcidPattern.MatchingType.values()
Returns an array containing the constants of this enum type, in
the order they are declared.
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Modifier and Type | Method and Description |
---|---|
void |
PTMFactory.checkFixedModifications(ModificationProfile modificationProfile,
Peptide peptide,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance)
Removes the fixed modifications of the peptide and remaps the one
searched for according to the ModificationProfile.
|
void |
PTMFactory.checkFixedModifications(ModificationProfile modificationProfile,
Tag tag,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance)
Removes the fixed modifications of the given tag and remaps the one
searched for according to the ModificationProfile.
|
int |
AminoAcidPattern.firstIndex(AminoAcidPattern aminoAcidPattern,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance)
Returns the first index where the amino acid pattern is found.
|
int |
AminoAcidPattern.firstIndex(AminoAcidPattern aminoAcidPattern,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance,
int startIndex)
Returns the first index where the amino acid pattern is found.
|
int |
AminoAcidPattern.firstIndex(String aminoAcidSequence,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance)
Returns the first index where the amino acid pattern is found.
|
int |
AminoAcidPattern.firstIndex(String aminoAcidSequence,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance,
int startIndex)
Returns the first index where the amino acid pattern is found.
|
Pattern |
AminoAcidPattern.getAsStringPattern(AminoAcidPattern.MatchingType matchingType,
Double massTolerance)
Returns the amino acid pattern as case insensitive pattern for String
matching.
|
HashMap<Integer,ArrayList<String>> |
PTMFactory.getExpectedPTMs(ModificationProfile modificationProfile,
Peptide peptide,
double modificationMass,
double ptmMassTolerance,
double ms2Tolerance,
AminoAcidPattern.MatchingType matchingType)
Returns the expected modifications based on the modification profile, the
peptide found and the modification details.
|
HashMap<Integer,ArrayList<String>> |
PTMFactory.getExpectedPTMs(ModificationProfile modificationProfile,
Peptide peptide,
String ptmName,
AminoAcidPattern.MatchingType matchingType,
Double ptmMassTolerance,
double ms2Tolerance)
Returns the names of the possibly expected modification based on the name
of the expected modification in a map where the PTM names are indexed by
their potential site on the sequence.
|
ArrayList<Integer> |
AminoAcidPattern.getIndexes(AminoAcidPattern input,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance)
Returns the indexes where the amino acid pattern was found in the input.
|
ArrayList<Integer> |
AminoAcidPattern.getIndexes(String input,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance)
Returns the indexes where the amino acid pattern was found in the input.
|
static String |
AminoAcid.getMatchingAminoAcid(String aminoAcid,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance)
Returns a matching amino acid using the given matching type and
massTolerance.
|
String |
Peptide.getMatchingKey(AminoAcidPattern.MatchingType matchingType,
Double massTolerance)
Returns a unique key for the peptide when considering the given matching
type and mass tolerance.
|
static String |
AminoAcid.getMatchingSequence(String sequence,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance)
Returns the matching sequence of a given sequence.
|
ArrayList<String> |
Peptide.getParentProteins(AminoAcidPattern.MatchingType matchingType,
Double massTolerance)
Returns the parent proteins and remaps the peptide to the protein if no
protein mapping was set using the default protein tree of the sequence
factory.
|
ArrayList<String> |
Peptide.getParentProteins(AminoAcidPattern.MatchingType matchingType,
Double massTolerance,
ProteinTree proteinTree)
Returns the parent proteins and remaps the peptide to the protein if no
protein mapping was set.
|
ArrayList<String> |
Peptide.getParentProteins(boolean remap,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance)
Returns the parent proteins and eventually remaps the peptide to the
protein using the default protein tree.
|
ArrayList<String> |
Peptide.getParentProteins(boolean remap,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance,
ProteinTree proteinTree)
Returns the parent proteins and eventually remaps the peptide to the
protein.
|
ArrayList<Integer> |
Protein.getPeptideStart(String peptideSequence,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance)
Returns the list of indexes where a peptide can be found in the protein
sequence.
|
ArrayList<Integer> |
Peptide.getPotentialModificationSites(Double ptmMass,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance,
ModificationProfile modificationProfile)
Returns the potential modification sites as an ordered list of string.
|
ArrayList<Integer> |
Peptide.getPotentialModificationSites(PTM ptm,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance)
Returns the potential modification sites as an ordered list of string.
|
HashMap<Integer,String[]> |
Protein.getSurroundingAA(String peptide,
int nAA,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance)
Returns the amino acids surrounding a peptide in the sequence of the
given protein in a map: peptide start index -> (amino acids before, amino
acids after).
|
ArrayList<String> |
Peptide.isCterm(AminoAcidPattern.MatchingType matchingType,
Double massTolerance)
Returns a list of proteins where this peptide can be found in the
C-terminus.
|
boolean |
Protein.isCTerm(String peptideSequence,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance)
Returns a boolean indicating whether the protein ends with the given
peptide.
|
boolean |
Peptide.isDecoy(AminoAcidPattern.MatchingType matchingType,
Double massTolerance)
Indicates whether a peptide can be derived from a decoy protein.
|
boolean |
AminoAcidPattern.isEnding(AminoAcidPattern aminoAcidPattern,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance)
Indicates whether the given amino acid sequence ends with the pattern.
|
boolean |
AminoAcidPattern.isEnding(String aminoAcidSequence,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance)
Indicates whether the given amino acid sequence ends with the pattern.
|
boolean |
Protein.isEnzymaticPeptide(String peptideSequence,
Enzyme enzyme,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance)
Returns true of the peptide is non-enzymatic, i.e., has one or more end
points that cannot be caused by the enzyme alone.
|
boolean |
AminoAcidPattern.isExcluded(char aa,
int index,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance)
Indicates whether the given amino acid at the given index of the pattern
shall be excluded.
|
boolean |
Peptide.isModifiable(PTM ptm,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance)
Indicates whether the given modification can be found on the peptide.
|
ArrayList<String> |
Peptide.isNterm(AminoAcidPattern.MatchingType matchingType,
Double massTolerance)
Returns a list of proteins where this peptide can be found in the
N-terminus.
|
boolean |
Protein.isNTerm(String peptideSequence,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance)
Returns a boolean indicating whether the protein starts with the given
peptide.
|
boolean |
Peptide.isSameSequence(Peptide anotherPeptide,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance)
Returns a boolean indicating whether another peptide has the same
sequence as the given peptide
|
boolean |
Peptide.isSameSequenceAndModificationStatus(Peptide anotherPeptide,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance)
Indicates whether another peptide has the same sequence and modification
status without accounting for modification localization.
|
boolean |
AminoAcidPattern.isStarting(AminoAcidPattern aminoAcidPattern,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance)
Indicates whether the given amino acid sequence starts with the pattern.
|
boolean |
AminoAcidPattern.isStarting(String aminoAcidSequence,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance)
Indicates whether the given amino acid sequence starts with the pattern.
|
boolean |
AminoAcidPattern.isTargeted(char aa,
int index,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance)
Indicates whether the given amino acid at the given index of the pattern
is targeted.
|
boolean |
AminoAcidPattern.matches(AminoAcidPattern aminoAcidPattern,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance)
Indicates whether the pattern is found in the given amino acid sequence.
|
boolean |
AminoAcidPattern.matches(String aminoAcidSequence,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance)
Indicates whether the pattern is found in the given amino acid sequence.
|
Modifier and Type | Method and Description |
---|---|
void |
Identification.buildPeptidesAndProteins(String spectrumMatchKey,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance)
Creates the peptides and protein instances based on the given spectrum
match.
|
void |
Identification.buildPeptidesAndProteins(WaitingHandler waitingHandler,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance)
Creates the peptides and protein instances based on the spectrum matches.
|
static NeutralLossesMap |
SpectrumAnnotator.getDefaultLosses(SpectrumIdentificationAssumption spectrumIdentificationAssumption,
AminoAcidPattern.MatchingType matchingType,
double mzTolerance)
Returns the possible neutral losses expected by default for a given
peptide.
|
Modifier and Type | Method and Description |
---|---|
SpectrumMatch |
SpectrumMatch.getPeptidesFromTags(ProteinTree proteinTree,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance,
boolean scoreInAscendingOrder,
ArrayList<String> fixedModifications,
ArrayList<String> variableModifications,
boolean ascendingScore,
boolean reportFixedPtms)
Creates a peptide based spectrum match where peptide assumptions are
deduced from tag assumptions.
|
boolean |
ProteinMatch.hasEnzymaticPeptide(String accession,
Enzyme enzyme,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance)
Indicates whether the protein group has an enzymatic peptide when
considering the given accession as main accession.
|
Modifier and Type | Method and Description |
---|---|
HashMap<String,ArrayList<Integer>> |
ProteinTree.getMatchedPeptideSequences(String peptideSequence,
String proteinAccession,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance,
boolean limitXs)
Returns a list of peptides matched using the given peptide sequence in
the given protein according the provided matching settings.
|
HashMap<String,HashMap<String,ArrayList<Integer>>> |
Node.getProteinMapping(AminoAcidPattern query,
String currentSequence,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance,
boolean limitXs)
Returns the protein mappings for the given peptide sequence.
|
HashMap<String,HashMap<String,ArrayList<Integer>>> |
ProteinTree.getProteinMapping(String peptideSequence,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance,
boolean limitXs)
Returns the protein mapping in the sequence factory for the given peptide
sequence.
|
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.
|
Modifier and Type | Method and Description |
---|---|
static HashMap<Integer,Double> |
AScore.getAScore(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
AminoAcidPattern.MatchingType matchingType)
Returns the A-score for the best PTM location without accounting for
neutral losses.
|
static HashMap<Integer,Double> |
AScore.getAScore(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
AminoAcidPattern.MatchingType matchingType)
Returns the A-score for the best PTM location accounting for neutral
losses.
|
static HashMap<Integer,Double> |
AScore.getAScore(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
boolean accountNeutralLosses,
AminoAcidPattern.MatchingType matchingType)
Returns the A-score for the best PTM location.
|
static Double |
MDScore.getMDScore(SpectrumMatch spectrumMatch,
ArrayList<String> ptms,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance)
Returns the MD score for the best peptide in a spectrum match (the best
peptide has to be set before).
|
static Double |
MDScore.getMDScore(SpectrumMatch spectrumMatch,
Peptide peptideCandidate,
ArrayList<String> ptms,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance)
Returns the MD score for the given peptide in a spectrum match.
|
static HashMap<Integer,Double> |
PhosphoRS.getSequenceProbabilities(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
boolean accountNeutralLosses,
AminoAcidPattern.MatchingType matchingType)
Returns the PhosphoRS sequence probabilities for the PTM possible
locations.
|
Modifier and Type | Method and Description |
---|---|
static NeutralLossesMap |
PeptideSpectrumAnnotator.getDefaultLosses(Peptide peptide,
AminoAcidPattern.MatchingType matchingType,
double mzTolerance)
Returns the possible neutral losses expected by default for a given
peptide.
|
static NeutralLossesMap |
TagSpectrumAnnotator.getDefaultLosses(Tag tag,
AminoAcidPattern.MatchingType matchingType,
double mzTolerance)
Returns the possible neutral losses expected by default for a given
peptide.
|
Modifier and Type | Method and Description |
---|---|
HashMap<Integer,ArrayList<Peptide>> |
Tag.getPeptideMatches(String sequence,
int tagIndex,
int componentIndex,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance,
ArrayList<String> fixedModifications,
ArrayList<String> variableModifications,
boolean reportFixedPtms)
Returns the start and end indexes of the tag in the given sequence.
|
ArrayList<Integer> |
Tag.getPotentialModificationSites(PTM ptm,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance)
Returns the potential modification sites as an ordered list of string.
|
Modifier and Type | Method and Description |
---|---|
void |
AnnotationPreferences.resetAutomaticAnnotation(AminoAcidPattern.MatchingType matchingType,
double mzTolerance)
Updates the neutral losses and charge annotation settings.
|
void |
AnnotationPreferences.setCurrentSettings(SpectrumIdentificationAssumption spectrumIdentificationAssumption,
boolean newSpectrum,
AminoAcidPattern.MatchingType matchingType,
double mzTolerance)
Sets the annotation settings for the current peptide and precursor
charge.
|
boolean |
IdFilter.validateModifications(Peptide peptide,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance,
ModificationProfile modificationProfile)
Validates the modifications of a peptide.
|
boolean |
IdFilter.validateProteins(Peptide peptide,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance)
Validates a peptide depending on its protein inference status.
|
boolean |
IdFilter.validateProteins(Peptide peptide,
AminoAcidPattern.MatchingType matchingType,
Double massTolerance,
ProteinTree proteinTree)
Validates a peptide depending on its protein inference status.
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