|
||||||||||
PREV NEXT | FRAMES NO FRAMES |
Packages that use ProteinMatch.MatchingType | |
---|---|
com.compomics.util.experiment.biology | This package contains experiement classes related to biological entities. |
com.compomics.util.experiment.identification.matches | This package contains experiment classes releated to matches. |
com.compomics.util.experiment.identification.protein_inference.proteintree | |
com.compomics.util.preferences |
Uses of ProteinMatch.MatchingType in com.compomics.util.experiment.biology |
---|
Methods in com.compomics.util.experiment.biology with parameters of type ProteinMatch.MatchingType | |
---|---|
void |
PTMFactory.checkFixedModifications(ModificationProfile modificationProfile,
Peptide peptide,
ProteinMatch.MatchingType matchingType,
Double massTolerance)
Removes the fixed modifications of the peptide and remaps the one searched for according to the ModificationProfile. |
Pattern |
AminoAcidPattern.getAsStringPattern(ProteinMatch.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 massTolerance,
ProteinMatch.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,
ProteinMatch.MatchingType matchingType,
Double massTolerance)
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(String input,
ProteinMatch.MatchingType matchingType,
Double massTolerance)
Returns the indexes where the amino acid pattern was found in the input. |
ArrayList<Integer> |
Protein.getPeptideStart(String peptideSequence,
ProteinMatch.MatchingType matchingType,
Double massTolerance)
Returns the list of indexes where a peptide can be found in the protein sequence. |
ArrayList<Integer> |
Peptide.getPotentialModificationSites(PTM ptm,
ProteinMatch.MatchingType matchingType,
Double massTolerance)
Returns the potential modification sites as an ordered list of string. |
HashMap<Integer,String[]> |
Protein.getSurroundingAA(String peptide,
int nAA,
ProteinMatch.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(ProteinMatch.MatchingType matchingType,
Double massTolerance)
Returns a list of proteins where this peptide can be found in the C-terminus. |
boolean |
Protein.isCTerm(String peptideSequence,
ProteinMatch.MatchingType matchingType,
Double massTolerance)
Returns a boolean indicating whether the protein ends with the given peptide. |
boolean |
AminoAcidPattern.isEnding(String aminoAcidSequence,
ProteinMatch.MatchingType matchingType,
Double massTolerance)
Indicates whether the given amino acid sequence ends with the pattern. |
boolean |
Protein.isEnzymaticPeptide(String peptideSequence,
Enzyme enzyme,
ProteinMatch.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 |
Peptide.isModifiable(PTM ptm,
ProteinMatch.MatchingType matchingType,
Double massTolerance)
Indicates whether the given modification can be found on the peptide. |
ArrayList<String> |
Peptide.isNterm(ProteinMatch.MatchingType matchingType,
Double massTolerance)
Returns a list of proteins where this peptide can be found in the N-terminus. |
boolean |
Protein.isNTerm(String peptideSequence,
ProteinMatch.MatchingType matchingType,
Double massTolerance)
Returns a boolean indicating whether the protein starts with the given peptide. |
boolean |
AminoAcidPattern.isStarting(String aminoAcidSequence,
ProteinMatch.MatchingType matchingType,
Double massTolerance)
Indicates whether the given amino acid sequence starts with the pattern. |
boolean |
AminoAcidPattern.matches(String aminoAcidSequence,
ProteinMatch.MatchingType matchingType,
Double massTolerance)
Indicates whether the pattern is found in the given amino-acid sequence. |
Uses of ProteinMatch.MatchingType in com.compomics.util.experiment.identification.matches |
---|
Methods in com.compomics.util.experiment.identification.matches that return ProteinMatch.MatchingType | |
---|---|
static ProteinMatch.MatchingType |
ProteinMatch.MatchingType.valueOf(String name)
Returns the enum constant of this type with the specified name. |
static ProteinMatch.MatchingType[] |
ProteinMatch.MatchingType.values()
Returns an array containing the constants of this enum type, in the order they are declared. |
Methods in com.compomics.util.experiment.identification.matches with parameters of type ProteinMatch.MatchingType | |
---|---|
boolean |
ProteinMatch.hasEnzymaticPeptide(String accession,
Enzyme enzyme,
ProteinMatch.MatchingType matchingType,
Double massTolerance)
Indicates whether the protein group has an enzymatic peptide when considering the given accession as main accession. |
Uses of ProteinMatch.MatchingType in com.compomics.util.experiment.identification.protein_inference.proteintree |
---|
Methods in com.compomics.util.experiment.identification.protein_inference.proteintree with parameters of type ProteinMatch.MatchingType | |
---|---|
HashMap<String,ArrayList<Integer>> |
ProteinTree.getMatchedPeptideSequences(String peptideSequence,
String proteinAccession,
ProteinMatch.MatchingType matchingType,
Double massTolerance)
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>>> |
ProteinTree.getProteinMapping(String peptideSequence,
ProteinMatch.MatchingType matchingType,
Double massTolerance)
Returns the protein mapping in the sequence factory for the given peptide sequence. |
HashMap<String,HashMap<String,ArrayList<Integer>>> |
Node.getProteinMapping(String peptideSequence,
ProteinMatch.MatchingType matchingType,
Double massTolerance)
Returns the protein mappings for the given peptide sequence. |
Uses of ProteinMatch.MatchingType in com.compomics.util.preferences |
---|
Methods in com.compomics.util.preferences with parameters of type ProteinMatch.MatchingType | |
---|---|
boolean |
IdFilter.validateModifications(Peptide peptide,
ProteinMatch.MatchingType matchingType,
Double massTolerance)
Validates the modifications of a peptide. |
|
||||||||||
PREV NEXT | FRAMES NO FRAMES |