Uses of Class
com.compomics.util.experiment.identification.matches.ProteinMatch.MatchingType

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.
 



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