Package | Description |
---|---|
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.
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com.compomics.util.experiment.identification.protein_inference.proteintree | |
com.compomics.util.preferences |
Modifier and Type | Method and Description |
---|---|
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.
|
int |
AminoAcidPattern.firstIndex(String aminoAcidSequence,
ProteinMatch.MatchingType matchingType,
Double massTolerance)
Returns the first index where the amino acid pattern is found.
|
int |
AminoAcidPattern.firstIndex(String aminoAcidSequence,
ProteinMatch.MatchingType matchingType,
Double massTolerance,
int startIndex)
Returns the first index where the amino acid pattern is found.
|
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<String> |
Peptide.getParentProteins(boolean remap,
ProteinMatch.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,
ProteinMatch.MatchingType matchingType,
Double massTolerance,
ProteinTree proteinTree)
Returns the parent proteins and eventually remaps the peptide to the
protein
|
ArrayList<String> |
Peptide.getParentProteins(ProteinMatch.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(ProteinMatch.MatchingType matchingType,
Double massTolerance,
ProteinTree proteinTree)
Returns the parent proteins and remaps the peptide to the
protein if no protein mapping was set
|
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.
|
Modifier and Type | Method and Description |
---|---|
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.
|
Modifier and Type | Method and Description |
---|---|
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.
|
Modifier and Type | Method and Description |
---|---|
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.
|
Modifier and Type | Method and Description |
---|---|
boolean |
IdFilter.validateModifications(Peptide peptide,
ProteinMatch.MatchingType matchingType,
Double massTolerance)
Validates the modifications of a peptide.
|
boolean |
IdFilter.validateProteins(Peptide peptide,
ProteinMatch.MatchingType matchingType,
Double massTolerance)
Validates a peptide depending on its protein inference status.
|
boolean |
IdFilter.validateProteins(Peptide peptide,
ProteinMatch.MatchingType matchingType,
Double massTolerance,
ProteinTree proteinTree)
Validates a peptide depending on its protein inference status.
|
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