Class ProteinIteratorUtils
java.lang.Object
com.compomics.util.experiment.identification.protein_sequences.digestion.ProteinIteratorUtils
public class ProteinIteratorUtils extends Object
This class contains utilities used during the iteration of protein sequences.
- Author:
- Marc Vaudel
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Field Summary
Fields Modifier and Type Field Description static double
WATER_MASS
The mass of water (H2O). -
Constructor Summary
Constructors Constructor Description ProteinIteratorUtils()
Empty default constructorProteinIteratorUtils(ArrayList<String> fixedModifications, Integer maxX)
Constructor. -
Method Summary
Modifier and Type Method Description String
getCtermModification(PeptideDraft peptideDraft, String proteinSequence, int indexOnProtein)
Returns the c-terminal modification for the given peptide draft.String
getFixedModificationAtAa(char aa)
Returns the fixed modification that can be found at the given amino acid.int
getMaxXsInSequence()
Returns the maximal number of Xs to account for in a sequence.double
getMinCtermMass()
Returns the minimal mass to consider for a c-terminus.double
getModificationMass(String modificationName)
Returns the mass corresponding to a given modification.AminoAcidPattern
getModificationPattern(String modificationName)
Returns the modification pattern that is targeted by the given modification.String
getNtermModification(boolean proteinNTerm, char nTermAaChar, String proteinSequence)
Returns the N-term modification for the given amino acid.ExtendedPeptide
getPeptideFromProtein(char[] proteinSequence, int indexOnProtein, double massMin, double massMax)
Returns a peptide from the given sequence.ExtendedPeptide
getPeptideFromProtein(char[] peptideSequence, String proteinSequence, int indexOnProtein, double massMin, double massMax, BoxedObject<Boolean> smallMass)
Returns a peptide from the given sequence on the given protein.ExtendedPeptide
getPeptideFromProtein(char[] peptideSequence, String proteinSequence, int indexOnProtein, Double massMin, Double massMax)
Returns a peptide from the given sequence on the given protein.
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Field Details
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WATER_MASS
public static final double WATER_MASSThe mass of water (H2O).
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Constructor Details
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ProteinIteratorUtils
public ProteinIteratorUtils()Empty default constructor -
ProteinIteratorUtils
Constructor.- Parameters:
fixedModifications
- a list of fixed modifications to consider when iterating the protein sequences.maxX
- The maximal number of Xs allowed in a sequence to derive the possible peptides
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Method Details
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getNtermModification
Returns the N-term modification for the given amino acid. Null if no modification is found.- Parameters:
proteinNTerm
- boolean indicating whether the amino acid is at the protein N-terminusnTermAaChar
- the amino acid as characterproteinSequence
- the protein sequence- Returns:
- the N-term modification for the given amino acid.
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getCtermModification
public String getCtermModification(PeptideDraft peptideDraft, String proteinSequence, int indexOnProtein)Returns the c-terminal modification for the given peptide draft.- Parameters:
peptideDraft
- the peptide draft of interestproteinSequence
- the protein sequenceindexOnProtein
- the index of the peptide draft on the protein- Returns:
- the c-terminal modification for the given peptide draft
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getModificationMass
Returns the mass corresponding to a given modification.- Parameters:
modificationName
- the name of the modification- Returns:
- the mass of the modification
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getFixedModificationAtAa
Returns the fixed modification that can be found at the given amino acid. Null if none.- Parameters:
aa
- the one letter code of the amino acid- Returns:
- the fixed modification that can be found at the given amino acid
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getModificationPattern
Returns the modification pattern that is targeted by the given modification. Null if no pattern longer than one is targeted.- Parameters:
modificationName
- the name of the modification- Returns:
- the modification pattern that is targeted
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getMaxXsInSequence
public int getMaxXsInSequence()Returns the maximal number of Xs to account for in a sequence.- Returns:
- the maximal number of Xs to account for in a sequence
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getMinCtermMass
public double getMinCtermMass()Returns the minimal mass to consider for a c-terminus.- Returns:
- the minimal mass to consider for a c-terminus
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getPeptideFromProtein
public ExtendedPeptide getPeptideFromProtein(char[] proteinSequence, int indexOnProtein, double massMin, double massMax)Returns a peptide from the given sequence. The sequence should not contain ambiguous amino acids. Peptides are filtered according to the given masses. Filters are ignored if null.- Parameters:
proteinSequence
- the protein sequence where this peptide was foundindexOnProtein
- the index on the proteinmassMin
- the minimal massmassMax
- the maximal mass- Returns:
- a peptide from the given sequence
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getPeptideFromProtein
public ExtendedPeptide getPeptideFromProtein(char[] peptideSequence, String proteinSequence, int indexOnProtein, Double massMin, Double massMax)Returns a peptide from the given sequence on the given protein. The sequence should not contain ambiguous amino acids. Peptides are filtered according to the given masses. Filters are ignored if null.- Parameters:
peptideSequence
- the peptide sequenceproteinSequence
- the protein sequence where this peptide was foundindexOnProtein
- the index on the proteinmassMin
- the minimal massmassMax
- the maximal mass- Returns:
- a peptide from the given sequence
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getPeptideFromProtein
public ExtendedPeptide getPeptideFromProtein(char[] peptideSequence, String proteinSequence, int indexOnProtein, double massMin, double massMax, BoxedObject<Boolean> smallMass)Returns a peptide from the given sequence on the given protein. The sequence should not contain ambiguous amino acids. Peptides are filtered according to the given masses. Filters are ignored if null.- Parameters:
peptideSequence
- the peptide sequenceproteinSequence
- the protein sequence where this peptide was foundindexOnProtein
- the index on the proteinmassMin
- the minimal massmassMax
- the maximal masssmallMass
- an encapsulated boolean indicating whether the peptide passed the maximal mass filter- Returns:
- a peptide from the given sequence
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