public class ProteinIteratorUtils extends Object
Modifier and Type | Field and Description |
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static double |
WATER_MASS
The mass of water (H2O).
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Constructor and Description |
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ProteinIteratorUtils()
Empty default constructor
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ProteinIteratorUtils(ArrayList<String> fixedModifications,
Integer maxX)
Constructor.
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Modifier and Type | Method and Description |
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String |
getCtermModification(PeptideDraft peptideDraft,
String proteinSequence,
int indexOnProtein)
Returns the c-terminal modification for the given peptide draft.
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String |
getFixedModificationAtAa(char aa)
Returns the fixed modification that can be found at the given amino acid.
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int |
getMaxXsInSequence()
Returns the maximal number of Xs to account for in a sequence.
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double |
getMinCtermMass()
Returns the minimal mass to consider for a c-terminus.
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double |
getModificationMass(String modificationName)
Returns the mass corresponding to a given modification.
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AminoAcidPattern |
getModificationPattern(String modificationName)
Returns the modification pattern that is targeted by the given
modification.
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String |
getNtermModification(boolean proteinNTerm,
char nTermAaChar,
String proteinSequence)
Returns the N-term modification for the given amino acid.
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ExtendedPeptide |
getPeptideFromProtein(char[] proteinSequence,
int indexOnProtein,
double massMin,
double massMax)
Returns a peptide from the given sequence.
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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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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.
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public ProteinIteratorUtils()
public ProteinIteratorUtils(ArrayList<String> fixedModifications, Integer maxX)
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 peptidespublic String getNtermModification(boolean proteinNTerm, char nTermAaChar, String proteinSequence)
proteinNTerm
- boolean indicating whether the amino acid is at the
protein N-terminusnTermAaChar
- the amino acid as characterproteinSequence
- the protein sequencepublic String getCtermModification(PeptideDraft peptideDraft, String proteinSequence, int indexOnProtein)
peptideDraft
- the peptide draft of interestproteinSequence
- the protein sequenceindexOnProtein
- the index of the peptide draft on the proteinpublic double getModificationMass(String modificationName)
modificationName
- the name of the modificationpublic String getFixedModificationAtAa(char aa)
aa
- the one letter code of the amino acidpublic AminoAcidPattern getModificationPattern(String modificationName)
modificationName
- the name of the modificationpublic int getMaxXsInSequence()
public double getMinCtermMass()
public ExtendedPeptide getPeptideFromProtein(char[] proteinSequence, int indexOnProtein, double massMin, double massMax)
proteinSequence
- the protein sequence where this peptide was foundindexOnProtein
- the index on the proteinmassMin
- the minimal massmassMax
- the maximal masspublic ExtendedPeptide getPeptideFromProtein(char[] peptideSequence, String proteinSequence, int indexOnProtein, Double massMin, Double massMax)
peptideSequence
- the peptide sequenceproteinSequence
- the protein sequence where this peptide was foundindexOnProtein
- the index on the proteinmassMin
- the minimal massmassMax
- the maximal masspublic ExtendedPeptide getPeptideFromProtein(char[] peptideSequence, String proteinSequence, int indexOnProtein, double massMin, double massMax, BoxedObject<Boolean> smallMass)
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 filterCopyright © 2021. All rights reserved.