public class ProteinUtils extends Object
Constructor and Description |
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ProteinUtils() |
Modifier and Type | Method and Description |
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static double |
computeMolecularWeight(String sequence)
Returns the protein's molecular weight.
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static int |
getNCleavageSites(String sequence,
ArrayList<Enzyme> enzymes)
Returns the number of cleavage sites.
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static int[] |
getObservableAminoAcids(String sequence,
ArrayList<Enzyme> enzymes,
double pepMaxLength)
Returns the observable amino acids in the sequence when using the given
enzymes with the given maximal peptide length.
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static int |
getObservableLength(String sequence,
ArrayList<Enzyme> enzymes,
double pepMaxLength)
Returns the number of observable amino acids in the sequence.
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static boolean |
isDecoy(String accession,
FastaParameters fastaParameters)
Returns a boolean indicating whether the given accession corresponds to a decoy sequence according to the given fasta parameters.
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static boolean |
isDecoy(String accession,
SequenceProvider sequenceProvider)
Returns a boolean indicating whether the given accession corresponds to a decoy sequence according to the given sequence provider.
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public static boolean isDecoy(String accession, FastaParameters fastaParameters)
accession
- the protein accessionfastaParameters
- the fasta parameterspublic static boolean isDecoy(String accession, SequenceProvider sequenceProvider)
accession
- the protein accessionsequenceProvider
- the sequence providerpublic static int[] getObservableAminoAcids(String sequence, ArrayList<Enzyme> enzymes, double pepMaxLength)
sequence
- the protein sequenceenzymes
- the enzymes to usepepMaxLength
- the max peptide lengthpublic static int getObservableLength(String sequence, ArrayList<Enzyme> enzymes, double pepMaxLength)
sequence
- the protein sequenceenzymes
- the enzymes to usepepMaxLength
- the max peptide lengthpublic static int getNCleavageSites(String sequence, ArrayList<Enzyme> enzymes)
sequence
- the protein sequenceenzymes
- the enzymes to usepublic static double computeMolecularWeight(String sequence)
sequence
- the protein sequenceCopyright © 2018. All rights reserved.