Uses of Class
com.compomics.util.protein.Protein

Packages that use Protein

Package	Description
com.compomics.util.nucleotide	Useful objects for modeling and handling nucleotides.
com.compomics.util.protein	Classes concerning useful Objects and their operations for modeling and handling proteins.

Uses of Protein in com.compomics.util.nucleotide

Methods in com.compomics.util.nucleotide that return Protein

Modifier and Type	Method	Description
Protein[]	NucleotideSequence.translate()	This method translates the nucleotide sequence in six reading frames.

Uses of Protein in com.compomics.util.protein

Methods in com.compomics.util.protein that return Protein

Modifier and Type	Method	Description
Protein[]	DualEnzyme.cleave(Protein aProtein)	This method is the focus of the Enzyme instance.
Protein[]	Enzyme.cleave(Protein aProtein)	This method is the focus of the Enzyme instance.
Protein[]	Enzyme.cleave(Protein aProtein, int minPeptideLength, int maxPeptideLength)	This method is the focus of the Enzyme instance.
Protein[]	RegExEnzyme.cleave(Protein aProtein)
Protein	Protein.getCTermTruncatedProtein(int aSize)	This method truncates the sequence for this protein on the C-terminus to the requested size.
Protein	Protein.getNTermTruncatedProtein(int aSize)	This method truncates the sequence for this protein on the N-terminus to the requested size.
Protein[]	DualEnzyme.oldCleave(Protein aProtein)	This cleave method will process sequence XDYRZ solely into YR peptides.

Methods in com.compomics.util.protein with parameters of type Protein

Modifier and Type	Method	Description
Protein[]	DualEnzyme.cleave(Protein aProtein)	This method is the focus of the Enzyme instance.
Protein[]	Enzyme.cleave(Protein aProtein)	This method is the focus of the Enzyme instance.
Protein[]	Enzyme.cleave(Protein aProtein, int minPeptideLength, int maxPeptideLength)	This method is the focus of the Enzyme instance.
Protein[]	RegExEnzyme.cleave(Protein aProtein)
Protein[]	DualEnzyme.oldCleave(Protein aProtein)	This cleave method will process sequence XDYRZ solely into YR peptides.