Class ProteinTools


  • public class ProteinTools
    extends java.lang.Object
    The central port-of-call for all information and functionality specific to SymbolLists over the protein alphabet.
    Author:
    Matthew Pocock, Greg Cox, Thomas Down, MarkSchreiber, Jonathan Warren, gwaldon (pyrrolysine, pKs)
    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static AtomicSymbol a()
      Returns the AtomicSymbol for the amino acid Alanine
      static AtomicSymbol ala()
      Returns the AtomicSymbol for the amino acid Alanine (A)
      static AtomicSymbol arg()
      Returns the AtomicSymbol for the amino acid Arginine (R)
      static AtomicSymbol asn()
      Returns the AtomicSymbol for the amino acid Asparagine (N)
      static AtomicSymbol asp()
      Returns the AtomicSymbol for the amino acid Aspartic Acid (D)
      static AtomicSymbol c()
      Returns the AtomicSymbol for the amino acid Cysteine
      static GappedSequence createGappedProteinSequence​(java.lang.String theProtein, java.lang.String name)
      Get a new protein as a GappedSequence
      static SymbolList createProtein​(java.lang.String theProtein)
      Return a new Protein SymbolList for protein.
      static Sequence createProteinSequence​(java.lang.String protein, java.lang.String name)
      Return a new PROTEIN Sequence for protein.
      static AtomicSymbol cys()
      Returns the AtomicSymbol for the amino acid Cysteine (C)
      static AtomicSymbol d()
      Returns the AtomicSymbol for the amino acid Aspartic Acid
      static AtomicSymbol e()
      Returns the AtomicSymbol for the amino acid Glutamic Acid
      static AtomicSymbol f()
      Returns the AtomicSymbol for the amino acid Phenylalanine
      static AtomicSymbol g()
      Returns the AtomicSymbol for the amino acid Glycine
      static FiniteAlphabet getAlphabet()
      Gets the protein alphabet
      static SymbolPropertyTable getSymbolPropertyTable​(java.lang.String name)  
      static FiniteAlphabet getTAlphabet()
      Gets the protein alphabet including the translation termination symbols
      static AtomicSymbol gln()
      Returns the AtomicSymbol for the amino acid Glutamine (Q)
      static AtomicSymbol glu()
      Returns the AtomicSymbol for the amino acid Glutamic Acid (E)
      static AtomicSymbol gly()
      Returns the AtomicSymbol for the amino acid Glycine (G)
      static AtomicSymbol h()
      Returns the AtomicSymbol for the amino acid Histidine
      static AtomicSymbol his()
      Returns the AtomicSymbol for the amino acid Histidine (H)
      static AtomicSymbol i()
      Returns the AtomicSymbol for the amino acid Isoleucine
      static AtomicSymbol ile()
      Returns the AtomicSymbol for the amino acid Isoleucine (I)
      static AtomicSymbol k()
      Returns the AtomicSymbol for the amino acid Lysine
      static AtomicSymbol l()
      Returns the AtomicSymbol for the amino acid Leucine
      static AtomicSymbol leu()
      Returns the AtomicSymbol for the amino acid Leucine (L)
      static AtomicSymbol lys()
      Returns the AtomicSymbol for the amino acid Lysine (K)
      static AtomicSymbol m()
      Returns the AtomicSymbol for the amino acid Methionine
      static AtomicSymbol met()
      Returns the AtomicSymbol for the amino acid Methionine (M)
      static AtomicSymbol n()
      Returns the AtomicSymbol for the amino acid Asparagine
      static AtomicSymbol o()
      Returns the AtomicSymbol for the amino acid Pyrrolysine
      static AtomicSymbol p()
      Returns the AtomicSymbol for the amino acid Proline
      static AtomicSymbol phe()
      Returns the AtomicSymbol for the amino acid Phenylalanine (F)
      static AtomicSymbol pro()
      Returns the AtomicSymbol for the amino acid Proline (P)
      static AtomicSymbol pyl()
      Returns the AtomicSymbol for the amino acid Pyrrolysine (O)
      static AtomicSymbol q()
      Returns the AtomicSymbol for the amino acid Glutamine
      static AtomicSymbol r()
      Returns the AtomicSymbol for the amino acid Arginine
      static AtomicSymbol s()
      Returns the AtomicSymbol for the amino acid Serine
      static AtomicSymbol sec()
      Returns the AtomicSymbol for the amino acid Selenocysteine (U)
      static AtomicSymbol ser()
      Returns the AtomicSymbol for the amino acid Serine (S)
      static AtomicSymbol t()
      Returns the AtomicSymbol for the amino acid Threonine
      static AtomicSymbol ter()
      Returns the AtomicSymbol for the termination (*) placeholder
      static AtomicSymbol thr()
      Returns the AtomicSymbol for the amino acid Threonine (T)
      static AtomicSymbol trp()
      Returns the AtomicSymbol for the amino acid Tryptophan (W)
      static AtomicSymbol tyr()
      Returns the AtomicSymbol for the amino acid Tyrosine (Y)
      static AtomicSymbol u()
      Returns the AtomicSymbol for the amino acid Selenocysteine
      static AtomicSymbol v()
      Returns the AtomicSymbol for the amino acid Valine
      static AtomicSymbol val()
      Returns the AtomicSymbol for the amino acid Valine (V)
      static AtomicSymbol w()
      Returns the AtomicSymbol for the amino acid Tryptophan
      static AtomicSymbol y()
      Returns the AtomicSymbol for the amino acid Tyrosine
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Method Detail

      • getAlphabet

        public static final FiniteAlphabet getAlphabet()
        Gets the protein alphabet
      • getTAlphabet

        public static final FiniteAlphabet getTAlphabet()
        Gets the protein alphabet including the translation termination symbols
      • getSymbolPropertyTable

        public static final SymbolPropertyTable getSymbolPropertyTable​(java.lang.String name)
      • createProtein

        public static SymbolList createProtein​(java.lang.String theProtein)
                                        throws IllegalSymbolException
        Return a new Protein SymbolList for protein.
        Parameters:
        theProtein - a String to parse into Protein
        Returns:
        a SymbolList created form Protein
        Throws:
        IllegalSymbolException - if dna contains any non-Amino Acid characters.
      • createProteinSequence

        public static Sequence createProteinSequence​(java.lang.String protein,
                                                     java.lang.String name)
                                              throws IllegalSymbolException
        Return a new PROTEIN Sequence for protein.
        Parameters:
        protein - a String to parse into PROTEIN
        name - a String to use as the name
        Returns:
        a Sequence created form protein
        Throws:
        IllegalSymbolException - if protein contains any non-PROTEIN characters
      • ala

        public static AtomicSymbol ala()
        Returns the AtomicSymbol for the amino acid Alanine (A)
      • a

        public static AtomicSymbol a()
        Returns the AtomicSymbol for the amino acid Alanine
      • arg

        public static AtomicSymbol arg()
        Returns the AtomicSymbol for the amino acid Arginine (R)
      • r

        public static AtomicSymbol r()
        Returns the AtomicSymbol for the amino acid Arginine
      • asn

        public static AtomicSymbol asn()
        Returns the AtomicSymbol for the amino acid Asparagine (N)
      • n

        public static AtomicSymbol n()
        Returns the AtomicSymbol for the amino acid Asparagine
      • asp

        public static AtomicSymbol asp()
        Returns the AtomicSymbol for the amino acid Aspartic Acid (D)
      • d

        public static AtomicSymbol d()
        Returns the AtomicSymbol for the amino acid Aspartic Acid
      • cys

        public static AtomicSymbol cys()
        Returns the AtomicSymbol for the amino acid Cysteine (C)
      • c

        public static AtomicSymbol c()
        Returns the AtomicSymbol for the amino acid Cysteine
      • gln

        public static AtomicSymbol gln()
        Returns the AtomicSymbol for the amino acid Glutamine (Q)
      • q

        public static AtomicSymbol q()
        Returns the AtomicSymbol for the amino acid Glutamine
      • glu

        public static AtomicSymbol glu()
        Returns the AtomicSymbol for the amino acid Glutamic Acid (E)
      • e

        public static AtomicSymbol e()
        Returns the AtomicSymbol for the amino acid Glutamic Acid
      • gly

        public static AtomicSymbol gly()
        Returns the AtomicSymbol for the amino acid Glycine (G)
      • g

        public static AtomicSymbol g()
        Returns the AtomicSymbol for the amino acid Glycine
      • his

        public static AtomicSymbol his()
        Returns the AtomicSymbol for the amino acid Histidine (H)
      • h

        public static AtomicSymbol h()
        Returns the AtomicSymbol for the amino acid Histidine
      • ile

        public static AtomicSymbol ile()
        Returns the AtomicSymbol for the amino acid Isoleucine (I)
      • i

        public static AtomicSymbol i()
        Returns the AtomicSymbol for the amino acid Isoleucine
      • leu

        public static AtomicSymbol leu()
        Returns the AtomicSymbol for the amino acid Leucine (L)
      • l

        public static AtomicSymbol l()
        Returns the AtomicSymbol for the amino acid Leucine
      • lys

        public static AtomicSymbol lys()
        Returns the AtomicSymbol for the amino acid Lysine (K)
      • k

        public static AtomicSymbol k()
        Returns the AtomicSymbol for the amino acid Lysine
      • met

        public static AtomicSymbol met()
        Returns the AtomicSymbol for the amino acid Methionine (M)
      • m

        public static AtomicSymbol m()
        Returns the AtomicSymbol for the amino acid Methionine
      • phe

        public static AtomicSymbol phe()
        Returns the AtomicSymbol for the amino acid Phenylalanine (F)
      • f

        public static AtomicSymbol f()
        Returns the AtomicSymbol for the amino acid Phenylalanine
      • pro

        public static AtomicSymbol pro()
        Returns the AtomicSymbol for the amino acid Proline (P)
      • p

        public static AtomicSymbol p()
        Returns the AtomicSymbol for the amino acid Proline
      • pyl

        public static AtomicSymbol pyl()
        Returns the AtomicSymbol for the amino acid Pyrrolysine (O)
      • o

        public static AtomicSymbol o()
        Returns the AtomicSymbol for the amino acid Pyrrolysine
      • sec

        public static AtomicSymbol sec()
        Returns the AtomicSymbol for the amino acid Selenocysteine (U)
      • u

        public static AtomicSymbol u()
        Returns the AtomicSymbol for the amino acid Selenocysteine
      • ser

        public static AtomicSymbol ser()
        Returns the AtomicSymbol for the amino acid Serine (S)
      • s

        public static AtomicSymbol s()
        Returns the AtomicSymbol for the amino acid Serine
      • thr

        public static AtomicSymbol thr()
        Returns the AtomicSymbol for the amino acid Threonine (T)
      • t

        public static AtomicSymbol t()
        Returns the AtomicSymbol for the amino acid Threonine
      • trp

        public static AtomicSymbol trp()
        Returns the AtomicSymbol for the amino acid Tryptophan (W)
      • w

        public static AtomicSymbol w()
        Returns the AtomicSymbol for the amino acid Tryptophan
      • tyr

        public static AtomicSymbol tyr()
        Returns the AtomicSymbol for the amino acid Tyrosine (Y)
      • y

        public static AtomicSymbol y()
        Returns the AtomicSymbol for the amino acid Tyrosine
      • val

        public static AtomicSymbol val()
        Returns the AtomicSymbol for the amino acid Valine (V)
      • v

        public static AtomicSymbol v()
        Returns the AtomicSymbol for the amino acid Valine
      • ter

        public static AtomicSymbol ter()
        Returns the AtomicSymbol for the termination (*) placeholder