org.expasy.mzjava.proteomics.mol

Class Peptide

java.lang.Object

org.expasy.mzjava.proteomics.mol.AminoAcidSequence

org.expasy.mzjava.proteomics.mol.Peptide

All Implemented Interfaces:

SymbolSequence<AminoAcid>, Weighable

public class Peptide
extends AminoAcidSequence
implements Weighable

Version:

1.0

Author:

Oliver Horlacher, fnikitin

Constructor Summary

Constructors

Constructor and Description
Peptide(AminoAcid firstResidue, AminoAcid... residues) Construct an Peptide by copying the residues.
Peptide(AminoAcidSequence src) Copy constructor.
Peptide(AminoAcidSequence src, int beginIndex, int endIndex) Constructs a Peptide by copying the residues and modifications from src.
Peptide(List<AminoAcid> residues) Constructs an Peptide by copying the residues.
Peptide(List<AminoAcid> residues, com.google.common.collect.Multimap<Integer,Modification> sideChainModMap, com.google.common.collect.Multimap<ModAttachment,Modification> termModMap) Constructs an Peptide from the list of residues with the modifications contained in side chain and term mod map.
Peptide(Peptide peptide, Set<AminoAcid> oldAAs, AminoAcid newAa)

Method Summary

Methods

Modifier and Type	Method and Description
double	calculateMz(int charge) Calculate the m/z of this peptide at the given charge
PeptideFragment	createFragment(int beginIndex, int endIndex, FragmentType fragmentType) Returns a new peptide fragment that is a subsequence of this peptide.
PeptideFragment	createFragment(IonType ionType, int residueNumber) Create PeptideFragment that is sub sequence for the give ion type and residue number Given peptide CERVILAS createFragment(y, 1) will return S, createFragment(b, 1) will return C createFragment(b, 3) will return CER.
double	getMolecularMass() Returns the mass of this peptide
static Peptide	parse(String s) Parse s to build a Peptide.
static Peptide	parse(String s, ModificationResolver modResolver) Parse s to build a Peptide using the modResolver to convert modification strings to Modification
Peptide	replace(Set<AminoAcid> oldAAs, AminoAcid newAa)
Peptide	subSequence(int beginIndex, int endIndex) Returns a new peptide that is a sub sequence of this peptide.
Peptide	subSequence(IonType ionType, int residueNumber) Create a sub sequence for the give ion type and residue number Given peptide CERVILAS subSequence(y, 1) will return S, subSequence(b, 1) will return C subSequence(b, 3) will return CER.

Methods inherited from class org.expasy.mzjava.proteomics.mol.AminoAcidSequence

calculateMonomerMassDefect, calculateMonomerMassSum, countAminoAcidsIn, equals, getAmbiguousAminoAcids, getModificationCount, getModificationCount, getModificationIndexes, getModifications, getModificationsAt, getModifiedResidueCount, getSymbol, getSymbolIndexes, hasAmbiguousAminoAcids, hashCode, hasModificationAt, hasModificationAt, hasModificationAt, hasModificationAt, hasModifications, hasSameSequence, hasSameSequence, isEmpty, size, toString, toSymbolString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

Peptide

public Peptide(AminoAcid firstResidue,
       AminoAcid... residues)

Construct an Peptide by copying the residues.

Parameters:

firstResidue - the first residue

residues - the rest of the residues

Peptide

public Peptide(List<AminoAcid> residues)

Constructs an Peptide by copying the residues.

Parameters:

residues - the residues, the array cannot be empty

Peptide

public Peptide(AminoAcidSequence src)

Copy constructor.

Parameters:

src - the peptide to copy.

Peptide

public Peptide(AminoAcidSequence src,
       int beginIndex,
       int endIndex)

Constructs a Peptide by copying the residues and modifications from src. The new Peptide begins at the specified beginIndex and extends to the residue at index endIndex - 1.

Parameters:

src - the AminoAcidSequence from which to copy the sequence and modifications

beginIndex - beginIndex the beginning index, inclusive.

endIndex - the ending index, exclusive.

Peptide

public Peptide(List<AminoAcid> residues,
       com.google.common.collect.Multimap<Integer,Modification> sideChainModMap,
       com.google.common.collect.Multimap<ModAttachment,Modification> termModMap)

Constructs an Peptide from the list of residues with the modifications contained in side chain and term mod map.

Parameters:

residues - the residues, this list must have at least one amino acid

sideChainModMap - the side chain modifications, this map can be empty

termModMap - the terminal modifications, this map can be empty

Peptide

public Peptide(Peptide peptide,
       Set<AminoAcid> oldAAs,
       AminoAcid newAa)

Method Detail

parse

public static Peptide parse(String s)

Parse s to build a Peptide.

The expected format is a string of amino acids. Each amino acid can have an optional list of modifications. The modifications can either be formulas as defined by Composition, or PSI-MS Names found in Uni Mod.

 PEPTIDE              : the peptide PEPTIDE
 PEPTM(O)IDE          : the peptide PEPTIDE with an oxidation on M
 PEPTM(O, Phospho)IDE : the peptide PEPTIDE with an oxidation and phosphorylation on M
 (Acetyl)_PEPTIDE_(O) : the peptide PEPTIDE with a n-term Acetylation and c_term oxidation modification
 

Parameters:

s - the string

Returns:

the Peptide

Throws:

PeptideParseException - if s is not a valid string

parse

public static Peptide parse(String s,
            ModificationResolver modResolver)

Parse s to build a Peptide using the modResolver to convert modification strings to Modification

Parameters:

s - the string

modResolver - Function to convert modification string to Modification

Returns:

the Peptide

Throws:

PeptideParseException - if s is not a valid string

subSequence

public Peptide subSequence(int beginIndex,
                  int endIndex)

Returns a new peptide that is a sub sequence of this peptide. The sub sequence begins at the specified beginIndex and extends to the amino acid at index endIndex - 1. Thus the length of the sub sequence is endIndex-beginIndex.

Parameters:

beginIndex - the beginning index, inclusive.

endIndex - the ending index, exclusive.

Returns:

the specified substring.

Throws:

IndexOutOfBoundsException - if the beginIndex is negative, or endIndex is larger than the length of this Peptide object, or beginIndex is larger than endIndex.

createFragment

public PeptideFragment createFragment(int beginIndex,
                             int endIndex,
                             FragmentType fragmentType)

Returns a new peptide fragment that is a subsequence of this peptide. The subsequence begins at the specified beginIndex and extends to the amino acid at index endIndex - 1. Thus the length of the subsequence is endIndex-beginIndex.

Parameters:

beginIndex - the beginning index, inclusive.

endIndex - the ending index, exclusive.

fragmentType - the type of the fragment

Returns:

a new PeptideFragment with the specified sub sequence.

Throws:

IndexOutOfBoundsException - if the beginIndex is negative, or endIndex is larger than the length of this String object, or beginIndex is larger than endIndex.

createFragment

public PeptideFragment createFragment(IonType ionType,
                             int residueNumber)

Create PeptideFragment that is sub sequence for the give ion type and residue number Given peptide CERVILAS createFragment(y, 1) will return S, createFragment(b, 1) will return C createFragment(b, 3) will return CER. If the IonType is i (immonium) the residue at residueNumber - 1 is returned: createFragment(i, 1) is C, createFragment(i, 2) is E

Parameters:

ionType - the type of the ion, only accepts ions that are FORWARD, REVERSE and MONOMER fragments

residueNumber - the index of the residue. The index of the first residue is 1

Returns:

the new PeptideFragment

subSequence

public Peptide subSequence(IonType ionType,
                  int residueNumber)

Create a sub sequence for the give ion type and residue number Given peptide CERVILAS subSequence(y, 1) will return S, subSequence(b, 1) will return C subSequence(b, 3) will return CER. If the IonType is i (immonium) the residue at residueNumber - 1 is returned: subSequence(i, 1) is C, subSequence(i, 2) is E

Parameters:

ionType - the type of the ion, only accepts ions that are FORWARD, REVERSE and MONOMER fragments

residueNumber - the index of the residue. The index of the first residue is 1

Returns:

the sub sequence

calculateMz

public double calculateMz(int charge)

Calculate the m/z of this peptide at the given charge

Parameters:

charge - the charge

Returns:

the m/z of this peptide

getMolecularMass

public double getMolecularMass()

Returns the mass of this peptide

Specified by:

getMolecularMass in interface Weighable

Returns:

the mass of this peptide

replace

public Peptide replace(Set<AminoAcid> oldAAs,
              AminoAcid newAa)