org.expasy.mzjava.proteomics.mol

Class PeptideFragment

java.lang.Object

org.expasy.mzjava.proteomics.mol.AminoAcidSequence

org.expasy.mzjava.proteomics.mol.PeptideFragment

All Implemented Interfaces:

SymbolSequence<AminoAcid>

public class PeptideFragment
extends AminoAcidSequence

Version:

1.0

Author:

Oliver Horlacher

Constructor Summary

Constructors

Constructor and Description
PeptideFragment(FragmentType fragmentType, AminoAcid firstResidue, AminoAcid... residues) Construct an PeptideFragment by copying the residues
PeptideFragment(FragmentType fragmentType, AminoAcidSequence src, int beginIndex, int endIndex) Constructor that copies the residues and modifications from src.
PeptideFragment(FragmentType fragmentType, List<AminoAcid> residues, com.google.common.collect.Multimap<Integer,Modification> sideChainModMap, com.google.common.collect.Multimap<ModAttachment,Modification> termModMap) Constructs an PeptideFragment from the list of residues with the modifications contained in side chain and term mod map.

Method Summary

Methods

Modifier and Type	Method and Description
double	calculateMass(IonType ionType) Calculate the mass of this PeptideFragment given the ionType
double	calculateMz(IonType ionType, int charge) Calculate the m/z of this PeptideFragment given the charge and ionType
boolean	equals(Object o)
FragmentType	getFragmentType() Return the fragmentType
int	hashCode()
static PeptideFragment	parse(String s, FragmentType fragmentType) Parse s to build a PeptideFragment.
static PeptideFragment	parse(String s, FragmentType fragmentType, ModificationResolver modResolver) Parse s to build a PeptideFragment using the modResolver to convert modification strings to Modification

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

calculateMonomerMassDefect, calculateMonomerMassSum, countAminoAcidsIn, getAmbiguousAminoAcids, getModificationCount, getModificationCount, getModificationIndexes, getModifications, getModificationsAt, getModifiedResidueCount, getSymbol, getSymbolIndexes, hasAmbiguousAminoAcids, 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

PeptideFragment

public PeptideFragment(FragmentType fragmentType,
               AminoAcid firstResidue,
               AminoAcid... residues)

Construct an PeptideFragment by copying the residues

Parameters:

fragmentType - the fragment type

firstResidue - the first residue

residues - the rest of the residues

PeptideFragment

public PeptideFragment(FragmentType fragmentType,
               AminoAcidSequence src,
               int beginIndex,
               int endIndex)

Constructor that copies the residues and modifications from src. The new PeptideFragment begins at the specified beginIndex and extends to the residue at index endIndex - 1. Thus the length of the new PeptideFragment is endIndex-beginIndex.

Parameters:

fragmentType - the fragment type

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

beginIndex - the beginning index, inclusive.

endIndex - the ending index, exclusive.

PeptideFragment

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

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

Parameters:

fragmentType - the fragment type

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

Method Detail

parse

public static PeptideFragment parse(String s,
                    FragmentType fragmentType)

Parse s to build a PeptideFragment.

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

fragmentType - the fragment type

Returns:

the PeptideFragment

Throws:

PeptideParseException - if s is not a valid string

parse

public static PeptideFragment parse(String s,
                    FragmentType fragmentType,
                    ModificationResolver modResolver)

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

Parameters:

s - the string

fragmentType - the fragment type

modResolver - Function to convert modification string to Modification

Returns:

the Peptide

Throws:

PeptideParseException - if s is not a valid string

getFragmentType

public FragmentType getFragmentType()

Return the fragmentType

Returns:

the fragmentType

calculateMz

public double calculateMz(IonType ionType,
                 int charge)

Calculate the m/z of this PeptideFragment given the charge and ionType

Parameters:

ionType - the ionType

charge - the charge

Returns:

the m/z

calculateMass

public double calculateMass(IonType ionType)

Calculate the mass of this PeptideFragment given the ionType

Parameters:

ionType - the ionType

Returns:

the mass

equals

public boolean equals(Object o)

Overrides:

equals in class AminoAcidSequence

hashCode

public int hashCode()

Overrides:

hashCode in class AminoAcidSequence