org.expasy.mzjava.proteomics.mol

Class PeptideBuilder

java.lang.Object

org.expasy.mzjava.proteomics.mol.PeptideBuilder

public class PeptideBuilder
extends Object

A builder for constructing Peptides

Version:

sqrt -1

Author:

Oliver Horlacher

Constructor Summary

Constructors

Constructor and Description
PeptideBuilder(AminoAcid... seq) Construct a PeptideBuilder initialised to contain the amino acids from seq
PeptideBuilder(AminoAcid[] residues, int fromInclusive, int toExclusive) Constructs an PeptideBuilder by copying the residues from residues starting at fromInclusive to toExclusive.
PeptideBuilder(List<AminoAcid> sequence) Construct a PeptideBuilder initialised to contain the amino acids from sequence
PeptideBuilder(Peptide peptide) Construct a PeptideBuilder initialised to contain the amino acids sequence and modifications copied from the peptide
PeptideBuilder(String peptide) Construct a peptide builder initialised by parsing the peptide string

Method Summary

Methods

Modifier and Type	Method and Description
PeptideBuilder	add(AminoAcid aminoAcid) Add an amino acid
PeptideBuilder	addModification(int index, Modification modification) Add a the modification to the side chain of residue at index
PeptideBuilder	addModification(ModAttachment modAttachment, Modification modification) Add a the modification to either end of the the peptide.
PeptideBuilder	addModificationToAll(Collection<Modification> modifications, AminoAcid aminoAcid) Add all of the Modification's in modifications to all amino acids that are equal to aminoAcid
PeptideBuilder	addModificationToAll(Modification modification, AminoAcid aminoAcid) Add the modification to all amino acids that are equal to aminoAcid
Peptide	build() Build a Peptide
PeptideFragment	buildFragment(FragmentType fragmentType) Build a PeptideFragment
void	clear() Reset this builder
PeptideBuilder	parseAndAdd(String peptideSequence) Parse the peptideSequence string and add the sequence and modifications to this builder
int	size() Return the number of amino acids

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

PeptideBuilder

public PeptideBuilder(String peptide)

Construct a peptide builder initialised by parsing the peptide string

Parameters:

peptide - the initial state of the builder

PeptideBuilder

public PeptideBuilder(List<AminoAcid> sequence)

Construct a PeptideBuilder initialised to contain the amino acids from sequence

Parameters:

sequence - the initial amino acids

PeptideBuilder

public PeptideBuilder(AminoAcid... seq)

Construct a PeptideBuilder initialised to contain the amino acids from seq

Parameters:

seq - the initial amino acids

PeptideBuilder

public PeptideBuilder(AminoAcid[] residues,
              int fromInclusive,
              int toExclusive)

Constructs an PeptideBuilder by copying the residues from residues starting at fromInclusive to toExclusive.

Parameters:

residues - the residues, the array cannot be empty

fromInclusive - the beginning index, inclusive

toExclusive - the ending index, exclusive

PeptideBuilder

public PeptideBuilder(Peptide peptide)

Construct a PeptideBuilder initialised to contain the amino acids sequence and modifications copied from the peptide

Parameters:

peptide - the peptide from which to copy the seqence and modifications

Method Detail

addModification

public PeptideBuilder addModification(ModAttachment modAttachment,
                             Modification modification)

Add a the modification to either end of the the peptide. The end is specified busing the modAttachment

Parameters:

modAttachment - specifies which end of the peptide the modification is to be added

modification - the Modification that is to be added

Returns:

the builder

parseAndAdd

public PeptideBuilder parseAndAdd(String peptideSequence)

Parse the peptideSequence string and add the sequence and modifications to this builder

Parameters:

peptideSequence - the string to parse

Returns:

the builder

add

public PeptideBuilder add(AminoAcid aminoAcid)

Add an amino acid

Parameters:

aminoAcid - the amino acid to add

Returns:

this builder

addModification

public PeptideBuilder addModification(int index,
                             Modification modification)

Add a the modification to the side chain of residue at index

Parameters:

index - the index of the reside where the Modification is to be added

modification - the ModificationMatch that is to be added

Returns:

this builder

addModificationToAll

public PeptideBuilder addModificationToAll(Modification modification,
                                  AminoAcid aminoAcid)

Add the modification to all amino acids that are equal to aminoAcid

Parameters:

modification - the modification to add

aminoAcid - the amino acid to which the modification is to be added

Returns:

this builder

addModificationToAll

public PeptideBuilder addModificationToAll(Collection<Modification> modifications,
                                  AminoAcid aminoAcid)

Add all of the Modification's in modifications to all amino acids that are equal to aminoAcid

Parameters:

modifications - the modifications to add

aminoAcid - the amino acid to which the modification is to be added

Returns:

this builder

clear

public void clear()

Reset this builder

size

public int size()

Return the number of amino acids

Returns:

the number of amino acids

build

public Peptide build()

Build a Peptide

Returns:

the new Peptide

buildFragment

public PeptideFragment buildFragment(FragmentType fragmentType)

Build a PeptideFragment

Parameters:

fragmentType - the fragment type for the PeptideFragment

Returns:

the new PeptideFragment