org.expasy.mzjava.proteomics.mol

Class AminoAcidSequence

java.lang.Object

org.expasy.mzjava.proteomics.mol.AminoAcidSequence

All Implemented Interfaces:

SymbolSequence<AminoAcid>

Direct Known Subclasses:

Peptide, PeptideFragment

public abstract class AminoAcidSequence
extends Object
implements SymbolSequence<AminoAcid>

Abstract amino acid sequence base class. This class holds the amino acid sequence along with the modifications to the amino acids.

Modifications can be attached to the side chains of any amino acid residue or the sequence n-term or c-term.

Each modification site can have 0 or more Modifications

Version:

sqrt -1

Author:

Oliver Horlacher

Constructor Summary

Constructors

Constructor and Description
AminoAcidSequence(AminoAcid[] residues) Constructs an AminoAcidSequence by copying the residues.
AminoAcidSequence(AminoAcid firstResidue, AminoAcid... residues) Construct an AminoAcidSequence by copying the residues
AminoAcidSequence(AminoAcidSequence src, int fromInclusive, int toExclusive) Constructor that copies the residues and modifications from src.
AminoAcidSequence(AminoAcidSequence src, Set<AminoAcid> oldAAs, AminoAcid newAA) Constructor that copies the source AminoAcidSequence and replaces any amino acids in oldAAs with newAA.
AminoAcidSequence(List<AminoAcid> residues, com.google.common.collect.Multimap<Integer,Modification> sideChainModMap, com.google.common.collect.Multimap<ModAttachment,Modification> termModMap) Constructs an AminoAcidSequence 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
protected double	calculateMonomerMassDefect()
protected double	calculateMonomerMassSum() Sums the mass of all the monomers
int	countAminoAcidsIn(Set<AminoAcid> aminoAcidSet) Counts sums the number of times each of the amino acid in aminoAcidSet is contained in this Peptide.
boolean	equals(Object o)
Set<AminoAcid>	getAmbiguousAminoAcids() Returns a set containing all the amino acids that are ambiguous.
int	getModificationCount() Return the number of modifications that this peptide has.
int	getModificationCount(ModAttachment attachment) Returns the number of modifications that are attached to the given attachment
int[]	getModificationIndexes(Set<ModAttachment> modAttachments) Returns a sorted Array containing the indexes of the modified amino acids
ModificationList	getModifications(Set<ModAttachment> attachments) Returns a ModificationList containing all the modifications for the given attachments.
ModificationList	getModificationsAt(int index, Set<ModAttachment> attachments) Returns a ModificationList containing all the modifications for the given index and attachments.
int	getModifiedResidueCount() Returns the number of residues that have a modification
AminoAcid	getSymbol(int index) Returns the symbol at the specified position in this symbol sequence.
int[]	getSymbolIndexes(AminoAcid symbol) Returns an array containing the indexes of where symbol is found in this sequence.
boolean	hasAmbiguousAminoAcids() Returns true if this AminoAcidSequence has amino acids that are ambiguous such as X or B.
int	hashCode()
boolean	hasModificationAt(int index) Returns true if the residue at index has a modification.
boolean	hasModificationAt(int index, Set<ModAttachment> modAttachments) Returns true if the residue at index has a modification attached by modAttachment.
boolean	hasModificationAt(ModAttachment modAttachment) Returns true if there are modifications attached via the given modAttachment
boolean	hasModificationAt(Set<ModAttachment> modAttachments) Returns true if there are modifications attached via any of the ModAttachments in modAttachments
boolean	hasModifications() Returns true if this AminoAcidSequence has modifications.
boolean	hasSameSequence(AminoAcidSequence sequence) Returns true if this and sequence have the same AA sequence even if the two sequences have different modifications.
boolean	hasSameSequence(SymbolSequence<AminoAcid> sequence) Returns true if this and sequence have the same AA sequence.
boolean	isEmpty() Returns true if this AminoAcidSequence contains no residues.
int	size() Returns the number of residues in this amino acid sequence.
String	toString()
String	toSymbolString() Returns a string containing the amino acids and ignores the modifications.

Methods inherited from class java.lang.Object

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

Constructor Detail

AminoAcidSequence

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

Construct an AminoAcidSequence by copying the residues

Parameters:

firstResidue - the first residue

residues - the rest of the residues

AminoAcidSequence

public AminoAcidSequence(AminoAcid[] residues)

Constructs an AminoAcidSequence by copying the residues.

Parameters:

residues - the residues, the array cannot be empty

AminoAcidSequence

public AminoAcidSequence(AminoAcidSequence src,
                 int fromInclusive,
                 int toExclusive)

Constructor that copies the residues and modifications from src. The new AminoAcidSequence begins at the specified fromInclusive and extends to the residue at index toExclusive - 1.

Thus the length of the new AminoAcidSequence is toExclusive-fromInclusive.

Parameters:

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

fromInclusive - the beginning index, inclusive.

toExclusive - the ending index, exclusive.

AminoAcidSequence

public AminoAcidSequence(AminoAcidSequence src,
                 Set<AminoAcid> oldAAs,
                 AminoAcid newAA)

Constructor that copies the source AminoAcidSequence and replaces any amino acids in oldAAs with newAA.

Parameters:

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

oldAAs - set containing the old amino acids

newAA - the new amino acid

AminoAcidSequence

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

Constructs an AminoAcidSequence 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

Method Detail

hasModifications

public boolean hasModifications()

Returns true if this AminoAcidSequence has modifications.

Returns:

true if this AminoAcidSequence has modifications

toString

public String toString()

Overrides:

toString in class Object

hasSameSequence

public boolean hasSameSequence(AminoAcidSequence sequence)

Returns true if this and sequence have the same AA sequence even if the two sequences have different modifications.

Parameters:

sequence - the sequence to check against

Returns:

true if this and sequence have the same AA sequence

hasSameSequence

public boolean hasSameSequence(SymbolSequence<AminoAcid> sequence)

Returns true if this and sequence have the same AA sequence.

Parameters:

sequence - the sequence to check against

Returns:

true if this and sequence have the same AA sequence

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

getModificationCount

public int getModificationCount()

Return the number of modifications that this peptide has.

Returns:

the number of modifications that this peptide has

getModificationCount

public int getModificationCount(ModAttachment attachment)

Returns the number of modifications that are attached to the given attachment

Parameters:

attachment - where the modification is attached

Returns:

the number of modifications that are attached to the given attachment

getAmbiguousAminoAcids

public Set<AminoAcid> getAmbiguousAminoAcids()

Returns a set containing all the amino acids that are ambiguous.

Returns:

a set containing all the amino acids that are ambiguous

hasAmbiguousAminoAcids

public boolean hasAmbiguousAminoAcids()

Returns true if this AminoAcidSequence has amino acids that are ambiguous such as X or B.

Returns:

true if there are ambiguous amino acids false otherwise

toSymbolString

public String toSymbolString()

Returns a string containing the amino acids and ignores the modifications.

Specified by:

toSymbolString in interface SymbolSequence<AminoAcid>

Returns:

a string containing the amino acids and ignores the modifications

getModifiedResidueCount

public int getModifiedResidueCount()

Returns the number of residues that have a modification

Returns:

the number of residues that have a modification

getModifications

public ModificationList getModifications(Set<ModAttachment> attachments)

Returns a ModificationList containing all the modifications for the given attachments.

For example given the peptide (n-term)_PE(m1)PS(m2, m3)IDE_(c-term1, c-term2):

 getModifications(EnumSet.of(ModAttachment.N_TERM) will return {n-term}
 getModifications(EnumSet.of(ModAttachment.C_TERM) will return {c-term1, c-term2}
 getModifications(EnumSet.of(ModAttachment.SIDE_CHAIN) will return {m1, m2, m3}
 getModifications(EnumSet.of(ModAttachment.all) will return {n-term, m1, m2, m3, c-term1, c-term2}
 

Parameters:

attachments - the ModAttachments to include

Returns:

a ModificationList containing all the modifications for the given attachments

getModificationsAt

public ModificationList getModificationsAt(int index,
                                  Set<ModAttachment> attachments)

Returns a ModificationList containing all the modifications for the given index and attachments.

For example given the peptide (n-term)_PE(m1)PS(m2, m3)IDE_(c-term1, c-term2):

 getModifications(0, EnumSet.of(ModAttachment.N_TERM) will return {n-term}
 getModifications(6, EnumSet.of(ModAttachment.N_TERM) will return {}
 getModifications(6, EnumSet.of(ModAttachment.C_TERM) will return {c-term1, c-term2}
 getModifications(3, EnumSet.of(ModAttachment.SIDE_CHAIN) will return {m2, m3}
 

Parameters:

attachments - the ModAttachments to include

Returns:

a ModificationList containing all the modifications for the given attachments

hasModificationAt

public boolean hasModificationAt(int index)

Returns true if the residue at index has a modification.

Parameters:

index - the index

Returns:

true if the residue at index has a modification

hasModificationAt

public boolean hasModificationAt(int index,
                        Set<ModAttachment> modAttachments)

Returns true if the residue at index has a modification attached by modAttachment.

Parameters:

index - the index

modAttachments - set of mod attachments to check

Returns:

true if the residue at index has a modification

hasModificationAt

public boolean hasModificationAt(ModAttachment modAttachment)

Returns true if there are modifications attached via the given modAttachment

Parameters:

modAttachment - the mod attachments to check

Returns:

true if there are modifications attached via the given modAttachment

hasModificationAt

public boolean hasModificationAt(Set<ModAttachment> modAttachments)

Returns true if there are modifications attached via any of the ModAttachments in modAttachments

Parameters:

modAttachments - the mod attachments to check

Returns:

true if there are modifications attached via the given modAttachment

size

public int size()

Returns the number of residues in this amino acid sequence.

Specified by:

size in interface SymbolSequence<AminoAcid>

Returns:

the number of residues in this amino acid sequence

getModificationIndexes

public int[] getModificationIndexes(Set<ModAttachment> modAttachments)

Returns a sorted Array containing the indexes of the modified amino acids

Returns:

a sorted Array containing the indexes of the modified amino acids

getSymbolIndexes

public int[] getSymbolIndexes(AminoAcid symbol)

Returns an array containing the indexes of where symbol is found in this sequence.

For example:

the indexes of S in PSPSK is {1, 3}

Parameters:

symbol - the symbol for which the indexes are to be returned

Returns:

an array containing the indexes of where symbol is found in this sequence

getSymbol

public AminoAcid getSymbol(int index)

Description copied from interface: SymbolSequence

Returns the symbol at the specified position in this symbol sequence.

Specified by:

getSymbol in interface SymbolSequence<AminoAcid>

Parameters:

index - index of the symbol to return

Returns:

the symbol at the specified position in this symbol sequence

calculateMonomerMassSum

protected double calculateMonomerMassSum()

Sums the mass of all the monomers

Returns:

the sum of all the monomer mass

calculateMonomerMassDefect

protected double calculateMonomerMassDefect()

countAminoAcidsIn

public int countAminoAcidsIn(Set<AminoAcid> aminoAcidSet)

Counts sums the number of times each of the amino acid in aminoAcidSet is contained in this Peptide.

For example PEPSIDE.countAminoAcidsIn((P, I)) returns 3

Parameters:

aminoAcidSet - the amino acids to check

Returns:

the sum of the number of times each of the amino acid in aminoAcidSet is contained in this Peptide

isEmpty

public boolean isEmpty()

Returns true if this AminoAcidSequence contains no residues.

Returns:

true if this AminoAcidSequence contains no residues