Package de.isas.lipidomics.domain

Class LipidSpecies

java.lang.Object

de.isas.lipidomics.domain.LipidSpecies

Direct Known Subclasses:

LipidMolecularSubspecies

public class LipidSpecies
extends Object

A lipid species is the factual root of the object hierarchy. Lipid category and class are used as taxonomic roots of a lipid species. Partial structural knowledge, apart from the head group, is first encoded in the lipid species. A typical lipid species is PC 32:0 (SwissLipids SLM:000056493), where the head group is defined as PC (Glycerophosphocholines), with fatty acyl chains of unknown individual composition, but known total composition (32 carbon atoms, zero double bonds, no hydroxylations).

Author:

nils.hoffmann

See Also:

LipidCategory, LipidClass, LipidMolecularSubspecies, LipidStructuralSubspecies, LipidIsomericSubspecies

Field Summary

Fields

Modifier and Type	Field	Description
protected LipidSpeciesInfo	info
static LipidSpecies	NONE

Constructor Summary

Constructors

Constructor	Description
LipidSpecies(HeadGroup headGroup)	Create a lipid species using the provided head group and a lipid species info LipidSpeciesInfo.NONE.
LipidSpecies(HeadGroup headGroup, Optional<LipidSpeciesInfo> lipidSpeciesInfo)	Create a lipid species from a head group and an optional LipidSpeciesInfo.

Method Summary

Modifier and Type	Method	Description
protected String	buildLipidString(LipidLevel level, String headGroup, boolean isNormalized)
protected StringBuilder	buildSpeciesHeadGroupString(String headGroup, boolean normalizeHeadGroup)
ElementTable	getElements()	Returns the element count table for this lipid.
Map<String,FattyAcid>	getFa()	Returns the fatty acyls registered for this lipid.
LipidSpeciesInfo	getInfo()	Returns the LipidSpeciesInfo for this lipid.
LipidCategory	getLipidCategory()
LipidClass	getLipidClass()
String	getLipidString()	Returns a lipid string representation for the LipidLevel, e.g.
String	getLipidString(LipidLevel level)	Returns a lipid string representation for the given LipidLevel, e.g.
String	getLipidString(LipidLevel level, boolean normalizeHeadGroup)	Returns a lipid string representation for the given LipidLevel, e.g.
String	getNormalizedHeadGroup()	Returns a lipid string representation for the head group of this lipid.
String	getNormalizedLipidString()	Returns a lipid string representation for the native LipidLevel, e.g.
boolean	isEtherLipid()	Returns true, if the head group ends with ' O' or if the lipid fa bond type is either LipidFaBondType.ETHER_UNSPECIFIED, LipidFaBondType.ETHER_PLASMANYL or LipidFaBondType.ETHER_PLASMENYL.
String	toString()
boolean	validate()	Validate this lipid against the class-specific available FA types and slots.

Methods inherited from class java.lang.Object

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

Field Detail

NONE

public static final LipidSpecies NONE

info

protected LipidSpeciesInfo info

Constructor Detail

LipidSpecies

public LipidSpecies(HeadGroup headGroup)

Create a lipid species using the provided head group and a lipid species info LipidSpeciesInfo.NONE.

Parameters:

headGroup - the lipid species head group.

LipidSpecies

public LipidSpecies(HeadGroup headGroup,
                    Optional<LipidSpeciesInfo> lipidSpeciesInfo)

Create a lipid species from a head group and an optional LipidSpeciesInfo. This constructor will infer the lipid class from the head group automatically. It then uses the lipid class to retrieve the category of this lipid automatically, or sets the category to LipidCategory.UNDEFINED. The lipid species info, which contains details about the total no. of carbons in FA chains, no. of double bonds etc., is used as provided.

Parameters:

headGroup - the lipid species head group.

lipidSpeciesInfo - the lipid species info object.

Method Detail

getInfo

public LipidSpeciesInfo getInfo()

Returns the LipidSpeciesInfo for this lipid.

Returns:

the lipid species info.

isEtherLipid

public boolean isEtherLipid()

Returns true, if the head group ends with ' O' or if the lipid fa bond type is either LipidFaBondType.ETHER_UNSPECIFIED, LipidFaBondType.ETHER_PLASMANYL or LipidFaBondType.ETHER_PLASMENYL.

Returns:

whether this is an 'ether' lipid, e.g. a unspecified ether species, a Plasmanyl or Plasmenyl species.

getLipidString

public String getLipidString()

Returns a lipid string representation for the LipidLevel, e.g. Category, Species, etc, as returned by getInfo(). Will return the head group name if the level is LipidSpeciesInfo.NONE.

Returns:

the lipid name for the native level.

getLipidString

public String getLipidString(LipidLevel level)

Returns a lipid string representation for the given LipidLevel, e.g. Category, Species, etc. Please note that this method is overridden by specific implementations for molecular, structural and isomeric subspecies levels. This method does not normalize the head group.

Parameters:

level - the lipid level to report the name of this lipid on.

Returns:

the lipid name.

getLipidString

public String getLipidString(LipidLevel level,
                             boolean normalizeHeadGroup)

Returns a lipid string representation for the given LipidLevel, e.g. Category, Species, etc. Please note that this method is overridden by specific implementations for molecular, structural and isomeric subspecies levels. This method normalizes the head group to the primary class-specific synonym. E.g. TG would be normalized to TAG.

Parameters:

level - the lipid level to report the name of this lipid on.

normalizeHeadGroup - if true, use class specific synonym for headGroup, if false, use head group as parsed.

Returns:

the lipid name.

buildSpeciesHeadGroupString

protected StringBuilder buildSpeciesHeadGroupString(String headGroup,
                                                    boolean normalizeHeadGroup)

buildLipidString

protected String buildLipidString(LipidLevel level,
                                  String headGroup,
                                  boolean isNormalized)
                           throws ConstraintViolationException

Throws:

ConstraintViolationException

getNormalizedHeadGroup

public String getNormalizedHeadGroup()

Returns a lipid string representation for the head group of this lipid. This method normalizes the original head group name to the class specific primary alias, if the level and class are known. E.g. TG is normalized to TAG.

Returns:

the normalized lipid head group.

getNormalizedLipidString

public String getNormalizedLipidString()

Returns a lipid string representation for the native LipidLevel, e.g. Category, Species, etc, as returned by getInfo() of this lipid. This method normalizes the head group to the primary class-specific synonym. E.g. TG would be normalized to TAG.

Returns:

the normalized lipid name.

validate

public boolean validate()

Validate this lipid against the class-specific available FA types and slots.

Returns:

true if this lipid's FA types and their number match the class definition, false otherwise.

getFa

public Map<String,FattyAcid> getFa()

Returns the fatty acyls registered for this lipid.

Returns:

the fatty acyls.

getElements

public ElementTable getElements()

Returns the element count table for this lipid.

Returns:

the element count table.

getLipidClass

public LipidClass getLipidClass()

getLipidCategory

public LipidCategory getLipidCategory()

toString

public String toString()

Overrides:

toString in class Object