ambit2.base.relation.composition

Class CompositionRelation

java.lang.Object

ambit2.base.relation.AbstractRelation<STRUCTURE_RELATION,Proportion,SubstanceRecord,IStructureRecord>

ambit2.base.relation.composition.CompositionRelation

All Implemented Interfaces:

IChemical, IStructureRecord, IStructureRelation<STRUCTURE_RELATION,Proportion,SubstanceRecord,IStructureRecord>, Serializable

Direct Known Subclasses:

Additive, Constituent, Impurity

public class CompositionRelation
extends AbstractRelation<STRUCTURE_RELATION,Proportion,SubstanceRecord,IStructureRecord>
implements IStructureRecord

Substance composition

Author:

nina

{
    "composition": [
        {
            "substance": {
                "URI": "http://apps.ideaconsult.net:8080/data/substance/1"
            },
            "component": {
                "compound": {
                    "URI": "http://apps.ideaconsult.net:8080/data/compound/21219/conformer/39738",
                    "structype": "NA",
                    "metric": null,
                    "name": "",
                    "cas": "",
                    "einecs": ""
                },
                "values": {
                    "http://apps.ideaconsult.net:8080/data/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23ChemicalNameDefault": "formaldehyde|Formaldehyde",
                    "http://apps.ideaconsult.net:8080/data/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23CASRNDefault": "50-00-0",
                    "http://apps.ideaconsult.net:8080/data/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23EINECSDefault": "200-001-8",
                    "http://apps.ideaconsult.net:8080/data/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23TradeNameDefault": "Formaldehyde, gas|Oxomethane|Methanal|Formaldehyde (8CI, 9CI)|Paraform|Formaldehyde solution|Methylene oxide|Formol|Formaldehyd|Formalin|Morbicid|Oxymethylene|Methyl aldehyde|Formic aldehyde|Formalith|Methaldehyde|TRA0001"
                },
                "facets": []
            },
            "compositionUUID": "L-340e87fb-e95f-3743-823d-1b9b25a94d56",
            "compositionName": "other: pure",
            "relation": "HAS_CONSTITUENT",
            "proportion": {
                "typical": {
                    "precision": "",
                    "value": 100,
                    "unit": "% (w/w)"
                },
                "real": {
                    "lowerPrecision": "",
                    "lowerValue": 0,
                    "upperPrecision": "",
                    "upperValue": 0,
                    "unit": ""
                },
                "function_as_additive": null
            }
        },
        {
            "substance": {
                "URI": "http://apps.ideaconsult.net:8080/data/substance/1"
            },
            "component": {
                "compound": {
                    "URI": "http://apps.ideaconsult.net:8080/data/compound/21219/conformer/39738",
                    "structype": "NA",
                    "metric": null,
                    "name": "",
                    "cas": "",
                    "einecs": ""
                },
                "values": {
                    "http://apps.ideaconsult.net:8080/data/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23ChemicalNameDefault": "formaldehyde|Formaldehyde",
                    "http://apps.ideaconsult.net:8080/data/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23CASRNDefault": "50-00-0",
                    "http://apps.ideaconsult.net:8080/data/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23EINECSDefault": "200-001-8",
                    "http://apps.ideaconsult.net:8080/data/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23TradeNameDefault": "Formaldehyde, gas|Oxomethane|Methanal|Formaldehyde (8CI, 9CI)|Paraform|Formaldehyde solution|Methylene oxide|Formol|Formaldehyd|Formalin|Morbicid|Oxymethylene|Methyl aldehyde|Formic aldehyde|Formalith|Methaldehyde|TRA0001"
                },
                "facets": []
            },
            "compositionUUID": "L-cf10d721-b0e7-37cd-a233-e9a2483c4d3c",
            "compositionName": "other: sales products in aqueous solution",
            "relation": "HAS_CONSTITUENT",
            "proportion": {
                "typical": {
                    "precision": "",
                    "value": 0,
                    "unit": ""
                },
                "real": {
                    "lowerPrecision": "",
                    "lowerValue": 0,
                    "upperPrecision": "",
                    "upperValue": 0,
                    "unit": ""
                },
                "function_as_additive": null
            }
        },
        {
            "substance": {
                "URI": "http://apps.ideaconsult.net:8080/data/substance/1"
            },
            "component": {
                "compound": {
                    "URI": "http://apps.ideaconsult.net:8080/data/compound/21220/conformer/39739",
                    "structype": "NA",
                    "metric": null,
                    "name": "",
                    "cas": "",
                    "einecs": ""
                },
                "values": {
                    "http://apps.ideaconsult.net:8080/data/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23ChemicalNameDefault": "water|Water",
                    "http://apps.ideaconsult.net:8080/data/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23CASRNDefault": "7732-18-5",
                    "http://apps.ideaconsult.net:8080/data/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23EINECSDefault": "231-791-2"
                },
                "facets": []
            },
            "compositionUUID": "L-f2d0bc7e-a154-3f6d-babd-22ea28467466",
            "compositionName": "",
            "relation": "HAS_ADDITIVE",
            "proportion": {
                "typical": {
                    "precision": "ca.",
                    "value": 49,
                    "unit": "% (w/w)"
                },
                "real": {
                    "lowerPrecision": "",
                    "lowerValue": 0,
                    "upperPrecision": "",
                    "upperValue": 0,
                    "unit": ""
                },
                "function_as_additive": "solvent"
            }
        },
        {
            "substance": {
                "URI": "http://apps.ideaconsult.net:8080/data/substance/1"
            },
            "component": {
                "compound": {
                    "URI": "http://apps.ideaconsult.net:8080/data/compound/21221/conformer/39740",
                    "structype": "NA",
                    "metric": null,
                    "name": "",
                    "cas": "",
                    "einecs": ""
                },
                "values": {
                    "http://apps.ideaconsult.net:8080/data/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23ChemicalNameDefault": "6,6'-(m-phenylene)bis(1,3,5-triazine-2,4-diamine)",
                    "http://apps.ideaconsult.net:8080/data/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23CASRNDefault": "5118-80-9",
                    "http://apps.ideaconsult.net:8080/data/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23EINECSDefault": "225-859-0"
                },
                "facets": []
            },
            "compositionUUID": "L-f2d0bc7e-a154-3f6d-babd-22ea28467466",
            "compositionName": "",
            "relation": "HAS_ADDITIVE",
            "proportion": {
                "typical": {
                    "precision": "",
                    "value": 0,
                    "unit": ""
                },
                "real": {
                    "lowerPrecision": "",
                    "lowerValue": 0,
                    "upperPrecision": "",
                    "upperValue": 0,
                    "unit": ""
                },
                "function_as_additive": ""
            }
        },
        {
            "substance": {
                "URI": "http://apps.ideaconsult.net:8080/data/substance/1"
            },
            "component": {
                "compound": {
                    "URI": "http://apps.ideaconsult.net:8080/data/compound/21222/conformer/39741",
                    "structype": "NA",
                    "metric": null,
                    "name": "",
                    "cas": "",
                    "einecs": ""
                },
                "values": {
                    "http://apps.ideaconsult.net:8080/data/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23ChemicalNameDefault": "methanol|Methanol",
                    "http://apps.ideaconsult.net:8080/data/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23CASRNDefault": "67-56-1",
                    "http://apps.ideaconsult.net:8080/data/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23EINECSDefault": "200-659-6"
                },
                "facets": []
            },
            "compositionUUID": "L-f2d0bc7e-a154-3f6d-babd-22ea28467466",
            "compositionName": "",
            "relation": "HAS_IMPURITY",
            "proportion": {
                "typical": {
                    "precision": "",
                    "value": 0,
                    "unit": ""
                },
                "real": {
                    "lowerPrecision": "",
                    "lowerValue": 0.5,
                    "upperPrecision": "",
                    "upperValue": 2,
                    "unit": "% (w/w)"
                },
                "function_as_additive": null
            }
        }
        
    ],
    "feature": {
        "http://apps.ideaconsult.net:8080/data/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23IUPACNameDefault": {
            "type": "Feature",
            "title": "IUPAC name",
            "units": "",
            "isNominal": "false",
            "isNumeric": "false",
            "sameAs": "http://www.opentox.org/api/1.1#IUPACName",
            "isModelPredictionFeature": false,
            "creator": "http://ambit.sourceforge.net",
            "order": 1,
            "source": {
                "URI": "http://apps.ideaconsult.net:8080/data/dataset/Default",
                "type": "Dataset"
            },
            "annotation": []
        },
        "http://apps.ideaconsult.net:8080/data/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23ChemicalNameDefault": {
            "type": "Feature",
            "title": "Names",
            "units": "",
            "isNominal": "false",
            "isNumeric": "false",
            "sameAs": "http://www.opentox.org/api/1.1#ChemicalName",
            "isModelPredictionFeature": false,
            "creator": "http://ambit.sourceforge.net",
            "order": 2,
            "source": {
                "URI": "http://apps.ideaconsult.net:8080/data/dataset/Default",
                "type": "Dataset"
            },
            "annotation": []
        }
    }
}

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	CompositionRelation.jsonFeature

Nested classes/interfaces inherited from interface ambit2.base.interfaces.IStructureRecord

IStructureRecord.MOL_TYPE, IStructureRecord.STRUC_TYPE

Field Summary

Fields

Modifier and Type	Field and Description
protected String	compositionUUID
protected boolean	hidden

Fields inherited from class ambit2.base.relation.AbstractRelation

name

Constructor Summary

Constructors

Constructor and Description
CompositionRelation(SubstanceRecord structure1, IStructureRecord structure2, Proportion proportion)
CompositionRelation(SubstanceRecord structure1, IStructureRecord structure2, STRUCTURE_RELATION type, Proportion proportion)

Method Summary

Modifier and Type	Method and Description
void	addFacet(net.idea.modbcum.i.facet.IFacet facet)
void	addRecordProperties(Map newProperties)
void	clearFacets()
void	clearProperties()
Object	clone()
String	getCompositionUUID() Composition UUID
String	getContent()
int	getDataEntryID() Data entry (tuples) in a dataset, i.e.
int	getDatasetID()
Iterable<net.idea.modbcum.i.facet.IFacet>	getFacets()
String	getFormat()
String	getFormula()
int	getIdchemical()
int	getIdstructure()
String	getInchi()
String	getInchiKey()
int	getNumberOfProperties()
Iterable<Property>	getRecordProperties()
Object	getRecordProperty(Property key)
ILiteratureEntry	getReference()
String	getSmiles()
IStructureRecord.STRUC_TYPE	getType()
String	getWritableContent()
boolean	isHidden()
boolean	isSelected()
void	removeFacet(net.idea.modbcum.i.facet.IFacet facet)
Object	removeRecordProperty(Property key)
void	setCompositionUUID(String compositionUUID)
void	setContent(String content)
void	setDataEntryID(int id)
void	setDatasetID(int id)
void	setFormat(String format)
void	setFormula(String formula)
void	setHidden(boolean hidden)
void	setIdchemical(int idchemical)
void	setIdstructure(int idstructure)
void	setInchi(String inchi)
void	setInchiKey(String key)
void	setRecordProperty(Property key, Object value)
void	setReference(ILiteratureEntry reference)
void	setSelected(boolean value)
void	setSmiles(String smiles)
void	setType(IStructureRecord.STRUC_TYPE type)
void	setUsePreferedStructure(boolean value)
String	toJSON(String substanceURI, String component)
boolean	usePreferedStructure()

Methods inherited from class ambit2.base.relation.AbstractRelation

clear, getFirstStructure, getName, getRelation, getRelationType, getSecondStructure, setFirstStructure, setName, setRelation, setRelationType, setSecondStructure

Methods inherited from class java.lang.Object

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

Methods inherited from interface ambit2.base.interfaces.IStructureRecord

clear

Field Detail

hidden

protected boolean hidden

compositionUUID

protected String compositionUUID

Constructor Detail

CompositionRelation

public CompositionRelation(SubstanceRecord structure1,
                           IStructureRecord structure2,
                           Proportion proportion)

CompositionRelation

public CompositionRelation(SubstanceRecord structure1,
                           IStructureRecord structure2,
                           STRUCTURE_RELATION type,
                           Proportion proportion)

Method Detail

isHidden

public boolean isHidden()

setHidden

public void setHidden(boolean hidden)

getCompositionUUID

public String getCompositionUUID()

Composition UUID

Returns:

setCompositionUUID

public void setCompositionUUID(String compositionUUID)

getFormula

public String getFormula()

Specified by:

getFormula in interface IChemical

setFormula

public void setFormula(String formula)

Specified by:

setFormula in interface IChemical

getSmiles

public String getSmiles()

Specified by:

getSmiles in interface IChemical

setSmiles

public void setSmiles(String smiles)

Specified by:

setSmiles in interface IChemical

getInchi

public String getInchi()

Specified by:

getInchi in interface IChemical

setInchi

public void setInchi(String inchi)

Specified by:

setInchi in interface IChemical

getInchiKey

public String getInchiKey()

Specified by:

getInchiKey in interface IChemical

setInchiKey

public void setInchiKey(String key)

Specified by:

setInchiKey in interface IChemical

getIdchemical

public int getIdchemical()

Specified by:

getIdchemical in interface IChemical

setIdchemical

public void setIdchemical(int idchemical)

Specified by:

setIdchemical in interface IChemical

getFormat

public String getFormat()

Specified by:

getFormat in interface IStructureRecord

setFormat

public void setFormat(String format)

Specified by:

setFormat in interface IStructureRecord

getIdstructure

public int getIdstructure()

Specified by:

getIdstructure in interface IStructureRecord

setIdstructure

public void setIdstructure(int idstructure)

Specified by:

setIdstructure in interface IStructureRecord

getContent

public String getContent()

Specified by:

getContent in interface IStructureRecord

setContent

public void setContent(String content)

Specified by:

setContent in interface IStructureRecord

isSelected

public boolean isSelected()

Specified by:

isSelected in interface IStructureRecord

setSelected

public void setSelected(boolean value)

Specified by:

setSelected in interface IStructureRecord

getNumberOfProperties

public int getNumberOfProperties()

Specified by:

getNumberOfProperties in interface IStructureRecord

getRecordProperties

public Iterable<Property> getRecordProperties()

Specified by:

getRecordProperties in interface IStructureRecord

setRecordProperty

public void setRecordProperty(Property key,
                              Object value)

Specified by:

setRecordProperty in interface IStructureRecord

getRecordProperty

public Object getRecordProperty(Property key)

Specified by:

getRecordProperty in interface IStructureRecord

removeRecordProperty

public Object removeRecordProperty(Property key)

Specified by:

removeRecordProperty in interface IStructureRecord

clearProperties

public void clearProperties()

Specified by:

clearProperties in interface IStructureRecord

addRecordProperties

public void addRecordProperties(Map newProperties)

Specified by:

addRecordProperties in interface IStructureRecord

getWritableContent

public String getWritableContent()

Specified by:

getWritableContent in interface IStructureRecord

getReference

public ILiteratureEntry getReference()

Specified by:

getReference in interface IStructureRecord

setReference

public void setReference(ILiteratureEntry reference)

Specified by:

setReference in interface IStructureRecord

getType

public IStructureRecord.STRUC_TYPE getType()

Specified by:

getType in interface IStructureRecord

setType

public void setType(IStructureRecord.STRUC_TYPE type)

Specified by:

setType in interface IStructureRecord

getDataEntryID

public int getDataEntryID()

Description copied from interface: IStructureRecord

Data entry (tuples) in a dataset, i.e. row identifier

Specified by:

getDataEntryID in interface IStructureRecord

Returns:

setDataEntryID

public void setDataEntryID(int id)

Specified by:

setDataEntryID in interface IStructureRecord

getDatasetID

public int getDatasetID()

Specified by:

getDatasetID in interface IStructureRecord

setDatasetID

public void setDatasetID(int id)

Specified by:

setDatasetID in interface IStructureRecord

usePreferedStructure

public boolean usePreferedStructure()

Specified by:

usePreferedStructure in interface IChemical

Specified by:

usePreferedStructure in interface IStructureRecord

setUsePreferedStructure

public void setUsePreferedStructure(boolean value)

Specified by:

setUsePreferedStructure in interface IChemical

Specified by:

setUsePreferedStructure in interface IStructureRecord

getFacets

public Iterable<net.idea.modbcum.i.facet.IFacet> getFacets()

Specified by:

getFacets in interface IStructureRecord

addFacet

public void addFacet(net.idea.modbcum.i.facet.IFacet facet)

Specified by:

addFacet in interface IStructureRecord

removeFacet

public void removeFacet(net.idea.modbcum.i.facet.IFacet facet)

Specified by:

removeFacet in interface IStructureRecord

clearFacets

public void clearFacets()

Specified by:

clearFacets in interface IStructureRecord

clone

public Object clone()
             throws CloneNotSupportedException

Specified by:

clone in interface IStructureRecord

Overrides:

clone in class Object

Throws:

CloneNotSupportedException

toJSON

public String toJSON(String substanceURI,
                     String component)