ambit2.db.search.structure

Class QuerySimilarityStructure

java.lang.Object

ambit2.db.search.AbstractQuery<F,T,C,IStructureRecord>

ambit2.db.search.structure.AbstractStructureQuery<F,T,C>

ambit2.db.search.structure.QuerySimilarity<ClassHolder,org.openscience.cdk.interfaces.IAtomContainerSet,net.idea.modbcum.q.conditions.NumberCondition>

ambit2.db.search.structure.QuerySimilarityStructure

All Implemented Interfaces:

Serializable, net.idea.modbcum.i.IParameterizedQuery<ClassHolder,org.openscience.cdk.interfaces.IAtomContainerSet,net.idea.modbcum.q.conditions.NumberCondition>, net.idea.modbcum.i.IQueryObject<IStructureRecord>, net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>, net.idea.modbcum.i.IRetrieval<IStructureRecord>, net.idea.modbcum.i.IStatement

public class QuerySimilarityStructure
extends QuerySimilarity<ClassHolder,org.openscience.cdk.interfaces.IAtomContainerSet,net.idea.modbcum.q.conditions.NumberCondition>

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class ambit2.db.search.structure.AbstractStructureQuery

AbstractStructureQuery.FIELD_NAMES

Field Summary

Fields

Modifier and Type	Field and Description
protected FingerprintGenerator	g
static ClassHolder[]	methods
protected MoleculeReader	molReader
protected AbstractStructureQuery	query
protected org.openscience.cdk.isomorphism.UniversalIsomorphismTester	uit

Fields inherited from class ambit2.db.search.structure.QuerySimilarity

forceOrdering, threshold

Fields inherited from class ambit2.db.search.structure.AbstractStructureQuery

chemicalsOnly, group, nanomaterial, order_descendant, where_group

Fields inherited from class ambit2.db.search.AbstractQuery

condition, fieldname, id, logger, maxRecords, name, page, selected, value

Fields inherited from interface net.idea.modbcum.i.IQueryRetrieval

NaN

Constructor Summary

Constructors

Constructor and Description
QuerySimilarityStructure()

Method Summary

Modifier and Type	Method and Description
double	calculateMetric(IStructureRecord object)
net.idea.modbcum.q.conditions.NumberCondition	getCondition()
Integer	getId()
String	getName()
List<net.idea.modbcum.i.query.QueryParam>	getParameters()
String	getSQL()
double	getThreshold()
boolean	isForceOrdering()
boolean	isPrescreen()
void	setCondition(net.idea.modbcum.q.conditions.NumberCondition condition)
void	setFieldname(ClassHolder method)
void	setForceOrdering(boolean forceOrdering)
void	setId(Integer id)
void	setName(String name)
void	setStructure(org.openscience.cdk.interfaces.IAtomContainer structure)
void	setThreshold(double threshold)
void	setValue(org.openscience.cdk.interfaces.IAtomContainerSet set)
String	toString()

Methods inherited from class ambit2.db.search.structure.QuerySimilarity

retrieveMetric

Methods inherited from class ambit2.db.search.structure.AbstractStructureQuery

getObject, isChemicalsOnly, isNanomaterial, isOrder_descendant, isPreferredStructure, retrieveStrucType, retrieveValue, setChemicalsOnly, setNanomaterial, setOrder_descendant

Methods inherited from class ambit2.db.search.AbstractQuery

getCategory, getFieldname, getKey, getPage, getPageSize, getValue, isSelected, setPage, setPageSize, setSelected, stringify, supportsPaging, test

Methods inherited from class java.lang.Object

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

Methods inherited from interface net.idea.modbcum.i.IQueryObject

getCategory, getKey, getPage, getPageSize, setPage, setPageSize, supportsPaging

Field Detail

query

protected AbstractStructureQuery query

g

protected FingerprintGenerator g

molReader

protected MoleculeReader molReader

uit

protected org.openscience.cdk.isomorphism.UniversalIsomorphismTester uit

methods

public static ClassHolder[] methods

Constructor Detail

QuerySimilarityStructure

public QuerySimilarityStructure()

Method Detail

setFieldname

public void setFieldname(ClassHolder method)

Specified by:

setFieldname in interface net.idea.modbcum.i.IParameterizedQuery<ClassHolder,org.openscience.cdk.interfaces.IAtomContainerSet,net.idea.modbcum.q.conditions.NumberCondition>

Overrides:

setFieldname in class AbstractQuery<ClassHolder,org.openscience.cdk.interfaces.IAtomContainerSet,net.idea.modbcum.q.conditions.NumberCondition,IStructureRecord>

setForceOrdering

public void setForceOrdering(boolean forceOrdering)

Overrides:

setForceOrdering in class QuerySimilarity<ClassHolder,org.openscience.cdk.interfaces.IAtomContainerSet,net.idea.modbcum.q.conditions.NumberCondition>

isForceOrdering

public boolean isForceOrdering()

Overrides:

isForceOrdering in class QuerySimilarity<ClassHolder,org.openscience.cdk.interfaces.IAtomContainerSet,net.idea.modbcum.q.conditions.NumberCondition>

getParameters

public List<net.idea.modbcum.i.query.QueryParam> getParameters()
                                                        throws net.idea.modbcum.i.exceptions.AmbitException

Throws:

net.idea.modbcum.i.exceptions.AmbitException

setThreshold

public void setThreshold(double threshold)

Overrides:

setThreshold in class QuerySimilarity<ClassHolder,org.openscience.cdk.interfaces.IAtomContainerSet,net.idea.modbcum.q.conditions.NumberCondition>

getThreshold

public double getThreshold()

Overrides:

getThreshold in class QuerySimilarity<ClassHolder,org.openscience.cdk.interfaces.IAtomContainerSet,net.idea.modbcum.q.conditions.NumberCondition>

setCondition

public void setCondition(net.idea.modbcum.q.conditions.NumberCondition condition)

Specified by:

setCondition in interface net.idea.modbcum.i.IParameterizedQuery<ClassHolder,org.openscience.cdk.interfaces.IAtomContainerSet,net.idea.modbcum.q.conditions.NumberCondition>

Overrides:

setCondition in class AbstractQuery<ClassHolder,org.openscience.cdk.interfaces.IAtomContainerSet,net.idea.modbcum.q.conditions.NumberCondition,IStructureRecord>

getCondition

public net.idea.modbcum.q.conditions.NumberCondition getCondition()

Specified by:

getCondition in interface net.idea.modbcum.i.IParameterizedQuery<ClassHolder,org.openscience.cdk.interfaces.IAtomContainerSet,net.idea.modbcum.q.conditions.NumberCondition>

Overrides:

getCondition in class AbstractQuery<ClassHolder,org.openscience.cdk.interfaces.IAtomContainerSet,net.idea.modbcum.q.conditions.NumberCondition,IStructureRecord>

getSQL

public String getSQL()
              throws net.idea.modbcum.i.exceptions.AmbitException

Throws:

net.idea.modbcum.i.exceptions.AmbitException

setStructure

public void setStructure(org.openscience.cdk.interfaces.IAtomContainer structure)

setValue

public void setValue(org.openscience.cdk.interfaces.IAtomContainerSet set)

Specified by:

setValue in interface net.idea.modbcum.i.IParameterizedQuery<ClassHolder,org.openscience.cdk.interfaces.IAtomContainerSet,net.idea.modbcum.q.conditions.NumberCondition>

Overrides:

setValue in class AbstractQuery<ClassHolder,org.openscience.cdk.interfaces.IAtomContainerSet,net.idea.modbcum.q.conditions.NumberCondition,IStructureRecord>

setId

public void setId(Integer id)

Specified by:

setId in interface net.idea.modbcum.i.IQueryObject<IStructureRecord>

Overrides:

setId in class AbstractQuery<ClassHolder,org.openscience.cdk.interfaces.IAtomContainerSet,net.idea.modbcum.q.conditions.NumberCondition,IStructureRecord>

getId

public Integer getId()

Specified by:

getId in interface net.idea.modbcum.i.IQueryObject<IStructureRecord>

Overrides:

getId in class AbstractQuery<ClassHolder,org.openscience.cdk.interfaces.IAtomContainerSet,net.idea.modbcum.q.conditions.NumberCondition,IStructureRecord>

getName

public String getName()

Overrides:

getName in class AbstractQuery<ClassHolder,org.openscience.cdk.interfaces.IAtomContainerSet,net.idea.modbcum.q.conditions.NumberCondition,IStructureRecord>

setName

public void setName(String name)

Overrides:

setName in class AbstractQuery<ClassHolder,org.openscience.cdk.interfaces.IAtomContainerSet,net.idea.modbcum.q.conditions.NumberCondition,IStructureRecord>

toString

public String toString()

Overrides:

toString in class QuerySimilarity<ClassHolder,org.openscience.cdk.interfaces.IAtomContainerSet,net.idea.modbcum.q.conditions.NumberCondition>

isPrescreen

public boolean isPrescreen()

Specified by:

isPrescreen in interface net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>

Overrides:

isPrescreen in class AbstractStructureQuery<ClassHolder,org.openscience.cdk.interfaces.IAtomContainerSet,net.idea.modbcum.q.conditions.NumberCondition>

calculateMetric

public double calculateMetric(IStructureRecord object)

Specified by:

calculateMetric in interface net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>

Overrides:

calculateMetric in class AbstractStructureQuery<ClassHolder,org.openscience.cdk.interfaces.IAtomContainerSet,net.idea.modbcum.q.conditions.NumberCondition>