ambit2.db.search.structure

Class QuerySimilarityBitset

java.lang.Object

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

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

ambit2.db.search.structure.QuerySimilarity<String,BitSet,net.idea.modbcum.q.conditions.NumberCondition>

ambit2.db.search.structure.QuerySimilarityBitset

All Implemented Interfaces:

Serializable, net.idea.modbcum.i.IParameterizedQuery<String,BitSet,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 QuerySimilarityBitset
extends QuerySimilarity<String,BitSet,net.idea.modbcum.q.conditions.NumberCondition>

Tanimoto similarity of BitSet. Use FingerprintGenerator to obtain Bitset of IAtomContainer.

Author:

Nina Jeliazkova nina@acad.bg order by metric forces filesort! ordering not necessary if results go into query_results table introduce query caching - in this case via BitSet

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 FPTable	mode
protected String	order
protected String	sql_similarity

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
QuerySimilarityBitset()

Method Summary

Modifier and Type	Method and Description
double	calculateMetric(IStructureRecord object)
FPTable	getMode()
List<net.idea.modbcum.i.query.QueryParam>	getParameters()
String	getSQL() select ? as idquery,idchemical,idstructure,1 as selected,Tanimoto as metric
boolean	isPrescreen()
void	setMode(FPTable mode)

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

getThreshold, isForceOrdering, retrieveMetric, setForceOrdering, setThreshold, toString

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, getCondition, getFieldname, getId, getKey, getName, getPage, getPageSize, getValue, isSelected, setCondition, setFieldname, setId, setName, setPage, setPageSize, setSelected, setValue, 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, getId, getKey, getPage, getPageSize, setId, setPage, setPageSize, supportsPaging

Field Detail

mode

protected FPTable mode

order

protected final String order

See Also:

Constant Field Values

sql_similarity

protected final String sql_similarity

See Also:

Constant Field Values

Constructor Detail

QuerySimilarityBitset

public QuerySimilarityBitset()

Method Detail

getMode

public FPTable getMode()

setMode

public void setMode(FPTable mode)

getSQL

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

select ? as idquery,idchemical,idstructure,1 as selected,Tanimoto as metric

Throws:

net.idea.modbcum.i.exceptions.AmbitException

getParameters

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

Throws:

net.idea.modbcum.i.exceptions.AmbitException

isPrescreen

public boolean isPrescreen()

Specified by:

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

Overrides:

isPrescreen in class AbstractStructureQuery<String,BitSet,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<String,BitSet,net.idea.modbcum.q.conditions.NumberCondition>