ambit2.db.reporters

Class SDFReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>>

java.lang.Object

net.idea.modbcum.p.DefaultAmbitProcessor<Target,Result>

net.idea.modbcum.p.AbstractDBProcessor<Q,Output>

net.idea.modbcum.r.QueryAbstractReporter<T,Q,Output>

net.idea.modbcum.r.QueryReporter<IStructureRecord,Q,Output>

ambit2.db.reporters.QueryStructureReporter<Q,Writer>

ambit2.db.reporters.SDFReporter<Q>

All Implemented Interfaces:

Serializable, net.idea.modbcum.i.IDBProcessor<Q,Writer>, net.idea.modbcum.i.processors.IProcessor<Q,Writer>, net.idea.modbcum.i.reporter.Reporter<Q,Writer>

public class SDFReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>>
extends QueryStructureReporter<Q,Writer>

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected boolean	changeLineSeparators
protected boolean	first
protected Profile	groupProperties
protected boolean	MOLONLY
protected MoleculeReader	reader
protected Template	template

Fields inherited from class net.idea.modbcum.r.QueryAbstractReporter

autoCommit, batch, licenseURI, maxRecords, output, processors, showFooter, showHeader, startTime, timeout

Fields inherited from class net.idea.modbcum.p.AbstractDBProcessor

closeConnection, connection

Fields inherited from class net.idea.modbcum.p.DefaultAmbitProcessor

enabled, logger, propertyChangeSupport

Constructor Summary

Constructors

Constructor and Description
SDFReporter()
SDFReporter(Template template, Profile groupedProperties, boolean changeLineSeparator)
SDFReporter(Template template, Profile groupedProperties, boolean molOnly, boolean changeLineSeparator)

Method Summary

Modifier and Type	Method and Description
void	footer(Writer output, Q query)
String	getFileExtension()
Profile	getGroupProperties()
protected String	getSDFContent(IStructureRecord item)
Template	getTemplate()
void	header(Writer output, Q query)
boolean	isChangeLineSeparators()
boolean	isMOLONLY()
void	open()
Object	processItem(IStructureRecord item)
void	setChangeLineSeparators(boolean changeLineSeparators)
void	setGroupProperties(Profile gp)
void	setMOLONLY(boolean molonly)
void	setTemplate(Template template)

Methods inherited from class ambit2.db.reporters.QueryStructureReporter

createBatch, isIncludeLicenseInTextFiles

Methods inherited from class net.idea.modbcum.r.QueryAbstractReporter

getLicenseURI, getMaxRecords, getOutput, getProcessors, getStartTime, getTimeout, isAutoCommit, isShowFooter, isShowHeader, process, setAutoCommit, setCloseConnection, setLicenseURI, setMaxRecords, setOutput, setProcessors, setShowFooter, setShowHeader, setStartTime, setTimeout, wrapup

Methods inherited from class net.idea.modbcum.p.AbstractDBProcessor

close, getConnection, isCloseConnection, isEnabled, setConnection

Methods inherited from class net.idea.modbcum.p.DefaultAmbitProcessor

addPropertyChangeListener, addPropertyChangeListener, getID, removePropertyChangeListener, removePropertyChangeListener, setEnabled, toString

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.reporter.Reporter

close

Methods inherited from interface net.idea.modbcum.i.processors.IProcessor

getID, isEnabled, setEnabled

Field Detail

template

protected Template template

MOLONLY

protected boolean MOLONLY

reader

protected MoleculeReader reader

first

protected boolean first

changeLineSeparators

protected boolean changeLineSeparators

groupProperties

protected Profile groupProperties

Constructor Detail

SDFReporter

public SDFReporter()

SDFReporter

public SDFReporter(Template template,
                   Profile groupedProperties,
                   boolean changeLineSeparator)

SDFReporter

public SDFReporter(Template template,
                   Profile groupedProperties,
                   boolean molOnly,
                   boolean changeLineSeparator)

Method Detail

isChangeLineSeparators

public boolean isChangeLineSeparators()

setChangeLineSeparators

public void setChangeLineSeparators(boolean changeLineSeparators)

getGroupProperties

public Profile getGroupProperties()

setGroupProperties

public void setGroupProperties(Profile gp)

isMOLONLY

public boolean isMOLONLY()

setMOLONLY

public void setMOLONLY(boolean molonly)

getTemplate

public Template getTemplate()

setTemplate

public void setTemplate(Template template)

processItem

public Object processItem(IStructureRecord item)
                   throws net.idea.modbcum.i.exceptions.AmbitException

Specified by:

processItem in class net.idea.modbcum.r.QueryAbstractReporter<IStructureRecord,Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>,Writer>

Throws:

net.idea.modbcum.i.exceptions.AmbitException

getSDFContent

protected String getSDFContent(IStructureRecord item)
                        throws net.idea.modbcum.i.exceptions.AmbitException

Throws:

net.idea.modbcum.i.exceptions.AmbitException

open

public void open()
          throws net.idea.modbcum.i.exceptions.DbAmbitException

Specified by:

open in interface net.idea.modbcum.i.processors.IProcessor<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>,Writer>

Overrides:

open in class net.idea.modbcum.p.DefaultAmbitProcessor<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>,Writer>

Throws:

net.idea.modbcum.i.exceptions.DbAmbitException

footer

public void footer(Writer output,
                   Q query)

Specified by:

footer in class net.idea.modbcum.r.QueryAbstractReporter<IStructureRecord,Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>,Writer>

header

public void header(Writer output,
                   Q query)

Specified by:

header in class net.idea.modbcum.r.QueryAbstractReporter<IStructureRecord,Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>,Writer>

getFileExtension

public String getFileExtension()

Specified by:

getFileExtension in interface net.idea.modbcum.i.reporter.Reporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>,Writer>

Overrides:

getFileExtension in class net.idea.modbcum.r.QueryAbstractReporter<IStructureRecord,Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>,Writer>