ambit2.db.reporters

Class CSVReporter<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,Output>

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

ambit2.db.reporters.CSVReporter<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 CSVReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>>
extends QueryHeaderReporter<Q,Writer>

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected SubstanceEndpointsBundle[]	bundles
protected String[]	folders
protected String	licenseColumn
protected String	lineseparator
protected int	numberofHeaderLines
protected String	separator
protected Property	similarityColumn
protected String	urlPrefix
protected boolean	writeCompoundURI

Fields inherited from class ambit2.db.reporters.QueryHeaderReporter

groupProperties, header, includeMol, 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
CSVReporter()
CSVReporter(String baseRef, Template template)
CSVReporter(String baseRef, Template template, Profile groupedProperties, String urlPrefix)
CSVReporter(String baseRef, Template template, Profile groupedProperties, String[] folders, SubstanceEndpointsBundle[] bundles, String urlPrefix, boolean includeMol)

Method Summary

Modifier and Type	Method and Description
protected void	configureCollectionProcessors(String baseURI)
protected void	configurePropertyProcessors()
void	footer(Writer output, Q query)
SubstanceEndpointsBundle[]	getBundles()
String	getFileExtension()
String[]	getFolders()
int	getNumberofHeaderLines()
String	getSeparator()
Property	getSimilarityColumn()
protected String	getUnits(Property p)
protected String	getURI(IStructureRecord item)
String	getUrlPrefix()
void	header(Writer writer, Q query)
boolean	isWriteCompoundURI()
void	open()
Object	processItem(IStructureRecord item)
void	setBundles(SubstanceEndpointsBundle[] bundles)
void	setFolders(String[] folders)
void	setLicenseURI(String licenseURI)
void	setNumberofHeaderLines(int numberofHeaderLines)
void	setSeparator(String separator)
void	setSimilarityColumn(Property similarityColumn)
void	setUrlPrefix(String urlPrefix)
void	setWriteCompoundURI(boolean writeCompoundURI)
protected List<Property>	template2Header(Template template, boolean propertiesOnly)
protected void	writeHeader(Writer writer)

Methods inherited from class ambit2.db.reporters.QueryHeaderReporter

configureProcessors, getGroupProperties, getHeader, getTemplate, isIncludeMol, setGroupProperties, setTemplate

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, 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

numberofHeaderLines

protected int numberofHeaderLines

writeCompoundURI

protected boolean writeCompoundURI

similarityColumn

protected Property similarityColumn

licenseColumn

protected String licenseColumn

folders

protected String[] folders

bundles

protected SubstanceEndpointsBundle[] bundles

urlPrefix

protected String urlPrefix

separator

protected String separator

lineseparator

protected String lineseparator

Constructor Detail

CSVReporter

public CSVReporter()

CSVReporter

public CSVReporter(String baseRef,
                   Template template)

CSVReporter

public CSVReporter(String baseRef,
                   Template template,
                   Profile groupedProperties,
                   String urlPrefix)

CSVReporter

public CSVReporter(String baseRef,
                   Template template,
                   Profile groupedProperties,
                   String[] folders,
                   SubstanceEndpointsBundle[] bundles,
                   String urlPrefix,
                   boolean includeMol)

Method Detail

getBundles

public SubstanceEndpointsBundle[] getBundles()

setBundles

public void setBundles(SubstanceEndpointsBundle[] bundles)

getFolders

public String[] getFolders()

setFolders

public void setFolders(String[] folders)

getSimilarityColumn

public Property getSimilarityColumn()

setSimilarityColumn

public void setSimilarityColumn(Property similarityColumn)

isWriteCompoundURI

public boolean isWriteCompoundURI()

setWriteCompoundURI

public void setWriteCompoundURI(boolean writeCompoundURI)

getNumberofHeaderLines

public int getNumberofHeaderLines()

setNumberofHeaderLines

public void setNumberofHeaderLines(int numberofHeaderLines)

getSeparator

public String getSeparator()

setSeparator

public void setSeparator(String separator)

getUrlPrefix

public String getUrlPrefix()

setUrlPrefix

public void setUrlPrefix(String urlPrefix)

configureCollectionProcessors

protected void configureCollectionProcessors(String baseURI)

setLicenseURI

public void setLicenseURI(String licenseURI)

Specified by:

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

Overrides:

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

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>

template2Header

protected List<Property> template2Header(Template template,
                                         boolean propertiesOnly)

Overrides:

template2Header in class QueryHeaderReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>,Writer>

getUnits

protected String getUnits(Property p)

writeHeader

protected void writeHeader(Writer writer)
                    throws IOException

Throws:

IOException

header

public void header(Writer writer,
                   Q query)

Specified by:

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

getURI

protected String getURI(IStructureRecord item)

processItem

public Object processItem(IStructureRecord item)
                   throws Exception

Specified by:

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

Throws:

Exception

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

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>

configurePropertyProcessors

protected void configurePropertyProcessors()

Overrides:

configurePropertyProcessors in class QueryHeaderReporter<Q extends net.idea.modbcum.i.IQueryRetrieval<IStructureRecord>,Writer>