ambit2.pubchem

Class EntrezSearchProcessor

java.lang.Object

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

ambit2.pubchem.HTTPRequest<String,List<IStructureRecord>>

ambit2.pubchem.EntrezSearchProcessor

All Implemented Interfaces:

Serializable, net.idea.modbcum.i.processors.IProcessor<String,List<IStructureRecord>>

public class EntrezSearchProcessor
extends HTTPRequest<String,List<IStructureRecord>>

Searches PubChem for structures given search terms (via Entrez) and returns SDF files.

Author:

nina

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static String	entrezURL
protected EntrezESearchParser	parser
protected PUGProcessor	pug
protected boolean	retrieve_sdf

Fields inherited from class ambit2.pubchem.HTTPRequest

cancelled, httpMethod, maxretry, timeout, url

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

enabled, logger, propertyChangeSupport

Constructor Summary

Constructors

Constructor and Description
EntrezSearchProcessor()

Method Summary

Modifier and Type	Method and Description
protected String	format(IStructureRecord record, String source, String einecs)
boolean	isRetrieve_conformers()
boolean	isRetrieve_sdf()
protected List<IStructureRecord>	parseInput(String target, InputStream in)
protected void	prepareOutput(String target, OutputStream out)
List<IStructureRecord>	process(String target)
void	setRetrieve_conformers(boolean retrieve_conformers)
void	setRetrieve_sdf(boolean retrieve_sdf) If true (default) retrieves SDF via two stage query (Entrez + PUG).

Methods inherited from class ambit2.pubchem.HTTPRequest

getHttpMethod, getTimeout, getUrl, isCancelled, setCancelled, setHttpMethod, setTimeout, setUrl

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

addPropertyChangeListener, addPropertyChangeListener, close, getID, isEnabled, open, removePropertyChangeListener, removePropertyChangeListener, setEnabled, toString

Methods inherited from class java.lang.Object

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

Field Detail

entrezURL

public static String entrezURL

parser

protected final EntrezESearchParser parser

pug

protected final PUGProcessor pug

retrieve_sdf

protected boolean retrieve_sdf

Constructor Detail

EntrezSearchProcessor

public EntrezSearchProcessor()

Method Detail

isRetrieve_conformers

public boolean isRetrieve_conformers()

setRetrieve_conformers

public void setRetrieve_conformers(boolean retrieve_conformers)

isRetrieve_sdf

public boolean isRetrieve_sdf()

setRetrieve_sdf

public void setRetrieve_sdf(boolean retrieve_sdf)

If true (default) retrieves SDF via two stage query (Entrez + PUG). if false, retrieves only Pubchem CIDs by Entrez query.

Parameters:

retrieve_sdf -

parseInput

protected List<IStructureRecord> parseInput(String target,
                                            InputStream in)
                                     throws ProcessorException

Specified by:

parseInput in class HTTPRequest<String,List<IStructureRecord>>

Throws:

ProcessorException

prepareOutput

protected void prepareOutput(String target,
                             OutputStream out)
                      throws ProcessorException

Specified by:

prepareOutput in class HTTPRequest<String,List<IStructureRecord>>

Throws:

ProcessorException

process

public List<IStructureRecord> process(String target)
                               throws net.idea.modbcum.i.exceptions.AmbitException

Specified by:

process in interface net.idea.modbcum.i.processors.IProcessor<String,List<IStructureRecord>>

Overrides:

process in class HTTPRequest<String,List<IStructureRecord>>

Throws:

net.idea.modbcum.i.exceptions.AmbitException

format

protected String format(IStructureRecord record,
                        String source,
                        String einecs)