ambit2.pubchem

Class NCISearchProcessor

java.lang.Object

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

ambit2.pubchem.HTTPRequest<String,String>

ambit2.pubchem.NCISearchProcessor

All Implemented Interfaces:

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

public class NCISearchProcessor
extends HTTPRequest<String,String>

The general format of the URLS are http://cactus.nci.nih.gov/chemical/structure/{identifier}/{method} Allowed identifier values are: SMILES, Std. InChI/InChIKey (~50 million InChIKeys are available for lookup), chemical names (~70 million), NCI/CADD Identifier (FICuS, uuuuu), RN numbers Methods are currently /smiles, /inchi, /inchikey, /names,/image, /ficus, /ficts, and /uuuuu but there is more to come

Author:

nina

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	NCISearchProcessor.METHODS

Field Summary

Fields

Modifier and Type	Field and Description
protected String	host
protected String	nci_url
protected NCISearchProcessor.METHODS	option
protected long	wait_ms

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
NCISearchProcessor()

Method Summary

Modifier and Type	Method and Description
String	getHost()
NCISearchProcessor.METHODS	getOption()
long	getWait_ms()
protected String	parseInput(String target, InputStream in)
protected void	prepareOutput(String target, OutputStream out)
String	process(String target)
void	setHost(String host)
void	setOption(NCISearchProcessor.METHODS option)
void	setWait_ms(long wait_ms)

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

wait_ms

protected long wait_ms

nci_url

protected String nci_url

host

protected String host

option

protected NCISearchProcessor.METHODS option

Constructor Detail

NCISearchProcessor

public NCISearchProcessor()

Method Detail

getWait_ms

public long getWait_ms()

setWait_ms

public void setWait_ms(long wait_ms)

getHost

public String getHost()

setHost

public void setHost(String host)

getOption

public NCISearchProcessor.METHODS getOption()

setOption

public void setOption(NCISearchProcessor.METHODS option)

parseInput

protected String parseInput(String target,
                            InputStream in)
                     throws ProcessorException

Specified by:

parseInput in class HTTPRequest<String,String>

Throws:

ProcessorException

process

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

Specified by:

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

Overrides:

process in class HTTPRequest<String,String>

Throws:

net.idea.modbcum.i.exceptions.AmbitException

prepareOutput

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

Specified by:

prepareOutput in class HTTPRequest<String,String>

Throws:

ProcessorException