Package net.bioclipse.managers

Class PubChemManager

java.lang.Object

net.bioclipse.managers.PubChemManager

All Implemented Interfaces:

IBactingManager, net.bioclipse.managers.business.IBioclipseManager

public class PubChemManager
extends Object
implements IBactingManager

Bioclipse manager that provides functionality to interact with the PubChem database.

Constructor Summary

Constructors

Constructor	Description
PubChemManager(String workspaceRoot)	Creates a new PubChemManager.

Method Summary

Modifier and Type	Method	Description
List<String>	doi()	Lists the DOIs of the articles associated to this manager.
net.bioclipse.core.domain.IMolecule	download(Integer cid)
List<net.bioclipse.core.domain.IMolecule>	download(List<Integer> cids)
net.bioclipse.core.domain.IMolecule	download3d(Integer cid)
List<net.bioclipse.core.domain.IMolecule>	download3d(List<Integer> cids)
String	download3dAsString(Integer cid)
String	downloadAsString(Integer cid)
net.bioclipse.rdf.business.IRDFStore	downloadRDF(Integer cid, net.bioclipse.rdf.business.IRDFStore store)
String	getManagerName()
String	loadCompound(int cid, String target)
String	loadCompound3d(int cid, String target)
String	loadCompoundRDF(int cid, String target)
List<Integer>	search(String query)	Searches PubChem for compounds using the given query.

Methods inherited from class java.lang.Object

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

Constructor Details

PubChemManager

public PubChemManager(String workspaceRoot)

Creates a new PubChemManager.

Parameters:

workspaceRoot - location of the workspace, e.g. "."

Method Details

search

public List<Integer> search(String query)
                     throws IOException,
net.bioclipse.core.business.BioclipseException,
org.eclipse.core.runtime.CoreException

Searches PubChem for compounds using the given query.

Parameters:

query - the string to search in PubChem

Returns:

a Java List of PubChem compound identifiers

Throws:

IOException

net.bioclipse.core.business.BioclipseException

org.eclipse.core.runtime.CoreException

getManagerName

public String getManagerName()

Specified by:

getManagerName in interface net.bioclipse.managers.business.IBioclipseManager

doi

public List<String> doi()

Description copied from interface: IBactingManager

Lists the DOIs of the articles associated to this manager.

Specified by:

doi in interface IBactingManager

Returns:

a List of String with DOIs

download

public net.bioclipse.core.domain.IMolecule download(Integer cid)
                                             throws IOException,
net.bioclipse.core.business.BioclipseException,
org.eclipse.core.runtime.CoreException

Throws:

IOException

net.bioclipse.core.business.BioclipseException

org.eclipse.core.runtime.CoreException

downloadAsString

public String downloadAsString(Integer cid)
                        throws IOException,
net.bioclipse.core.business.BioclipseException,
org.eclipse.core.runtime.CoreException

Throws:

IOException

net.bioclipse.core.business.BioclipseException

org.eclipse.core.runtime.CoreException

downloadRDF

public net.bioclipse.rdf.business.IRDFStore downloadRDF(Integer cid,
 net.bioclipse.rdf.business.IRDFStore store)
                                                 throws IOException,
net.bioclipse.core.business.BioclipseException,
org.eclipse.core.runtime.CoreException

Throws:

IOException

net.bioclipse.core.business.BioclipseException

org.eclipse.core.runtime.CoreException

download3d

public net.bioclipse.core.domain.IMolecule download3d(Integer cid)
                                               throws IOException,
net.bioclipse.core.business.BioclipseException,
org.eclipse.core.runtime.CoreException

Throws:

IOException

net.bioclipse.core.business.BioclipseException

org.eclipse.core.runtime.CoreException

download3dAsString

public String download3dAsString(Integer cid)
                          throws IOException,
net.bioclipse.core.business.BioclipseException,
org.eclipse.core.runtime.CoreException

Throws:

IOException

net.bioclipse.core.business.BioclipseException

org.eclipse.core.runtime.CoreException

download

public List<net.bioclipse.core.domain.IMolecule> download(List<Integer> cids)
                                                   throws IOException,
net.bioclipse.core.business.BioclipseException,
org.eclipse.core.runtime.CoreException

Throws:

IOException

net.bioclipse.core.business.BioclipseException

org.eclipse.core.runtime.CoreException

download3d

public List<net.bioclipse.core.domain.IMolecule> download3d(List<Integer> cids)
                                                     throws IOException,
net.bioclipse.core.business.BioclipseException,
org.eclipse.core.runtime.CoreException

Throws:

IOException

net.bioclipse.core.business.BioclipseException

org.eclipse.core.runtime.CoreException

loadCompound

public String loadCompound(int cid,
 String target)
                    throws IOException,
net.bioclipse.core.business.BioclipseException,
org.eclipse.core.runtime.CoreException

Throws:

IOException

net.bioclipse.core.business.BioclipseException

org.eclipse.core.runtime.CoreException

loadCompound3d

public String loadCompound3d(int cid,
 String target)
                      throws IOException,
net.bioclipse.core.business.BioclipseException,
org.eclipse.core.runtime.CoreException

Throws:

IOException

net.bioclipse.core.business.BioclipseException

org.eclipse.core.runtime.CoreException

loadCompoundRDF

public String loadCompoundRDF(int cid,
 String target)
                       throws IOException,
net.bioclipse.core.business.BioclipseException,
org.eclipse.core.runtime.CoreException

Throws:

IOException

net.bioclipse.core.business.BioclipseException

org.eclipse.core.runtime.CoreException