Package net.bioclipse.managers.cdkdebug

Class CDKDebugManager

java.lang.Object

net.bioclipse.managers.cdkdebug.CDKDebugManager

All Implemented Interfaces:

IBactingManager, net.bioclipse.managers.business.IBioclipseManager

public class CDKDebugManager
extends Object
implements IBactingManager

Bioclipse manager that provides functionality by the Chemistry Development Kit that give access to less used functionality and exposes more details of the underlying data model.

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
String	diff(net.bioclipse.cdk.domain.ICDKMolecule mol, net.bioclipse.cdk.domain.ICDKMolecule mol2)	Returns the differences between the two molecules.
List<String>	doi()	Lists the DOIs of the articles associated to this manager.
String	getManagerName()
String	perceiveCDKAtomTypes(net.bioclipse.core.domain.IMolecule mol)	Returns a string of atom types as recognized by the CDK.

Methods inherited from class java.lang.Object

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

Constructor Details

CDKDebugManager

public CDKDebugManager(String workspaceRoot)

Creates a new CDKDebugManager.

Parameters:

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

Method Details

perceiveCDKAtomTypes

public String perceiveCDKAtomTypes(net.bioclipse.core.domain.IMolecule mol)
                            throws InvocationTargetException

Returns a string of atom types as recognized by the CDK.

Parameters:

mol - molecule for which the atoms are typed

Returns:

a String with the results

Throws:

InvocationTargetException

diff

public String diff(net.bioclipse.cdk.domain.ICDKMolecule mol,
 net.bioclipse.cdk.domain.ICDKMolecule mol2)

Returns the differences between the two molecules.

Parameters:

mol - One of the two ICDKMolecules to compare

mol2 - One of the two ICDKMolecules to compare

Returns:

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