org.opentox.toxotis.core
Interface IDescriptorCalculation

All Known Implementing Classes:
Compound, Conformer, DescriptorCaclulation

public interface IDescriptorCalculation

An interface implemented by OpenTox components on which descriptor calculation can be applied such as Datasets and Compounds.

Author:
Pantelis Sopasakis, Charalampos Chomenides

Method Summary
 Task calculateDescriptors(VRI descriptorCalculationAlgorithm, AuthenticationToken token)
          Calculates all available descriptors using a remote descriptor calculation service.
 Task calculateDescriptors(VRI descriptorCalculationAlgorithm, AuthenticationToken token, String... serviceConfiguration)
          Calculates descriptors for this compound empoying a descriptor calculation web service at the specified location.
 Future<VRI> futureCDKPhysChemDescriptors(AuthenticationToken token, VRI datasetService)
           
 Future<VRI> futureDescriptors(VRI descriptorCalculationAlgorithm, AuthenticationToken token, ExecutorService executor, String... serviceConfiguration)
          Use a remote Service to calculate (some or all available) descriptors for a chemical compound.
 Future<VRI> futureDescriptors(VRI descriptorCalculationAlgorithm, AuthenticationToken token, String... serviceConfiguration)
           
 Future<VRI> futureDescriptors(VRI descriptorCalculationAlgorithm, AuthenticationToken token, VRI datasetService)
          Calculate descriptors for a chemical compound or a dataset providing the URI of the descriptor calculation algorithm, the URI of a dataset service where the result should be stored and an authentication token for accessing the various services.
 Future<VRI> futureJoeLibDescriptors(AuthenticationToken token, VRI datasetService)
           
 

Method Detail

calculateDescriptors

Task calculateDescriptors(VRI descriptorCalculationAlgorithm,
                          AuthenticationToken token,
                          String... serviceConfiguration)
                          throws ServiceInvocationException
Calculates descriptors for this compound empoying a descriptor calculation web service at the specified location. The method accepts a set or parameters as a String array (String[]) for fine tuning of the remote service.

Parameters:
descriptorCalculationAlgorithm - A descriptor calculation algorithm. Some descriptor calculation algorithm URIs are found in the collection org.opentox.toxotis.client.collection. Services.DescriptorCalculation such as TUM's implementation using CDK and JOELib descriptors.
token - Token used to authenticate the client and grant it access to the various OpenTox resources.
serviceConfiguration - A string array (String[]) used for fine tuning of the remote service. Successive pairs of values act as a parameter name - parameter value pair which is posted to the remote service.
Returns:
The task returned by the remote service that will be used to monitor the progress of the descriptor calculation process.
Throws:
ToxOtisException - In case some communication or connection error occurs between the client and the descriptor calculation service or the stream cannot open or close.
ServiceInvocationException

calculateDescriptors

Task calculateDescriptors(VRI descriptorCalculationAlgorithm,
                          AuthenticationToken token)
                          throws ServiceInvocationException
Calculates all available descriptors using a remote descriptor calculation service.

Parameters:
descriptorCalculationAlgorithm - A descriptor calculation algorithm. Some descriptor calculation algorithm URIs are found in the collection org.opentox.toxotis.client.collection. Services.DescriptorCalculation such as TUM's implementation using CDK and JOELib descriptors.
token - Token used to authenticate the client and grant it access to the various OpenTox resources.
Returns:
The task returned by the remote service that will be used to monitor the progress of the descriptor calculation process.
Throws:
ToxOtisException - In case some communication or connection error occurs between the client and the descriptor calculation service or the stream cannot open or close.
ServiceInvocationException

futureDescriptors

Future<VRI> futureDescriptors(VRI descriptorCalculationAlgorithm,
                              AuthenticationToken token,
                              ExecutorService executor,
                              String... serviceConfiguration)
Use a remote Service to calculate (some or all available) descriptors for a chemical compound. Such processes might take long to complete so are usually executed asynchronously or put in an execution pool.

Parameters:
descriptorCalculationAlgorithm - The URI of an OpenTox descriptor calculation algorithm. A compound or a dataset is posted to a descriptor calculation algorithm and the expected result is a dataset containing the submitted compound(s) and the calculated descriptor values for each compound.
token - Authentication token used for accessing the descriptor calculation service.
executor - An executor used to sumbit the thread in. Be aware that the executor is not shutdown in this method so it is up to the user whether it should be shutdown or not.
serviceConfiguration - A string array (String[]) used for fine tuning of the remote service. Successive pairs of values act as a parameter name - parameter value pair which is posted to the remote service. You can choose the features to be calculated using this argument. For instance if you want only the descriptor Zagreb Index calculated, you should set the options to {"ALL","false","ZagrebIndexDescriptor", "true"}.
Returns:
A Future waiting for the background job to complete and and return the URI of a Dataset with the calculated descriptors for this Compound.

futureDescriptors

Future<VRI> futureDescriptors(VRI descriptorCalculationAlgorithm,
                              AuthenticationToken token,
                              VRI datasetService)
                              throws ServiceInvocationException
Calculate descriptors for a chemical compound or a dataset providing the URI of the descriptor calculation algorithm, the URI of a dataset service where the result should be stored and an authentication token for accessing the various services.

Parameters:
descriptorCalculationAlgorithm - URI of an OpenTox descriptor calculation algorithm
token - Authentication token used for accessing the descriptor calculation service.
datasetService - The URI of a dataset service, i.e. a URI of the form http://domain_name.ext:1234/ blah/blah/dataset.
Returns:
A Future result of an asynchronous job initiated
Throws:
ToxOtisException
ServiceInvocationException

futureJoeLibDescriptors

Future<VRI> futureJoeLibDescriptors(AuthenticationToken token,
                                    VRI datasetService)
                                    throws ServiceInvocationException
Throws:
ServiceInvocationException

futureCDKPhysChemDescriptors

Future<VRI> futureCDKPhysChemDescriptors(AuthenticationToken token,
                                         VRI datasetService)
                                         throws ServiceInvocationException
Throws:
ServiceInvocationException

futureDescriptors

Future<VRI> futureDescriptors(VRI descriptorCalculationAlgorithm,
                              AuthenticationToken token,
                              String... serviceConfiguration)
                              throws ServiceInvocationException
Throws:
ServiceInvocationException


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