com.chemaxon.overlap.cli.util.pipeline

Class TransformMolecule

java.lang.Object

com.chemaxon.overlap.cli.util.pipeline.TransformMolecule

All Implemented Interfaces:

PipelineStep

public class TransformMolecule
extends Object
implements PipelineStep

Standardize-like Molecule transformation. This step exposes a StandardizerWrapper as a pipeline step.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	TransformMolecule.Method

Constructor Summary

Constructors

Constructor and Description
TransformMolecule()

Method Summary

Modifier and Type	Method and Description
static void	addToLinenote(LinenoteBuilder<PipelineStep> linenoteBuilder)
void	addToPipeline(PipelineContext pipeline) Wire step into the pipeline.
void	cfgxml(String xml)
void	init() Initialize the step.
void	method(TransformMolecule.Method m)
String	toString()

Methods inherited from class java.lang.Object

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

Methods inherited from interface com.chemaxon.overlap.cli.util.pipeline.PipelineStep

close

Constructor Detail

TransformMolecule

public TransformMolecule()

Method Detail

method

public void method(TransformMolecule.Method m)

cfgxml

public void cfgxml(String xml)

init

public void init()
          throws Exception

Description copied from interface: PipelineStep

Initialize the step. Open required files, connections, etc. Be prepared to start stream data from now. Contracts:

• This method might not be invoked during the life cycle of an implementing instance.
• Method PipelineStep.addToPipeline(com.chemaxon.overlap.cli.util.pipeline.PipelineContext) will be invoked before this method.
• File presence, possibly validity checking should be done here.
• Values for single inputs are all set from upstream nodes before invoking this method..
• Outputs are queried after this method returned.
• Method PipelineStep.close() is expected to be invoked sometimes later, regardless of possible error(s) thrown.

Specified by:

init in interface PipelineStep

Throws:

Exception - In case of initialization failure

addToPipeline

public void addToPipeline(PipelineContext pipeline)

Description copied from interface: PipelineStep

Wire step into the pipeline. Contracts:

• Introduce the step using PipelineContext.addStep(com.chemaxon.overlap.cli.util.pipeline.PipelineStep)
• Introduce inputs and outputs. The actual inputs, outputs and their types might depend on the parameterization.
• Invoked before PipelineStep.init().
• Default parameterization is expected to be valid to invoke this method.
• Validity checks based on the parameterization might happen (consistency of the set parameters). Environment (other nodes, file system, etc) based verifications are expected to be executed in PipelineStep.init().
• Apart from interacting with the passed PipelineContext reference this method is side effect free
• Parameterization is expected to be not changed after invoking this method.

Specified by:

addToPipeline in interface PipelineStep

Parameters:

pipeline - Target pipeline.

toString

public String toString()

Overrides:

toString in class Object

addToLinenote

public static void addToLinenote(LinenoteBuilder<PipelineStep> linenoteBuilder)