com.chemaxon.overlap.io

Class MasterStorages.MoleculeCallbackBuilder

java.lang.Object

com.chemaxon.overlap.io.MasterStorages.MoleculeCallbackBuilder

All Implemented Interfaces:

MoleculeCallback

Enclosing class:

MasterStorages

public static class MasterStorages.MoleculeCallbackBuilder
extends Object
implements MoleculeCallback

Molecule callback based builder.

Constructor Summary

Constructors

Constructor and Description
MoleculeCallbackBuilder() Construct new empty builder.

Method Summary

Modifier and Type	Method and Description
MasterMoleculeStorage	build() Create immutable representation.
void	notifyMolecule(int readno, Optional<String> molString, Molecule m, int index) Introduce new processed molecule.
void	notifyParseError(int readno, Optional<String> molString, Throwable t) Notify a parsing error.
void	notifyProcessingError(int readno, Optional<String> molString, Molecule m, Throwable t) Notify a processing error.

Methods inherited from class java.lang.Object

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

Constructor Detail

MoleculeCallbackBuilder

public MoleculeCallbackBuilder()

Construct new empty builder.

Method Detail

notifyMolecule

public void notifyMolecule(int readno,
                           Optional<String> molString,
                           Molecule m,
                           int index)

Description copied from interface: MoleculeCallback

Introduce new processed molecule.

Specified by:

notifyMolecule in interface MoleculeCallback

Parameters:

readno - Read molecule count for this event (0 for the first molecule/record in the file). Note that value does not depend on possible index shift value specified for the import method.

molString - Molecule string from underlying MRecord.getMolString() if applicable

m - The given structure. If standardization was specified invocation is made after standardization. In this case the structure represents the standardized structure. In case the descriptor generation alters the molecule the altered molecule is passed.

index - Internal index which will refer to the given structure

notifyProcessingError

public void notifyProcessingError(int readno,
                                  Optional<String> molString,
                                  Molecule m,
                                  Throwable t)

Description copied from interface: MoleculeCallback

Notify a processing error.

This method is invoked when molecule parse was successfull but processing (standardization, descriptor generation, etc. failed

Specified by:

notifyProcessingError in interface MoleculeCallback

Parameters:

readno - Read molecule count for this event (0 for the first molecule/record in the file). Note that value does not depend on possible index shift value specified for the import method.

molString - Molecule string from underlying MRecord.getMolString() if applicable

m - The given structure when error caught. If standardization was specified and error occured during standardization then the state of the structure (original or partially/fully standardized) depends of the internal contracts realized by Standardizer.

t - Processing error

notifyParseError

public void notifyParseError(int readno,
                             Optional<String> molString,
                             Throwable t)

Description copied from interface: MoleculeCallback

Notify a parsing error.

This method is invoked when molecule parse from String format failed.

Specified by:

notifyParseError in interface MoleculeCallback

Parameters:

readno - Read molecule count for this event (0 for the first molecule/record in the file). Note that value does not depend on possible index shift value specified for the import method.

molString - Molecule string from underlying MRecord.getMolString() if applicable

t - Parsing error

build

public MasterMoleculeStorage build()

Create immutable representation.

Returns:

Immutable representation