com.chemaxon.overlap.io

Class MoleculeCallbacks.IndexToNameStoringCallback

java.lang.Object

com.chemaxon.overlap.io.MoleculeCallbacks.IndexToNameStoringCallback

All Implemented Interfaces:

MoleculeCallback

Enclosing class:

MoleculeCallbacks

public static class MoleculeCallbacks.IndexToNameStoringCallback
extends Object
implements MoleculeCallback

A callback storing indexes.

Note that errors are not stored or reported.

Constructor Summary

Constructors

Constructor and Description
IndexToNameStoringCallback() Construct.
IndexToNameStoringCallback(MoleculeCallback with) Construct.

Method Summary

Modifier and Type	Method and Description
ImmutableList<String>	getIndexToName() Get a clone of index to name association.
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.
String	toString()
void	toStrings(PrintStream ps, SubProgressObserver po) Print index to name associations into escaped strings.

Methods inherited from class java.lang.Object

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

Constructor Detail

IndexToNameStoringCallback

public IndexToNameStoringCallback(MoleculeCallback with)

Construct.

Parameters:

with - Callback to also invoke

IndexToNameStoringCallback

public IndexToNameStoringCallback()

Construct.

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

getIndexToName

public ImmutableList<String> getIndexToName()

Get a clone of index to name association.

Note that an ImmutableList is constructed on every invocation which is not cached.

Returns:

Index to name asspcoayopn

toStrings

public void toStrings(PrintStream ps,
                      SubProgressObserver po)

Print index to name associations into escaped strings.

Each line will be scaped using StringEscapeUtils.escapeJava(java.lang.String).

Parameters:

ps - Stream to write; will not be closed

po - Progress Observer to track progress; will be closed

Throws:

CancellationException - when cancelled

toString

public String toString()

Overrides:

toString in class Object