Package org.openscience.cdk.io
Class DefaultChemObjectReader
java.lang.Object
org.openscience.cdk.io.ChemObjectIO
org.openscience.cdk.io.DefaultChemObjectReader
- All Implemented Interfaces:
Closeable
,AutoCloseable
,IChemObjectIO
,IChemObjectReader
,ISimpleChemObjectReader
- Direct Known Subclasses:
CDKOWLReader
,CIFReader
,CMLReader
,CrystClustReader
,CTXReader
,GamessReader
,Gaussian03Reader
,Gaussian98Reader
,GhemicalMMReader
,HINReader
,INChIPlainTextReader
,INChIReader
,MDLReader
,MDLRXNReader
,MDLRXNV2000Reader
,MDLRXNV3000Reader
,MDLV2000Reader
,MDLV3000Reader
,Mol2Reader
,Mopac7Reader
,MoSSOutputReader
,PCCompoundASNReader
,PCCompoundXMLReader
,PCSubstanceXMLReader
,PDBReader
,PMPReader
,RGroupQueryReader
,ShelXReader
,SMILESReader
,VASPReader
,XYZReader
,ZMatrixReader
public abstract class DefaultChemObjectReader
extends ChemObjectIO
implements ISimpleChemObjectReader
Abstract class that ChemObjectReader's can implement to have it
take care of basic stuff, like managing the ReaderListeners.
- Source code:
- main
- Belongs to CDK module:
- io
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Nested Class Summary
Nested classes/interfaces inherited from interface org.openscience.cdk.io.IChemObjectReader
IChemObjectReader.Mode
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Field Summary
FieldsModifier and TypeFieldDescriptionprotected IChemObjectReaderErrorHandler
protected IChemObjectReader.Mode
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected void
Sends a frame read event to the registered ReaderListeners.void
handleError
(String message) Redirects an error message to theIChemObjectReaderErrorHandler
.void
handleError
(String message, int row, int colStart, int colEnd) Redirects an error message to theIChemObjectReaderErrorHandler
.void
handleError
(String message, int row, int colStart, int colEnd, Exception exception) Redirects an error message to theIChemObjectReaderErrorHandler
.void
handleError
(String message, Exception exception) Redirects an error message to theIChemObjectReaderErrorHandler
.void
Sets an error handler that is sent events when file format issues occur.void
Sets the reader mode.Methods inherited from class org.openscience.cdk.io.ChemObjectIO
addChemObjectIOListener, addSetting, addSettings, fireIOSettingQuestion, getIOSettings, getListeners, getSetting, getSetting, getSettings, hasSetting, removeChemObjectIOListener
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface org.openscience.cdk.io.IChemObjectIO
accepts, addChemObjectIOListener, addSetting, addSettings, close, getFormat, getIOSettings, getListeners, getSetting, getSetting, getSettings, hasSetting, removeChemObjectIOListener
Methods inherited from interface org.openscience.cdk.io.IChemObjectReader
setReader, setReader
Methods inherited from interface org.openscience.cdk.io.ISimpleChemObjectReader
read
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Field Details
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mode
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errorHandler
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Constructor Details
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DefaultChemObjectReader
public DefaultChemObjectReader()
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Method Details
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fireFrameRead
protected void fireFrameRead()Sends a frame read event to the registered ReaderListeners. -
setReaderMode
Description copied from interface:IChemObjectReader
Sets the reader mode. If Mode.STRICT, then the reader will fail on any problem in the format of the read file, instead of trying to recover from that.- Specified by:
setReaderMode
in interfaceIChemObjectReader
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setErrorHandler
Sets an error handler that is sent events when file format issues occur.- Specified by:
setErrorHandler
in interfaceIChemObjectReader
- Parameters:
handler
-IChemObjectReaderErrorHandler
to send error messages to.
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handleError
Redirects an error message to theIChemObjectReaderErrorHandler
. Throws anCDKException
when in STRICTIChemObjectReader.Mode
.- Specified by:
handleError
in interfaceIChemObjectReader
- Parameters:
message
- the error message.- Throws:
CDKException
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handleError
Redirects an error message to theIChemObjectReaderErrorHandler
. Throws anCDKException
when in STRICTIChemObjectReader.Mode
.- Specified by:
handleError
in interfaceIChemObjectReader
- Parameters:
message
- the error message.exception
- the correspondingException
.- Throws:
CDKException
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handleError
Redirects an error message to theIChemObjectReaderErrorHandler
. Throws anCDKException
when in STRICTIChemObjectReader.Mode
.- Specified by:
handleError
in interfaceIChemObjectReader
- Parameters:
message
- the error message.row
- Row in the file where the error is found.colStart
- Start column in the file where the error is found.colEnd
- End column in the file where the error is found.- Throws:
CDKException
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handleError
public void handleError(String message, int row, int colStart, int colEnd, Exception exception) throws CDKException Redirects an error message to theIChemObjectReaderErrorHandler
. Throws anCDKException
when in STRICTIChemObjectReader.Mode
.- Specified by:
handleError
in interfaceIChemObjectReader
- Parameters:
message
- the error message.row
- Row in the file where the error is found.colStart
- Start column in the file where the error is found.colEnd
- End column in the file where the error is found.exception
- the correspondingException
.- Throws:
CDKException
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