Package org.openscience.cdk.io
Class CMLReader
- java.lang.Object
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- org.openscience.cdk.io.ChemObjectIO
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- org.openscience.cdk.io.DefaultChemObjectReader
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- org.openscience.cdk.io.CMLReader
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- All Implemented Interfaces:
Closeable
,AutoCloseable
,IChemObjectIO
,IChemObjectReader
,ISimpleChemObjectReader
public class CMLReader extends DefaultChemObjectReader
Reads a molecule in CML 1.x and 2.0 format. CML is an XML based application [Murray-Rust, P. and Rzepa, H.S.. Journal of Chemical Information and Computer Sciences. 1999. 39], and this Reader applies the method described in [Willighagen, E.L.. Internet Journal of Chemistry. 2001. 4].
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Nested Class Summary
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Nested classes/interfaces inherited from interface org.openscience.cdk.io.IChemObjectReader
IChemObjectReader.Mode
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Field Summary
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Fields inherited from class org.openscience.cdk.io.DefaultChemObjectReader
errorHandler, mode
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Constructor Summary
Constructors Constructor Description CMLReader()
CMLReader(InputStream input)
Reads CML from an java.io.InputStream, for example the FileInputStream.CMLReader(String url)
Define this CMLReader to take the input from a java.io.Reader class.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
accepts(Class<? extends IChemObject> classObject)
Returns whether the givenIChemObject
can be read or written.void
close()
Closes this IChemObjectIO's resources.IResourceFormat
getFormat()
Returns theIResourceFormat
class for this IO class.<T extends IChemObject>
Tread(T object)
Read a IChemObject from input.void
registerConvention(String convention, ICMLModule conv)
void
setReader(InputStream input)
Sets the InputStream from which this ChemObjectReader should read the contents.void
setReader(Reader reader)
This method must not be used; XML reading requires the use of an InputStream.-
Methods inherited from class org.openscience.cdk.io.DefaultChemObjectReader
fireFrameRead, handleError, handleError, handleError, handleError, setErrorHandler, setReaderMode
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Methods inherited from class org.openscience.cdk.io.ChemObjectIO
addChemObjectIOListener, addSetting, addSettings, fireIOSettingQuestion, getIOSettings, getListeners, getSetting, getSetting, getSettings, hasSetting, removeChemObjectIOListener
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface org.openscience.cdk.io.IChemObjectIO
addChemObjectIOListener, addSetting, addSettings, getIOSettings, getListeners, getSetting, getSetting, getSettings, hasSetting, removeChemObjectIOListener
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Constructor Detail
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CMLReader
public CMLReader(InputStream input)
Reads CML from an java.io.InputStream, for example the FileInputStream.- Parameters:
input
- InputStream type input
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CMLReader
public CMLReader()
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CMLReader
public CMLReader(String url)
Define this CMLReader to take the input from a java.io.Reader class. Possible readers are (among others) StringReader and FileReader.- Parameters:
url
- String url which points to the file to be read
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Method Detail
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registerConvention
public void registerConvention(String convention, ICMLModule conv)
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getFormat
public IResourceFormat getFormat()
Description copied from interface:IChemObjectIO
Returns theIResourceFormat
class for this IO class.
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setReader
public void setReader(Reader reader) throws CDKException
This method must not be used; XML reading requires the use of an InputStream. Use setReader(InputStream) instead.- Throws:
CDKException
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setReader
public void setReader(InputStream input) throws CDKException
Description copied from interface:IChemObjectReader
Sets the InputStream from which this ChemObjectReader should read the contents.- Throws:
CDKException
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accepts
public boolean accepts(Class<? extends IChemObject> classObject)
Description copied from interface:IChemObjectIO
Returns whether the givenIChemObject
can be read or written.- Parameters:
classObject
-IChemObject
of which is tested if it can be handled.- Returns:
- true, if the
IChemObject
can be handled.
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read
public <T extends IChemObject> T read(T object) throws CDKException
Read a IChemObject from input.- Parameters:
object
- the type of object to return- Returns:
- the content in a ChemFile object
- Throws:
CDKException
- it is thrown if the type of information is not available from the input
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close
public void close() throws IOException
Description copied from interface:IChemObjectIO
Closes this IChemObjectIO's resources.- Throws:
IOException
- when the wrapper IO class cannot be closed.
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