org.openscience.cdk.io

Class ChemObjectIO

java.lang.Object

org.openscience.cdk.io.ChemObjectIO

All Implemented Interfaces:

Closeable, AutoCloseable, IChemObjectIO

Direct Known Subclasses:

DefaultChemObjectReader, DefaultChemObjectWriter, DefaultEventChemObjectReader, DefaultIteratingChemObjectReader

public abstract class ChemObjectIO
extends Object
implements IChemObjectIO

Provides some basic functionality for readers and writers. This includes managing the IChemObjectIOListener's and managing of IOSetting's. The IOSettings are managed via the SettingManager class with most method's wrapped to more descriptive method names (e.g. SettingManager.get(String) is invoked by getSetting(String)).

Author:

johnmay

Source code:

master

Belongs to CDK module:

io

Created on:

20.03.2012

Constructor Summary

Constructors

Constructor and Description
ChemObjectIO()

Method Summary

Modifier and Type	Method and Description
void	addChemObjectIOListener(IChemObjectIOListener listener) Adds a IChemObjectIOListener to this IChemObjectIO.
<S extends IOSetting> S	addSetting(IOSetting setting) Add an IOSetting to the reader/writer.
void	addSettings(Collection<IOSetting> settings) Adds a collection of IOSettings to the reader/writer.
protected void	fireIOSettingQuestion(IOSetting setting) Fires IChemObjectIOListener.processIOSettingQuestion(org.openscience.cdk.io.setting.IOSetting) for all managed listeners.
IOSetting[]	getIOSettings() Returns an array of IOSettings defined by this IChemObjectIO class.
List<IChemObjectIOListener>	getListeners() Access all the listeners for this ChemObject Reader or Writer.
<S extends IOSetting> S	getSetting(String name) Access a named setting managed by this reader/writer.
<S extends IOSetting> S	getSetting(String name, Class<S> c) Access a named setting managed by this reader/writer.
Collection<IOSetting>	getSettings() Access a collection of IOSettings for this reader/writer.
boolean	hasSetting(String name) Determine whether this reader/writer has a setting of the provided name.
void	removeChemObjectIOListener(IChemObjectIOListener listener) Removes a IChemObjectIOListener from this IChemObjectIO.

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, close, getFormat

Constructor Detail

ChemObjectIO

public ChemObjectIO()

Method Detail

getListeners

public List<IChemObjectIOListener> getListeners()

Access all the listeners for this ChemObject Reader or Writer. This will returned an unmodifiable list of listeners. Listeners should be added to and removed from the reader/writer using IChemObjectIO.addChemObjectIOListener(org.openscience.cdk.io.listener.IChemObjectIOListener) and IChemObjectIO.removeChemObjectIOListener(org.openscience.cdk.io.listener.IChemObjectIOListener)

Specified by:

getListeners in interface IChemObjectIO

Returns:

all listeners managed by this IO object

addChemObjectIOListener

public void addChemObjectIOListener(IChemObjectIOListener listener)

Adds a IChemObjectIOListener to this IChemObjectIO.

Specified by:

addChemObjectIOListener in interface IChemObjectIO

Parameters:

listener - the reader listener to add.

removeChemObjectIOListener

public void removeChemObjectIOListener(IChemObjectIOListener listener)

Removes a IChemObjectIOListener from this IChemObjectIO.

Specified by:

removeChemObjectIOListener in interface IChemObjectIO

Parameters:

listener - the listener to be removed.

addSetting

public <S extends IOSetting> S addSetting(IOSetting setting)

Add an IOSetting to the reader/writer. If the name clashes with another setting the original setting will be returned. This method should be called when assigning field settings:

 private BooleanIOSetting setting; // field

 ...

 setting = addSetting(new BooleanIOSetting("setting", ...));
 // if setting was already added we are now using the correct instance

Specified by:

addSetting in interface IChemObjectIO

Parameters:

setting - setting to add

Returns:

usable setting

See Also:

SettingManager.add(org.openscience.cdk.interfaces.ISetting)

addSettings

public void addSettings(Collection<IOSetting> settings)

Adds a collection of IOSettings to the reader/writer. This is useful for transferring/propagating settings between different reader/writer. When the new settings are added if there is a setting with the same name already stored the value for the new setting is set on the managed setting (See. IteratingSDFReader/SDFWriter for propagation examples). Note that if the setting is invalid (a CDKException thrown) then the setting will not be set.

 // two different readers (of same or different type)
 IChemObjectReader reader1 = ...;
 IChemObjectReader reader2 = ...;

 // settings transferred from reader2 to reader1
 reader1.addSettings(reader2.getSettings());
 

Specified by:

addSettings in interface IChemObjectIO

Parameters:

settings - collection of settings to add

See Also:

IChemObjectIO.getSettings()

hasSetting

public boolean hasSetting(String name)

Determine whether this reader/writer has a setting of the provided name.

Specified by:

hasSetting in interface IChemObjectIO

Parameters:

name - name of a setting

Returns:

whether the setting is available

See Also:

SettingManager.has(String)

getSetting

public <S extends IOSetting> S getSetting(String name)

Access a named setting managed by this reader/writer.

Specified by:

getSetting in interface IChemObjectIO

Type Parameters:

S - type to cast to

Parameters:

name - name of the setting

Returns:

instance of the setting for the name (InvalidParameterException is thrown if no setting for the provided name is found)

See Also:

IChemObjectIO.getSetting(String, Class), SettingManager.get(String)

getSetting

public <S extends IOSetting> S getSetting(String name,
                                          Class<S> c)

Access a named setting managed by this reader/writer.

Specified by:

getSetting in interface IChemObjectIO

Type Parameters:

S - type to cast to

Parameters:

name - name of the setting

c - the class of the setting (matching generic return type). This is need as due to type erasure we don't know the class of 'S' at runtime.

Returns:

instance of the setting for the name (InvalidParameterException is thrown if no setting for the provided name is found)

See Also:

IChemObjectIO.getSetting(String), SettingManager.get(String, Class)

getIOSettings

public IOSetting[] getIOSettings()

Returns an array of IOSettings defined by this IChemObjectIO class.

Specified by:

getIOSettings in interface IChemObjectIO

Returns:

the IOSettings for this class.

getSettings

public Collection<IOSetting> getSettings()

Access a collection of IOSettings for this reader/writer.

Specified by:

getSettings in interface IChemObjectIO

Returns:

collection of IOSetting's

See Also:

IChemObjectIO.addSettings(java.util.Collection)

fireIOSettingQuestion

protected void fireIOSettingQuestion(IOSetting setting)

Fires IChemObjectIOListener.processIOSettingQuestion(org.openscience.cdk.io.setting.IOSetting) for all managed listeners.

Parameters:

setting - the setting to process