info.bioinfweb.jphyloio.formats.nexus.commandreaders

Class AbstractNexusCommandEventReader

java.lang.Object

info.bioinfweb.jphyloio.formats.nexus.commandreaders.AbstractNexusCommandEventReader

All Implemented Interfaces:

NexusCommandEventReader

Direct Known Subclasses:

AbstractCharLabelsReader, AbstractKeyValueCommandReader, AbstractNexusSetReader, DefaultCommandReader, MatrixReader, TaxLabelsReader, TitleReader, TranslateReader, TreeReader

public abstract class AbstractNexusCommandEventReader
extends java.lang.Object
implements NexusCommandEventReader

Implements shared functionality for classes implementing NexusCommandEventReader.

Author:

Ben Stöver

Constructor Summary

Constructors

Constructor and Description
AbstractNexusCommandEventReader(java.lang.String commandName, java.lang.String[] validBlocks, NexusReaderStreamDataProvider streamDataProvider) Creates a new instance of this class.

Method Summary

Modifier and Type	Method and Description
protected void	consumeWhiteSpaceAndCommentsToBuffer(java.util.Collection<JPhyloIOEvent> buffer)
protected abstract boolean	doReadNextEvent()
java.lang.String	getCommandName() Returns the name of the Nexus command that can be parsed by this instance.
protected NexusReaderStreamDataProvider	getStreamDataProvider()
java.util.Collection<java.lang.String>	getValidBlocks() Returns a collection with the names of the Nexus blocks the command parsed by the implementing class may be contained in.
protected boolean	isAllDataProcessed() Returns true if the whole command this instance was created on has been parsed or false if another events can be generated by the next call of readNextEvent().
boolean	readNextEvent() Adds at least one additional event (generated from the current Nexus command) to the event queue.
protected void	setAllDataProcessed(boolean allDataProcessed)

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractNexusCommandEventReader

public AbstractNexusCommandEventReader(java.lang.String commandName,
                                       java.lang.String[] validBlocks,
                                       NexusReaderStreamDataProvider streamDataProvider)

Creates a new instance of this class.

Note that non-abstract inherited classes need to specify a constructor matching the requirements defined by NexusCommandEventReader.

Parameters:

validBlocks - an array with the names of the Nexus blocks the command parsed by the implementing class may be contained in

Method Detail

getCommandName

public java.lang.String getCommandName()

Description copied from interface: NexusCommandEventReader

Returns the name of the Nexus command that can be parsed by this instance.

Specified by:

getCommandName in interface NexusCommandEventReader

Returns:

a non-empty string

getValidBlocks

public java.util.Collection<java.lang.String> getValidBlocks()

Description copied from interface: NexusCommandEventReader

Returns a collection with the names of the Nexus blocks the command parsed by the implementing class may be contained in.

An empty collection returned here indicates that this reader is valid in all Nexus blocks.

Specified by:

getValidBlocks in interface NexusCommandEventReader

Returns:

a collection with the block names

isAllDataProcessed

protected boolean isAllDataProcessed()

Returns true if the whole command this instance was created on has been parsed or false if another events can be generated by the next call of readNextEvent().

Returns:

whether more events are available

setAllDataProcessed

protected void setAllDataProcessed(boolean allDataProcessed)

getStreamDataProvider

protected NexusReaderStreamDataProvider getStreamDataProvider()

consumeWhiteSpaceAndCommentsToBuffer

protected void consumeWhiteSpaceAndCommentsToBuffer(java.util.Collection<JPhyloIOEvent> buffer)
                                             throws java.io.IOException

Throws:

java.io.IOException

doReadNextEvent

protected abstract boolean doReadNextEvent()
                                    throws java.io.IOException

Throws:

java.io.IOException

readNextEvent

public boolean readNextEvent()
                      throws java.io.IOException

Description copied from interface: NexusCommandEventReader

Adds at least one additional event (generated from the current Nexus command) to the event queue.

Specified by:

readNextEvent in interface NexusCommandEventReader

Returns:

true if at least one additional event was added or false if the underlying Nexus command was already completely processed an no more events can generated from it

Throws:

java.io.IOException