info.bioinfweb.jphyloio.formats.nexus.receivers

Class AbstractNexusSetsEventReceiver

java.lang.Object

info.bioinfweb.jphyloio.dataadapters.implementations.receivers.BasicEventReceiver<P>

info.bioinfweb.jphyloio.formats.text.BasicTextCommentEventReceiver<NexusWriterStreamDataProvider>

info.bioinfweb.jphyloio.formats.nexus.receivers.AbstractNexusEventReceiver

info.bioinfweb.jphyloio.formats.nexus.receivers.AbstractNexusSetsEventReceiver

All Implemented Interfaces:

JPhyloIOEventReceiver, NexusConstants

Direct Known Subclasses:

CharacterSetEventReceiver, ReferenceOnlySetReceiver

public abstract class AbstractNexusSetsEventReceiver
extends AbstractNexusEventReceiver

General implementation for event receivers writing Nexus set commands.

Since:

0.0.0

Author:

Ben Stöver

Field Summary

Fields inherited from interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants

ALTERNATIVE_END_COMMAND, BEGIN_COMMAND, BLOCK_NAME_CHARACTERS, BLOCK_NAME_DATA, BLOCK_NAME_NETWORKS, BLOCK_NAME_SETS, BLOCK_NAME_TAXA, BLOCK_NAME_TREES, BLOCK_NAME_UNALIGNED, CHARACTER_NAME_STATES_SEPARATOR, COMMAND_END, COMMAND_NAME_CHAR_LABELS, COMMAND_NAME_CHAR_SET, COMMAND_NAME_CHAR_STATE_LABELS, COMMAND_NAME_DIMENSIONS, COMMAND_NAME_FORMAT, COMMAND_NAME_LINK, COMMAND_NAME_MATRIX, COMMAND_NAME_NETWORK, COMMAND_NAME_TAX_LABELS, COMMAND_NAME_TAXON_SET, COMMAND_NAME_TITLE, COMMAND_NAME_TRANSLATE, COMMAND_NAME_TREE, COMMAND_NAME_TREE_SET, COMMENT_END, COMMENT_START, DIMENSIONS_SUBCOMMAND_NCHAR, DIMENSIONS_SUBCOMMAND_NEW_TAXA, DIMENSIONS_SUBCOMMAND_NTAX, ELEMENT_SEPARATOR, END_COMMAND, FIRST_LINE, FORMAT_NAME_STANDARD, FORMAT_NAME_VECTOR, FORMAT_SUBCOMMAND_DATA_TYPE, FORMAT_SUBCOMMAND_GAP_CHAR, FORMAT_SUBCOMMAND_INTERLEAVE, FORMAT_SUBCOMMAND_MATCH_CHAR, FORMAT_SUBCOMMAND_MISSING_CHAR, FORMAT_SUBCOMMAND_NO_LABELS, FORMAT_SUBCOMMAND_NO_TOKENS, FORMAT_SUBCOMMAND_SYMBOLS, FORMAT_SUBCOMMAND_TOKENS, FORMAT_SUBCOMMAND_TRANSPOSE, FORMAT_VALUE_CONTINUOUS_DATA_TYPE, FORMAT_VALUE_DNA_DATA_TYPE, FORMAT_VALUE_MIXED_DATA_TYPE, FORMAT_VALUE_NUCLEOTIDE_DATA_TYPE, FORMAT_VALUE_PROTEIN_DATA_TYPE, FORMAT_VALUE_RNA_DATA_TYPE, FORMAT_VALUE_STANDARD_DATA_TYPE, KEY_VALUE_SEPARATOR, MATRIX_POLYMORPHIC_TOKEN_END, MATRIX_POLYMORPHIC_TOKEN_START, MATRIX_UNCERTAINS_TOKEN_END, MATRIX_UNCERTAINS_TOKEN_START, NEXUS_FORMAT_NAME, NEXUS_NAMESPACE_PREFIX, NEXUS_PREDICATE_NAMESPACE, SET_END_INDEX_SYMBOL, SET_KEY_WORD_ALL, SET_KEY_WORD_REMAINING, SET_REGULAR_INTERVAL_SYMBOL, SET_TO_SYMBOL, SET_VECTOR_CONTAINED, SET_VECTOR_NOT_CONTAINED, UNTIL_WHITESPACE_COMMENT_COMMAND_EQUAL_PATTERN, UNTIL_WHITESPACE_COMMENT_COMMAND_PATTERN, VALUE_DELIMITER, WORD_DELIMITER

Constructor Summary

Constructors

Constructor and Description
AbstractNexusSetsEventReceiver(NexusWriterStreamDataProvider streamDataProvider) Creates a new instance of this class.

Method Summary

Modifier and Type	Method and Description
protected boolean	doAdd(JPhyloIOEvent event) This method is called internally by BasicEventReceiver.add(JPhyloIOEvent) to process events that do not model metadata or comments.
protected boolean	handleCharacterSetInterval(CharacterSetIntervalEvent event) This method is called every time a CharacterSetIntervalEvent is encountered on the top level by this receiver.
protected abstract boolean	handleSetElement(SetElementEvent event) This method is called every time a SetElementEvent is encountered on the top level by this receiver and must be implemented by inherited classes.
protected void	writeElementReference(SetElementEvent event)

Methods inherited from class info.bioinfweb.jphyloio.formats.text.BasicTextCommentEventReceiver

getCommentEnd, getCommentStart, handleComment, writeComment

Methods inherited from class info.bioinfweb.jphyloio.dataadapters.implementations.receivers.BasicEventReceiver

add, addIgnoredComments, addIgnoredLiteralMetadata, addIgnoredResourceMetadata, addIgnoreLogMessage, didIgnoreComments, didIgnoreLiteralMetadata, didIgnoreMetadata, didIgnoreResourceMetadata, getIgnoredComments, getIgnoredLiteralMetadata, getIgnoredMetadata, getIgnoredResourceMetadata, getLogger, getParameterMap, getParentEvent, getParentEvents, getStreamDataProvider, handleLiteralContentMeta, handleLiteralMetaStart, handleMetaEndEvent, handleResourceMetaStart, isInComment

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractNexusSetsEventReceiver

public AbstractNexusSetsEventReceiver(NexusWriterStreamDataProvider streamDataProvider)

Creates a new instance of this class.

Parameters:

streamDataProvider - the stream data provider of the calling NexusEventWriter.

Method Detail

handleCharacterSetInterval

protected boolean handleCharacterSetInterval(CharacterSetIntervalEvent event)
                                      throws java.io.IOException

This method is called every time a CharacterSetIntervalEvent is encountered on the top level by this receiver.

This default implementation always returns false that leads to an IllegalEventException. Inherited classes that support CharacterSetIntervalEvents should overwrite this method.

Parameters:

event - the character set interval event that was encountered on the top level by this receiver

Returns:

true if the encountered event is legal at this position or false otherwise

Throws:

java.io.IOException - if an I/O error occurs while trying to write the contents of the event (This cannot happen in this default implementation, but may happen in overwritten implementations.)

handleSetElement

protected abstract boolean handleSetElement(SetElementEvent event)
                                     throws java.io.IOException

This method is called every time a SetElementEvent is encountered on the top level by this receiver and must be implemented by inherited classes.

Parameters:

event - the set element event that was encountered on the top level by this receiver

Returns:

true if the encountered event is legal at this position or false otherwise (If false is returned by inherited classes, an IllegalEventException will be thrown as a result afterwards.)

Throws:

java.io.IOException - if an I/O error occurs while trying to write the contents of the event

writeElementReference

protected void writeElementReference(SetElementEvent event)
                              throws java.io.IOException

Throws:

java.io.IOException

doAdd

protected boolean doAdd(JPhyloIOEvent event)
                 throws java.io.IOException,
                        javax.xml.stream.XMLStreamException

Description copied from class: BasicEventReceiver

This method is called internally by BasicEventReceiver.add(JPhyloIOEvent) to process events that do not model metadata or comments. (Such events are treated by the according special methods of this class).

This default implementation just throws an IllegalEventException. Inherited classes that need to support other events then these modeling metadata or comments, must overwrite this method.

Overrides:

doAdd in class BasicEventReceiver<NexusWriterStreamDataProvider>

Parameters:

event - the event to be processed

Returns:

true if more events can be written to this acceptor or false if writing should be aborted

Throws:

java.io.IOException - if an I/O error occurs when writing to the underlying stream

javax.xml.stream.XMLStreamException - if an XML stream error occurs when writing to the underlying stream