info.bioinfweb.jphyloio.formats.nexus.receivers

Class ReferenceOnlySetReceiver

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

info.bioinfweb.jphyloio.formats.nexus.receivers.ReferenceOnlySetReceiver

All Implemented Interfaces:

JPhyloIOEventReceiver, NexusConstants

public class ReferenceOnlySetReceiver
extends AbstractNexusSetsEventReceiver

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
ReferenceOnlySetReceiver(NexusWriterStreamDataProvider streamDataProvider, java.util.Set<EventContentType> allowedTypes)
ReferenceOnlySetReceiver(NexusWriterStreamDataProvider streamDataProvider, java.util.Set<EventContentType> allowedTypes, java.util.Set<EventContentType> ignoredTypes)

Method Summary

Modifier and Type	Method and Description
protected 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.

Methods inherited from class info.bioinfweb.jphyloio.formats.nexus.receivers.AbstractNexusSetsEventReceiver

doAdd, handleCharacterSetInterval, writeElementReference

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

ReferenceOnlySetReceiver

public ReferenceOnlySetReceiver(NexusWriterStreamDataProvider streamDataProvider,
                                java.util.Set<EventContentType> allowedTypes,
                                java.util.Set<EventContentType> ignoredTypes)

ReferenceOnlySetReceiver

public ReferenceOnlySetReceiver(NexusWriterStreamDataProvider streamDataProvider,
                                java.util.Set<EventContentType> allowedTypes)

Method Detail

handleSetElement

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

Description copied from class: AbstractNexusSetsEventReceiver

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

Specified by:

handleSetElement in class AbstractNexusSetsEventReceiver

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