public class LinkReader extends AbstractKeyValueCommandReader implements NexusConstants
LINK command of a Nexus block and stores the links in the shared information map of the
stream data provider under the key NexusReaderStreamDataProvider.INFO_KEY_BLOCK_LINKS.
Note that the LINK command is not part of the initial Nexus definition, but was used by Mesquite
as a custom command to allow references between blocks using the TITLE command.
This reader is valid for all blocks, therefore AbstractNexusCommandEventReader.getValidBlocks() returns an empty collection.
Example usage:
#NEXUS BEGIN TAXA; TITLE 'taxon list 1'; DIMENSIONS NTAX = 3; TAXLABELS A B C; END; BEGIN TAXA; TITLE TaxonList2; DIMENSIONS NTAX = 3; TAXLABELS D E F; END; BEGIN TREES; LINK TAXA = 'taxon list 1'; TREE someTree = (A, (B, C)); END; BEGIN TREES; LINK TAXA = TaxonList2; TREE someTree = (D, (E, F)); END;The
LINK command may also be used to link other blocks than the TAXA block, but JPhyloIO will
not use this information.TitleReaderALTERNATIVE_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 and Description |
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LinkReader(NexusReaderStreamDataProvider nexusDocument) |
| Modifier and Type | Method and Description |
|---|---|
protected boolean |
addStoredEvents()
Implementations that need to store events, until all generated events are known should add such events
to the queue, when this method is called.
|
protected boolean |
processSubcommand(KeyValueInformation info)
Inherited classes should implement this method by adding one or more events to the queue, which have
been generated from the specified key value pair.
|
doReadNextEventconsumeWhiteSpaceAndCommentsToBuffer, getCommandName, getStreamDataProvider, getValidBlocks, isAllDataProcessed, readNextEvent, setAllDataProcessedpublic LinkReader(NexusReaderStreamDataProvider nexusDocument)
protected boolean processSubcommand(KeyValueInformation info) throws java.io.IOException
AbstractKeyValueCommandReaderprocessSubcommand in class AbstractKeyValueCommandReaderinfo - the key and valuetrue if at least one event has been added to the queue by this or false otherwisejava.io.IOException - if an exception occurs when trying to read from the underlying streamprotected boolean addStoredEvents()
AbstractKeyValueCommandReaderAbstractKeyValueCommandReader, before the whole command was processed.addStoredEvents in class AbstractKeyValueCommandReadertrue if events were added by this method or false otherwise