info.bioinfweb.jphyloio.formats.nexus.commandreaders

Class AbstractKeyValueCommandReader

java.lang.Object

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

info.bioinfweb.jphyloio.formats.nexus.commandreaders.AbstractKeyValueCommandReader

All Implemented Interfaces:

NexusCommandEventReader, NexusConstants

Direct Known Subclasses:

DimensionsReader, FormatReader, LinkReader

public abstract class AbstractKeyValueCommandReader
extends AbstractNexusCommandEventReader
implements NexusConstants

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
AbstractKeyValueCommandReader(java.lang.String commandName, java.lang.String[] validBlocks, NexusReaderStreamDataProvider nexusDocument)

Method Summary

Modifier and Type	Method and Description
protected abstract 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	doReadNextEvent()
protected abstract 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.

Methods inherited from class info.bioinfweb.jphyloio.formats.nexus.commandreaders.AbstractNexusCommandEventReader

consumeWhiteSpaceAndCommentsToBuffer, getCommandName, getStreamDataProvider, getValidBlocks, isAllDataProcessed, readNextEvent, setAllDataProcessed

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractKeyValueCommandReader

public AbstractKeyValueCommandReader(java.lang.String commandName,
                                     java.lang.String[] validBlocks,
                                     NexusReaderStreamDataProvider nexusDocument)

Method Detail

processSubcommand

protected abstract boolean processSubcommand(KeyValueInformation info)
                                      throws java.io.IOException

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.

Parameters:

info - the key and value

Returns:

true if at least one event has been added to the queue by this or false otherwise

Throws:

java.io.IOException - if an exception occurs when trying to read from the underlying stream

addStoredEvents

protected abstract 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. It is guaranteed that this method will not be called by AbstractKeyValueCommandReader, before the whole command was processed.

Returns:

true if events were added by this method or false otherwise

doReadNextEvent

protected boolean doReadNextEvent()
                           throws java.io.IOException

Specified by:

doReadNextEvent in class AbstractNexusCommandEventReader

Throws:

java.io.IOException