info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters

Class FormatReader

java.lang.Object

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

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

info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters.FormatReader

All Implemented Interfaces:

NexusCommandEventReader, NexusConstants, ReadWriteConstants

public class FormatReader
extends AbstractKeyValueCommandReader
implements NexusConstants, ReadWriteConstants

Parser for the Format command in a Characters, Unaligned or Data block.

Author:

Ben Stöver

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	INFO_KEY_INTERLEAVE
static java.lang.String	INFO_KEY_LABELS
static java.lang.String	INFO_KEY_TOKENS_FORMAT
static java.lang.String	INFO_KEY_TRANSPOSE
static java.util.regex.Pattern	MIXED_DATA_TYPE_SINGLE_SET_PATTERN
static java.util.regex.Pattern	MIXED_DATA_TYPE_VALUE_PATTERN

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

Fields inherited from interface info.bioinfweb.jphyloio.ReadWriteConstants

ATTRIBUTE_STRING_KEY, ATTRIBUTES_NAMESPACE_FOLDER, DATA_TYPE_NAMESPACE_FOLDER, DATA_TYPE_SIMPLE_VALUE_LIST, DEFAULT_CHAR_SET_ID_PREFIX, DEFAULT_CHARACTER_DEFINITION_ID_PREFIX, DEFAULT_EDGE_ID_PREFIX, DEFAULT_GENERAL_ID_PREFIX, DEFAULT_MATRIX_ID_PREFIX, DEFAULT_MAX_COMMENT_LENGTH, DEFAULT_MAX_TOKENS_TO_READ, DEFAULT_META_ID_PREFIX, DEFAULT_NETWORK_ID_PREFIX, DEFAULT_NODE_EDGE_SET_ID_PREFIX, DEFAULT_NODE_ID_PREFIX, DEFAULT_OTU_ID_PREFIX, DEFAULT_OTU_LIST_ID_PREFIX, DEFAULT_OTU_SET_ID_PREFIX, DEFAULT_SEQUENCE_ID_PREFIX, DEFAULT_SEQUENCE_SET_ID_PREFIX, DEFAULT_TOKEN_DEFINITION_ID_PREFIX, DEFAULT_TOKEN_SET_ID_PREFIX, DEFAULT_TREE_ID_PREFIX, DEFAULT_TREE_NETWORK_GROUP_ID_PREFIX, DEFAULT_TREE_NETWORK_SET_ID_PREFIX, JPHYLOIO_ATTRIBUTES_NAMESPACE, JPHYLOIO_ATTRIBUTES_PREFIX, JPHYLOIO_DATA_TYPE_NAMESPACE, JPHYLOIO_DATA_TYPE_PREFIX, JPHYLOIO_FORMATS_NAMESPACE_PREFIX, JPHYLOIO_GENERAL_NAMESPACE, JPHYLOIO_NAMESPACE_PREFIX, JPHYLOIO_PREDICATE_NAMESPACE, JPHYLOIO_PREDICATE_PREFIX, PREDICATE_CHARACTER_COUNT, PREDICATE_EDGE_LENGTH, PREDICATE_EDGE_SOURCE_NODE, PREDICATE_EDGE_TARGET_NODE, PREDICATE_HAS_CUSTOM_XML, PREDICATE_HAS_LITERAL_METADATA, PREDICATE_HAS_RESOURCE_METADATA, PREDICATE_IS_CROSSLINK, PREDICATE_NAMESPACE_FOLDER, PREDICATE_PART_SEPERATOR, PREDICATE_SEQUENCE_COUNT, RESERVED_ID_PREFIX

Constructor Summary

Constructors

Constructor and Description
FormatReader(NexusReaderStreamDataProvider nexusDocument)

Method Summary

Modifier and Type	Method and Description
protected boolean	addStoredEvents() Adds the stored token set event with nested single token definition events to the queue, if present.
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.

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

doReadNextEvent

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

Field Detail

INFO_KEY_TOKENS_FORMAT

public static final java.lang.String INFO_KEY_TOKENS_FORMAT

See Also:

Constant Field Values

INFO_KEY_INTERLEAVE

public static final java.lang.String INFO_KEY_INTERLEAVE

See Also:

Constant Field Values

INFO_KEY_LABELS

public static final java.lang.String INFO_KEY_LABELS

See Also:

Constant Field Values

INFO_KEY_TRANSPOSE

public static final java.lang.String INFO_KEY_TRANSPOSE

See Also:

Constant Field Values

MIXED_DATA_TYPE_VALUE_PATTERN

public static final java.util.regex.Pattern MIXED_DATA_TYPE_VALUE_PATTERN

MIXED_DATA_TYPE_SINGLE_SET_PATTERN

public static final java.util.regex.Pattern MIXED_DATA_TYPE_SINGLE_SET_PATTERN

Constructor Detail

FormatReader

public FormatReader(NexusReaderStreamDataProvider nexusDocument)

Method Detail

processSubcommand

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

Description copied from class: AbstractKeyValueCommandReader

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.

Specified by:

processSubcommand in class AbstractKeyValueCommandReader

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 boolean addStoredEvents()

Adds the stored token set event with nested single token definition events to the queue, if present.

In the case of MrBayes MIXED data type more than one token set definition event may be added. The stored single token definition events are nested into each of these token set definition event, except for events with the meaning CharacterSymbolMeaning.CHARACTER_STATE, which are removed in this case, because they may not fit to all defined token sets.

If only single token definition events could be created from the format command and no token set, no events will be added.

Specified by:

addStoredEvents in class AbstractKeyValueCommandReader

Returns:

true if events were added by this method or false otherwise

See Also:

AbstractKeyValueCommandReader.addStoredEvents()