info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets

Class IDBasedSetsReader

java.lang.Object

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

info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets.AbstractNexusSetReader

info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets.IDBasedSetsReader

All Implemented Interfaces:

NexusCommandEventReader, NexusConstants, ReadWriteConstants

Direct Known Subclasses:

TaxSetReader, TreeSetReader

public class IDBasedSetsReader
extends AbstractNexusSetReader
implements NexusConstants, ReadWriteConstants

Base class for all Nexus readers that create set event streams that consist of SetElementEvents.

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

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
IDBasedSetsReader(EventContentType setType, java.lang.String commandName, java.lang.String linkedBlockTypeName, EventContentType elementType, NexusReaderStreamDataProvider streamDataProvider)

Method Summary

Modifier and Type	Method and Description
protected void	createEventsForInterval(long start, long end) Creates the event(s) representing the specified interval in the current set type
protected long	elementIndexByName(java.lang.String name) Converts the Nexus name of a set element to its index.
protected long	getElementCount() Returns the number of elements which can potentially be contained in this set (e.g.
protected java.lang.String	getLinkedID() Returns the ID if the object that is linked to this set (e.g.

Methods inherited from class info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets.AbstractNexusSetReader

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

Constructor Detail

IDBasedSetsReader

public IDBasedSetsReader(EventContentType setType,
                         java.lang.String commandName,
                         java.lang.String linkedBlockTypeName,
                         EventContentType elementType,
                         NexusReaderStreamDataProvider streamDataProvider)

Method Detail

getLinkedID

protected java.lang.String getLinkedID()

Description copied from class: AbstractNexusSetReader

Returns the ID if the object that is linked to this set (e.g. an alignment start event related to a character set or an OTU list related to an OTU set)

Specified by:

getLinkedID in class AbstractNexusSetReader

Returns:

the ID of the linked start element

getElementCount

protected long getElementCount()

Description copied from class: AbstractNexusSetReader

Returns the number of elements which can potentially be contained in this set (e.g. the number of declared taxa or the number of alignment columns).

Specified by:

getElementCount in class AbstractNexusSetReader

Returns:

the number of elements or -1 if the number is currently undefined (e.g. if no block is linked to the current SETS block

createEventsForInterval

protected void createEventsForInterval(long start,
                                       long end)
                                throws java.io.IOException

Description copied from class: AbstractNexusSetReader

Creates the event(s) representing the specified interval in the current set type

Specified by:

createEventsForInterval in class AbstractNexusSetReader

Parameters:

start - the fist index of the interval

end - the first index after the end of the interval

Throws:

java.io.IOException - if an I/O error occurs while writing the event(s)

elementIndexByName

protected long elementIndexByName(java.lang.String name)

Description copied from class: AbstractNexusSetReader

Converts the Nexus name of a set element to its index.

Specified by:

elementIndexByName in class AbstractNexusSetReader

Parameters:

name - the Nexus name of the element

Returns:

the index of the specified element or -1 if an element with the specified name could not be found