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

Class AbstractNexusSetReader

java.lang.Object

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

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

All Implemented Interfaces:

NexusCommandEventReader, NexusConstants, ReadWriteConstants

Direct Known Subclasses:

CharSetReader, IDBasedSetsReader

public abstract class AbstractNexusSetReader
extends AbstractNexusCommandEventReader
implements NexusConstants, ReadWriteConstants

General reader implementation to read the Nexus commands that define different kinds of sets.

It supports reading sets in Nexus standard and vector format.

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
AbstractNexusSetReader(EventContentType setType, java.lang.String commandName, java.lang.String[] validBlocks, NexusReaderStreamDataProvider nexusDocument)

Method Summary

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

AbstractNexusSetReader

public AbstractNexusSetReader(EventContentType setType,
                              java.lang.String commandName,
                              java.lang.String[] validBlocks,
                              NexusReaderStreamDataProvider nexusDocument)

Method Detail

getLinkedID

protected abstract java.lang.String getLinkedID()

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)

Returns:

the ID of the linked start element

Throws:

java.io.IOException

getElementCount

protected abstract long getElementCount()

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).

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

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

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 abstract long elementIndexByName(java.lang.String name)

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

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

doReadNextEvent

protected boolean doReadNextEvent()
                           throws java.io.IOException

Specified by:

doReadNextEvent in class AbstractNexusCommandEventReader

Throws:

java.io.IOException