info.bioinfweb.jphyloio.formats.nexus

Class AbstractNexusSetWriter

java.lang.Object

info.bioinfweb.jphyloio.formats.nexus.AbstractNexusSetWriter

All Implemented Interfaces:

NexusConstants

public abstract class AbstractNexusSetWriter
extends java.lang.Object
implements NexusConstants

Customizable implementation for writing different kinds of Nexus sets.

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

Constructor Summary

Constructors

Constructor and Description
AbstractNexusSetWriter(NexusWriterStreamDataProvider streamDataProvider, java.lang.String commandName, EventContentType linkedContentType, java.util.Iterator<? extends ElementDataAdapter<? extends LabeledIDEvent>> dataSourceIterator, AbstractNexusEventReceiver receiver)

Method Summary

Modifier and Type	Method and Description
protected abstract java.lang.String	getLinkedBlockName(ElementDataAdapter<? extends LabeledIDEvent> dataSource)
protected abstract ObjectListDataAdapter<LinkedLabeledIDEvent>	getSets(ElementDataAdapter<? extends LabeledIDEvent> dataSource)
void	write()

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractNexusSetWriter

public AbstractNexusSetWriter(NexusWriterStreamDataProvider streamDataProvider,
                              java.lang.String commandName,
                              EventContentType linkedContentType,
                              java.util.Iterator<? extends ElementDataAdapter<? extends LabeledIDEvent>> dataSourceIterator,
                              AbstractNexusEventReceiver receiver)

Method Detail

getSets

protected abstract ObjectListDataAdapter<LinkedLabeledIDEvent> getSets(ElementDataAdapter<? extends LabeledIDEvent> dataSource)

getLinkedBlockName

protected abstract java.lang.String getLinkedBlockName(ElementDataAdapter<? extends LabeledIDEvent> dataSource)

write

public void write()
           throws java.io.IOException

Throws:

java.io.IOException