info.bioinfweb.jphyloio.formats.nexus.commandreaders

Class DefaultCommandReader

java.lang.Object

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

info.bioinfweb.jphyloio.formats.nexus.commandreaders.DefaultCommandReader

All Implemented Interfaces:

NexusCommandEventReader, NexusConstants

public class DefaultCommandReader
extends AbstractNexusCommandEventReader
implements NexusConstants

Default Nexus command reader for all unsupported Nexus commands.

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
DefaultCommandReader(java.lang.String commandName, NexusReaderStreamDataProvider streamDataProvider) Creates a new instance of this class.

Method Summary

Modifier and Type	Method and Description
protected boolean	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

DefaultCommandReader

public DefaultCommandReader(java.lang.String commandName,
                            NexusReaderStreamDataProvider streamDataProvider)

Creates a new instance of this class.

This class does not provide a constructor according to the requirements defined in NexusCommandEventReader, because it is not meant to be used with NexusCommandReaderFactory but shall be directly created in NexusEventReader.

Parameters:

commandName - the name of the command to be parsed

streamDataProvider - the provider to access the shared Nexus data and the input stream

Method Detail

doReadNextEvent

protected boolean doReadNextEvent()
                           throws java.io.IOException

Specified by:

doReadNextEvent in class AbstractNexusCommandEventReader

Throws:

java.io.IOException