info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees

Class NexusNewickReaderNodeLabelProcessor

java.lang.Object

info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees.NexusNewickReaderNodeLabelProcessor

All Implemented Interfaces:

NewickReaderNodeLabelProcessor, NexusConstants

public class NexusNewickReaderNodeLabelProcessor
extends java.lang.Object
implements NewickReaderNodeLabelProcessor, NexusConstants

Field Summary

Fields

Modifier and Type	Field and Description
static boolean	DEFAULT_TRANSLATE_INTERNAL_NODE_NAMES

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
NexusNewickReaderNodeLabelProcessor(NexusReaderStreamDataProvider streamDataProvider)

Method Summary

Modifier and Type	Method and Description
java.lang.String	getLinkedOTUID(java.lang.String processedLabel) Returns the OTU ID that is associated with the specified label.
java.lang.String	processLabel(java.lang.String originalLabel, boolean isInternal) Processes a label according to the format modeled by this implementation.

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_TRANSLATE_INTERNAL_NODE_NAMES

public static final boolean DEFAULT_TRANSLATE_INTERNAL_NODE_NAMES

See Also:

Constant Field Values

Constructor Detail

NexusNewickReaderNodeLabelProcessor

public NexusNewickReaderNodeLabelProcessor(NexusReaderStreamDataProvider streamDataProvider)

Method Detail

processLabel

public java.lang.String processLabel(java.lang.String originalLabel,
                                     boolean isInternal)

Description copied from interface: NewickReaderNodeLabelProcessor

Processes a label according to the format modeled by this implementation.

Specified by:

processLabel in interface NewickReaderNodeLabelProcessor

Parameters:

originalLabel - the label as it was read from the Newick string

isInternal - defines whether the node carrying this label is an internal node or not

Returns:

the processed label

getLinkedOTUID

public java.lang.String getLinkedOTUID(java.lang.String processedLabel)

Description copied from interface: NewickReaderNodeLabelProcessor

Returns the OTU ID that is associated with the specified label.

Specified by:

getLinkedOTUID in interface NewickReaderNodeLabelProcessor

Parameters:

processedLabel - the processed label as it was returned by a call if #processLabel(String)

Returns:

the linked OTU ID or null if no associated OTU ID exists