public class NewickEventReader extends AbstractTextEventReader<TextReaderStreamDataProvider<NewickEventReader>> implements NewickConstants
';'. Any whitespace, as well as comments contained in '['
and ']' is allowed between all tokens.
Additionally this reader is able to parse hot comments associated with nodes or edges and the eNexus network formats
as described in the documentation of NewickStringReader.
lineConsumedALLOCATION_SEPARATOR_SYMBOL, ALLOCATION_SYMBOL, ALTERNATIVE_NAME_DELIMITER, COMMENT_END, COMMENT_START, DATA_TYPE_NEWICK_ARRAY, E_NEWICK_EDGE_TYPE_HYBRIDIZATION, E_NEWICK_EDGE_TYPE_LATERAL_GENE_TRANSFER, E_NEWICK_EDGE_TYPE_RECOMBINATION, E_NEWICK_NAMESPACE_PREFIX, E_NEWICK_NETWORK_DATA_SEPARATOR, ELEMENT_SEPERATOR, FIELD_END_SYMBOL, FIELD_START_SYMBOL, FIELD_VALUE_SEPARATOR_SYMBOL, FREE_NAME_BLANK, HOT_COMMENT_START_SYMBOL, INDEX_END_SYMBOL, INDEX_START_SYMBOL, LENGTH_SEPERATOR, NAME_DELIMITER, NEWICK_DATA_TYPE_NAMESPACE, NEWICK_FORMAT_NAME, NEWICK_NAMESPACE_PREFIX, NHX_KEY_CONFIDENCE, NHX_KEY_EVENT, NHX_KEY_GENE_NAME, NHX_KEY_PREFIX, NHX_KEY_SCIENTIFIC_NAME, NHX_KEY_SEQUENCE_ACCESSION, NHX_KEY_TAXONOMY_ID, NHX_START, NHX_VALUE_SEPARATOR_SYMBOL, PREDICATE_E_NEWICK_EDGE_TYPE, ROOTED_HOT_COMMENT, SUBTREE_END, SUBTREE_START, TERMINAL_SYMBOL, UNROOTED_HOT_COMMENTATTRIBUTE_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 and Description |
|---|
NewickEventReader(java.io.BufferedReader reader,
ReadWriteParameterMap parameters)
Creates a new instance of this class.
|
NewickEventReader(java.io.File file,
ReadWriteParameterMap parameters)
Creates a new instance of this class.
|
NewickEventReader(java.io.InputStream stream,
ReadWriteParameterMap parameters)
Creates a new instance of this class.
|
NewickEventReader(java.io.Reader reader,
ReadWriteParameterMap parameters)
Creates a new instance of this class.
|
| Modifier and Type | Method and Description |
|---|---|
java.lang.String |
getFormatID()
Returns a string ID uniquely identifying the target format of this instance.
|
protected void |
readNextEvent()
Method to be implemented be inherited classes that adds at least one additional event (determined from
the underlying data source) to the event queue.
|
close, consumeWhiteSpaceAndComments, createStreamDataProvider, createTokenList, getReader, readCharacters, readCharacters, readComment, readKeyValueInformation, readTokenaddEventListener, fireEvent, getCurrentEventCollection, getIDManager, getLastNonCommentEvent, getParameters, getParentInformation, getPreviousEvent, getSequenceTokensEventManager, getStreamDataProvider, getUpcomingEvents, hasNextEvent, hasSpecialEventCollection, isBeforeFirstAccess, next, nextOfType, peek, removeEventListener, resetCurrentEventCollection, setCurrentEventCollectionpublic NewickEventReader(java.io.BufferedReader reader, ReadWriteParameterMap parameters) throws java.io.IOException
reader - the reader providing the Newick data to be readparameters - the parameter map for this reader instancejava.io.IOException - if an I/O exception occurs while parsing the first eventpublic NewickEventReader(java.io.File file, ReadWriteParameterMap parameters) throws java.io.IOException
file - the Newick file to be readparameters - the parameter map for this reader instancejava.io.IOException - if an I/O exception occurs while parsing the first eventpublic NewickEventReader(java.io.InputStream stream, ReadWriteParameterMap parameters) throws java.io.IOException
stream - the stream providing the Newick data to be readparameters - the parameter map for this reader instancejava.io.IOException - if an I/O exception occurs while parsing the first eventpublic NewickEventReader(java.io.Reader reader, ReadWriteParameterMap parameters) throws java.io.IOException
reader - the reader providing the Newick data to be readparameters - the parameter map for this reader instancejava.io.IOException - if an I/O exception occurs while parsing the first eventpublic java.lang.String getFormatID()
JPhyloIOFormatSpecificObjectJPhyloIOReaderWriterFactory.getFormatInfo(String).
Third party developers that create readers or writers for additional formats must make sure to use a globally unique
format ID. It is strongly recommended to use owned reverse domain names for this (e.g.
org.example.additionalformat).
getFormatID in interface JPhyloIOFormatSpecificObjectJPhyloIOReaderWriterFactory.getFormatInfo(String)protected void readNextEvent() throws java.io.IOException
AbstractEventReaderreadNextEvent in class AbstractEventReader<TextReaderStreamDataProvider<NewickEventReader>>java.io.IOException