info.bioinfweb.jphyloio.formats.phylip

Class PhylipEventReader

java.lang.Object

info.bioinfweb.jphyloio.AbstractEventReader<P>

info.bioinfweb.jphyloio.formats.text.AbstractTextEventReader<P>

info.bioinfweb.jphyloio.formats.phylip.AbstractPhylipEventReader<TextReaderStreamDataProvider<PhylipEventReader>>

info.bioinfweb.jphyloio.formats.phylip.PhylipEventReader

All Implemented Interfaces:

PhylipConstants, JPhyloIOEventReader, JPhyloIOFormatSpecificObject, ReadWriteConstants

public class PhylipEventReader
extends AbstractPhylipEventReader<TextReaderStreamDataProvider<PhylipEventReader>>

Event based reader for Phylip alignment files.

The format is expected to be valid under the definition available here: http://evolution.genetics.washington.edu/phylip/doc/main.html#inputfiles. The extended Phylip format is supported according to this definition: http://www.phylo.org/index.php/help/relaxed_phylip.

Recognized parameters

• ReadWriteParameterNames.KEY_MATCH_TOKEN
• ReadWriteParameterNames.KEY_REPLACE_MATCH_TOKENS
• ReadWriteParameterNames.KEY_RELAXED_PHYLIP
• ReadWriteParameterNames.KEY_ALLOW_INTERLEAVED_PARSING
• ReadWriteParameterNames.KEY_LOGGER
• ReadWriteParameterNames.KEY_MAXIMUM_TOKENS_TO_READ

Author:

Ben Stöver

See Also:

SequentialPhylipEventReader

Field Summary

Fields inherited from class info.bioinfweb.jphyloio.formats.phylip.AbstractPhylipEventReader

currentSequenceName

Fields inherited from class info.bioinfweb.jphyloio.formats.text.AbstractTextEventReader

lineConsumed

Fields inherited from interface info.bioinfweb.jphyloio.formats.phylip.PhylipConstants

DEFAULT_NAME_LENGTH, PHYLIP_FORMAT_NAME, PREMATURE_NAME_END_CHARACTER, RELAXED_PHYLIP_NAME_PATTERN, SEQUENTIAL_PHYLIP_FORMAT_NAME

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
PhylipEventReader(java.io.BufferedReader reader, ReadWriteParameterMap parameters) Creates a new instance of this class.
PhylipEventReader(java.io.File file, ReadWriteParameterMap parameters) Creates a new instance of this class.
PhylipEventReader(java.io.InputStream stream, ReadWriteParameterMap parameters) Creates a new instance of this class.
PhylipEventReader(java.io.Reader reader, ReadWriteParameterMap parameters) Creates a new instance of this class.

Method Summary

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.

Methods inherited from class info.bioinfweb.jphyloio.formats.phylip.AbstractPhylipEventReader

getCharacterCount, getSequenceCount, isRelaxedPhylip, readMatrixDimensions, readSequenceName

Methods inherited from class info.bioinfweb.jphyloio.formats.text.AbstractTextEventReader

close, consumeWhiteSpaceAndComments, createStreamDataProvider, createTokenList, getReader, readCharacters, readCharacters, readComment, readKeyValueInformation, readToken

Methods inherited from class info.bioinfweb.jphyloio.AbstractEventReader

addEventListener, fireEvent, getCurrentEventCollection, getIDManager, getLastNonCommentEvent, getParameters, getParentInformation, getPreviousEvent, getSequenceTokensEventManager, getStreamDataProvider, getUpcomingEvents, hasNextEvent, hasSpecialEventCollection, isBeforeFirstAccess, next, nextOfType, peek, removeEventListener, resetCurrentEventCollection, setCurrentEventCollection

Methods inherited from class java.lang.Object

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

Constructor Detail

PhylipEventReader

public PhylipEventReader(java.io.BufferedReader reader,
                         ReadWriteParameterMap parameters)
                  throws java.io.IOException

Creates a new instance of this class.

Parameters:

reader - the reader providing the Phylip data to be read

parameters - the parameter map for this reader instance

Throws:

java.io.IOException - if an I/O exception occurs while parsing the first event

PhylipEventReader

public PhylipEventReader(java.io.File file,
                         ReadWriteParameterMap parameters)
                  throws java.io.IOException

Creates a new instance of this class.

Parameters:

file - the Phylip file to be read

parameters - the parameter map for this reader instance

Throws:

java.io.IOException - if an I/O exception occurs while parsing the first event

PhylipEventReader

public PhylipEventReader(java.io.InputStream stream,
                         ReadWriteParameterMap parameters)
                  throws java.io.IOException

Creates a new instance of this class.

Parameters:

stream - the stream providing the Phylip data to be read

parameters - the parameter map for this reader instance

Throws:

java.io.IOException - if an I/O exception occurs while parsing the first event

PhylipEventReader

public PhylipEventReader(java.io.Reader reader,
                         ReadWriteParameterMap parameters)
                  throws java.io.IOException

Creates a new instance of this class.

Parameters:

reader - the reader providing the Phylip data to be read

parameters - the parameter map for this reader instance

Throws:

java.io.IOException - if an I/O exception occurs while parsing the first event

Method Detail

getFormatID

public java.lang.String getFormatID()

Description copied from interface: JPhyloIOFormatSpecificObject

Returns a string ID uniquely identifying the target format of this instance. Additional information on the format can be retrieved by passing the returned ID to JPhyloIOReaderWriterFactory.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).

Returns:

the ID of the target format of this instance

See Also:

JPhyloIOReaderWriterFactory.getFormatInfo(String)

readNextEvent

protected void readNextEvent()
                      throws java.io.IOException

Description copied from class: AbstractEventReader

Method to be implemented be inherited classes that adds at least one additional event (determined from the underlying data source) to the event queue.

Specified by:

readNextEvent in class AbstractEventReader<TextReaderStreamDataProvider<PhylipEventReader>>

Throws:

java.io.IOException