info.bioinfweb.jphyloio.formats.phylip

Class AbstractPhylipEventReader<P extends TextReaderStreamDataProvider<? extends AbstractPhylipEventReader<P>>>

java.lang.Object

info.bioinfweb.jphyloio.AbstractEventReader<P>

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

info.bioinfweb.jphyloio.formats.phylip.AbstractPhylipEventReader<P>

All Implemented Interfaces:

PhylipConstants, JPhyloIOEventReader, JPhyloIOFormatSpecificObject, ReadWriteConstants

Direct Known Subclasses:

PhylipEventReader, SequentialPhylipEventReader

public abstract class AbstractPhylipEventReader<P extends TextReaderStreamDataProvider<? extends AbstractPhylipEventReader<P>>>
extends AbstractTextEventReader<P>
implements PhylipConstants

Implements shared functionality of Phylip event readers.

Author:

Ben Stöver

Field Summary

Fields

Modifier and Type	Field and Description
protected java.lang.String	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
AbstractPhylipEventReader(java.io.File file, ReadWriteParameterMap parameters)
AbstractPhylipEventReader(java.io.InputStream stream, ReadWriteParameterMap parameters)
AbstractPhylipEventReader(PeekReader reader, ReadWriteParameterMap parameters)
AbstractPhylipEventReader(java.io.Reader reader, ReadWriteParameterMap parameters)

Method Summary

Modifier and Type	Method and Description
protected long	getCharacterCount()
protected long	getSequenceCount()
boolean	isRelaxedPhylip()
protected void	readMatrixDimensions()
protected java.lang.String	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, readNextEvent, removeEventListener, resetCurrentEventCollection, setCurrentEventCollection

Methods inherited from class java.lang.Object

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

Methods inherited from interface info.bioinfweb.jphyloio.JPhyloIOFormatSpecificObject

getFormatID

Field Detail

currentSequenceName

protected java.lang.String currentSequenceName

Constructor Detail

AbstractPhylipEventReader

public AbstractPhylipEventReader(PeekReader reader,
                                 ReadWriteParameterMap parameters)

AbstractPhylipEventReader

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

Throws:

java.io.IOException

AbstractPhylipEventReader

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

Throws:

java.io.IOException

AbstractPhylipEventReader

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

Throws:

java.io.IOException

Method Detail

isRelaxedPhylip

public boolean isRelaxedPhylip()

getSequenceCount

protected long getSequenceCount()

getCharacterCount

protected long getCharacterCount()

readMatrixDimensions

protected void readMatrixDimensions()
                             throws java.io.IOException

Throws:

java.io.IOException

readSequenceName

protected java.lang.String readSequenceName()
                                     throws java.io.IOException

Throws:

java.io.IOException