info.bioinfweb.jphyloio.formats.text

Class AbstractTextEventReader<P extends TextReaderStreamDataProvider<? extends AbstractTextEventReader<P>>>

java.lang.Object

info.bioinfweb.jphyloio.AbstractEventReader<P>

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

All Implemented Interfaces:

JPhyloIOEventReader, JPhyloIOFormatSpecificObject, ReadWriteConstants

Direct Known Subclasses:

AbstractPhylipEventReader, FASTAEventReader, MEGAEventReader, NewickEventReader, NexusEventReader

public abstract class AbstractTextEventReader<P extends TextReaderStreamDataProvider<? extends AbstractTextEventReader<P>>>
extends AbstractEventReader<P>

Abstract base class for all readers that read their data from a file using a PeekReader.

Those are currently readers all reader reading non-XML formats from text files.

Author:

Ben Stöver

Field Summary

Fields

Modifier and Type	Field and Description
protected boolean	lineConsumed

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
AbstractTextEventReader(java.io.File file, ReadWriteParameterMap parameters, java.lang.String matchToken) Creates a new instance of this class.
AbstractTextEventReader(java.io.InputStream stream, ReadWriteParameterMap parameters, java.lang.String matchToken) Creates a new instance of this class.
AbstractTextEventReader(PeekReader reader, ReadWriteParameterMap parameters, java.lang.String matchToken) Creates a new instance of this class.
AbstractTextEventReader(java.io.Reader reader, ReadWriteParameterMap parameters, java.lang.String matchToken) Creates a new instance of this class.

Method Summary

Modifier and Type	Method and Description
void	close() Closes the underlying document source (usually a stream).
protected void	consumeWhiteSpaceAndComments(char commentStart, char commentEnd)
protected P	createStreamDataProvider() This method is called in the constructor of AbstractEventReader to initialize the stream data provider that will be returned by AbstractEventReader.getStreamDataProvider().
protected java.util.List<java.lang.String>	createTokenList(java.lang.CharSequence sequence)
protected PeekReader	getReader() Returns the reader providing the document contents.
protected JPhyloIOEvent	readCharacters(java.lang.String currentSequenceName)
protected JPhyloIOEvent	readCharacters(java.lang.String currentSequenceName, char commentStart, char commentEnd) Reads characters from the stream and adds a respective sequence tokens event to the queue.
protected void	readComment(char commentStart, char commentEnd) Reads a single comment from the reader.
protected KeyValueInformation	readKeyValueInformation(char commandEnd, char commentStart, char commentEnd, char keyValueSeparator)
protected java.lang.String	readToken(char commandEnd, char commentStart, char commentEnd, char keyValueSeparator)

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

lineConsumed

protected boolean lineConsumed

Constructor Detail

AbstractTextEventReader

public AbstractTextEventReader(PeekReader reader,
                               ReadWriteParameterMap parameters,
                               java.lang.String matchToken)

Creates a new instance of this class.

Parameters:

reader - the reader providing the document data to be read

parameters - the parameter map for this reader instance

matchToken - the match token to be replaced in sequences or null if no replacement shall be performed

AbstractTextEventReader

public AbstractTextEventReader(java.io.Reader reader,
                               ReadWriteParameterMap parameters,
                               java.lang.String matchToken)
                        throws java.io.IOException

Creates a new instance of this class.

Parameters:

reader - the reader providing the document data to be read

parameters - the parameter map for this reader instance

matchToken - the match token to be replaced in sequences or null if no replacement shall be performed

Throws:

java.io.IOException

AbstractTextEventReader

public AbstractTextEventReader(java.io.InputStream stream,
                               ReadWriteParameterMap parameters,
                               java.lang.String matchToken)
                        throws java.io.IOException

Creates a new instance of this class.

Parameters:

stream - the stream providing the document data to be read

parameters - the parameter map for this reader instance

matchToken - the match token to be replaced in sequences or null if no replacement shall be performed

Throws:

java.io.IOException

AbstractTextEventReader

public AbstractTextEventReader(java.io.File file,
                               ReadWriteParameterMap parameters,
                               java.lang.String matchToken)
                        throws java.io.IOException

Creates a new instance of this class.

Parameters:

file - the document file to be read

parameters - the parameter map for this reader instance

matchToken - the match token to be replaced in sequences or null if no replacement shall be performed

Throws:

java.io.IOException

Method Detail

createStreamDataProvider

protected P createStreamDataProvider()

Description copied from class: AbstractEventReader

This method is called in the constructor of AbstractEventReader to initialize the stream data provider that will be returned by AbstractEventReader.getStreamDataProvider(). Inherit classes that use their own stream data provider implementation should overwrite this method.

This default implementation creates a new instance of ReaderStreamDataProvider.

Overrides:

createStreamDataProvider in class AbstractEventReader<P extends TextReaderStreamDataProvider<? extends AbstractTextEventReader<P>>>

Returns:

the stream data provider to be used with this instance

createTokenList

protected java.util.List<java.lang.String> createTokenList(java.lang.CharSequence sequence)

consumeWhiteSpaceAndComments

protected void consumeWhiteSpaceAndComments(char commentStart,
                                            char commentEnd)
                                     throws java.io.IOException

Throws:

java.io.IOException

readComment

protected void readComment(char commentStart,
                           char commentEnd)
                    throws java.io.IOException

Reads a single comment from the reader. Only the first one of subsequent comments (e.g. [comment 1][comment 2]) would be read. Nested comments are included in the parsed comment.

This method assumes that the comment start symbol has already been consumed.

Throws:

java.io.IOException

readCharacters

protected JPhyloIOEvent readCharacters(java.lang.String currentSequenceName)
                                throws java.io.IOException

Throws:

java.io.IOException

readCharacters

protected JPhyloIOEvent readCharacters(java.lang.String currentSequenceName,
                                       char commentStart,
                                       char commentEnd)
                                throws java.io.IOException

Reads characters from the stream and adds a respective sequence tokens event to the queue. Additionally comment events are added to the queue, if comments are found.

Parameters:

currentSequenceName -

commentStart -

commentEnd -

Returns:

the sequence tokens event that was added to the event queue

Throws:

java.lang.Exception

java.io.IOException

readToken

protected java.lang.String readToken(char commandEnd,
                                     char commentStart,
                                     char commentEnd,
                                     char keyValueSeparator)
                              throws java.io.IOException

Throws:

java.io.IOException

readKeyValueInformation

protected KeyValueInformation readKeyValueInformation(char commandEnd,
                                                      char commentStart,
                                                      char commentEnd,
                                                      char keyValueSeparator)
                                               throws java.io.IOException

Throws:

java.io.IOException

getReader

protected PeekReader getReader()

Returns the reader providing the document contents.

Returns:

the reader to read the document data from

close

public void close()
           throws java.io.IOException

Description copied from interface: JPhyloIOEventReader

Closes the underlying document source (usually a stream).

Specified by:

close in interface JPhyloIOEventReader

Overrides:

close in class AbstractEventReader<P extends TextReaderStreamDataProvider<? extends AbstractTextEventReader<P>>>

Throws:

java.io.IOException - Implementing classes might throw different types of exceptions if the stream cannot be closed properly