info.bioinfweb.jphyloio.formats.newick

Class NewickFactory

java.lang.Object

info.bioinfweb.jphyloio.factory.AbstractSingleReaderWriterFactory

info.bioinfweb.jphyloio.formats.newick.NewickFactory

All Implemented Interfaces:

SingleReaderWriterFactory, JPhyloIOFormatIDs, NewickConstants

public class NewickFactory
extends AbstractSingleReaderWriterFactory
implements SingleReaderWriterFactory, JPhyloIOFormatIDs, NewickConstants

Reader and writer factory for the Newick format.

Since:

0.0.0

Author:

Ben Stöver

Field Summary

Fields inherited from interface info.bioinfweb.jphyloio.formats.JPhyloIOFormatIDs

FASTA_FORMAT_ID, FORMAT_ID_PREFIX, MEGA_FORMAT_ID, NEWICK_FORMAT_ID, NEXML_FORMAT_ID, NEXUS_FORMAT_ID, PDE_FORMAT_ID, PHYLIP_FORMAT_ID, PHYLOXML_FORMAT_ID, SEQUENTIAL_PHYLIP_FORMAT_ID, XTG_FORMAT_ID

Fields inherited from interface info.bioinfweb.jphyloio.formats.newick.NewickConstants

ALLOCATION_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_COMMENT

Constructor Summary

Constructors

Constructor and Description
NewickFactory()

Method Summary

Modifier and Type	Method and Description
boolean	checkFormat(java.io.Reader reader, ReadWriteParameterMap parameters) Since there is no real characteristic starting string for any Newick file, it is just checked whether at least five events (if available) can be created from the input without an exception.
protected JPhyloIOFormatInfo	createFormatInfo()
JPhyloIOEventReader	getReader(java.io.InputStream stream, ReadWriteParameterMap parameters) Creates a new reader instance for the target format of this factory.
JPhyloIOEventReader	getReader(java.io.Reader reader, ReadWriteParameterMap parameters) Creates a new reader instance for the target format of this factory.
JPhyloIOEventWriter	getWriter() Creates a new writer instance for the target format of this factory.
boolean	hasReader() Determines whether this factory is able to create reader instances for its target format.
boolean	hasWriter() Determines whether this factory is able to create writer instances for its target format.

Methods inherited from class info.bioinfweb.jphyloio.factory.AbstractSingleReaderWriterFactory

checkFormat, getFormatInfo

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.factory.SingleReaderWriterFactory

checkFormat, getFormatInfo

Constructor Detail

NewickFactory

public NewickFactory()

Method Detail

checkFormat

public boolean checkFormat(java.io.Reader reader,
                           ReadWriteParameterMap parameters)

Since there is no real characteristic starting string for any Newick file, it is just checked whether at least five events (if available) can be created from the input without an exception. Since this method may fail in some cases, factories should test this format after all the others have been tested unsuccessfully.

Specified by:

checkFormat in interface SingleReaderWriterFactory

Parameters:

reader - the reader to read the first bytes from

parameters - the parameters map that would also be used to create a reader

Returns:

true if the tested reader may return content in target format or false if the content is not in valid target format

See Also:

SingleReaderWriterFactory.checkFormat(java.io.Reader, info.bioinfweb.jphyloio.ReadWriteParameterMap)

getReader

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

Description copied from interface: SingleReaderWriterFactory

Creates a new reader instance for the target format of this factory.

Specified by:

getReader in interface SingleReaderWriterFactory

Parameters:

stream - the stream to provide the content for the reader

parameters - the parameter map for the new reader instance

Returns:

the new reader instance

Throws:

java.io.IOException

getReader

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

Description copied from interface: SingleReaderWriterFactory

Creates a new reader instance for the target format of this factory.

Specified by:

getReader in interface SingleReaderWriterFactory

parameters - the parameter map for the new reader instance

Returns:

the new reader instance or null if this factory is not able to create readers

Throws:

java.io.IOException

See Also:

SingleReaderWriterFactory.hasReader()

getWriter

public JPhyloIOEventWriter getWriter()

Description copied from interface: SingleReaderWriterFactory

Creates a new writer instance for the target format of this factory.

Specified by:

getWriter in interface SingleReaderWriterFactory

Returns:

the new writer instance or null if this factory is not able to create writers

See Also:

SingleReaderWriterFactory.hasWriter()

hasReader

public boolean hasReader()

Description copied from interface: SingleReaderWriterFactory

Determines whether this factory is able to create reader instances for its target format.

Specified by:

hasReader in interface SingleReaderWriterFactory

Returns:

true if creating readers is supported or false otherwise

hasWriter

public boolean hasWriter()

Description copied from interface: SingleReaderWriterFactory

Determines whether this factory is able to create writer instances for its target format.

Specified by:

hasWriter in interface SingleReaderWriterFactory

Returns:

true if creating writers is supported or false otherwise

createFormatInfo

protected JPhyloIOFormatInfo createFormatInfo()

Specified by:

createFormatInfo in class AbstractSingleReaderWriterFactory