info.bioinfweb.jphyloio.formats.newick

Class NewickStringWriter

java.lang.Object

info.bioinfweb.jphyloio.formats.newick.NewickStringWriter

All Implemented Interfaces:

NewickConstants

public class NewickStringWriter
extends java.lang.Object
implements NewickConstants

Implementation to write Newick tree definitions to be used by NewickEventWriter and NexusEventWriter.

Author:

Ben Stöver

See Also:

NewickEventWriter, NexusEventWriter, Metadata demo application

Field Summary

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
NewickStringWriter(TextWriterStreamDataProvider<?> streamDataProvider, TreeNetworkDataAdapter tree, NewickWriterNodeLabelProcessor nodeLabelProcessor, ReadWriteParameterMap parameters) Creates a new instance of this class.

Method Summary

Modifier and Type	Method and Description
static java.lang.String	formatToken(java.lang.String token, char delimiter)
static boolean	isFreeNameCharForWriting(char c)
void	write() Writes the tree data specified in the constructor to the specified stream.

Methods inherited from class java.lang.Object

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

Constructor Detail

NewickStringWriter

public NewickStringWriter(TextWriterStreamDataProvider<?> streamDataProvider,
                          TreeNetworkDataAdapter tree,
                          NewickWriterNodeLabelProcessor nodeLabelProcessor,
                          ReadWriteParameterMap parameters)

Creates a new instance of this class.

Parameters:

writer - the writer to write the Newick string to

tree - the tree data adapter providing the tree data to be written

otuList - the list of OTU definitions to be used to label unlabeled tree nodes (Maybe null.)

useOTUFirst - Specify true here, if AbstractEventWriter#getLinkedOTUNameOTUFirst(LinkedLabeledIDEvent, OTUListDataAdapter) shall be used to determine node names (e.g. for writing Nexus) or false if AbstractEventWriter#getLinkedOTUNameOwnFirst(LinkedLabeledIDEvent, OTUListDataAdapter) should be used instead (e.g. for writing Newick).

parameters - the write parameter map specified to the calling reader

Method Detail

isFreeNameCharForWriting

public static boolean isFreeNameCharForWriting(char c)

formatToken

public static java.lang.String formatToken(java.lang.String token,
                                           char delimiter)

write

public void write()
           throws java.io.IOException

Writes the tree data specified in the constructor to the specified stream.

If the specified tree/network data adapter models a phylogenetic network and not a tree, nothing is written and an according warning is logged. Additionally warnings are logged, if the tree adapter provides metadata or if multiple root edges are available.

If an empty tree definition (with no root edge) is specified, the written Newick string only consists of the terminal symbol ';'.

Throws:

java.io.IOException - if an I/O error occurs while writing to specified writer