info.bioinfweb.jphyloio.formats.newick

Class NewickScanner

java.lang.Object

info.bioinfweb.jphyloio.formats.newick.NewickScanner

All Implemented Interfaces:

NewickConstants

public class NewickScanner
extends java.lang.Object
implements NewickConstants

Reads Newick tokens from a stream. (This class is used internally by JPhyloIO reader reading Newick tree definitions.)

Author:

Ben Stöver

See Also:

NewickStringReader, NewickEventReader, TreeReader

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
NewickScanner(PeekReader reader, boolean readSequence) Creates a new instance of this class.

Method Summary

Modifier and Type	Method and Description
boolean	hasMoreTokens()
static boolean	isCharAfterLength(char c)
static boolean	isFreeNameChar(char c)
NewickToken	nextToken()
NewickToken	peek()

Methods inherited from class java.lang.Object

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

Constructor Detail

NewickScanner

public NewickScanner(PeekReader reader,
                     boolean readSequence)

Creates a new instance of this class.

Parameters:

reader - the underlying reader to read the tokens from

readSequence - Specify true here, if this reader shall read multiple Newick strings separated by ';' from the underlying stream or false if the reader shall stop at the first encountered tree end (';').

Method Detail

isCharAfterLength

public static boolean isCharAfterLength(char c)

isFreeNameChar

public static boolean isFreeNameChar(char c)

peek

public NewickToken peek()
                 throws java.io.IOException

Throws:

java.io.IOException

hasMoreTokens

public boolean hasMoreTokens()
                      throws java.io.IOException

Throws:

java.io.IOException

nextToken

public NewickToken nextToken()
                      throws java.io.IOException

Throws:

java.io.IOException