Available downloads of JPhyloIO - Core

JPhyloIO is distributed under GNU Lesser General Public License. Copyright (C) 2015 - 2018 by Ben Stöver and Sarah Wiechers. This program is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose. See the GNU Lesser General Public License for more details.

By downloading JPhyloIO you agree with the License. Please read it carefully.

Note that the releases 0.0.0 and 0.1.0 were distributed under GNU General Public License instead.

Downloads	Version	Since	Changes
Module binary JAR    Module sources	1.0.0-1681 beta	2019-06-12 15:30:00.0	The parameter ReadWriteParameterNames.KEY_TRANSLATE_INTERNAL_NODE_NAMES now allows to determine whether internal node names in [i]NEXUS[/i] documents should be translated using the taxon list from the [i]TAXA[/i] block of a translation table. Not translating them can be useful if support values are provided as internal node names.
Module binary JAR    Module sources	0.5.4-1672 alpha	2019-04-26 19:30:00.0	JAX-B dependency JARs added. (These have been removed from the JRE in Java 11.) MetaXMLStreamWriter adjusted to changes in Java 11.
Module binary JAR    Module sources	0.5.3-1657 alpha	2019-03-20 17:45:00.0	Fixed bug #275 that produced additional sequence end events when reading MEGA files with line breaks in sequences.
Module binary JAR    Module sources	0.5.2-1609 alpha	2018-02-26 14:55:00.0	Bug fix: AbstractEventWriter now creates a new stream data provider for each document that is written to avoid data from one document to interfere with writing the next.
Module binary JAR    Module sources	0.5.1-1604 alpha	2018-02-13 09:00:00.0	Bug fix: AbstractNeXMLElementReader does not loose tokens at the end of subsequent character XML events anymore.
Module binary JAR    Module sources	0.5.0-1597 alpha	2018-02-04 23:20:00.0	XTGConstants refactored to use only one constant per values in all contexts. Recently added pie chart label properties in XTG are now supported. XTGEventReader now supports scale bars and legends. XTG constants for width and height renamed. EnumTranslator, HexadecimalColorTranslator and ColorTranslator added. NeXMLWriterStreamDataProvider.idToAlignmentInfo renamed to alignmentInfoByIDMap. Warning messages in NeXMLCollectTokenSetDefinitionDataReceiver now differentiate between switching and specifying a token set. URIOrStringIdentifier.equalsStringOrURI() added. Bug fix (temporary workaround): The OutputStream version of AbstractEventWriter.writeDocument() now closes the decorator writer it uses internally after writing. This was necessary to prevent data loss, but also closes the passed stream, which cannot be used further by the application. Bug fix: XTG readers and writers now use the correct tag spelling for pie chart label IDs. Bug fix: JPhyloIOWritingUtils now allows to write empty literal metadata. Bug fix: AbstractXMLElementReader now handles unknown data types. Bug fix: XTGFormattedTextElementReader now produces correct empty literal metadata event sequences. Bug fix: Missing namespace declarations added to XTGConstants. Bug fixes in character set checking in NeXMLCollectTokenSetDefinitionDataReceiver. Bug fix: MatrixReader does not produce additional sequence end event if there is a line break without additional spaces between the end of the last sequence and the semicolon of a Nexus MATRIX command. Bug fix: NeXMLCollectTokenSetDefinitionDataReceiver now logs warnings at the correct positions. Bug fix: NeXMLEventWriter now clears its ID set after writing to allow to write another document using the same IDs. Bug fix: NeXMLEventWriter now considers gap tokens as atomic instead of uncertain and missing data tokens now also contain gaps und stop codons as their constituents. Bug fix: NeXMLTokenSetEventReceiver now also writes integer symbols for gaps and missing data for discrete token sets.
Module binary JAR    Module sources	0.4.0-1514 alpha	2017-05-13 12:32:00.0	Support for optionally reading Newick strings in eNewick format from Newick files and custom NETWORKS blocks in Nexus added. Internal code corrections.
Module binary JAR    Module sources	0.3.0-1475 alpha	2016-12-14 13:15:00.0	PhyloXMLEventWriter now checks event IDs before writing them to an id_source attribute. JPhyloIOReadingUtils.collectEvents() added. PhyloXMLConstants now defines the correct predicate namespace. PhyloXMLEventReader now fires meta events representing id_source attributes. PhyloXMLEventWriter now writes unique id_source attribute values. Added ReadWriteParameterNames.KEY_PHYLOXML_EVENT_ID_TRANSLATION_MAP to PhyloXMLFactory. PhyloXMLSpecificPredicatesDataReceiver now only writes meta events if their IDs are contained in the according set. A mapping of PhyloXML IDs and JPhyloIO IDs can now be obtained via the ReadWriteParameterMap. PhyloXMLEventReader now uses JPhyloIO event IDs in meta events created from clade relation tags. JPhyloIOEventFactory removed. StAX adapters refactored. Removed unused constant PREDICATE_IS_ALIGNED from ReadWriteConstants. LiteralMetadataContentEvent.toString() added. Static conversion methods added to ListTranslator. NewickStringWriter now writes empty hot comments if necessary in order to distinguish node from edge metadata, when necessary. ObjectTranslatorFactory now allows to use Nexus/Newick lists also in XML formats. PhyloXMLEventWriter now writes the schema location to the root tag of every document. Constants in PhyloXMLMetadataTreatment renamed. Tool methods added to JPhyloIOReadingUtils. NexusEventWriter now logs warning, if multiple token sets are encountered in a single matrix. AbstractNeXMLDataReceiverMixin.handleLiteralContentMeta() is now able to write XML representations of objects. Bug fix: NewickNodeEdgeEventReceiver does not ignore nested literal metadata anymore and throws no InternalError on such events anymore, when writing Newick or Nexus. Bug fix in PhyloXMLSpecificPredicatesDataReceiver: Writing texts now also works if content event does not provide a string representation. Bug fix: NewickScanner now skips terminal name delimiters. Bug fix in NexusEventWriter: TAXLABELS command is not repeated in matrix anymore. Bug fix in TokenSetEventReceiver: Does accept character set interval events now. JavaDoc extended.