Available downloads of JPhyloIO - Core

GNU Lesser General Public License, version 3

JPhyloIO is distributed under GNU Lesser General Public License. Copyright (C) 2015 - 2016 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.

First entry:    Number of entries:    alpha   beta   release candidate   release  
Downloads Version Since Changes
Download icon Module binary JAR    Download icon 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.
Download icon Module binary JAR    Download icon 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.
First entry:    Number of entries:    alpha   beta   release candidate   release  
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