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Download version 0.3.0 of JPhyloIO

You are downloading an older version (0.3.0-1475 alpha) of JPhyloIO which was released on 2016-12-14 13:15:00.0 The latest version can be found here.

License

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.

Downloads

Complete download

The complete download contains the classes of all components associated with this release.

Complete binary, sources, docs Download icon complete-0.3.0.zip
Complete binary only Download icon complete-0.3.0-bin.zip

[Browse source codes]    [Browse JavaDoc]

Single component downloads

The following components are associated with version 0.3.0. Components that were updated in this version are shown in bold.

Component Module binary JAR Module sources
Core Download icon core-0.3.0.jar Download icon core-0.3.0-source.zip

Subversion

Developers can also check out the source codes directly from the subversion repository under https://secure.bioinfweb.info/Code/svn/JPhyloIO/trunk/main/.

Maven

Developers can use the following code to add dependencies for the modules of JPhyloIO to their Maven project.

Dependencies

<dependency>
    <groupId>info.bioinfweb.jphyloio</groupId>
    <artifactId>jphyloio-core</artifactId>
    <version>0.3.0</version>
</dependency>

Repository

<repository>
    <id>bioinfweb-maven-repo</id>
    <name>bioinfweb repository</name>
    <url>http://bioinfweb.info/MavenRepository/</url>
</repository>

Changes in this version

  • Contains a new version of the core module.

Core

  • 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.

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