Download version 0.5.0 of JPhyloIO
You are downloading an older version (0.5.0-1597 alpha) of JPhyloIO which was released on 2018-02-04 23:20:00.0 The latest version can be found here.
License
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
Complete download
The complete download contains the classes of all components associated with this release.
| Complete binary, sources, docs |
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|---|---|
| Complete binary only |
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[Browse source codes] [Browse JavaDoc]
Single component downloads
The following components are associated with version 0.5.0. Components that were updated in this version are shown in bold.
| Component | Module binary JAR | Module sources |
|---|---|---|
| Core |
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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>0.5.0</version>
</dependency>
Repository
<repository>
<id>bioinfweb-maven-repo</id>
<name>bioinfweb repository</name>
<url>http://bioinfweb.info/MavenRepository/</url>
</repository>
Changes in this version
- New release of core.
- Warning: This release does not specify the correct version number of JPhyloIO when writing files. This has been fixed in version 0.5.1.
Core
- 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.
