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CHANGELOG.md

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Changelog

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

Unreleased

  • Updated minimum Java version from Java 11 to Java 17 (current LTS).
  • Used Spotless to clean up pom.xml, Markdown and Java files.
  • Added .mvn/jvm.config to work around an issue with Spotless.
  • Removed IDEA (IntelliJ) files.
  • Added a GitHub Action to check style, test and package.

v1.9: May 14, 2021

  • Replaced Ant-based build process with Maven build.
  • Changed minimum Java version from 1.8 to 11.
  • Consolidated all shared code into TaxonDNA.Common.
  • Added memory information in the SequenceMatrix About dialog box.
  • Added Spotless for code style checking.

v1.8.2: April 17, 2020

  • Updated Java version from 1.5 to 1.8. No Mac application is available for this release, but I'll try to fix that in #70 before the next release. You can run the JAR file on macOS by opening the Terminal and running:

v1.8.1: April 17, 2020

Older versions

  • 1.8: June 22, 2015
    • Used 'codesign' to sign "Sequence Matrix.app" as this might prevent it from being recognized on MacOS X systems.
    • Thanks to Shiyu Phan for this suggestion!
  • 1.7.9
    • Turned off displaying 'N's in the display, as we don't re-export those anyway.
    • Fixed a bug in the Cluster tool reported by Michael Balke: single species without conspecific sequences in the dataset were being reported as 'Split'.
  • 1.7.8
    • Added DOI to the citation for Sequence Matrix.
  • 1.7.7-dev4
    • Naked Nexus now replaces all non-alphanumeric characters with underscores.
  • 1.7.7-dev3
    • Fixed a minor bug with clustering in which the "% of valid comparisons above the threshold" number was always 0%.
    • Fixed a bug in which multiple "Cluster" analyses in the same session caused the ProgressDialog to never close, resulting in the program getting "stuck" and a forced quit becoming necessary.
  • 1.7.7-dev2
    • Rewrote SpeciesDetails to remove the old, bug-ridden algorithm. The new one will probably actually work.
    • Added discrimination between "Split only", "Lumped/Split" and "Lumped" for clusters in Cluster.
  • 1.7.6 (June 6, 2010)
    • Added code to detect overlapping codonsets on input (#19).
    • Fixed a bug relating to TNT files exported into directory (#55).