Information & Computational Sciences

New in Flapjack

By on 17/03/2014 in News

Flapjack has just been updated to version

  • NEW: The project format is now an sqlite database file, wrapped around the original Flapjack xml. Existing projects in xml (or compressed xml) should still load into Flapjack.
  • NEW: Flapjack can now save large analysis results (eg similarity matrices, dendrograms, etc) directly to its database file without needing to keep them in memory.
  • NEW: Flapjack now experimentally supports remote web services.
  • NEW: Changed the menu system to include a new entry for analysis options and also moved the existing simmatrix generation entry into it (from data).
  • NEW: Added a new remote analysis method that performs a PCoA analysis using a similarity matrix. The results can be visualized using CurlyWhirly.
  • NEW: Added a new remote analysis method that can generate a graphical dendrogram from a similarity matrix.
  • NEW: Added new views to support the new analysis methods, including a basic (initial) visualization of the existing similarity matrix result.
  • NEW: Added the ability to save a dendrogram as both PNG and PDF.
  • NEW: Further tweaked the similarity matrix generation code to make it even faster again.
  • NEW: Subsets of data (both lines and markers) can now be selected when generating matrices.
  • NEW: Added the ability to highlight homozygous alleles.
  • NEW: Added the ability to toggle gradient paint on or off.
  • NEW: Included a new “binned” data colour scheme, that will display genotypes binned from 0 to [n] bins on a low/high colour scale.
  • NEW: Long running allele frequencies calculations are progress tracked and can be cancelled.
  • NEW: Added quick sort options for the traits heatmap, along with a link to the existing advanced sort functionality.
  • NEW: Added a new command-line spin-off (creatematrix) for creating a similarity matrix.
  • NEW: Added an extension of the nucleotide colour scheme so that it also supports 0 and 1 alleles in addition to ACGT.
  • NEW: Added initial support for Spanish (Mexican) language translations.
  • NEW: Added a licence panel to Flapjack’s About Flapjack dialog box.
  • NEW: Implemented various changes to maintain compatibility with new security requirements in Web Start with Java 1.7.0_45 and above.
  • CHG: Flapjack now requires Java 7 as its minimum supported JRE version.
  • CHG: Dropped support for the Flapjack binary format. There are now no options for selecting the format in the Preferences dialog as only the sqlite format is available now.
  • CHG: Removed the option to toggle cloning hidden lines/markers on or off.
  • CHG: The calculation of allele frequencies (for the colour scheme) now correctly interprets the data at the allele level rather than the genotype (eg A/T can now have separate colours for the ratio of A and T).
  • BUG: Fixed some UI display issues with Windows 8.
  • BUG: Fixed an issue on Linux with the line names not (graphically) lining up with the genotypes on the main display.
  • BUG: Traits without an experiment no longer show “undefined” on their mouse over text.
  • BUG: Fixed a display issue with the traits/map canvases that caused them to misalign after performing a sort.
  • BUG: Cloning a view resulted in selected lines/markers affecting the line/marker state of the original view too.
  • BUG: Threaded off drag and drop file loading so that Windows Explorer no longer appears to hang after performing the drop.
  • BUG: Fixed a problem with the final row of the phenotypes table being missing.
  • BUG: Fixed encoding (lack of UTF-8) issues with reading text files.
  • BUG: Fixed an issue with cloning a view causing a complete crash.
  • BUG: Exporting large genotype files was unnecessarily slow.

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