Information & Computational Sciences

New in Flapjack

By on 31/10/2016 in News

Flapjack has just been updated to version

  • NEW: Implemented a new analysis method for calculating marker assisted back crossing (MABC) statistics.
  • NEW: Implemented MABC stats for recurrent parent percentage and linkage drag.
  • NEW: Added a initial dialog for MABC to enable selection of parent lines and MABC parameters.
  • NEW: MABC statistics are displayed in an Analysis Results Table (linked view).
  • NEW: Added a whole new view – the Analysis Results Table – that links statistical results to the graphical genotype visualizations.
  • NEW: Line order, selection state, visibility, etc between a view and a Results Table is mirrored at all times.
  • NEW: Added advanced line sort functionality to the Results Tables, including the ability to ignore sort order for certain lines.
  • NEW: Added advanced line filter functionality to the Results Tables, including the ability to ignore filter parameters for certain lines.
  • NEW: Added line selection functionality to the Results Tables.
  • NEW: Added the ability to export all, just the visible, or just the visible/selected lines from a Results Table.
  • NEW: Added a right-click menu option to the main view’s lines list to enable the display of data from a Results Table next to the normal visualizations.
  • NEW: Disabled the ability to add sort splitters, insert blank lines, etc when using a a view that contains a Results Table.
  • NEW: All Results Table data, as well as its options (sort order, filters etc) are saved as part of a project.
  • NEW: Implemented a new analysis method for pedigree verification of lines (PedVer); also using the Analysis Results Tables.
  • NEW: Implemented PedVer stats covering %age heterozygosity, %age deviation from expected F1, %age containment for parents, etc.
  • NEW: Added a initial dialog for PedVer to enable selection of options for parent lines, simulated F1, etc.
  • NEW: Added a special colour by similarity colour scheme which works on an exact match basis (for PedVer visualization).
  • NEW: Added command-line executables for running MABC and PedVer statistics (straight input->output).
  • NEW: Heterozygous rendering can now be forced to mono-colour “H” blocks at any time, regardless of the selected colour scheme.
  • NEW: Maps in the all chromosome view now alternate between having white and light blue backgrounds.
  • NEW: Added a special MABC-only option to ‘rank’ lines that is available via the table view.
  • NEW: Created a new map-based graphic to show ‘notches’ above any marker that is itself under a QTL.
  • NEW: Modified the similarity colour schemes so alleles compared against missing data are grey by default (rather than red).
  • NEW: Added new options to the Customize Colours dialog so the user can specify the ‘grey’ colour (or make it red like before).
  • NEW: Added an option to filter (and hide) monomorphic markers.
  • NEW: Added an option to filter (and hide) missing markers for a given line.
  • NEW: Added an option to filter (and hide) heterozygous markers for a given line.
  • NEW: Added the ability to access the filter markers options by right-clicking on the canvas.
  • NEW: Numerical summaries are now shown after filtering or selecting markers.
  • NEW: Flapjack now tracks the expansion state of the tree in the navpanel, as well as which node is selected.
  • NEW: Modified the loading code so that Flapjack can import data without a map file.
  • NEW: Modified the map loading code to look for entries defining the length of each chromosome.
  • NEW: Adjusted the map visualization to deal with chromosomes that can now be longer than the last marker’s position.
  • NEW: Added map start/end ‘notches’ to visually show when its start or end are on screen.
  • NEW: The list of line names now highlights the row under the mouse (just like mousing over on the main canvas).
  • NEW: Web service jobs (simmatrix and pcoa) can now be cancelled by the user.
  • NEW: Added a message to the final stages of PCoA generation to warn/inform of loading CurlyWhirly.
  • NEW: Flapjack now displays a dialog where the user can select the number of dimensions for the PCoA analysis to generate.
  • NEW: Flapjack will now allow views with zero lines and/or markers (because they’ve all been hidden).
  • NEW: Mousing over the map on the all chromosomes view now shows the position for the chromosome your mouse is over and its name.
  • NEW: Added the ability to rename analysis nodes in the NavPanel (eg MABC, PedVer, SimMatrix and Dendrogram).
  • NEW: Chromosome names now sort in a more natural order when data is first imported.
  • NEW: Added the ability to mirror the selection state of markers between the all chromosome view and normal views.
  • NEW: Updated and/or added many new help topics.
  • NEW: Added a new tab to the About Dialog to cover funding and/or acknowledgements.
  • CHG: Updated the Dendrogram and PCoA web services to utilise a combination of Restlet (REST) and DRAMM APIs.
  • CHG: Many of the analysis tasks now share a common UI for selecting which chromosomes to analyse.
  • CHG: Changing the coloured state of a traits table now marks a project as modified.
  • CHG: Switched the default colours for line/marker similarity so that green is a match and red is a non-match.
  • CHG: Comparison colour schemes will now render all grey if the comparison line/marker is removed from the view.
  • CHG: Removed all instances of the blue “Office/Windows XP” look and feel that were still present.
  • CHG: Disabled showing icons on any of the menus on OS X.
  • CHG: Adjusted the map scaling preference to use Global as its new default.
  • CHG: Many of the analysis methods now know whether it makes sense to run over the all-chromosomes view or not.
  • CHG: Removed all instances of the old blue “Windows XP” title panel that was still present in many of Flapjack’s dialogs.
  • CHG: Made various inner changes and improvements to get Flapjack ready for Java 9, mainly related to XML parsing and HiDPI support.
  • BUG: Any errors thrown during map loading probably had (a slightly) wrong line number given.
  • BUG: If a trait’s numerical value for every line is identical, then the colouring didn’t work (trait was black).
  • BUG: Fixed an issue when saving projects containing similarity matrices.
  • BUG: Fixed problems with floating point precision for datasets with very large (probably physical) marker or QTL positions.
  • BUG: Collapsing input files containing (for example) A/A into A wasn’t working for all cases.
  • BUG: Fixed an issue with combo boxes stretching beyond their panel bounds with very long text.
  • BUG: Nav/Marker/Line mode selections weren’t reflecting their correct state after certain operations.
  • BUG: Undo/redo wasn’t tracking filtering of marker changes across multiple chromosomes.
  • BUG: None of the filtering methods were correctly “undo-ing” their state if the operation was cancelled mid-way.
  • BUG: Fixed an issue when saving projects containing similarity matrices.
  • BUG: Fixed a bug with sorting by trait related to incorrect multi-row selection/deletion events in the dialog.
  • BUG: Updated all of the floating point parsing code to use methods that are locale-safe.
  • BUG: Some of the filtering/selecting marker methods were not tracking their progress properly.

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