Information & Computational Sciences

Flapjack Release Notes

This page describes the additions (NEW), changes (CHG) and bug fixes (BUG) that have been made to Flapjack in recent versions. For full details on all the changes between versions, please see the subversion change log.

New in 1.16.10.31

  • 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.

New in 1.16.03.04

  • NEW: (Experimental) Updated much of Flapjack’s UI to utilize 4K displays (probably Windows only for now).
  • NEW: Added options to the Preferences dialog to control UI scaling.
  • NEW: A trait’s categorical or numerical status is now reflected in its column header (and tooltip).
  • NEW: Tooltip headers are now enabled for the QTL table.
  • NEW: Added a new dialog to allow the user to customize the colours for traits.
  • NEW: Added a File->Optimize menu option that performs an sqlite vacuum on the project.
  • CHG: Tidied up a few of the menu options to make the use of ellipses a bit more consistent.
  • CHG: Updated scri-commons to the latest version (to allow for progress tracking dialogs that can’t be cancelled).
  • BUG: The option to allow data containing duplicate line names to be imported was missing when importing transposed data files.
  • BUG: Fixed a crash with CreateProject where binned data with 8 bins would cause an Exception in the MAGIC population detection code (which also uses 8 states).
  • BUG: The loading dialog would track the number of lines as zero when it reached 100%.
  • BUG: Data summaries were wrong when the number of alleles broke the 32bit INT limit.
  • BUG: QTL/features with single point values weren’t displaying properly, or allowing interaction.

New in 1.15.08.31

  • NEW: Updated all the installers to include the latest version of Java.
  • NEW: The traits table will now show the heatmap colours behind each table cell.
  • NEW: Flapjack can now load HDF5 files that are of a specific Flapjack defined format (experimental).
  • NEW: Importing of large genotype files is now faster.
  • NEW: Added an option to visually distinguish category boundaries on the traits heatmap.
  • NEW: The traits table now shows full trait names, plus experiment info if any, as a tooltip in the column headers.
  • NEW: Added an option to allow data sets with duplicate line (names) to still be imported.
  • CHG: Matrix calculations are now disabled when working with binned data.
  • CHG: Removed the write-file test when running installer-update code as it’s not compatible with UAC situations.
  • CHG: Updated all help links to point to the new help pages on the new ICS wiki.
  • BUG: Editing the phenotypes table is no longer possible.
  • BUG: Importing SSR data was failing when the number of allele states breaks 127.

New in 1.15.04.27

  • BUG: Fixed an issue with importing SSR style data where the number of possible allele states can get very high.

New in 1.15.03.02

  • CHG: Importing of very large genotype files is now significantly faster.
  • BUG: Fixed some NPE/HTTP 500 issues with the remote analysis services when using OS X or Linux clients.

New in 1.14.09.24

  • NEW: Implemented a new graph based view of each chromosome selectable from the Chromosomes Panel.
  • NEW: Optimised the hiding lines and markers code so it is now significantly faster.
  • NEW: The list of chromosomes is now always sorted and presented alphabetically.
  • NEW: Added a progress tracker dialog for filtering missing markers on very large datasets.
  • NEW: Improved the scrolling speed of the ChromosomesPanel (10 pixels rather than 1).
  • NEW: Added an option to allow the creation of a custom Chromosomes Panel view based on the currently selected set of lines (Edit->Create Custom…).
  • NEW: Flapjack will now default to using a Save-As prompt if a file being written to is read-only.
  • NEW: Tweaked the label on the dialog for importing sample projects to explain how to retrieve the original input files.
  • BUG: Fixed a critical bug where dendrogram-created similarity matrices had the wrong (internal) line order.
  • BUG: Enabling the Chromosomes Panel view now sets the rest of Flapjack’s menus to their correct enabled/disabled state.
  • BUG: Fixed some issues with .flapjack project files opened (as attachments) from Outlook.
  • BUG: Some of the projects in the MRU list were being duplicated.
  • BUG: The Chromosome Panel’s heatmap key wasn’t updating high/low values on dataset changes.

New in 1.14.07.21

  • NEW: Added a new colour scheme to visualize MAGIC population data in Flapjack.
  • NEW: Added a new (unfinished) “chromosomes” view of the data set.
  • CHG: Flapjack will now only send any traits active on the current view’s heatmap when passing data to CurlyWhirly.
  • CHG: The recently opened files list will now track up to ten recent projects.
  • CHG: Replaced the old mailing list panel with a link to the citation information.
  • CHG: Tweaked the binned data auto detection code to check for numerical data as well as binned data with bin headers.
  • BUG: Cancelling the imports of line or marker selection incorrectly caused their respective selection modes to be activated.
  • BUG: Hidden lines were not being ignored properly when generating a similarity matrix.
  • BUG: If the option to NOT collapse A/T into T/A was picked at import time, the matrix would score them as 0.5 rather than 1.0.

New in 1.14.04.29

  • NEW: Flapjack now recognises bin-headers (#bin) and displays this information when mousing over an entry.
  • NEW: Lines and markers can now be selected by loading in text files with the names of lines/markers to be selected.
  • NEW: The menus showing colour scheme options now highlight the active scheme.
  • BUG: The createproject command-line code wasn’t producing files in the new project format.
  • BUG: Unknown states were not being skipped properly in the new similarity matrix calculation code.
  • BUG: Dummy markers (on the all-chromosomes view) were still being included in any matrix calculations.

New in 1.14.03.17

  • 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.

New in 1.13.03.19

  • BUG: Searching for lines by name was no longer working.

New in 1.13.03.18

  • NEW: Added support for duplicating a line.
  • NEW: Optimised some of the similarity matrix calculation code to make it about 50% faster.
  • NEW: Enhanced SplitProject so it can selectively process datasets, with optional renaming of them.
  • BUG: Export options for all-chromosomes were not behaving properly based on the user’s selected chromosomes.
  • BUG: Filtering QTL on a freshly loaded project caused the Filter dialog to be blank.

New in 1.12.05.25

  • NEW: Sorting by trait can now be done on any number of sort levels.
  • NEW: Redesigned the Sort by Trait dialog to present a tabular control for defining the sort levels.
  • NEW: Added file header support so Flapjack can properly identify its input files.
  • NEW: Added drag and drop support for all input files (so long as they carry header information).
  • NEW: All generated output files now include header information in them.
  • NEW: Graph data can now be imported into Flapjack using the Wiggle data format.
  • NEW: Added a splitproject executable to handle importing .flapjack files and re-generating their component parts (map file, genotype file, etc).
  • NEW: Added a new dialog for quick exporting all project data back to disk in raw file format.
  • NEW: The split between the original chromosomes on the all-chromosomes view is now shown graphically.
  • NEW: QTL should now be correctly drawn on the super-chromosome view.
  • BUG: Fixed various selection state issues when using the all-chromosomes view.
  • BUG: The show/hide dialog now displays the correct marker count when dealing with the all-chromosomes view.
  • BUG: Fixed various display misc issues when sorting/finding/etc via the all-chromosomes view.
  • BUG: Importing graph data for an all-chromosomes set now works correctly.
  • BUG: The minimum and maximum values for a graph weren’t being calculated properly if some markers were missing data.
  • BUG: Fixed dialogs disappearing if the user’s screen resolution had changed since they were last visible.
  • BUG: Removing QTL from a project and then resaving was breaking the project file.
  • BUG: Cloning a view was not properly copying across the QTL information.
  • BUG: Selecting a QTL (and toggling marker states) switched the view to Marker Mode but left the toolbar/menu states incorrect.
  • BUG: Fixed the ‘Comparison method violates its general contract’ error with certain sort operations.
  • BUG: Exporting map and genotype data still included the duplicated markers and genotypes from any all-chromosomes view.
  • BUG: Fixed a problem that saw QTL being duplicated after (re)saving a project in XML format.

New in 1.11.12.13

  • NEW: Added the ability to export an all-by-all similarity matrix for the lines within the current view.
  • NEW: Added support for a sort splitter, that denotes that all lines above it are exempt from sorting and always keep their order. Lines below are sorted as normal.
  • CHG: It is now possible to cancel Line Sort operations.
  • CHG: Due to internal changes, existing projects with QTL will need to have their QTL re-imported.
  • BUG: Similarity scores for cases such as A vs A/T were incorrect (0 rather than 0.5).
  • BUG: Fixed a problem with incorrect chromosome positions being shown when moving the mouse over the chromosome map canvas.
  • BUG: Fixed a problem with saving dummy lines in binary projects.
  • BUG: Sorting with an imported sort order wasn’t updating the progress dialog when it was running.
  • BUG: QTL groups could disappear due to a quirk of their elements being in reverse order.

New in 1.11.07.06

  • NEW: Added a new option to the edit menu – Filter missing markers – that allows the removal of markers with missing data over a given threshold limit.
  • NEW: You can now select up to three graphs to be displayed alongside the genotypes at one time.
  • NEW: Added a new option to createproject.exe so it can be forced to always use UK English settings for reading decimal numbers in its input.
  • NEW: Added a new Prefs option that allows the locale (language) settings to be overridden so that decimal formatting is always displayed (and read from files) in UK English style.
  • NEW: Added support for a new (optional) QTL data column – RGB – that if specified will allow the user to override the default trait-based colouring that the QTLs normally use.
  • NEW: Added the concept of an “experiment” to a trait.
  • NEW: The project format (xml, zipped xml, binary) for createproject.exe can can now be specified.
  • BUG: The keyboard handling for page left/right wasn’t dealing with multiple events in quick succession.
  • BUG: Exporting phenotypic trait data for lines without trait data resulted in traits being written to the file with zero (or default categorical) values.
  • BUG: Cloning a view didn’t copy over the selected graph index, so the new view reverted to the first graph available.
  • BUG: Markers included in the genotypes file that weren’t listed in the map file were not being ignored.

New in 1.11.04.21

  • NEW: The CreateProject executable will now append datasets into existing projects if the file already exists.
  • NEW: Phenotypic trait data can now be exported from Flapjack to a file on disk.
  • NEW: QTL data can now be exported from Flapjack to a file on disk.
  • BUG: Exporting images from data sets without graph data was failing.
  • BUG: Importing graph data into data sets that didn’t contain markers for that graph was causing Flapjack’s rendering to fail.

New in 1.11.04.19

  • NEW: Flapjack is now a version 1.x release, after being published in Bioinformatics.
  • NEW: SCRI become the The James Hutton Institute in April 2011, and Flapjack has been branded accordingly.
  • NEW: Flapjack now supports importing and displaying graph data (http://bioinf.hutton.ac.uk/flapjack/help/graphs.shtml).
  • NEW: Added a Filter QTLs button to the QTL Table.
  • NEW: Added functionality to move the view one “page” left or right at a time.
  • NEW: Moving the mouse over the chromosome canvas now displays the current chromosome position.
  • CHG: Various tweaks to try to reduce memory consumption a little more.
  • CHG: Tweaked the Castor XML mapping to remove spurious xsi:type entries, resulting in smaller XML project files.
  • BUG: The displayed number-of-lines (during importing) was incorrect when transposed data was loaded.
  • BUG: File loading progress wasn’t being properly tracked when importing QTL or phenotype data.
  • BUG: Trait values weren’t being written properly during binary serialization.

New in 0.10.10.07

  • NEW: Projects can now be saved in a new Flapjack-specific binary format (at least 50x faster than the XML format).
  • NEW: Added an option at import time to create a “super” chromosome, containing all the markers across all chromosomes.
  • NEW: Flapjack can now load its project files from local and remote (http) addresses.
  • NEW: The Bookmark right-click menu option is now disabled unless over a genuine allele.
  • NEW: Redesigned the Import Dialog to include all options (map/genotype data, traits, and QTL) in a single tabbed display.
  • NEW: Genotype data can now be imported in a transposed form (if the advanced option checkbox for it is selected).
  • NEW: Added an additional new tab to support opening example projects from the web server.
  • NEW: Split the additional options from the map/genotype importing dialog into a separate “Advanced Options” dialog.
  • NEW: Updated the line similarity code to score 1 for a homozygous match, and 0.5 for a heterozygous match (previously zero) for cases like A against A/T.
  • NEW: Added summary messages at the end of importing either traits or QTL.
  • NEW: The number of markers found while importing data is now tracked by the progress dialog.
  • NEW: Added a link to the front page to go directly to opening an example project.
  • NEW: Added Java Web Start support.
  • NEW: Added 64bit support and installers.
  • CHG: Changed the internal format for object ID, reducing memory usage and project file size.
  • CHG: Changed the source code to be compatible with Java 6 only.
  • CHG: Marker frequencies are no longer stored in the project file. They are now simply (re)calculated whenever needed.
  • BUG: Fixed the bad number formatting on the chromosome length label (at the top of the screen).
  • BUG: Fixed a bug when (right) clicking on deselected entries in the Find dialog.
  • BUG: Fixed a small issue with the TaskBar icon being stretched on Windows 7 because it wasn’t 32×32.
  • BUG: Fixed a rare, but critical error with threading when the progress tracking dialog was active.
  • BUG: The “PowerPoint” wipe when new data sets are first opened now works properly.
  • BUG: Fixed a problem with the line similarity analysis generating NaN values for scores.
  • BUG: Loading a project that was saved after all its views were deleted would result in a silent exception and Flapjack acting as if nothing had been loaded.

New in 0.10.05.17

  • NEW: Implemented a more robust method for version checking and updating of Flapjack
  • CHG: Added the “Close” button back to the Filter QTLs dialog.
  • BUG: Filtering QTL using the Filter dialog wasn’t working until after the display had been manually refreshed.

New in 0.10.05.07

  • CHG: Minor modifications (for Windows only) to improve compatibility with Windows 7.

New in 0.10.04.27

  • NEW: Implemented multicore/cpu rendering for the main canvas.
  • NEW: Added an option to sort lines by importing an external file that contains the order to put them in (one “line” per line).
  • CHG: Removed the ability to back-buffer the entire main canvas.
  • BUG: Fixed some rendering bugs on OS X systems.

New in 0.10.03.10

  • NEW: Implemented three new methods of scaling and displaying the chromosome map: local, global, and classic.
  • NEW: Added a new summary “mini map” display that shows where on the chromosome the markers currently on screen are.
  • NEW: Gaps in the data set (lines with no value for a given marker) can now be graphically highlighted.
  • NEW: Internet proxy settings can now be configured using the Preferences Dialog.
  • CHG: Some of the options from the Visualization menu now form part of a new View top-level menu.
  • CHG: The chromosome map is now drawn in real-time rather than back buffered, freeing up memory.
  • CHG: Removed the “Flapjack has encountered an error” dialog due to it not working probably with EDT errors.
  • BUG: Fixed various miscellaneous rendering issues.
  • BUG: Fixed some number formatting problems when large numbers were displayed.
  • BUG: Some of the error messages displayed during file loading were incorrect.
  • BUG: Fixed a critical problem with loading data that goes beyond the byte limit for Flapjack’s state table (eg with SSR data).
  • BUG: Fixed a problem with the small overview inset window that resulted in it disappearing completely at times.

New in 0.09.10.29

  • NEW: Importing very large chromosomes (> 20,000 markers) is now significantly quicker.
  • NEW: You can now choose which chromosomes are including when exporting data as text.
  • NEW: The number of tracks used for QTLs is now dynamic, based on a draggable slider below their display.
  • NEW: QTLs are now painted bottom-to-top, keeping them closer to the map than before.
  • NEW: QTLs that overlap one another on the same track are now outlined in black.
  • CHG: As QTL layout is now dynamic based on the slider position, support for CTRL/CMD movement of QTL between tracks has been removed.
  • CHG: QTL changes have meant a slight change to the .flapjack project format, so any existing projects will need any QTL data reimported.
  • CHG: Simplified the settings dialog for exporting data as text.
  • BUG: The status labels at the bottom of the screen were not resetting properly after mousing-over QTLs.

New in 0.09.10.02

  • BUG: Fixed a rendering bug that was causing the chromosome map to incorrectly link its lines to the markers.

New in 0.09.10.01

  • NEW: Exported images now include any phenotype heat map and/or QTL visualization as part of the output.
  • NEW: Added keyboard shortcuts for zooming (CTRL++, CTRL+-).
  • CHG: Made various changes to the installers to improve Linux compatibility and to provide “What’s New” information at update time.
  • BUG: Fixed a problem with hidden QTLs reappearing if the mouse moved over their position.
  • BUG: Fixed a problem with some QTLs not responding to mouse over events.

New in 0.09.08.26

  • NEW: The heatmap of phenotypic trait data now supports any number of displayable columns (it used to be fixed at three).
  • NEW: QTLs can now be imported that contain supplementary columns of textual data (previously only numerical was support).
  • NEW: Flapjack now maintains a history of recently accessed files in all of its open-file dialogs.
  • NEW: Optimized the rendering of QTLs; large datasets should now draw significantly faster.
  • NEW: The CreateProject (command line) attachment to Flapjack can now import QTLs as part of project creation.
  • CHG: The dialog used for selecting which traits to be displayed now lists all the traits in a table along with a checkbox to toggle it on or off.
  • CHG: The option to select displayable traits via a right-click has been removed. The menu now provides a link to the Select Traits dialog instead.
  • BUG: Fixed a crash that occurs if Flapjack is resized to a size small enough to make the chromosome map disappear.
  • BUG: Fixed an issue that was occuring on some systems that was stopping Flapjack from exiting properly.

New in 0.09.07.27

  • NEW: Added an option for sorting lines alphabetically by their name.
  • CHG: Similarity sorting is now much faster.
  • CHG: Implemented some minor changes to reduce the total number of threads in use.
  • BUG: Fixed a critical bug that effected QTL data that didn’t have any additional/optional data columns.

New in 0.09.06.19

  • NEW: Significant improvements to real-time rendering speeds should be noticeable to Windows users.
  • NEW: Overview displays are now created much faster than before.
  • NEW: The random colour scheme now has two choices of style (HSB or WebSafe).
  • NEW: A lot more help topics have been added to the web site.

New in 0.09.03.09

  • NEW: Flapjack now supports the import of supplementary QTL data.
  • NEW: QTLs data files can have any number of additional (optional) numerical columns (LOD, r2, etc).
  • NEW: Added support for graphically rendering QTLs across multiple “tracks”.
  • NEW: QTLs can now be colour-coded according to the trait they are associated with.
  • NEW: Flapjack will automatically lay out QTLs over multiple tracks to avoid overlaps.
  • NEW: Added support for mouse interactions (info popups) for QTLs and for moving QTLs between tracks.
  • NEW: QTLs can be clicked on and all markers associated with them with toggle their selection state.
  • NEW: QTLs can be manually moved between tracks by CTRL clicking and dragging.
  • NEW: Added a new front-end to the program that provides quick links to recent projects, help, etc.
  • NEW: Added a QTL summary table with controls to toggle the visibility of individual QTLs.
  • NEW: Added a Filter QTLs dialog to assist in visibility selection based on trait and experiment.
  • NEW: Added toolbar shortcut buttons for inverting the selection state of lines and markers.
  • NEW: Added many new help topics and placeholders for areas still to be included.
  • NEW: Hovering the mouse over a QTL that is drawn under its neighbours will now render that QTL on top.
  • CHG: The Traits folder on the project navigation tree now supports QTL and phenotype trait data.
  • CHG: The similarity colour schemes will now do half-and-half colouring of heterozygotes.
  • CHG: Colour-boxes (such as in the Customize Colours dialog) now render using gradients.
  • CHG: All “floating” dialog boxes (such as Find By Name) will now auto-close when navigating to another view or data set.
  • CHG: Importing an additional set of phenotype traits will now overwrite rather than append the existing set.
  • BUG: Fixed a problem with importing genotype data files that contain non zero length lines that held no data.

New in 0.09.02.03

  • NEW: Flapjack can now read files containing genotype data that does not include heterozygous separator characters, for example “AT” can be read as “A/T” or “A” and “T” (depending on import options).
  • CHG: Flapjack is now better at estimating what default colour scheme to use when a data set is first imported.
  • BUG: Importing the sample data set after modifying the import options away from their defaults no longer results in the sample not loading correctly.
  • BUG: Re-clicking on the same row again in the Find Dialog will now graphically highlight the result again.
  • BUG: The two-colour scheme now properly colours heterozygotes to match the colours selected for the primary homozygotes.

New in 0.09.01.27

  • NEW: The line and marker under the mouse is now graphically highlighted on the main canvas and in the names list.
  • NEW: Lines names in the list are now graphically highlighted as the mouse moves over the canvas.
  • NEW: Added an option for right-click deletion of dummy lines that have been inserted.
  • NEW: Added a proper selection dialog for loading trait data.
  • CHG: Flapjack now has an enhanced visual scheme that should appear less grey/drab, especially in dialog boxes.
  • CHG: Highlighted lines and markers (eg from the Find Dialog) now appear in the centre of the display.
  • BUG: Fixed a crash that could occur when CTRL+click moving a line from a position outside of the visible list.
  • BUG: Fixed some redraw issues with the traits heat-map when scrolling the display.
  • BUG: Fixed issues with importing data containing blank lines BEFORE the end of the file was reached.
  • BUG: Fixed issues with importing data that mixed the case of genotypes (eg ‘a’ and ‘A’).

New in 0.08.09.05

  • NEW: Added a new option for right-clicking on a line and inserting a “dummy” line at that position.
  • NEW: Added many more help topics, including a start menu shortcut to the help that is now added at install time.
  • NEW: Flapjack can now export views back to disk in raw-data format.
  • NEW: Flapjack license information is now included as part of its install routine.
  • NEW: Flapjack will detect when a new version has been installed and link the user to a web page describing the major changes.
  • BUG: Fixed errors relating to mixing numerical and categorical data for a single trait.
  • BUG: Fixed a bug that caused inverting the selection states of lines to run incorrectly.

New in 0.08.08.08

  • NEW: “Bookmarks” can now be assigned to any location within a view, allowing the user to quickly return to regions of interest.
  • NEW: Flapjack can now be linked with Germinate-like database websites for display of additional line or marker information. When exporting data from Germinate in Flapjack format this information will be included automatically.
  • NEW: Added displayable sort scores to the list of line names (that appears after performing a similarity sort).
  • NEW: Added a right-click pop-up menu option to the list of line names to toggle the sort scores on or off.
  • NEW: The colours used for the traits heatmap can now be customized by the user.
  • CHG: Flapjack’s data modal has been updated to allow it to cope with data sets that use large numbers of unique alleles per locus (eg SSR data).
  • CHG: The random colour scheme now correctly displays heterozygous alleles as a diagonal split with appropriate colour coding for each half.
  • BUG: Fixed a bug in the Find by Name dialog that could cause Flapjack to crash when quickly selecting multiple results.
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