What's New

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 1.11.12.13

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 32x32.
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.