Version History
[5.7.1] June 10th, 2005
[5.6.1] March 30th, 2005
[5.5] January 31st, 2005
[5.4.5] December 31st, 2004
[5.4.4] October 8th, 2004
[5.4.3] September 10th, 2004
[5.4.2] August 13th, 2004
[5.4.1] August 5th, 2004
[5.4] July 5th, 2004
[5.3] May 14th, 2004
[5.2] April 7th, 2004
[5.1] Feb 23rd 2004
[5.03] Dec.11th 2003
[5.01] Nov. 6th 2003
[5.0] Oct 15th 2003
[Beta27] Oct. 10th 2003
[Beta24] Sep. 29th 2003
[Beta22] Sep. 18th 2003
[Beta20] Sep. 9th 2003
[Beta19] Sep. 3rd 2003
[Beta18] Aug. 29th 2003
[Beta17] Aug 25th 2003
[Beta16] Aug 20th 2003
[Beta15] Aug 12th 2003
[Beta13] Aug 5th 2003
June10th 2005 - Version 5.7.1 released
notes include changes in 5.7
Fixed since 5.6:
Workspace
- The prev/next buttons in open graph windows should be updated based upon workspace operations
- Adding a directory containing no samples still creates a group for that directory
- Can create a statistic node for a sample on a parameter that does not exist for the sample
- Shortcut key is the same for add keyword and add remote sample
- Would like a preference setting to automatically sort by any keyword
- Adding a keyword column resizes the columns in table editor
- Changing a group resets the size of the group panel
- Renaming a population should not allow duplicates
- Would like to be able to define keyword value series
- If you fill up the visible workspace panel with samples, you can not drag-n-drop any more
- In the group create/edit dialog, the auto-enter values are not sorted
- In the group create/edit dialog, keyword comparision evaluation fails
- Would like an option to make quad gate naming are cumulative
- When selecting a file in the File Chooser dialog, the Cancel All option does not work
- Workspace 'close' operation causes FlowJo to exit
- The Collapse All menu selection does not collapse nested gates
- Changing the text properties of a group causes populations to appear to no longer belong to the group
- Would like a status dialog to display when drag-n-dropping files into a workspace
Graph Window
- If multiple gates are selected, the Active Gate info should be disabled
- The output of copy statistics should be tab-delimited
- For dot plots, dots directly on the x-axis are not visible
- The manual gate entry dialog stays open, even when checkbox indicates to close
- If two gates are overlapped, need a way to select the gate underneath
- Would like the option to show gate names in the graph window and layout editor
- Opening a graph Window from a chart in the layout editor doesn't change the axes if the graph window is already open
- Preference settings for text style (bold, italic) are not observed in the graph window and layout editor
- Manual entry of quad gates using absolute intensity (scale values) yields bad gates
- Using the polygon gating tool, sometimes don't get 100% of events when the polygon extends beyond the visible graph window
Layout Editor
- % angle in graph info dialog grayed out when it should not be
- Performing undo in the layout editor de-selects the current selection
- Performing undo of multiple graph property change only restores the first graph
- The items in a legend can not be reordered if not viewing the layout at 100% scale
- Histogram overlay gates should be color coded
- Changing the histogram offset to a high number can causes a stack
- Legend does not display control population in italics
- Choosing to show ancestry for multiple graphs in the group properties dialog doesn't work
- Performing undo after a new object is created in layout editor doesn't work
- Display of histogram gates lose correct y position when layout re-generated
- A graph with legend visible and show ancestry selected should only contain one entry in the legend
- Deleting a sample from workspace leaves it in layout
- Would like to have shortkut keys to change tool in layout editor
- Deleting a row from the legend removes the entire legend
- Deleting a statistic node in the workspace will remove it's parent graph from the layout editor
- Deleting a single statistic node will remove the entire statistics text in layout editor
- The current sample iteration value gets out of synch when switching between groups
- Statistics in the layout editor do not always dynamically update If you name a batch layout same as the originating layout, it overwrites the original layout
- Batch layout name not retained when batch completed
Table Editor
- No help documentation for the table editor
- Would like option to save the table data as xml in a file
- Single line headers in a table aren't legible
- Cannot rename a statistic
- If you add too many columns to the table editor you can not scroll it all
- Deleting a sample changes table back to default layout
- Deleting a sample does not always delete the corresponding row from a table
- Table column headers get too big in some circumstances
Preferences
- Would like a preference setting to specify threshold number for 'too many cells on the axis'
- Would like a preference setting to hide uncompensated parameters in pulldown menus
- Would like a preference setting for the order in which quad gate are named
- Would like a preference setting to display the gate name in graph windows and layout editor
Compensation and Transformation
- When defining a compensation matrix, show the assigned gate name in compensation dialog
- Graph windows sometimes show warning for events on axis from previous graph
- The pulldown menu for compensation matrices is too narrow to see full path of compensation matrix file
Documentation
- The help menu from a generated table does nothing
Derived Parameters
- Can open multiple derived parameters dialog on the same sample
- Cancelling the creation of a time derived parameter still creates the derived parameter
Cell Cycle
- RMS value says 'invalid' on histogram with a tightly synchronized peak
- When cell cycle node created on gated population, use the x axis of the parent population by default
Kinetics
- Creating a kinetics node for a gated population uses the samples entire time series
- Would like the ability to copy the time series values for pasting into a spreadsheet
- When graphing kinetics time series by percentile, empty percent field defaults to 90
Other
- Closing a graph window always brings the workspace window to the front
- The next/previous buttons work strangely for platform nodes
Performance
- Zoom in, Zoom out buttons are slow with large layouts
- Moving gates on large files is slow
Known Issues
- Layouts saved as .svg files cannot always be ungrouped in third party graphics editors.
Workaround - for ungoupable graphs, save SVG files from the GRAPH WINDOW one at a time. For overlays, save individual histo's from GW and merge them in your software package. - Saving a layout as a .emf or .swf file produces bad results and may crash some browsers. This functionality has been removed, pending a re-evaluation of the 3rd party code
- Guava FCS data - some files may have problems gating on the time parameter saved by the Guava machine. Workaround - derive a time parameter using Platforms/Derive Parameters.
- Table font resize - if you generate a table, then add it to the layout, and resize it - you may lose the font styling. Workaround - don't resize layout tables for now ;)
- opening charts from Layout Editor sometimes renders graphs that look like the correct plot, but labeled with axes from another file. We're still working on this bug, and expecting a fix shortly. Workaround - always check the axes of the graph you're looking at when using the ctrl+o keystroke in the LE.
March 30th 2005 - Version 5.6.1 released
Fixed since 5.6/5.5.1:
Batching
- legend rows all point to same sample after batched overlay
Calibration
- applying calibration to other samples does not work right calibration windows does not open can not create a calibrated parameter
- Cell Cycle Gaussian figs are deselected after edited controls for Watson & DJF should be radio buttons, not checkboxes performance problem for some calculations changing y-axis scaling in layout editor makes cell cycle, proliferation graphs incorrect
Derived Parameters
- Deleting a derived parameter does not reset graph window current graph time derived parameter can be created with no start or end time
DiVa
- data being transformed before compensation (mac and PC)
Documentation
- missing page http://www.flowjo.com/win/html/kintimeslicenamer.html Proliferation window Help - inactive menu options getting "no files were added" dialog -- help url fails
Engine
- VM crash when compensating fcs file with 8 bit data
Graph
- arrow and diamond tools should be disabled if sample is not viewable up/down hierarchy buttons
- diamond menu comes up on left side of GW
- can't create manually entered gate histogram overlays rendered with errors
- can't graph parameters where there is a colon in the name
- deleting a group owned child of a node does not remove it all the time
- divide by zero exception when parent gate changes to 0 events
Kinetics
- hide/show axis properties doesn't work for kinetics chart
- kinetics chart in LE is scaled
- timeslice naming dialog should be placed relative to kinetics window
- kinetics smoothing, threshold not saved with workspace
- edited timeslice loses order in tree
- want ability to copy time series for pasting into Excel
Layout
- remove annotation does not remove handles
- annotation stays selected after hiding
- figs that are grouped bring up a generic dialog that does not work
- cut and paste into new layout has problems
- chart annotations are not resizable
- stack on double-clicking in empty chart properties control box
- ancestry with platform nodes draws an extra parent graph
- quality of ancestry graphs is bad
- workspace breaks if you change a group owned gate and reapply it to the group
- template name with "-" throws stack
- pasting from LE to MSWord yields blank graphics
- setting controls in layout chart def
- user annotation in figChart properties doesn't make it to text box
- right click -> duplicate from figchart box is broken
- text (stat) editor doesn't grow field to show full definition
- stack on chart drag to LE when all templates are selected
- deleting a sample from the workspace does not really remove it
- figchart not updated when overlay that depends upon a gate is moved
Other
- default email sender of anonymous@treestar.com is annoying
- Can open stat dialog multiple times
- .swf image format crashes ie sometimes
- missing conversions between Mac and Windows workspaces
- New license agreement must be displayed for release 5.6
Performance
- Opening a workspace performs engine requests for layout editor
Preferences
- "show gate frequency" pref not honored
- Null pointer in PrefsAdditional,
- preferences for LE chart axes font do not work
Proliferation
- proliferation graphs do not dynamically update in the layout editor
- proliferation curves drawn incorrectly in layout editor
- when annotation shown show ancestry of a proliferation node in the layout editor loses curves
- changing axis values for a proliferation node in the layout editor yields strange results
- proliferation statistics not displayed with annotation in the layout editor
- opening/closing a prolif window loses fit
- proliferation chart in LE suboptimal quality
- graph name appears near top left corner of graph
- Can't drag proliferation node to other sample
- Can't open a saved workspace with a proliferation node
- can not delete a proliferation node
- no dynamic update of proliferation chart in layout editor
- curves not remembered in proliferation window
- null pointer on load of workspace with proliferation
Workspace
- Frequency stats were not working in 5.6, fixed for 5.6.1
- overwriting gates require you to delete the original gate
- significant figures in FlowJo calc's
- 'Platforms' menu should be enabled if only a population node is selected
- can't create child gate with same as parent by drag n drop menu
- enabled/disabled broken in workspace when sample selected
- command line should list flowjo.jar version number
- time parameter scaled wrong
- save as template is broken
- group pane scrollbar doesn't show until resize
- sort by cells in sample list table doesn't work
- adding samples to workspace doesn't add to groups correctly
- no help button in Group definition dlog
- adding samples resets list to All Samples, but doesn't change group
- Group definitions referencing other groups don't work
- Group definition - changing keywords and applying includes wrong samples
- 'Revert' menu item doesn't do anything
- using AnyKeyword in first search criterion ignored the second
- not able to resize compensation dialog
- get stain name mismatch when dragging gate to a parm that has the same parameter
January 31st 2005 - Version 5.5 released
This release includes the first implementation of platforms.
Authorization
- launching flowjo checks the wrong FLS site, http code 400 returned
- copy to clipboard button broken
- would like a global prefs file and global serial number
- flowjo crashes when server is slow
Batching
- annotation window position and text/line/color properties not retained
- Java error in layout editor when batching more than one node /show ancestry selected
- batching with extra figs (like lines) produces bad layout
Derived Parameters
- label switched in DP platform window
DiVa
- transform buttons in GW
- setting Linear Channel Number to 0 yields blank plots
Engine
Graph
- data file shows label axes incorrectly in GW
- changing a histogram to a different kind of graph does not change label
- openParentPopulation can't switch display to Histogram if nec
- quads when broken up don't retain stats inside of rects
- y axis numbering problem - rounds inappropriately
Layout
- annotation window doesnt resize for long sample names
- leditor window title always says "Untitled" even after WS is saved
- File/Save in LE misleading...
- iterate by N does not function via panel pulldown
- clicks on annotation and legend should be handled appropriately
- dots and contours show in red, not foreground color
- annotation & legend don't move when parent chart is resized
- batched grouped charts shift annotation after ungrouping
- Show Gates & Show Gate Frequency options ignored
- avoid page breaks does not pay attention to figchart dependants
- fit to page in layout editor sets a new page size that is global
- annotations lose carriage returns on restore from save
- iterate by panel - # of samples not evenly divisible by panel size
- Caption box and stats box overlap after batching
- Close button on print preview is not functional
- show ansestry does not size correctly
- show ansestry needs to be greyed out if there are no parents
- object tab in the layout editor should be greyed out if no object is selected
- When more than one node in layout is selected object properties has no effect
- overlays of samples with different parameters is allowed
- batched layouts are grouped, must ungroup before double-click to get chart definition
Other
- transformation prefs ignored
- define transformation window lacks navigation for matrix files
- FCS3.0 data from cyan/summit 4.1
Preferences
- gate freqs should be on by default
- graphic output prefs don't match actual output options
Table
- table attempts to summarize keyword columns
- table does not show stats for gates
Workspace
- please add memory to Create Group window's position
- opening saved workspace says "error adding files"
- Java error when trying to delete nodes from sample.
- Error adding files when opening saved workspace
- In graph window under graph options show outliers fuctionality is backwards
- Samples with same group owned gate have different gate values
December 31st 2004 - Version 5.4.5 released
Engine
- fixed FLOS problems
- improved first launch in FJ
- fixed support for European decimal point annotation
- expiration removed
- friendlier versions of error dialogs
Graph
- data file shows labels incorrectly in graph winow
- rect gate gets stuck in mode when drawing equilateral sides
- resizing gate with CTRL key down
- auth failure results in immediate GW refresh
Layout
- no legends in LE
- add samples dialog doesn't show correctly
- zooming in layouts causes shift of the canvas
- avoid page break fixed for batching
- deleting a sample in WS removes unrelated sample in LE
Other
- when email to FJ is turned off, you do not get repeated errors
- dongle removal issues
Table
- open spreadsheet doesn't work
Preferences
Workspace
- samples left behind in layout editor after being deleted
- no clean way to abort add samples operation
- can't add sample after workspace redo operation
- compensation definition window doesn't list a parameter
Known Issues
- platforms not yet implemented
- performance somewhat slower compared to the Mac version
- workspace format is not yet compatible with the Mac version
October 8th 2004 - Version 5.4.4 released
Engine
- url connection not closed in Engine.CheckSiteLicense
Graph
- moving quad gates severely broken
- Null pointer when opening graph window
- moving a gate causes the graph axis to change
- data file shows label axes incorrectly in graph window
Layout
- changing histogram line properties lost after other annotation changes
- Setting control sample in Chart Definition dialog has no effect
- selection problem in layout editor
- default layout Iteration Options is set to "don't allow"
- scrolling moves to fast
- change deault color of histograms in layout editor to black
- zoom breaks layout editors scolling ability.
Other
- remote samples directory won't get removed upon exit
Preferences
- can select 'Specify Keywords' without making a selection
- Mute sounds preference can't be turned off
Workspace
- accented chars in file paths produce parse error
- Edit Column Names can't remove multiple columns
- Column Editing dialog allows separator lines to become columns
- duplicate columns abort add column operation
- stack when deleting sample
- editing of parameter based keywords not preserved thru save
- samples left behind in layout editor after being deleted
- alt-clicking a disclosure triangle hides all levels, not just current level
- problem with loading samples into a template
- statistic not calculated when dragged to group node with > 2 parents
September 10th 2004 - Version 5.4.3 released
Batching
- cant add columns to workspace in attached workspace file
- same errors pop up multiple times
- ip site license serial number allows empty string to work
- layout editor scolling problem
- stain name mismatch results in unexpected boxes
- erroneous warning of events on axis
DiVa
- gating problem with DiVa data - quad gates calc'd wrong
Engine
- Need better error messages from the engine when serial number validation fails
Graph
- density plots Mac vs. PC
- save as SVG from GW is different than save as PNG
- manual gate entry buttons confusing
- transformed gates when recalc'd change value when xform pref is toggled
- dialog problem with gates applied to all samples
- Y axis on CDF plot wrong
- manual gate dialog won't make quad gates
- specifying manual gate by percentiles doesn't work
- down arrow enabled when no gate selected
- freq on gates not updated when gates are moved by arrow keys
- sample pulldown throws exception on parameter mismatch
- multiple graph windows on same sample can be inconsistent
- renamed keywords not displayed anywhere other than the workspace
- deleting gate, drawing gate, undo, causes odd behavior
- even when disabled, ancestry popup will display menu
- manual gate in graph window not dynamically updated in LE
- deleting gates takes too long
- Down button arrow not enabled after gate created
- Edit >> Clear does not delete selected gate
Layout
- copying a part of a batched layout creates sizing issues in the clipboard
- min Y axis scaling produces strange graph
- page size not saved in layouts
- shift key and snap-to-angle for line tool
- range gate in histogram overlays
- changing scale values in chart def followed by ctrl+z returns stack
- layout editor window resets position on open/close
- layout editor undo buffer doesn't remember which layout
- gate change to population in non-displayed layout is not reflected
- open layout editor shows wrong layout when new workspace loaded
Other
- wifi serial numbers dont work
- display property change hides windows
- Want feedback if browser or other 3rd party application doesn't launch
Preferences
- Would like a preference for FlowJo to check for more recent version
Workspace
- sort columns both ways
- unify analyses does not work
- sort order doesn't put cd8 before cd16 (always alpha sorts)
- deleting child node that has same name of a parents sibling throws error
- dragging parent and child into a child node and then deleting the child node thows error
- undo problem when changing gate applied to all groups
- delete group owned node that is present in layout crashes layout
- drag and drop for workspaces
- want 'collapse all' option in Edit menu
- editing columns does not touch dirty flag
- Workspace does not save dimensions when you save the workspace.
- reopening saved workspaces does not preserve disclosure
- quad gate sort order might be confusing
- Cancelling 'sample find' operation for multiple samples
- right click menu for group pane
- Percentile stat can be added with no argument
- drag to all samples with a node in the way causes stack
- default first choice of sort order is decreasing values
- moved group owned when deleted are replaced by group owned node w/o dialog
- Samples with CD reagents not sorted
- only keywords starting in $ are editable
- stain mismatch not recognized when dragging gates
- stain combinations not sorted in group creation dialog
Known Issues
- platforms not yet implemented
- performance somewhat slower compared to the Mac version
- workspace format is not yet compatible with the Mac version
Batching
- Problems with batching fixed
Engine
- Attempt to assign comp matrix file with a parameter not present in the sample, engine crashes
Graph
- Added free hand gating tool
- More info and navigation ability in graph window
- Creating multiple quad gates loses previous one when graph window re-opened when you select the last nodes in a freehand gate and drag it
- Snap to grid causes funny movement in graph window with box gates
Layout
- Overlay of contour graphs still shows contour in overlay
- Dragging fig always causes a scroll
- Resizing sample in layout doesnt work
- Mmenu buttons overlap when layout windows is resized to very small
- Save and print dont show entire window when zoomed in
- Null pointer thrown in checkForStainCompatibility
- When custom iterator is used, legend's file name does not update
- Grayed layout when switching between layouts with scrollbars
Other
- Want user feedback when an attempt to auto-assign +/- gates fails in compensation definition dialog
- NullPointerException in email dialog responding to Send
Preferences
- Dialog indicating gated events may change is too broad
- Remind to save preference does not work when set, then reminds too often when restarted
- Want button to reset preferences back to factory defaults
Workspace
- Added 'any keyword' to the group creation dialog
- Extra keywords are drawn for all populuations
- Renaming great grandparent node causes problem in workspace
- 'Create archive' and 'Email archive' should be moved to help menu
- Need 'Email FlowJo' operation
- Uncaught exceptions should bring up email dialog to report bug to FlowJo
- Want 'Select Equivalent Nodes' in Workspace->Edit' menu
- Cannot graph comp'd parameters after assigning comp matrix
- Previous samples remain in workspace when new workspace opened
- LastQuery.txt access denied error
- File/save sometimes grayed out
August 5th 2004 - version 5.4.1 is released
Batching
- batch analysis status bar problem, incorrect progress feedback when batching in layout editor
- Basic and Advanced tutorial data does not work together in batching
- Snap to grid doesn't work with starting point of rects, lines allow stain name mismach always on
DiVa
- DiVa data and statistics not correct
- Gates not moved after pref in DiVa setting changed comp matrix files not loaded from some DiVa files
Graph
- no warning for 0th channel events
- background on saved graph image files is grey not white
- problem with deleting quad gate
- graph window axes label and scientific notation
- manually entered gates do not show correct frequency
- can't undo moving a gate
- export to photoshop/illustrator
- graphs of zero events are not drawn
- file -> export vector has *.png selected as file type
- going to next/prev sample button needs to check if visible axes are in next sample
cannot manually enter range gates
Layout
- offset histogram overlay Y axis label missing
- resizing issue with layout editor
- Dragging statistic from workspace to text editor in layout editor does not work
- drag and drop of images does not work
- no horizontal scrollbars in certain circumstances
- none of the buttons in the layout editor have mouse-over text
- can't select objects under other objects easily
- problem with adding sample after creating overlay in layout editor
- undoing FigChart deletion does not restore annotation
- layout scrollbars when automatically extended reset layout position to upper left corner
- snap to grid doesn't work when dragging objects
- can't get to prefs directly from Layout Editor
- deleting sample doesn't remove related graphs in layouts
- parameter mismatch not handled correctly in non-batch view
- no cut and past from system clipboard into or out of layout editor
- ctl select through objects in layout editor does not work properly
- need to change line selection area to be just the line
- color problem with deleting root layer in overlay
- you are able to drag an object in layout editor out of the editor window
- right click menu for overlay legend box does not work for same sample gates
- problem with how layout editor looks and acts when it is dragged to a smaller size
Other
- No 'undo' command
- tabbing through fields should select existing value
- problem when saving image file
Preferences
- would like to be able to launch excel from table editor
- changing transform setting for comp'd data doesnt refresh GW's
- need preference for grid size & visibility
- default path of vector and bitmap should be C: drive
- deleting/regenerating new prefs throws exceptions
- wording on Edit 32 bit data settings dialog
Workspace
- Would like undo operation after dragging pop node to a group
- not all menu items are dimmed appropriately
- dragging a selection doesnt scroll the workspace as needed
- cant select sample when only one is in the workspace under some instances
- workspaces do not open unless all FCS data is present
- ignoring of gate change updates to all samples
- group owned stat nodes don't work right
- two hardware addresses on one machine can be problematic
- gating on transformed data causes gate offset
- clicking selected node of unfocussed table doesn't switch focus
- updating a group-owned gate turns non-group owned gates bold
- accented chars in file paths produce parse error
- workspaces that reference networked shared files do not load
- compensations def widow doesn't accept a selection of multiple gates in Autoassign box
- DiVa 3.0 and EXP files load with linear labels for FL channels
- change window title to differentiate "open workspace" and "add samples"
- Unify Analysis under the workspace menu doesn't seem to work
- workspace dirty flag not set by changes in table or layout editors
Batching
- ancestry is ignored during a batch operation
- iteration problem when reopening a saved workspace
- batch analysis name is wrong in batch dialog
- when you create a batch of a layout there is a problem with the naming
- batch analysis on overlays only prints top graph
- when you iterate between samples in the layout editor the statistics stay the same
- Statistic boxes in layouts show as *, regardless of iteration
- statistic boxes in batched layout have no text
- charts and "accessory boxes" in layouts are divorced
- iteration by nth in batching does not work
DiVa
- the transformation definition dialog doesn't list acquisition defined comp's
- diva gating problems
Engine
- flowjo accepts any valid serial number.
Graph
- count values for ellipse gates wrong, Workspace.Recalculate doesn't correct
- graph type in graph window is set to wrong type
Layout
- Avoid page breaks moves charts unnecessarily
- can't draw rectangles beyond certain x / y values
- FigChart Anotation Text box does not get created when sample is placed in layout ditor.
- holding shift when drawing a line in layout editor should shift line
- saving an image from the layout window doesn't work right
- selecting cancel in text editor problem
- can't draw straight lines in layout editor.
- cant get property page on multiply selected graphs in layout editor
- image import file type problem
- Can't delete all the letters in the name of a layout.
- file path for inserting image into layout editor is wrong
- when you insert an image into layout editor. Only part of it appears.
- deleting anotation box doesn't delete the entire box
- saving a layout only saves the visible area of the layout editor
- chart definition problem, legend "show statistic"
- when you uncheck the show annotation box in the layout properties, it is not saved
Table
- a generated table in the table editor needs horizontal slide bar
Workspace
- Default color for new groups should choose unique color
- define group by more than one staining protocol
- Groups do not get sorted into alphabetical order
- problem with saved workspaces - layout graphs show blank
- Dragging gates to all samples does not retain axis settings.
- node should remember graph axes
- freq. statistics applied to a group do not change from the original sample's values
- applying gate to a group does not retain the gates graphical settings
- summit software acquisition defined compmatrix not supported
- statistics added to sample before sample is graphed are 0.3
- analysis dragged to groups doesn't correctly adopt the group's color
- dragging a folder to the workspace creates a new group of the same name
- group stats changed when new stat added
- add more options to Workspace->Edit->Select Every menu
- when adding samples recursively, groups names uniqueness not ensured
- Add sample dialog always starts at My Docs for each new wsp
Engine
- reduced number of calls to calculation engine for improved performance
- added caching of samples in calculation engine for improved performance
Graph Window
- better positioning and retention of annotations
- copying histogram and then pasting into a spreadsheet creates two columns of data
- workspace is updated when gate is moved in graph window
Layout Editor
- added iteration option by keyword and by Nth panel
- added ability to make histogram overlays drawn in dotted or dashed lines
- fixed errors with histograms, legends, and text boxes when generating batches
- header and footer generated when printed out
- fixed algorithm to reposition charts to avoid page boundaries
- fixed bug where deleted charts were resurrected after workspace is saved
- default iteration option is to iterate by panel
- can now save svg files from layout editor
- charts are zoomed to 100% for copy/paste operation
- statistic nodes can be dragged to layout editor
Other
- FlowJo can now be started by double-clicking on a workspace (*.wsp) file
Preferences
- FlowJo preferences file now stored in users 'My Documents' directory
Workspace
- added ability to load remote sample data files
- menus are grayed out if operations not possible
- added ability to save templates
- workspace files now include the FlowJo version number
- quad gates are named and ordered the same as the Mac version
- can cancel when attempting to overwrite an existing workspace file
- can only select a single group in the workspace
- gates must have unique names at the same level
Engine
- Fixed: problem with gating on LMD files (coulter)
- Fixed: crash in diva files
- Fixed: compensation errors on engine side
- Fixed: Better error reporting from Engine
- Fixed: ctrl c ctrl v keystrokes in LE
- Fixed: need different error if no dongle
- Fixed: transform doesn't work for axes
- Fixed: Can't graph sample with stat on a compensated parameter
Graph window fixes
- transforming option bug
- graphing options in graph window don't cause window refresh
- outliers drawn inside contours
- histogram refreshing misbehavior
- deleting gates from GW doesn't delete them from WS
- histo gating tool allowed on bivariate plots
- statistics disclosure triangle
- wrong graph type in options panel
- polygon gate inverted
- delete gate population doesn't update active gate option panel
- duplication of gates by applying to all samples
- diva gating problems
- histogram axis labeled wrong
- y axis scaling should be disabled for 2 dimensional plots
- null pointer exception thrown when changing graph and Y axis type
- changing transform prefs can yield incorrect graph
- glitch in histogram Y axis, parameter and file specific
- CDF on Y axis values and label are wrong
- graph color change when auto scaling changed
- histogram and CDF Y axis label gets reset but graph stays the same
- when a change in a gate is made and is updated for all graphs it adds a new gate.
Layout Editor fixes
- Screen update during batch operation leads to multiple screen paints
- histogram overlay legend problems (line style, coloring)
- saved layouts too big in area
- copy and paste from LE to powerpoint doesn't work
- outliers in LE charts drawn on top
- count stat nodes not calculated
- Annotating layout editor graph with full path produces empty legend
- Disable arrow buttons when no previous or next option
- layout editor copying and pasting bug
- Layout graphs and gates wrong
- paste from one layout editor to another only displays placeholder
- image copied from layout editor to external target is too large
- opened layout editor may be off screen
- all figs in Layout Editor, rather than selected figs, are pasted to external target
- text editor not working correctly in layout window
- only histogram overlay works in layout window
- scale to page problem
Other
- data files from different vendors don't open in same workspace
- platforms/define transformation
- creating quad gate causes unnecessary plotting
- Confirmation dialog's "Don't ask again" checkbox assumes you selected yes
Preferences
- hardware address field
- prefs for stat text size in GW doesn't work
- FlowJo not multi-user aware under XP
- diva looks for nondiva transform pref settings
Table
- column name field typing problems
- custom column names ignored
Workspace
- group overlapping doesn't work
- adding folders with non-fcs data
- duplicate files allowed in groups
- gate frequencies decimal places
- Change color of group not taking effect
- deleting stat in ws doesn't delete stat description in graph window
- Save As function from Workspace menu
- nested gate nodes that are dragged to a population cannot be graphed
- workspace saved with samples graphed as histograms get error when graph type changed
- statistic node error
- data files in same directory as workspace should be found automatically
- new workspaces come up on top of old ones
- drag sample from desktop does not get added to selected group
- drag sample from one workspace to another broken
- count and freq stats not calculated when dragged to all samples
- data related bug - gating on Cy7 PE
- problem adding stats
- removing samples from workspace doesn't decrement affected group count
progress bar - works for most tasks throughout flowjo * Workspace:
- diva data is supported in all modes.
- improved support for European characters in path names
- fixed clipboard support for pasting things into power point/excel etc
- renaming top level node should be OK if sample name keyword is used
- fixed group creating behavior (manual addition of samples) * Graph Window:
- NOT option for gates wouldn't refresh dependent graph windows and layouts
- transposing axes handles gates and gate freq's properly
- assigning a new compensation matrix forces an update of the axes pulldown * layout editor
- fixed improper scrolling/display of batched layouts
- fixed manual histogram Y axis scaling
*New in 5.03
* Known 'high priority' issues:
- Transforming compensated data
- No Mac/PC format convergence at this point
- speed and optimizations
- Microsoft Clipboard support for PowerPoint
- no support for directories with non-English characters in the name path
- outliers drawn in wrong layer in LE and saved graph window/LE dumps
*New Features
- Offline documentation has been added to the installer. This will work for anyone
with no internet access. FlowJo will automatically look for the documentation whenever
a help button is pressed.
- The installer will quit unless windows version is 2000, XP, or 2003.
- better SVG compliance with Illustrator
- USB Dongle support
* Workspace:
- made dialogs less repetitive, added "don't ask again" to most dialogs
- shift-clicking is fixed (for selecting consecutive nodes/samples)
- "adding stats" window is no longer "on top", it is now same level as workspace
- added support for keyboard usage for most menu items and navigation
- dragging a folder into "all samples" will create a group with that folder's name
- all nodes should recalculate immediately
- added stain mismatch dialog with a "don't ask again" feature
- Improved group-analysis related operations
- Fixing workspaces whose data files have been moved is more functional
* Graph Window:
- live quad stats update
- Save as SVG, JPG, PNG works ('save as' file format must match the one in preferences)
- Gate stats showing in Graph Window are now Frequency of Parent, not Frequency.
- edit/copy gate and edit/paste gate menu items are functional
- background color works
- transformed axis labels (transformed graphs will come later)
- added the "not" option for gates (this will include events OUTSIDE the gate)
* layout editor
- FlowJo will remember chart definition options
- fixed stat box length in batched layouts
- Remove overlay component without having to start over (right click on legend, remove this layer)
- batching from custom group
- Histogram overlay Y Axis label will show counts
- show ancestry works
- Chart Definition window will remember settings
- added Undo action
* Table editor
- added support for custom keyword identification in preferences (by default, FJ will use file name)
* Engine:
- copy protection via. USB dongle
please install the drivers for your Windows 2000/XP. You can get them here:
http://www.ealaddin.com/support/hasp/enduser.asp
look for the "HASP Device Driver GUI Installation"
* Preferences:
- scientific notation works
- custom keyword can be used to identify samples in graph windows, table editor, and layout editor
*New in 5.01
# Workspace:
made dialogs less repetitive, added "don't ask again" to most dialogs
shift-clicking is fixed (for selecting consecutive nodes/samples)
"adding stats" window is no longer "on top", it is now same level as workspace
added support for keyboard usage for most menu items and navigation
dragging a folder into "all samples" will create a group with that folder's name
all nodes should recalculate immediately
# Graph Window:
live quad stats update
Save as SVG, JPG, PNG works ('save as' file format must match the one in preferences)
Gate stats showing in Graph Window are now Frequency of Parent, not Frequency.
edit/copy gate and edit/paste gate menu items are functional
background color works
transformed axis labels (transformed graphs will come later)
# layout editor
FlowJo will remember chart definition options
fixed stat box length in batched layouts
Remove overlay component without having to start over (right click on legend, remove this layer)
batching from custom group
# Table editor
works.
# Engine:
copy protection via. USB dongle
please install the drivers for your Windows 2000/XP. You can get them here:
http://www.ealaddin.com/support/hasp/enduser.asp
look for the "HASP Device Driver GUI Installation"
# Preferences:
scientific notation works
New in 5.0 / Beta27:
* new/fixed in b27:
Global:
update program: the last posted Beta installer has a "update.exe" program.
If your computer is connected to the internet, this program will update your
Beta FlowJo whenever a new version is posted. This reduces the size and
length of the download.
Workspace:
- fixed the node selection bug
- fixed the %ile stat returning 0.3 bug
- added a "select none" item in the edit menu
- dragging a new node to a group will overwrite and update all other
equivalent gates in that group
- right click menu added in workspace
- no more preference crashes.
- engine errors will come up for each required computation.
Layout:
- Improved SVG output, Adobe Illustrator will open them fine (and modify)
- improved header/footer annotation and spacing
- alt-dragging graphs will duplicate them in Layout Editor
- right-click functions added in Layout Editor
- images can be inserted into the layout now, but only through the Object
menu item
New in Beta24:
Update client:
the installer will put a shortcut to "update" to the destination you specify. From future versions on, this program will allow for smaller downloads to update the critical components of flowjo (the .dll engine and flowjo.jar). This will reduce the download size from 20MB to about 2.
Workspace:
- put restraints on gating space, gates will be 'caught' by the boundries of GW
Layout:
- fill color in graphs
- frequencies in graphs
- histogram y axis
- histogram overlays fixed up
- batching fixed up
- control sample works
- saving batch settings
Graph Window:
- now able to delete populations from GW
- paste gate fixed
- saving as SVG fixed
- gate tinting fixed
- fixed elliptic gate movement
Engine:
- outliers added to pseudocolor, zebra, density plots
New in Beta22:
Workspace:
- fixed LMD data support (text2fcs)
- fixed LMD data support (winMDI)
- FlowJo "remembers" graph types in the workspace
Layout:
- fixed up overlays
- added ancestry
- fixed contour plots
Graph Window:
- transformation of graphs
- fixed contours
- made histograms nicer
- changed quad gate naming
New in Beta20:
WORKSPACE
- the blank graph problem
- compensation is possible of more than one sample at a time
- folders and files alike can be added to workspace by dragging on "all samples"
- fixed FJ's inability to read HWA's on non-English versions of windows
LAYOUT EDITOR
- batched layouts will display correct axes labels and the stats will be calculated properly
- layout names are now saved
TABLE EDITOR
- table editor output can be copied to the clipboard and pasted elsewhere
- table's are now named right
- added support for custom table header names
ENGINE
- annotated engine error codes
PREFERENCES
- specifying cell number per dot plot will work
New in Beta19:
WORKSPACE
- added "show time since last save" feature
- fixed Cyan data support
- added DiVa data support, but the parameters still need work
- fixed compensation. how to compensate -
http://www.flowjo.com/win/html/compensation.html
GRAPH WINDOW
- fixed histogram gate pinning
- space bar implemented as polygon gate abort key
- deleted populations will no longer show as 'gates' in graph windows
New in Beta18:
WORKSPACE
- show $pns as reagent in group definition dialog
- make a new group, make a subpop, # samples in group gets flooded from the all samples group
- it is possible to open multiple compensation definition dialogs
- users should be able to open our test data (http://www.flowjo.com/demo_data.html) without a serial number
New in Beta17:
WORKSPACE
* some LSR data contains blank spaces in keywords. This caused FJ to display
statistics as "0", this is now fixed.
* users should now be able to save workspaces anywhere (desktop, user folders, etc..)
and open them, too ;)
LAYOUT EDITOR
* statistics would show as "*", this is now fixed.
* pressing the print button in LE prints the layout with the scroll bar (fixed)
New in Beta16:
*serial numbers
* When renaming a node in the workspace, delete key or arrow keys are not enabled.
* edit/copy menu item does not work (table editor)
* 'forward scatter on X axis by default' preference does not work
* fixed histograms (triangle defect)
* saving workspaces: you should now be able to save workspaces to flowjo's home directory (c:\program files\flowjo\), but the data files can be anywhere on your computer
New in Beta15:
*Force recalc stats upon generating a table for all involved statistics
doesn't happen (TE assumes they are calc'ed)
*Rectangle line in LE: dotted doesn't work; text box: line weight is the
same no matter what the choice
*Gate frequency shows in graphs in LE only if they're enabled in GW prefs
*Some graph annotations exceed the length of the annotation box (text
sticks out). I noticed this happens after batching - both in original
and batched layouts.
*Offset histograms needs improvement, %angle, and Y axis
*'Checked items remain locked' - in chart def, doesn't work. the triangle
icon changes once clicked, but does not change back.
*Show gates/freq on graphs doesn't work
*Problems with printing more than one graph on the layout.
*Newly batched layouts show the first sample info over and over.
*'Forward scatter on X axis by default' in preferences doesn't work
New in Beta13:
* added support for large (>300K events) multi parameter files (now able to plot/gate etc)
* references to FCS files are relative, program will ask for missing files if the
workspace is moved (relative to the data files) but it will ask for each file ;)
* keyword-defined columns saved in preferences will show in a new workspace
regardless of data having those keywords
* $FIL will now only show the file name, not the whole path.
