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Delta2D Changelog

The user benefits are described in the What's New document.

Delta2D 4.7

4.7.2 Final 03 (201705081334)

  • The included Java engine was updated to Java 8 Update 131 (JRE 1.8.0_131) under Windows and MacOSX (not yet under Linux).

4.7.2 Final 02 (201704281529)

  • Added interpolation as alternative method for mW estimation. Usually regression is the most suitable method, but the results sometimes are not satisfying, e.g. when you included precise markers in your gel. In this case, interpolation produces better estimations.
    To use interpolation, please make sure Delta2D is not running and append the following line to your Delta.ini in <your userhome>\.Delta2D:
    calibration.mw.interpolate=true
    If you start Delta2D again, it will use interpolation for estimation of mW on your gel Images.
    To revert this behaviour, simply set the above value to 'false' in the Delta2D.ini or remove the line completely.

4.7.2 Final 01 (201704121723)

  • Added support for gel image type *.mel produced by ImageScanner / LabScan
  • DualView now opens gel image pairs with respect to their order in the Project Explorer: the upper sorted image will always be the the unwarped master image and the lower will be the warped sample image in the DualView. Pressing the SHIFT key while double clicking on a image pair still swaps the roles.
  • Fixed an error occuring occasionally on moving images around in the Project Explorer.

4.7.1 Final 01 (201703281946)

  • The stability of pI estimation has been improved.

4.7.0 Final 16 (201703241352)

  • Fixed a problem where installation on Mac OS finished with an IO-Error in some cases.
  • Installation on Windows can now be done also without adminstrator rights in private places on the computer.
  • Manual was updated to current version.

4.7.0 Final 15 (201703101213)

  • Fixed a problem where Delta2D did not always use the system default browser for showing reports under Windows 10.

4.7.0 Final 14 (201703061509)

  • Improved usability: When opening Gel Image Pairs in Dual View by clicking on the pair connection in the Project Explorer or the Warping Setup window you can now open the image pair with inverted roles by holding the Shift key while clicking.
    Example: Klicking on the Pair GelA_vs_GelB normally opens GelA as so called 'Master Gel', the gel out of the two on which the other one, GelB in this case, will be warped to. If you now press Shift while clicking on the same pair, GelB will be the unwarped 'Master Gel' and GelA will be warped onto GelB.

4.7.0 Final 13 (201702231806)

  • Fixed problems with transferring spots when a modeled spot could not be computed. [7917]
  • Gels in Gel Image Attributes dialogue are now sorted alphanumerically instead of alphabetically before.

4.7.0 Final 12 (201701301758)

  • Improved labeling: When labeling spots with numbers, they are assigned according the position of the spot from top to bottom.
  • Sorting of Gel Attributes is now alphanumerical instead of alphabetical before.
  • Fixed a problem where in new, not yet saved projects the quantitation table opened initially empty.
  • The spot numbers (all/visible/selected) at the bottom of Quantitation Tables was not always correct.
  • Fixed a problem with right click on column header without filter in Quantitation Tables.
  • Fixed a problem with representation of ratio filter dialog.

4.7.0 Final 11 (201611031939)

(cumulated changes from versions 4.7.0 Final 01 through Final 11)

  • Blotting Report was introduced.
  • Numerous improvements, mainly of performance, related to generation of reports.
  • Numerous small glitches and problems related to reports were fixed and details polished.
  • Installation routines were cleaned up, unnecessary elements removed.
  • Updated some third party elements.
  • Updated included Java engine to Java 8 Update 102 (JRE 1.8.0_102).
  • The installer got a new 'EV' signature to avoid Windows Smartscreen warnings.

Note: The versions 4.7.0 Final 01 to 4.7.0 Final 10 have not been released.

Delta2D 4.6

4.6.3 Final 08 (201610131247)

  • Updated developer certificate in installer to avoid complaints by Windows SmartScreen on attempting installation.

4.6.3 Final 07 (201607141842)

  • Fixed a problem with saving all reports at once (Reports Index).

4.6.3 Final 06 (201606031858)

  • Fixed several small problems with reports.
  • Fixed problems with reopening projects with saved filters or importing filters.

Note: the versions 4.6.3 Final 04 and 4.6.3 Final 05 have not been released.

4.6.3 Final 03 (201605111742)

  • Fixed a problem loading Fuji files with uppercase file suffixes.
  • Fixed a potential deadlock on closing Delta2D.
  • Fixed problems with saving a project when only filters have been modified.

4.6.3 Final 01 (201603171119)

  • Fixed a problem where some windows were not resizable in certain constellations of windows.
  • Changed initial values for filters activated from the context menu (right click on column header in tables).
  • Fixed a problem where project was not saveable if 'Clear all filters' was the only modification.
  • Fixed a problem with deleting all labels if there were groups of labels before on the same gel.
  • Continued preparation for future enhancements.

4.6.2 Final 02 (201603041621)

  • Fixed a problem with spot matching in reports when gel images without spots were included in project

4.6.2 Final 01 (201603031925)

  • Fixed a problem where the Quantitation Tables were not resizable in certain constellations of windows.
  • Improved filter dialog to show infinity ( ) values as well.
  • Fixed several problems (technical and cosmetical) with negative values and logarithmic representation in filter dialog.
  • Modifications of filters now also enable project saving, even if they are the only modifications on project.
  • Fixed problems with inverse filters saved in previous sessions.
  • Several mostly cosmetical issues were fixed in reports.
  • Several enhancements, improvements and fixes for special reports (not included in standard installation)

4.6.1 Final 06 (201601251000)

  • Fixed a problem in Quantitation Tables where actions for selected elements sometimes were not available.

4.6.1 Final 05 (201601181129)

  • Some cosmetic issues were fixed.
  • Improved usability of update installer: does not ask unnecessary questions any more.

4.6.1 Final 04 (201601141759)

  • Adapted size of Warping Strategy dialogue to fit larger description texts as well.
  • Fixed Delta2D asking whether to use logarythmic values when opening an empty DIGE project.
  • Fixed a problem with the filter active checkbox and an sometimes inactive apply button in filter dialogues.
  • Fixed a problem with initial color of table cells with negated filters.
  • Impoved usability: main quantitation table is now opened and activated after spot transfer
  • Fixed a problem with initial spot filter state when creating report after opening project or transfering spots.
  • Started preparation for future report enhancements
  • Small fixes and adaptations for special reports.

4.6.0 Final 30 (201510281938)

  • Fixed a problem with opening and saving certain statistical analysis (TMEV).

4.6.0 Final 29 (201510231917)

  • Updated Java 8 from version 8u60 (8u45 on Mac OS X and Linux) to 8u66 in full installers on all platforms.
  • Updated 3D library (JOGL) to version 2.3.2 to fix problem with Java8u60 under Mac OS X.
  • Fixed problems with proxy settings for update checks and web-based license-check.
  • Significally reduced size of deployed Java Runtime by stripping libraries not needed by Delta2D anymore.

4.6.0 Final 28 (201510061526)

  • Fixed a bug for consumable mode: proxy settings are now used properly.
  • Fixed a bug for exporting presentation slides: fill state of label arrow heads is now considered.

4.6.0 Final 27 (201509152320)

  • Unified hover effects for spots, spot markers and labels using the corresponding layer color.

4.6.0 Final 26 (201509142039)

  • Show mouse-over effect (hover) for spots and spot markers, too.

4.6.0 Final 25 (201509111948)

  • Fixed active (mouse-hover) positions for label groups.

4.6.0 Final 24 (201509102326)

  • Label Management: Group and select labels, create multiple labels during translation.
  • Increased performance of reports.
  • Adjusted synchronous spot matching status across different views.
  • Delta2D now based on Java 8.
  • Fixed a couple of exceptions.

Note: The versions 4.6.0 Final 01 to 4.6.0 Final 23 have not been released.

Delta2D 4.5

4.5.3 Final 18 (201508281445)

  • Fixed problem with installer for Mac OS X
  • Fixed problem with 3D Representation (flickering on first start)

4.5.3 Final 17 (201508181711)

  • Sign installers and updaters for Mac OS X with code signing certificate.

4.5.3 Final 16 (201508141507)

  • Sign installers and updaters for Windows systems with code signing certificate.
  • Enable opening projects saved with upcoming Delta2D 4.6.
  • Initially deselect in-gel-standard images in the fusion dialog.
  • Increased zoom-out limit (5x) for Gel Image Regions.
  • Allow to open "All Gel images" table with data after opening a single gel table.
  • Activated missing spot match info again.
  • Fixed missing pptx/xlsx extension for custom export files names.
  • Fixed a number of exceptions.
Note: The versions 4.5.3 Final 14 and 4.5.3 Final 15 have not been released.

4.5.3 Final 13 (201504131828)

  • Fixed a bug in windows installers.

4.5.3 Final 12 (201503252226)

  • Facilitated Spot Transfer, enabling it for imported spot patterns.
  • Slightly changed formula for Spot Match Quality - making it even more meaningful.
  • Installation on Mac OS X with private Java.
  • Mac OS X Yosemite: Solved problem with Spot Editing.
  • Some minor bugs have been removed.

Note: The version 4.5.3 Final 11 has not been released.

4.5.3 Final 10 (201410271321)

  • Reduced risk of erraneous 3D view deactivation, added improvements for diagnosis of problems with 3D views.

4.5.3 Final 09 (201410201907)

  • Export of images as slides now compatible with latest Windows Office version (pptx format), slides can also be opened with LibreOffice and OpenOffice, and also with older Windows Office versions by using the official "Microsoft Office Compatibility Pack" (available for different languages)
  • Export of tables now compatible with latest Windows Office version (xlsx format), tables also readable with LibreOffice and OpenOffice (because of a known bug, LibreOffice has a problem with displaying boolean values properly - Delta2D includes a workaround for this)

Note: The versions 4.5.3 Final 03 to 4.5.3 Final 08 have not been released.

4.5.3 Final 02 (201409151214)

  • Fixed a problem with Filters on empty columns in Quantitation Tables
  • Fixed a problem with 3D Representation on MacOSX
  • p-value in projects using an internal standard (e.g. DIGE) is now calculated based on logarithmized spot volumes

Note: The versions 4.5.2 Final 03 and 4.5.3 Final 01 have not been released.

4.5.2 Final 02 (201408151633)

Please Note: due to a problem with packaging version 4.5.2 Final 01 is withdrawn.

  • fixed the reason for withdrawing version Final 01
  • reports now showing labels on image report (click in image to hide / show labels)
  • increased convenience for using new Delta2D Consumable infrastructure for certain uses

4.5.1 Final 06 (201407151720)

  • increased convenience for using new Delta2D Consumable infrastructure

Note: This version is mandatory for Delta2D Consumable users. The version Delta2D 4.5.1 Final 5 has not been released.

4.5.1 Final 04 (201407071420)

  • new Delta2D Consumable infrastructure in use
  • plus some bug fixes and resolved exceptions

Note: The versions Delta2D 4.5.1 Final 1 to Final 3 have not been released.

4.5.0 Final 13 (201405091553)

  • rois3D: fixed wrong viewports in 3D mode if prescale is effective (disabled using prescale in rois at all)
  • dualview: initially do not show background in dual view

4.5.0 Final 12 (201405052314)

  • light-table/warping-setup: remember the free last layout  and save the current layout as project aspect in the pool
  • dualview: added "Save" button to snapshot dialog
  • dualview: removed menu item "Export Dual Channel", replaced "Export Sample" by "Export Image" for the currently visible image
  • dualview: use the currently exported gel image name(s) as default file name for exporting images and saving snapshots, include warp partner name for the sample layer, if warped, and append "_snapshot" as suffix
  • reports: reports can be saved completely or separetely
  • reports: show spot profile as overlay
  • reports: allow to save all reports (including index) at once
  • reports: alpha-numeric table columns can be sorted also in saved reports
  • rois3D: allow to view rois in 3D
  • dualview: allow to choose the spot tool, even if there are no spots - this allows clicking on points of interest to scroll rois
  • spot detection: show parameter dialog only if there are already spots or markers on the image
  • tmev: add file extension to saved image file (if not explicitely typed)
  • tmev: remember last directory and image type for file chooser to save images
  • rois: initially scroll to first selected spot or dual view center if there is no such spot
  • rois: scrolling in dual view should move ROIs in either X- or Y-direction, but not in both directions to the new center
  • rois: scroll rois on mouse click in dual view, even if there is no spot at that point
  • rois: scroll to selected spot, even if the roi was not visible when the spot was selected
  • rois: unlinked zoom factors between dual view and rois
  • rollup3D: show region of interest when selecting spots, even if there are no spots in the dual view
  • rollup3D: show region of interest when selecting spots, even if the spot/profile was selected outside the dual view
  • 3D: drag (rotate) in 3D view could change the spot selection
  • rollup3D: by default show wire frame in dual mode (but gray gradient in single mode)
  • reports: scroll to a spot in the dual view (when selected via expression profile or roi report) even if another selected spot already was in the viewport
  • reports: do not deselect other spots if one is selected via expression profile or roi report
  • reports: removed label title from bar charts
  • reports: creating a spot album is 5 times faster now, saving reports even up to 20 times
  • plus some bug fixes and resolved exceptions

Note: The versions Delta2D 4.5 Final 01 to Final 11 have not been released.

Delta2D 4.4

4.4.1 Final 02 (201503192130)

Fixed spot editing under Mac OS X Yosemite

4.4.1 Final 01 (201409112005)

This is a recommended update.

  • Fixed a problem with Filters on empty columns in quantitation tables.

4.4.0 Final 18 (201311221210)

  • fixed: bug in ROI when changing project
  • compilation error
  • problem with Java3D during startup

Note: the versions Delta2D 4.4 Final 16 and Final 17 have not been released.

4.4.0 Final 15 (201310171623)

  • fixed: a serious problem which has been introduced in version 4.4 Final 14

4.4.0 Final 14 (201310162135)

  • fixed: performance problem of Dual View
  • improved: performance of table views after canceling of spots
  • fixed: some exceptions and reported errors of minor importance

Note: the versions Delta2D 4.4 Final 12 and Final 13 have not been released.

4.4.0 Final 11 (201309252323)

  • fixed: Menuitems in Quantitation Tables were disabeled under certain circumstances
  • improved: Error message in case of connection problems with license server is now more clear and allows to retry to connect
  • improved: licensing should be more robust now
  • fixed: automatic update check does not pop up if there is no update available.

Note: the versions Delta2D 4.4 Final 08 to Final 10 have not been released.

4.4.0 Final 07 (201307101904)

Note: this update is shipped as a full installer

  • Labels: Allow to delete multiple Labels for selected spots in Dual View and Quantitation Tables
  • Labels: Label visibility is linked to spot visibility by default: labels connected to invisible spots are hidden, too
  • Spots: When selecting a spot on a hidden gel image (e.g.a fusion) the Gel Image Regions will scroll to the corresponding region even without any matching spots
  • Spots: Hidden gel images are now excluded by default from Expression Profile bar charts
  • Spots: Selecting a single spot (in image views, tables, statistics) now always will select the complete expression profile (resp. deselect)
  • Reports: Tables in web reports can be sorted
  • Reports: Reflect a changed project when modifying a setting in an open report
  • Statistics: The visibility state of sample clusters will be saved now
  • Statistics: By default use "Complete linkage Clustering" for HCL and ST analyses
  • Statistics: By default use "Euclidian Distance" for T-Test analyses in HCL dialogs, too
  • Statistics: Show sample clusters for HCL analyses, if requested
  • Statistics: Try hard to avoid crashes under Windows related 3D driver conflicts when opening a PCA analysis
  • Statistics: Fixed multiple minor issues
  • Licensing: Under Windows it is now possible to import, register, or replace license files without administrative privileges
  • Licensing: Improved security when contacting the consumable server
  • Licensing: Improved error messages for license issues and fixed other minor problems with handling licenses
  • Other: Fixed broken Workflow in case of special characters in User home directory
  • Other: Remote assistance action opens a page on our website to start a screen sharing session
  • Other: The current pool can be changed in the "New Project" dialog, too
  • Other: Fixed missing permissions in installation folder when installed under Linux as root
  • Other: Show the version, the name of the current project, and the path to the pool in main window title bar
  • Other: Minor fixes to overall usability and stability

Note: the versions Delta2D 4.4 Final 01 to Final 06 were not released.

Delta2D 4.3

4.3.5 Final 01 (201409111703)

This is a recommended update.

  • Fixed a problem with Filters on empty columns in quantitation tables.

4.3.4 Final 01 (201305061429)

Note: This update is shipped as a full installer.

  • Automatically adapt memory settings for Delta2D during installation if not yet customized.
  • Improved robustness: start Delta2D with decreased memory (RAM) if preset amount of memory is not available.
  • Importing data from MS Repo is much faster for large protein lists.
  • More informative error messages from web license server, including "too many users".
  • Polished installer screen layout on Mac OS X.
  • Fixed some rare startup problems: "No splash screen available", "Pool has already been initialized".
  • Fixed a rare NullPointerException that occurred when changing the pool.
  • Fixed empty gel image regions window after changing the project.
  • Use the most recent Java 6 Runtime for improved stability and performance.

4.3.3 Final 02 (201212030156)

This is a recommended update.

  • Fixed a problem where TMEV analyses files were saved incompletely.
  • Fixed loading a TMEV analysis saved with Delta2D 4.2.1.
  • Fixed errors on "Export Sample…" and "Snapshot…" in the dual view.
  • Fixed a problem where importing a new gel image would delete a group due to a clash between sample name and group name.
  • Mac OS X: make file chooser more Mac-like, includes quick access to Desktop and other favorite folders.
  • Show larger points and gel image names for sample PCAs.
  • Improved error messages for Delta2D consumable.

Note: Version 4.3.3 Final 01 was not released.

4.3.2 Final 04 (201206081345)

This is a recommended update.

  • Considerably improved performance of autowarp for large images, slightly improved quality.
  • Added "G100", "G200", and "G300" as default gel image channels to better support NHD's Refraction-2D.
  • Scroll to selected profile after (freshly) showing Region of Interest frame.
  • Fixed a problem with initial slider values in table filter dialog of Quantitation Table.
  • Fixed an exception when adding a lot of gel images to a project.
  • Saving *.bak files also for matchmaps in pool now.
  • Bugfix for TMEV: after loading an external analysis, new analysises never again could be saved with the project.
  • Fixed a problem when renaming gel image attributes.
  • Ensure unique gel image names in UI to avoid exceptions on saving/loading pool.
  • Fixed a couple of rare exceptions related to image import and image fusion, TMEV, Dual View, Quantitation Table, and ROI.

Note: versions 4.3.1 final 1 to 4.3.2 final 3 were not released.

4.3.0 Final 04 (201111072145)

This is a recommended update.

  • Fixed a rare problem when opening a valid pool (message: "pool is corrupt").
  • Fixed problems with illegal refererences when saving reports.
  • Fixed problem with transferring data to TMEV.

4.3.0 Final 03 was not released.

4.3.0 Final 02 (201108301706)

This is a recommended update.

  • Changes in memory settings are saved properly again.

4.3.0 Final 01 (201108171453)

  • Introduced project import / export.

Delta2D 4.2

4.2.1 Final 08 (201503201502)

  • Fixed a problem with spot editing under Mac OS X 10.10 (Yosemite)
  • Fixed a problem whith saving project after importing gel images under certain circumstances ([7380] "Could not save image...")
  • Fixed a Concurrent Modification Exception related to table filters [7396]
  • Fixed a NullpointerException related to profiles [7391]

4.2.1 Final 07 (201112222216)

  • Scouts: list PCHProperties scout as source for pI/mW-estimation and preselect the correct pI/mW properties.
  • Proteome maps: synchronize correctly between dual view and color coding frame. Show correct color in selected cell in subset color coding dialog.
  • Fixed a potential deadlock on spot-editing.
  • Fixed a rare condition where reading gelImages.xml could fail even for valid XML resulting in "Pool is corrupt".
  • Project explorer: do not show match vectors as "Unused" for pairs with automatic warp mode.
  • Fixed several other exceptions
  • Updated Java from version 6u22 to 6u23 in full installers, includes version 19.0 of the Java HotSpot VM with improvements to overall performance and reliability.

4.2.0 Final 02 (201012011539)

  • Deactivated experimental feature: check warping quality.

4.2.0 Final 01 (20101201)

  • GenoList/AureoList scouts did not show result of fetching in editor.

Delta2D 4.1

4.1.2 Final 01 (201009290008)

  • Improved responsiveness when selecting files for gel image import.
  • In the workflow: open the correct gel image pair even when the gel image pairs table was sorted.
  • Fixed: spot transfer was not canceled when "Cancel" button was clicked.
  • Fixed an exception when opening the quantitation table.
  • Fixed missing line-breaks in some dialog texts (e.g. in hint when saving in demo version).

4.1.1 Final 02 (201007231619)

  • Fixed a problem with the Delta2D update installer for Mac OS X.

4.1.1 Final 01 (201007211555)

  • Fixed: rotating and mirroring an image in the image properties dialog did not always behave as expected (e.g. for 270 degrees rotation).

4.1.0 Final 01 (201006221049)

  • Fixed hanging progress bars on image import/edit.

Delta2D 4.0

4.0.8 Final 06 (201009281522)

  • Fixed: spot transfer was not canceled when "Cancel" button was clicked.
  • Fixed an exception when opening the quantitation table.

4.0.8 Final 05 (201006081455)

  • Fixed a ConcurrentModificationException at startup.
  • The t-test Dialog in Statistics Module was too big when opening it.

4.0.8 Final 04 (201005171443)

  • Color and name can now be changed for empty groups.
  • On Mac, Delta2D would not start if there was a space in the application path name.
  • On Mac, fixed inconsistent background colors, e.g. in dual view toolbar.

4.0.8 Final 03 (201004281713)

  • Fixed: Delta2D was not starting on Windows (32 bit) after updating to 4.0.8. This occurred when reserved memory (RAM) was set to maximum before.

4.0.8 Final 02 (201004201503)

  • Fixed: Delta2D on Mac did not start after last update.
  • Fixed: on Mac, the license file had to be imported multiple times when Delta2D was started once in the last installation step.
  • The link to show reports in the workflow works again.

4.0.8 Final 01 (201003301339)

  • Numeric label names in pick lists are now sorted correctly.
  • Workflow: link to add gel images on "Setup Project" task pane fixed.
  • Reports: correctly disable/enable reports on de-/reactivating the license.
  • Pick list menu is now correctly enabled after switching to another project with shared gel images.
  • Fixed incorrect image display in dual view and ROIs after changing "Amplitude Rescale" option.
  • Fixed issues with Quaqua Look&Feel for MacOS X.
  • Made various performance improvements, e.g. in image import.
  • Fixed an imaging exception on gel image import.
  • Fixed various other exceptions.

4.0.7 Final 01 (200912161409)

This is a recommended update because it fixes a potential data loss issue.
  • Fixed a potential loss of data: warping info became inaccessible after removing gel images from a pool.
  • Added key shortcuts: use Ctrl-F for "Find Label…" and F3 for "Find Next Label" in tables.
  • Searching for labels now tolerates leading or trailing spaces in label names.
  • Improved display of Gel Image Regions display.
  • Polished generation of pick lists, added Herolab Spot Picker to picklist menu.
  • Moved pick list actions from spots menu into export menu in the dual view.
  • Fixed a rare problem where spot transfer hanged while consuming 100% CPU.
  • Fixed several exceptions in reports.
  • Fixed: Delta2D was not starting in Turkish version of Windows.
  • Fixed: User interface indicated that project changes need saving (Save button was enabled) even though there were no changes.
  • Note: If you want to use this version of Delta2D with Protecs then you need Protecs version 1.28 or higher on the server side.
  • Reactivated buttons to show/hide spots/labels in Gel Image Regions display.
  • Removed menu item for generating Excel Report (Export to Excel is still there).
  • Fixed various other exceptions.

Note: Version 4.0.6 was not released.

4.0.5 Final 07 (20091028)

  • Significantly improved performance when changing warp modes (or the whole warp strategy) in large projects.
  • Visibility of spot boundaries in reports can be switched on/off again.
  • Fixed several exceptions related to modifying warp modes in large projects.
  • Fixed a deadlock situation that occurred sporadically when saving large projects.
  • Fixed an exception when browsing an expression profile with missing spots.
  • Fixed a problem where some transferred spots unexpectedly have been canceled.

Note: versions 4.0.5 final 3 to 4.0.5 final 6 were not released.

4.0.5 Final 02 (20090929)

  • Menu bar is now shown consistently on Mac.
  • Fixed problem with wrapped labels in PowerPoint.
  • Borders now leave enough padding around labels in the dual view in all zoom levels.
  • Dropping multiple images into project or images node will create a new group.
  • Update project's name in workflow when it is renamed.
  • Fixed: spot shapes were not exactly congruent in some cases after transfer without remodeling.
  • Fixed missing spot shapes on first image in Gel Image Region display.
  • Scouts: adapted to recent changes in NCBI webseite format.
  • Fixed exceptions that occurred when saving reports.
  • Fixed several other exceptions.

Note: version 4.0.5 final 1 was not released

4.0.4 Final 05 (20090716)

  • Fixed: Correspondences between expression profiles in TMEV window and spots in gel images were not correct after saving and loading an analysis.
  • Scouts: fixed a problem with parsing response from genolist.pasteur.fr (changed since July 1, 2009).
  • Improved gel image attributes dialog, e.g. you can drag and drop multiple selections.
  • Fixed problems related to "Save Project As…".
  • Fixed exceptions occurring under certain circumstances when opening a statistics table.
  • Fixed exceptions in spot quantity report, and project report when there are no connected gel image pairs.
  • Fixed exceptions when choosing an alternate data source in TMEV.
  • Fixed several exceptions in other areas.
  • The current project is shown in bold in the project manager dialog.
  • Fixed gray stripes in "Create Consensus Spot Pattern" workflow step.

Note: versions 4.0.4 final 3 and final 4 were not released

4.0.4 Final 02 (20090626)

  • Fixed several exceptions that occurred on opening a gel image pair in the dual view.
  • Fixed several exceptions related to warping.
  • Fixed a problem where some spot quantities were not updated in the table after changes in normalization.
  • Click on dual view with zoom tool scrolls to the correct position when gel image regions have been opened.
  • Selected spot remains visible when clicking on zoom button in gel image regions.
  • Complete profile is now selected when first clicking on a spot in gel image regions.
  • Workflow shows the path to the pool folder when no project is open.

4.0.4 Final 01 (20090619)

  • Available physical memory on Macs with more than 2GB of memory is now detected correctly
  • Added menu item Approve Warping to context menu of gel image pairs, use this to approve all match vectors in one operation.
  • Added standard context menu to tabs in Dual View.
  • Dialog for modifying the color coding settings now always stays on top.
  • Insert space between multiple label names in table CSV export.
  • Quantitation tables: Fixed unwanted resorting of rows after Mark Selected Spots.
  • Quantitation tables: Fixed a ClassCastException in quantitation tables.
  • Reports: Fixed several exceptions in spot album.
  • Reports: Fixed several problems that occurred after opening a new project, or when loading reports without a project.
  • Reports: Spot album now displays spot shapes by default.
  • Statistics: Fixed a problem where t-test dialog was listing gel images from a previous project.
  • Statistics: Re-enabled progress bars for TMeV-analyses
  • The full installer uses the Java 6 update 14 release notes.
  • The Groups node in Project Explorer was renamed to Gel Images.
  • Clarified text in Add Gel Images dialog.

4.0.3 Final 04 (20090515)

  • Fixed Excel reports.

4.0.3 Final 03 (20090508)

  • Fixed a problem where match vectors were not added correctly.
  • Fixed an error for missing calibration curves after changing the pool.
  • Fixed an error in spot quantities report: do not offer to use spots marked on an internal standard image.
  • Fixed: Installer was unresponsive on machines with locales that are not built-in installer options.
  • Fixed a problem with opening web browser under Linux.
  • Added the ability to choose a custom browser for reports (in preferences).

Note: version 4.0.3 final 2 was not released.

4.0.3 Final 01 (20090422)

  • Fixed a problem where a missing license could cause an exception.
  • Fixed an exception on matching.
  • Fixed an exception on invoking popup menu in project explorer, light table, or warping setup.
  • Fixed a rare exception on opening the dual view.
  • Dual view is always emptied properly after opening a new project.
  • Enable selection of user-generated calibration curves for gelimages.
  • Updated Java3D to version 1.5.2. This fixes a crash on Windows that occurred with some graphics card / driver combinations. Improves 3D performance on Mac. You need to use the complete installer to take advantage of this.

4.0.2 Final 06 (20090415)

  • Usability: re-enabled accelerator key strokes Ctrl-W/Ctrl-U to warp/unwarp in dual view.
  • Fixed an exception when warping with close match vectors.
  • Usability: prevent creation of match-vectors with one end too close to an existing vector, beep when this happens.
  • Usability: do not beep when cancelling spots or deleting match vectors with the Delete key in dual view.
  • Fixed some exceptions for a project with only a single gel image.
  • Fixed a rare exception on modifying warping setup or closing/opening projects.
  • Fixed an exception on zooming the light table or warping setup.
  • Fixed an exception on warping in dual view.

4.0.2 Final 05 (20090406)

  • Fixed a problem that caused out of memory error when doing spot transfer on certain images.
  • Label text bounding box is now closer to the text. Makes label selection easier, and the arrow points more directly to the text.

4.0.2 Final 04 (20090327)

This is a recommended update.

  • Fixed a rare problem that resulted in a corrupted (but recoverable) pool after switching between large projects.
  • Fixed an exception that occurred in the gel image import dialog.

Note: Versions 4.0.2 final 2 and final 3 were not released.

4.0.2 Final 01 (20090309)

This is a recommended update.

  • Fixed a problem with TMEV t-tests: they used the wrong test design (grouped, paired, etc.). The problem was introduced in version 4.0.1 Final 01 (released on 13 February 2009).
  • Fixed an exception related to manipulating match vectors, spots, labels, etc. in image views.
  • Fixed: I/O error writing PNG file when closing browser before spot album report is finished.
  • Installer: improved text in warning dialog when a running application was detected.
  • Fixed several exceptions.

4.0.1 Final 06 (20090227)

  • Now Hide Selected Spots operates only on the image / images that are currently visible in the quantitation table. Similar problem was fixed for other operations on selected spots.
  • Fixed an exception in spot quantities report that occurred when you included all spots in the report.
  • Fixed an exception related to 3D view when changing the Show Canceled Spots setting.

Note: Version 4.0.1 final 5 was not released.

4.0.1 Final 04 (20090225)

  • Project menu now includes item New Project
  • Added keyboard shortcuts in Project menu.
  • Added a new item to Delta2D's start menu: Use Reset Startup Configuration to recover from problems in setting memory.
  • Color coding displays is now updated correctly when settings are changed.
  • Fixed an exception when creating a color-coding that uses a gel image with labels as reference.
  • Fixed an exception on activating license files combined with license import.
  • TMeV: Fixed an exception when doing K-median Clustering (KMC) with Cluster Samples.
  • Fixed an exception on changing pool with open quantitation tables.
  • Fixed opening the spot table from the dual view.
  • Fixed exception on opening statistics table in new project.
  • Fixed exception related to tooltips on gel images in project matrix.
  • Fixed several minor exceptions.
  • Added more information to some error reports (ArithmeticException on creating a exact warp transform)

Note: Versions 4.0.1 final 2 and 4.0.1 final 3 were not released.

4.0.1 Final 01 (20090211)

  • Delta2D's installer, uninstaller, and updater now ask you to close a running Delta2D instance.
  • Better error notifications for web reports, uses Delta2D's error dialog.
  • In toolbar, the visibility button now controls "Gel Image Visibility".
  • Fixed an exception that occurred on opening statistics table or spot quantities report in certain projects.
  • Fixed an exception that occurred on opening the dual view with Java 6u12.
  • Fixed an exception when using gel images from a Protecs database pool.
  • TMeV: 3D PCA view shows spheres by default.
  • TMeV: Fixed a problem with entering p-value cutoffs in ANOVAs and t-Tests.
  • TMeV: T-test setup dialog now has "between subjects" as default.
  • TMeV: Setup dialogs for t-test and one way ANOVA now use a split pane for group assignments and parameters.

4.0.0 Final 04 (20090202)

This is a recommended update.

  • Fixed performance problems (especially graphics performance) that occurred in certain graphics hardware configurations.
  • Fixed several exceptions.
  • Fixed a problem with web reports when files from version 3.6 were left over in .Delta2D folder.
  • Pool-related menu items are available again when no project is open.
  • Fixed a problem when verifying workflow scripts in Turkish locale.
  • Make automatic reassignment of an image to a new group to solve a situation where a gel image without a group occurs.
  • Selection in explorer follows dual view more closely.
  • Added online help window for nonparametric tests.
  • Show a useful message instead of an exception when setting spot edit markers on invalid locations.
  • Fixed an access rights problem where debugging info was written into programs folder.
  • TMeV icons for HCL and support trees were swapped.

Note: Versions 4.0.0 final 2 and 4.0.0 final 3 were not released.

4.0.0 Final 01 (20081215)

  • Introduced completely new user interface.
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