DNA BASER - Changes (Version tracker)

[admin]

Read the last post for the most recent changes!







Legend:
+ New feature added or improvments
> Item recently introduced
- New bug introduced
* Bug fixed

Full history here

[admin]

[DNA Baser v2.9]

IMPROVEMENTS/CHANGES:

Speed of the assembly algorithm improved with 50%
Better detection of file type by magic header not by extension. Stop the process if the file has wrong extension and let the user know.
Brand new (better and easy to use) licensing system. We can send now the keys as plain text via email (instead of binary attachments). We can issue now temporary keys.
ENABLE/DISABLE menus according with the status of the selected column.
User is informed what to do when no contig was made.
Less memory required while opening chromatogram files (ABI, AB, SCF)
Dramatic speed improvement while scrolling the contig/chromatograms
[Contig window] The primers (when detected) are shown in the tool tips, while moving the mouse over the contig
Better search function
'View RC of contig' menu added the Pop-up menu of picture window (at user request)
[Chromatogram viewer] Remembers last used position of 'Bases line pos' track bar
[Chromatogram viewer] Improved chromatogram viewer
[Chromatogram viewer] Height of the peaks in chromatogram ('Chromaviewer') can be adjusted in a larger range
Better handling of errors in corrupted ABI files
Better handling of contig that are made from chromatogram and non-chromatogram (plain text) files
Better handling of SCF file type conflict
Better on screen sizing for Contig Window
Better debugger
Do not allow user to open MultiFasta files. DNA Baser does not directly support MultiFasta. Please use instead our free 'MultiFasta to Fasta converter'.
Better auto generation of project name when user keeps the samples in folder with very long name
Opening warning (for non-admin users) message changed
Better navigation in 'Project manager -> FileList'
Info about saved file in status bar was too long sometimes. Now it shows only the short file name.
Better tool tips in picture window (grid)
'Save contig as...' function added (at user request)
Word-Wrap button added in the RC window
Cursor can be moved with ArrowUp/ArrowDown keys
Feature added: Search function is working now also for files containing non-capital letters. DNA Baser will convert all letters to uppercase for search. [Takanaka]
The 'Primers' database is not overwritten when the user install a new version on top of an old version of Baser
The Search function is invoked every time you press the ENTER in the Search box
Added horizontal scrollbar in JobList
Batch by name pattern. Better actions handling.
Batch by name pattern. Better log.
Batch by name pattern. The user can stop now the process by pressing Escape or by closing the 'Project Manager'.
Do not draw the chromatogram peaks for the chromatogram that are not visible on screen. Great speed improvement.
Display in TitleBar how many hours/minutes are left from the current trial period (if in Trial mode)
When accessing an empty CDROM drive: Message 'Error I/O 21' change with 'Error: Could not access drive.'
It can open files over the network (partial support).

[admin]

DNA Baser v2.9.92

- Minor change in 'Project Manager' in 'File type' drop down box
- Color of arrows change in 'Contig Map'
- User is not lowed anymore to insert invalid characters in contig's name (in 'Project manager' window)
- Added 'Show hidden folders' and 'Show system folders' checkboxes
- Show 'You do not have administrator rights' message when limited users try to associate DNA Baser with chromatogram files
- Show 'Administrator privileges' in About window
- 'File Explorer' renamed to 'Sample Explorer'
- 'Log window' and 'Sample explorer' was moved in TPageControl
- Better handling of error when user tries to access a not ready drive (like a CD unit without inserted CD)
- Tool tips added to every Arrow in 'Contig map' window
- The 'Hide Peaks height track bar' was replaced with 'Toggle Peaks height spin box' menu
- Cross cursor is not visible anymore by default (you can enable it from 'Settings')
- Added tool tip to explain that GREY color in Grid means that the end of the sequence was trimmed
- Function 'Mark as Trusted' and 'Mark as Not Trusted' added
- Moving the cursor outside the Grid while selecting some bases repositioned the cursor which made the selection to be lost. Now the user can select any amount of bases.
- Added IUPAC ambiguity code table
- Fixed: clicking a FASTA file in contig window will not activate it’s arrow in ContigMap
- Better pre-contig betection
- New feature added: 'Show a button for Settings window in taskbar'

[admin]

DNA Baser v2.10

- Fixed: in some occasions editing a base in Assembly Viewer from did not changed the color of the column from red (Mismatch) to green (Solved)
- Fixed: problems when inserting long names for Primers
- Fixed: Minor: The 'Previous' button was visible also when opening single chromatograms (non-assembly mode)
- Enhancement: Better pre-contig detection
- Enhancement: the button for error navigation now also jumps to corrected/green bases (not only to errors/red)
- Enhancement: Better windows resizing
- Enhancement: Differences (mismatches) between the reference sequence and the other sequences is highlighted in purple.

[admin]

DNA Baser v2.11

+ Menu and window ‘Primers' renamed to 'Vector cleaning'
+ Better embedded help in ‘Vector cleaning’
+ No active vector cleaning sequence (primer) by default
+ Trial period changed to 6 hours (time lapse only when the program is running)
+ Better handling of invalid ABI files
+ Gray regions representing low quality ends are now bigger (same height as the viewer)
+ Now Baser can highlight not only the mismatches between chromatograms but also between the chromatograms and the reference sequence [request by Adam Rabinowitz]

[admin]

DNA Baser v2.675

NEW

Metadata and batch metadata integration (RNA Baser only).
Button to open Windows Explorer in contig's folder, after sequence assembly.
Remove vectors from single chromatograms.
SEQUENCE ANALYSIS - mark all bases with a confidence level (QV) below a specified threshold, in red.
Batch convert from chromatogram to Fasta with vector removal and automatic metadata integration.
Resizable chromatograms.
Full support for low quality sample ends editing.
Better Windows Vista compatibility for users without Admin privileges (Guest users)
"Gbk (GenBank) to Fasta converter" tool was integrated in DNA Baser Assembler
"Clone library de-replicator" tool was integrated in DNA Baser Assembler
"Fasta to MultiFasta converter" tool was integrated in DNA Baser Assembler
"MultiFasta to Fasta converter" tool was integrated in DNA Baser Assembler
Double clicking a sample file (SCF/ABI/FASTA/SEQ) in Windows Explorer will open that file in DNA Baser instead of opening only the folder where the file was located.
Allow only one instance of DNA Baser: If the user double clicks a sequence and DNA Baser instance is already open, the sequence will be loaded into that existing instance (instead of opening a new instance). You can change this behavior by placing/creating a file called 'OnlyOneInstance' into the 'DNA Baser\System' folder.
A new menu button called 'Request a feature' was added under the "Info" main menu. You can use this button to communicate with us, request new features or send feedback about our sequence assembler.
Batch metadata integration



IMPROVMENTS

* Speed improvement in "Mark as trusted/un-trusted" function
* Improved MultiFasta to Fasta converter
* High resolution icon incorporated into the EXE file (Vista-style icon).
* Show Desktop Alternative tool was updated to display more than 2GB of free RAM (for computers with more than 2GB or RAM).
* Colors in log. Save log as RTF.
* Open external Windows Explorer window in explore mode instead of browse mode.
* Show some messages only five times (make the interface less annoying and at the same time let the user to learn about the operation that will be executed automatically by DNA Baser Assembler in the future).
* Integrated "batch assembly" wizard: Teach the user that s/he needs to set the "template" before starting a batch assembly process (show the 'Did you check the ''file pattern'' parameters in the Settings window?' message box).
* Show error message while trying to open empty FASTA files
* 100% compatible with Mac via Parallels/Bootcamp/VMWare.
* Improved handling of corrupted/invalid ABI/SCF files.
* Improved contig editor.
* Improved file association.
* Improved 'Assemble to reference'.
* Improved log window. Show removed primers in log.
* Improved file handling: Before starting the contig, check if all files in the JobList are valid. Invalid samples are automatically removed from Job List so the assembly process can continue without human intervention. Build a list of invalid files and report it.
* Improved user interface: new toolbar, improved embedded help, interactive help, workflow...
* Improved sample viewer: 'Mark as trusted/un-trusted' can now be used also in Sample viewer window
* New: Show error message while trying to open empty/invalid FASTA files
* Improved: Correctly handle multiple contigs resulted when assembling to a reference.
* Improved: menu 'Save as Fasta/Seq/Scf' was replaced with 'Save all as...' and 'Save selected as...'. Now the user can choose where to save the file.
* Double click on a CSV file in DNA Baser Assembler will insert that file in "CSV file" box to be used as default.
* Check if project's name/path is too long (see Microsoft's 255 chars limit)
* Announce when project's path/name is too long, then automatically truncate it
* The folder to store the INI file (DNA Baser settings file) is choose based on disk write-access permissions instead of users privileges.
* The trial period was changed.
* Auto-detect invalid path of CSV files