Release Notes for Genome Workbench 2.6.0 (August 31, 2012)
New Features
- Search View: Implemented SNP Search (search by NCBI rs id)
- File Open: implemented support of direct file open from compressed formats .gz and .bz2
- Generic Table View and Tree View now remember old queries and search terms
- Generic Table View: new context menu option to filter on this cell
- Tree View: implemented broadcasting of taxonomic ids (tax-id property) to facilitate interactive comparison of trees
- Multiple Alignment View: new tooltips with detailed statistics for row and column
Bug Fixes and Improvements
- Format auto-detection for opening multiple files improved. First file is used for format detection analysis.
- Graphical Sequence View: major improvement in speed of rendering of BAM/cSRA alignments
- Graphical Sequence View: when selecting a region by mouse show exact boundary coordinates to improve position accuracy
- Graphical Sequence View: "Go to Sequence Position/Range..." fixed bug with focus in the dialog
- Graphical Sequence View: various fixes and improvements displaying of alignments
- Search View: fixed crash on feature search (“Select Feature Types”)
- Search View: fixed crash on closing the view while search in progress
- SPLIGN Tool: exposed more parameters for the algorithm
- Improved Drag-n-Drop of files into Project Tree
- Graphical View and Alignment Span View discrepancy fixed (rows selection made visible in Selection View)
- MacOS-X: improved windows docking
- MacOS-X: Application specific data now put into more conventional location for Mac platform
- MacOS-X: fixed bug with scroll bar disappearance in Graphical Sequence Viewer
- ORF/Kozak finder: fixed crash related to multi-threading
- File Open Dialog: improved layout to fix some cosmetic issues
- Tree View: Fixed bug with OpenGL rendering of mini-map (“m” key)
- Tree View: fixed issues in scaling of bounding boxes (cladogram mode)
- Window Manager: fixed number of issues which could cause crashes and incorrect window layouts
- Genome Assemblies – Generic Table View: added new columns: 'Assembly unit' and 'Patch type'
- Genome Assemblies – Grahical Sequence View: added support and visualization of of alignments coming with assembly
- Run Tool Dialog: improved default selection of target project for result
- Text View: fixed crash
- Feedback tool: improved e-mail address validation
- BLAST Search Tool: new improved categorization of available BLAST databases
- NG Align tool: algorithm rework and code cleanup
- Added support of new types of molecule accessions
- Linux: fixed number of dialogs where radio buttons did not work
- File Open/Import: improved default naming of project items, added meaningful track title for Graphical Sequence View
- File Open/Import: filename validation improved to be more responsive when used for slow network drives or locations
- Generic Table View: format of accession columns changed to include version number
- Generic Table View: fixed bug in query language, causing string interpretation of certain numeric types (like distance between nodes)
Release Notes for Genome Workbench 2.5.5 (May 17, 2012)
New Features
- Graphical Sequence View: saves markers and visual ranges (positions) on the sequence in the project file, reopening project now restores the context, making it easier to navigate.
- Graphical Sequence View: New rendering for clone features
- RMO format: added support for RepeatMasker RMP files (Feature Table)
- VCF format: added as supported file format for Open Dialog
- Implemented multiple-column sort option for tables (Search results, etc)
- BAM/cSRA: added support for SRA accessions in the Open Dialog
- Tree View: Search now supports wildcard espressions ‘?’ and ‘*’
Bug Fixes and Improvements
- Fixed multiple issues in processing and displaying alignments, due to switch to the new Alignment Manager (C++ Toolkit)
- Open Dialog (Genomes): fixed crash opening certain genomes like 'Escherichia coli'
- Open Dialog (Genomes): improved discovery of certain genomes (GRCm38)
- MacOSX: Fixed bug when you click on list icon Float/Minimize/Close options are disabled when docked
- MacOSX: Fixed bug with menu items not always available
- MacOSX, Windows: certain command shortcuts changed to better satisfy platform standards
- MacOSX: Solved stability issues related to OpenGL on dual GPU MacBook Pro machines
- MacOSX: solved drag-n-drop issues between Project Tree elements
- MacOSX: fixed a major issue in windows layout
- File Export: added default extensions for files of different formats
- Tree View: performance optimization for various versions of OpenGL
- Linux: Fixed compatibility issues, related to various versions of libpng and its APIs
- Project Load: load of large project can now be canceled using context menu
- Labels generation: fixed crash
- Labels generation: improved performance of taxon labels bulk retrieval
- FASTA import/export: fixed bug with exporting duplicate sequence ids (which prevented opening the exported file)
- Graphical Sequence View: Fixed bug in selection broadcasting for results of Component Search
- Graphical Sequence View: improved rendering of backgrounds for mRNA features
- Graphical Sequence View: fixed direction of transcription are drawn backwards in alignments
- Graphical Sequence View: more options for alignment height
- Graphical Sequence View: improved rendering of mixed strand alignments
- Graphical Sequence View: improved rendering of protein to genomic alignments
- Graphical Sequence View: fixed bug with ProSplign alignments don't project up from NT to NC
- Graphical Sequence View: fixed crash related to hotkeys and local menu
- Generic Table View: added export into a separated file, readable by MS Excel (use context menu)
- SPLIGN Tool: crash fixed
- Tree View: fixed rendering of area markup
- Tree View: fixed crash if node is deleted in one tree and user goes to another tree
- Tree View: improved broadcasting of certain local sequence ids
- Multiple Alignment View: fixed crash on certain BLAST alignments
- Search View: fixed issues with server-side compatibility sometimes showing empty columns
- ORF Search: crash fixed
- Genome Workbench now uses wxWidgets 2.9.3, fixing lots of issues on various platforms
- Close Workspace Dialog: layout fixed
- Alignment Summary Report: fixed to show 1-based coordinates (was: 0-based)
- BED Import: improved compatibility with BED format
Genome Workbench 2.5.0 Release Notes (1/11/12)
New Features
- Added support of Genomes (user can now search and load genome information (collection of sequences) from NCBI into project.
- BAM files loader now integrated with genome information from NCBI
- Added support for a new cSRA file format
- MacOS-X 64-bit build added to our distribution list
Bug Fixes
- GFF reader optimized for better performance, file size and memory footprint
- Improved communication protocol for clients working with certain versions of not so standard firewalls
- Graphical Sequence View: improved clone feature rendering
- Graphical Sequence View: fixed incorrect selection broadcasting
- Multiple Alignment View: fixed memory leak causing major slow down or crash on large data
- Text View: can now show ASN.1 type information
- Text View: fixed bug in range display for FASTA format
- Tree View: fixed crash on entering letters for cluster ids
- Tree View: improved performance and fixed some issues with radial layout
- Improved performance of generating a meaningful description for sequences
- Export of annotations in ASN.1 format: fixed issues of files written incorrectly, so binary ASN cannot import back to Genome Workbench
- Generic Table View: implemented cell de-selection, improved object broadcasting
- Generic Table View: accessions and locations made clickable
- Search View: fixed bug with incorrect row selection when sorting
- Search View: fixed bug on searching for components
- New version notification dialog: improved UI to offer a clickable URL
- BAM file loader: fixed file permission issues on MacOS-X
- BAM file loader: allow to select more than one file at once
- Open Dialog: improved performance opening a project item with large number of objects (like Genome collection)
- Open File Dialog: fixed issue with sometimes incorrect file opening on Windows
- FASTA load: performance optimization
- Project Save and Load: improved progress reporting, so Genome Workbench does not look dead while it is just busy
Genome Workbench 2.4.5 Release Notes (10/18/11)
New Features
- Open Dialog now implements a default view functionality, user can now open default view with a mouse double click in the project tree
- Generic Table View: implemented search function and query language
- Generic Table View: implemented new option to open trees as tables
- Tree View: implemented distance (scale) bar for trees with distances (like phylotrees)
- Graphical Sequence View: improved tooltips, links to RefSeq Gene, Entrez WEB pages added
- GFF3: major version upgrade for GFF reader
- Text View: implemented data types display for ASN.1 mode
Bug Fixes
- Multiple Alignment View: fixed memory consumption and crashing issues
- Graphical Sequence View: optimization of density graph computation
- Graphical Sequence View: fixed tooltips popup when dialog is shown
- Graphical Sequence View: fixed duplicate genes when project items annotate gene twice with an additional location
- Graphical Sequence View: fixed function of Undo-Redo buttons
- Graphical Sequence View: Fixed rendering issues of alignment statistics graphs at certain zoom levels
- BAM files compatibility:
- Tree View: improved search function
- Tree View: fixed crash when large tree is viewed with a change of layouts
- Tree View: fixed some sizing errors when certain trees become not fully visible after changes in zooming mode from vertical to proportional
- Tree View: fixed layout calculations and display of small single-node trees
- Tree View: fixed function of Undo-Redo buttons
- Tree View: fixed issues with nodes expand-collapse actions
- Tree View: fixed rendering issues with not always cleaning the view port area
- Local data caching: fixed bug in the internal SQL statements causing old data to stay in the database longer than expected
- Selection Inspector: fixed bug with scope selector disabled on MacOS
- Project Tree View: fixed crash when project item moved from one project to another
- Improvements and fixes of communication protocol to better work with older version semi-compliant proxy servers. This improvement results in better connection to NCBI data servers.
- Search View: MacOS version fixed autocomplete prevented entering new data
- Open View dialog: fixed location duplications
- FASTA export for BLAST alignments, fixed issues with showing incorrect locations in dialogs
- FASTA loading performance optimizations, use more advanced memory mapped I/O where possible
- Generic Table View: fixed graphical rendering issues (extra vertical lines) on MacOS
- Text View: now saves view settings (fonts, etc)
- MacOS: fixed various GUI issues related to keyboard commands and zooming using main menu, About not working, etc
Genome Workbench 2.4.0 Release Notes
New Features
- Tree View: implemented tree filtering using query language with logical expressions
- Implemented a brand new view: Alignment Summary to display various alignment properties (Identity %, Coverage %, mismatches, gaps, e-value, etc) in form of a tabular grid
- Implemented new column options for all table views to show/hide column, specify sorting and sort order
- Graphical Sequence View: ergonomics improvement, view now preserves collapse/expand state of track during Genome Workbench execution session
- Search Tool: overhaul of ORF Finder and Kozak Scan algorithms
- Graphical Sequence View: implemented context menu item Rename me to change track name
- Graphical Sequence View: user interaction improvements: '+' or '-' sign clickable on the left side of a track title bar, implemented track cloning
- Graphical Sequence View: 6-frame translation and protein translation are now context aware and can use alternative genetic code tables
- Graphical Sequence View: implemented alignment summary and statistics graph for alignment tracks (like BAM)
- Graphical Sequence View: implemented easy access to help and documentation
Fixes
- Fixed bug with incorrect taxonomic id when searching for a nucleotide in NCBI public databases
- Fixed Merge Alignment tool to use the same engine as Cleanup Alignment only with more exposed parameters
- Fixed bug with BLAST tool not honor multiple query sequences
- Fixed bug with tooltips sometimes stealing focus from views, so keyboard shortcuts may not work as a result
- Implemented new BLAST results retrieval from NCBI to improve stability over unfavorable network conditions
- Graphical Sequence View: fixed display of component map in multiple level layout
- Graphical Sequence Viewer: fixed bug in reading self-alignments, which caused alignments visualization duplication
- Graphical Sequence View: fixed rendering of multi-location fuzz rendering
- Graphical Sequence View: fixed alignment coloration mismatch
- Graphical Sequence View: fixed freezing opening more than one view at the same time
- Graphical Sequence View: fixed crash in six frame translation track when switching between multiple layout mode and default mode
- Fixed bug in reading alignment segments, which in some cases manifested as failure to open Multiple Alignment View
- MacOS-X: fixed bug with loading local caching plugin
- MacOS-X: fixed crash on drag-n-drop project items
- MacOS-X: fixed WindowMasker tar file download creates incorrect file permissions on Mac and Linux
- Selection View: fixed coordinate discrepancy bug
- Open View Dialog: fixed object grouping mode (feature tables failed to open)
- Open View Dialog: fixed "attempt to access NULL pointer" error
- Alignment Views: fixed view opening to better categorize alignments
- Fixed serious issues in layout and windows management
- Tree View: fixed crash on closing
- Search View: fixed thread races crash
- Search View: fixed issues with buttons Start and Stop became enabled simultaneously
- Search View: fixed component search coordinate error (it was giving +1)
- Search View: improved stability of ENTREZ search
- Search View: column width changes are now saved
- BAM reader: fixed bug opening files on network drives
- BAM reader: fixed issue with canceled opening tasks stays on in the Task View
- GTF/GFF import: incorporate better reader
Genome Workbench 2.3.2 Release Notes
New Features
- Sequence Viewer: implemented fake end rendering for clone features
- ORF Search: implemented new column (Start Context), showing residues preceding and following ATG
Fixes
- BLAST and Windowmasker cannot start on Windows (missing manifest files)
- Sequence Viewer: fixed Marker navigation direction issue (Alt+left arrow)
- Tree View: performance optimization for large tree label assignment
Genome Workbench 2.3.1 Release Notes
New Features
- BAM/SRA format support. Please see tutorial 6
- CLUSTAL execution added (as an external tool).
- Tree View: implemented image export to assemble panorama images and/or printing
- Tree View: implemented support for Zoom to Selection
- Implemented progress indicator when Genome Workbench accessing network services.
- Implemented progress indicator and cancel for View Open function (if it takes too long to convert objects)
- Graphical Sequence View: multiple rendering improvements to better visualize large clusters of features (icicles), improve rendering of component color maps
- Graphical Sequence View: Improved six frame translation track, better codon detection, and visualization parameters
- BLAST tool: new option to link related hits together (for better visualization).
- Options dialog: checkbox to quickly enable/disable use of PROXY (for roaming users)
- Linux binary build is now based on Ubuntu 10.04 LTS (Lucid Lynx)
Fixes
- Multiple Alignment Viewer: fixed crashes on opening certain alignments with version-less accessions, fixed tooltip crashes.
- Fixed crash with View opening (improperly sent notifications)
- Graphical Sequence View: fixed crash in tooltips at the end of a sequence
- Window Masker directory path now saved between Genome Workbench executions
- Selection View fixed crash related to internal event races
- Tree View: fixed rendering for trees with negative distances
- Export Alignments: crash fixed
- BLAST tool: fixed algorithmic crash related to incorrect location mapping
- Newick tree loader: improved standard conformance
- Tooltips: made multiple improvements to better conform to standards of target platform (Windows, Linux, MacOS)
- Windows manager: fixed issues in panel configuration, making impossible to resize things to invisibility (and loss of GUI control), fixed bugs on loading incorrect configurations
- On-disk cache: improved automatic recovery if database got corrupted.
- MacOS support: cosmetic fixes in the status bar
- MUSCLE tool: fixed execution failure if path includes spaces
Genome Workbench 2.2.2 Release Notes
New features
- More advanced network traversal for clients behind restrictive firewalls
- Documented Graphical Sequence Viewer rendering styles (http://www.ncbi.nlm.nih.gov/projects/sviewer/help/legends.pdf)
- Tree View: Implemented new markup styles (http://www.ncbi.nlm.nih.gov/projects/gbench/tutorials/tutorial3/step7.html)
- Search for Repetitive Sequences Tool: integrated with Window Masker stats files
- Improved support for opening files located in directories containing international symbols
- Improved progress messages to inform user if Genome Workbench needs to run a network transaction and may look frozen
Bug fixes
- BLAST tool execution: advanced parameters are better understood by in-core BLAST
- Feature Table View: improved functionality to show features on chromosomes (used recursive lookup for features if annotations are placed on components)
- Open Dialog: improved performance for clipboard pasting long list of accessions
- Dot Matrix Viewer: fixed bug with combining certain alignments into one view
- Dot Matrix Viewer: fixed cases when open dialog shows empty list
- Dot Matrix View: fixed bug with opening objects (in some cases view incorrectly complained "Please select at least one object")
- Graphical Sequence Viewer: fixed crash on mouse over certain alignments
- Fixed cache database corruption, when running multiple Genome Workbench instances
- Fixed incorrect handling of certain Trace Archive Ti accessions
- Tree Viewer: fixed minimap corruption
- MacOS-X: cosmetic improvements in look and feel
- Open Dialog fixed number of copy-paste issues when working with large accession lists and on Linux
- Tree Export: added default file extension to file selection dialog
Genome Workbench 2.2.1 Release Notes
Genome Workbench version 2.2.1 was an internal NCBI only release.
Genome Workbench 2.2.0 Release Notes
New features
- New tool: NCBI Genomic Aligner (also known as NG Aligner)
- Feature Table View reworked to support more input types (locations, annotations, sequence ids)
- BLAST tool (local): implemented integration with WindowMasker, user can download a WindowMasker statistics from NCBI FTP and use it as a filtering option in Genome Workbench
- Tree View: implemented sticky tooltips. Genome Workbench now implements dialog to automate masks download
- Graphical Sequence Viewer: implemented meta-information load to quickly discover NAs (named Annotations), improved performance, reduced memory footprint
- Graphical Sequence Viewer: new tooltip system with sticky tooltips (works as a bookmark)
- Graphical Sequence Viewer: improved alignment tooltips to reflect PolyA and Unaligned tails
- Multiple Alignment View: added a new column sorting option: non-sorted
- Open Dialog: implemented ability to open data from Genbank (Accession) with a selected region
- SPLIGN tool: added "Max Intron Size" option (user defined Maximum Genomic Extent limit)
- Text View: supports opening with a molecule range (selection in Graphical Sequence View) to show list of features in flat GenBank mode
Bug fixes
- Tree View: fixed broadcast selection to better support various alternative sequence ids (GIs, accessions)
- Tree View: fixes and improvements in GUI switch to black-and-white color scheme
- Tree View: fixed zooming inconsistencies
- Tree View: fixed bug with failing to create a sub-tree with one single node
- Tree View: MacOS X: removed hard-coded font size, fixed size issue in Properties dialog, fixed empty space above scrollbar, lack of background color in search bar, incorrect button sizes
- Graphical Sequence View: fixed bug to show features (genes) that contain seq-loc with multiple seq-ids
- Graphical Sequence View: fixed display for trans-splicing (exons are on mixed strands). Example: AE014297.2, gene name: mod(mdg4), transcript name: CG32491-RT
- Graphical Sequence View: fixed massive feature duplication when user loads a local feature into the same workbench project
- Multiple Alignment View: fixed compatibility issues with alignments produced by MUSCLE, fixed crashes
- Multiple Alignment View: optimization to quickly stop background data processing if view closes or user collapses a row
- Dot Matrix View: fixed issue with unnecessarily opening multiple views, better support for multiple alignments display in one view
- Dot Matrix View: fixed bug with opening (not opening) certain types of alignments (Sparse-segs for multiple sequence)
- Text View: fixed FASTA mode crash on certain incorrectly formulated data (non-existing local accessions) (Supercontigs from Broad)
- Text View: Fixed flat file display for single feature (was: "feature not found")
- Text View: memory footprint reduced up to 30%
- Gene Model Tool: removed "Copy other features from record" option (disabled)
- Gene Model Tool: fixed crash in the algorithm
- BLAST tool (local): fixed bug in running tBLASTn (protein to nucleotide) in standalone mode
- BLAST tool (local): tuned parameters of BLASTn to make it more like MegaBLAST (failed to find certain hits before)
- Remote BLAST load: fixed thread race crash when loading results from an NCBI BLAST farm
- Sequence Search tool: Fixed bug with unimplemented reverse complement search
- Sequence Search Tool: Fixed bug with search in selected range
- Fixed GUI long lock on view closing
- Tooltips: fixed multiple bugs related to cross platform tooltip implementation (Linux, MacOS-X)
- Open Dialog: fixed bug with incorrect accession list save between Genome Workbench sessions
- Feedback report: Improved internal diagnostics to better track time of certain events
- Improved performance of saving options and settings
- Window Manager: restore minimized view by a single mouse click (ergonomics improvement)
- MS Windows build: discontinued support for Visual Studio 2005, base build platform becomes VS 2008
Genome Workbench 2.1.2 Release Notes
Special Thanks
We are especially indebted to the NCBI C++ Toolkit team, whose patience and help in establishing a capable network setup and in establishing a baseline for Windows 7 installation was invaluable. We are particularly indebted to Aaron Ucko for his help with FASTA parsing issues; Eugene Vasilchenko for general help with object manager issues and debugging memory consumption issues; Anton Lavrentiev and Sergey Satsky for help in improving network setup; Vladimir Ivanov for help with Windows 7 setup; and Denis Vakatov for general support and dealing with our compressed schedule.
New features
- Added special build for 64-bit Windows 7, enables more views to be opened simulteneously.
-
Graphical Sequnece Viewer:
- new rendering styles for feature qulity characteristics
- new feature to center view around marker position (available through context menu)
-
Tree View:
- added black and white color scheme
- added mouse dragging and panning for trees
- added font size customization
-
Multiple Alignment View:
- anchor row interaction improved to allow selection/expansion
Bug fixes
- Added an option to run BLAST as standalone, out-of-process program, fixes a lot of Genome Workbench stability issues.
-
Graphical Sequnece Viewer:
- fixed hang on selection of certain CDS fetures
- fixed crash in tooltip for exon feature
- Reduced memory consumption of highly repetitive alignments
-
BLAST search:
- fixed passing Repeats argument to NCBI server
- fixed error reporting from BLAST farm to client
- Fixed various errors related to GFF import
- Improved network connectivity test for clients behind firewalls with closed high ports
- Search tool: fixed error when searching for incorrect or misspelled words
- FASTA import/export: improved compatibility with gene export FASTA files or files with non-standard symbols in defline
- Improved local data cache corruption detection, implemented automatic recovery
-
Tree View:
- fixed bug in edge color customization
- fixed Undo/Redo
- fixed issues with minimap drag
- fixed issues with search
Genome Workbench 2.1.1 Release Notes
New features
- Implemented network availability diagnostics, report issues if Genome Workbench cannot connect to NCBI servers
- Graphical Sequence Viewer: added new tracks (OMIM genes, CCDS genes, pseudogenes, ncRNAs and non-protein-coding genes)
- Graphical Sequence Viewer: implemented '..' as a delimiter for sequence ranges
- Graphical Sequence Viewer: multiple improvements in variation features coloring
- Graphical Sequence Viewer: improved labels layout (side labels) for alignments and component maps
- Graphical Sequence Viewer: major improvements in component map visualization and coloring
- Tree View: implemented mouse based scroll/pan, improved user interaction consistency between grapghical sequence view and tree view
- Tree View: implemented sub-tree extraction
- Tree View: new rendering mode to highlight collapsed sub-trees (Ctrl-L)
- Search: Added sequence location to results
- MUSCLE tool: added support for the newer version 3.8
- Installer: improved installation for users without admin priviledges
Bug fixes
- Fixed crashes related to threading and multi-tasking
- Graphical Sequence Viewer: bug fix in rendering conceptual translation relative to protein product
- Tree View: fixed tree attributes and labels inconsistency for (Phylogenetic Tree and Common Tax Tree)
- Tree View: fixed crash on Undo
- Fixed crash on shutdown if user closes application immediately after start
- Dot Matrix View: fixed issues with displaying self-alignments
- Dot Matrix View: fixed issues related to lost high score hits (floating point rounding errors)
- Text View: fixed crash when displaying certain features
- Text View: fixed bugs with not showing protein sequences in Flat File mode
- Fixed issues with tooltips over OpenGL graphics for Linux and MacOS X
- Multiple Alignment View: [+] button now works for the Master row
- WindowMasker tool: improved stability
- Selection Inspector: fixed crash on switching between modes
- Selection Inspector: fixed MacOS X compatibility issues (support for Apple key)
- Project Tree View: improved MacOS X compatibility for tree elements editing
Genome Workbench 2.1.0 Release Notes
New features
- New Tree Viewer rendering with improved labels visibility, better support of clusters (coloring), function to load external attributes, node selection broadcasting (based on sequence id)
- Improved Tutorial
- Added integration with external MUSCLE tool
- Graphical Sequence View: feature quality visualization (rendering styles for .partial., .pseudo.,
- Graphical Sequence View: support for non-consensus splice sites
- Alignment Span View: support for
- Graphical Sequence View: mouse over alignment reports sequence base position in tooltip
- Graphical Sequence View: new rendering for parent-child feature relationships
- Graphical Sequence View: New content options for Gene Model Track to show/hide genes distribution histogram
- Linux build: added 64-bit Linux build (Ubuntu 8.4 Hardy), implemented DEB distribution file creation
- File Open Dialog: Implemented dead item removal from most recently used list
- Implemented Common Taxonomic Tree for sequences tool, with support of FASTA files as a legitimate data source for sequence ids
- Project Tree View: Folder open/closed state preserved in the project file
- File Open dialog: added list of recently open files
- Graphical Sequence View: added support for the new Clone feature subtype
- BLAST search tool: added RID (task id) for the details box, implemented copy-paste for easier WEB integration
- Alignment Span View: added support for unaligned head-tail, support Introl-Exon(In/Del) (splign alignments)
Bug fixes
- Fixed GUI logic in the Project Save dialog
- Graphical Sequence View: fixed Zoom handler behavior (.z. key processing)
- Improved Windows installer and plugin loading mechanism to be Windows Vista and Windows 2003 compatible
- Graphical Sequence View: Fixed serious performance degradation when zoomed to sequence level
- Graphical Sequence View: corrected positions for CDS translation and protein sequence
- Fixed disappearing scrollbar (windows manager)
- Fixed Project Item description editing / saving
- Fixed Needleman-Wunsch aligner
- Multiple Alignment View: fixed thick lines rendering issue
- Graphical Sequence View: fixed View redraw in multi-level mode after a project change
- Improved alignment labels for Spliced Alignments
- ASN export: improved file name validation
- Graphical Sequence View: Fixed Disc alignment rendering
- Project Tree View: Folder Delete/Cut/Paste/Drag-n-Drop function fixed
- Open File Dialog: fixed bug when Back button was showing empty or incorrect page
- Graphical Sequence View: fixed bug in alignment statistics (coverage) displayed in tooltips
- Fixed crash when editing label for unloaded project
- MacOS-X Color Picker Dialog: fixed dialog to correctly apply color changes
- MacOS-X: Implemented About box dialog
- Graphical Sequence View: fixed crash in flipped strand mode
- Search Edit Box: fixed upper-lower case history editing
- Tree View: fixed context menu radio button display to better reflect changes in the layout
- Multiple Alignment View: fixed unnecessary redraw happened on unrelated change in the project
- Feature Table View: fixed crash when the view is closed before loading content
- Text View: fixed crash in renderer
- Fixed GUI stalls generating labels for objects containing multiple alignments
- Fixed crash in Search Panel
- Fixed multiple issues related to internal thread/task processing
- Fixed selection inspector update/refresh related to multi-pane alignment viewer
Download
Current Version is 2.6.0 (released August 31, 2012)
- Release Notes
- Windows
- Mac OS X
- Linux (Ubuntu 10.04 LTS (Lucid Lynx))
- Source
- Older Versions