Change Log

Version 1.1
  • Added load and down load time to the info bar (for benchmarking).
  • Added annotation length (in bases) to the annotation info dialog.
  • Fixed length() in annotation.h (off by one base)
  • Enabled the primer prediction code and UI.
  • WYSIWYG image export now enabled (i.e. special code for Postscript was required to work around the lack of Postscript alpha support).
  • Fixed a lighting bug in the genome clipping rectangle (i.e. the rectangle did not match the background color for non-white backgrounds)

Version 1.2
  • Fixed orientation of displayed probe binding matches.
  • Fixed bug in sequence display (picking 0 for the first or last base caused infinite loop)
  • Improved the verbosity of error messages when trying to read incomplete EMBL and GBK files.
  • Lowered the %identity threshold for hybridization to 50%
  • Added a multiple sequence consensus measure based on base composition
  • Improved the hybridization calculation (now using a circular buffer to scan sequences instead of std::list).
  • Modifed the middle mouse button behavior to scroll *and* shift all genomes (regardless of selection).
  • Removed 3D shadow from Motif menu bar to modernize appearance.
  • Fixed formating error (for amplicon sequence output)
  • Fixed guide rendering (guide now renders on top of all other annotation)
  • Fixed find dialog option persistence in Motif version.

Version 1.3
  • Fixed Motif canvas offset bug (that partially obscured the selection box)
  • Added mouse and keyboard translations to the status bar and window frame (Motif).
  • Added 3' exact match information to primer searching output.
  • Fixed Motif open file dialog bug (Ctrl+O from the frame caused crash).
  • Fixed writable result windows (OSX).
  • Fixed hybridization bug (exact match of 0 3' bases not processed correctly).
  • Fixed Motif copy, paste and cut operations.
  • Added an optional lower bound to predicted amplicon lengths.
  • Improved error handling when processing GBK files.
  • Added support for GBK keyword "order" (as a synonym for "join").
  • Fixed bug that caused incorrect display of inverted, multi-segment annotations.
  • Fixed bug in calculation of %G+C when reading from some GenBank files.
  • Full screen anti-aliasing (FSAA) for OSX and annotation antialiasing for win32 (via antialiased edge overlay).
  • Fixed the wheel mouse scroll direction (Motif).
  • Fixed Motif segmentation fault on some linux systems (caused by bug in processing key strokes)
  • Added multisample FSAA support for Motif (when sufficient hardware is available).

Version 1.4
  • Added a selection guide for picking nucleotide sequence to display and translate into amino acids.
  • Fixed bug that caused clipping rectange to overlap neighbooring genomes.
  • Fixed bug in sequence selection (a selection that ended on the last base of the genome caused an infinite loop!).
  • Added a new annotation key to the GBK file parser -- "signature".
  • Fixed bug when inverting genome plot.
  • Fixed bug when parsing genome files with no genomes.
  • Fixed bug when clipping multiple genomes.
  • No longer throw an error when the GIF color table is exhausted -- use the closest color available instead.
  • Added the ability to import genome annotations from Protein Translation Table (ptt) files.
  • Fixed a bug in exact match DNA searching.
  • Added the ability to import annotations from any genome file that contains annotation (i.e. asn, gbk, embl, ptt). As with loading files, the file type is autodetected!
  • Fixed a import bug in the GBK file format (assigning GI values)
  • Added a horizontal scroll bar for scrolling all genomes left and right
  • Added a vertical scroll bar for zooming all genomes
  • Added the ability to export genome data (i.e. sequence and annotation) to the following formats: Fasta (protein and DNA), PTT and GBK
  • Fixed line numbers on GBK parse error messages.
  • Fixed lack of intergenic space for certain annotation combinations.
  • Fixed bug in the translation guide rendering (that could cause infinite loop under certain conditions).
  • Pressing the esc key now cancels any pending translation.
  • Added the ability to load multiple genomes from a single ASN file.
  • Fixed the rendering of *multiple* annotations that all overlap the origin.
  • Added search by genome name.
  • Modifed the EMBL parser to handle Artemis files.
  •  Fixed bug in searching for Padlock/MOL-PCR probes
  • Added an annotation editor

Version 1.5
  • Fixed bug in highlighting matched regions when searching with primers or probes that contain degenerate bases.
  • Fixed bug in parsing gbk files that contain single base annotations on the complement strand.
  • Fixed bug in DNA3Seq::find() that missed exact matches at 3' end of target sequence.
  • [OSX] Fixed bug in annotation editor (annotation type control was not enabled).
  • Fixed bug that required the selection of a genome when loading a genome plot when only a single genome is loaded. When only a single genome is present, assume implicit selection.
  • Custom color records are now saved to and read from GBK files.
  • Fixed bug when downloading multi-entry records from NCBI (i.e. gi|46810958)
  • Fixed fragile parsing of annotation range in the annotation edit dialog.
  • Changed all displayed ranges to match the Genbank range format (i.e. "start..stop").
  • [Motif] Fixed download dialog bug.
  • Fixed bug that prevented downloading of very large Genbank records (i.e. human chromosomes).
  • Fixed bug that omitted intergenic space following single base annotations (i.e. SNP's).
  • [OSX] Added an OS X Intel-specific executable and made the information dialog box resizable.
  • Added the number of Watson and Crick matches to all hybridization based search results.

Version 1.51
  • Fixed bug in rendering right hand annotation clipping[OSX]
  • Fixed bug in copying text from dialog boxes (accidently removed menu copy command ...).

Version 1.52
  • Added a "magnify" feature (under the view menu) that displays the annotation currently under the mouse pointer in the center of the screen (useful for crowed annotations that would otherwise be illegible).
  • Added a menu option to restore the default genome view (useful for quickly returning to a high level view without needing to resort to manual zooming).

Version 1.53
  • Fixed a bug when downloading large genomes from NCBI (i.e. human chromosome 1).
  • Changed the behavior of Genomorama when loading large genomes in ASN.1 format. If the file does not contain sequence data, only the annotation information will be read and all sequence bases will be shown as 'N' (i.e. unknown base). This allows large eukaryotic genomes to be downloaded much faster.
  • Improved the parsing of IMP records stored in ASN.1 files (STS labels will now be shown in the Note section of an annotation record).

Version 1.54
  • Fixed a bug that could result in a crash when editing annotations (a list iterator was not properly invalidated after a list sort). The crash has only been observed on a PPC OSX machine.

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