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Commits on Jul 14, 2003
  1. flybase changed the format of their GO cofiguration reporting. Changi…

    …ng parser to compensate
    
    svn path=/bioperl-gui/trunk/; revision=771
    mwilkinson committed Jul 14, 2003
Commits on Jun 3, 2003
  1. take advantage of the awsome power of the go API and allow filtering …

    …by organism when starting up the browser
    
    svn path=/bioperl-gui/trunk/; revision=770
    mwilkinson committed Jun 3, 2003
  2. POD fixes

    svn path=/bioperl-gui/trunk/; revision=769
    heikkil committed Jun 3, 2003
Commits on Jun 2, 2003
  1. various updates, added DESTROY method to GO Anotation to avoid those …

    …pesky error messages on destruction
    
    svn path=/bioperl-gui/trunk/; revision=768
    mwilkinson committed Jun 2, 2003
Commits on Apr 23, 2003
  1. scrollregion values are not set until a zoom event has been triggered…

    … (??) so do this by default. This allows for free-selection of sequence in genquire as soon as a contig is loaded
    
    svn path=/bioperl-gui/trunk/; revision=767
    mwilkinson committed Apr 23, 2003
Commits on Apr 22, 2003
  1. various changes to get rid of t-test non-critical errors

    svn path=/bioperl-gui/trunk/; revision=766
    mwilkinson committed Apr 22, 2003
Commits on Jun 3, 2002
  1. removed all copyright notices from gui software written by Dave and I…

    …. Fortuitously, it turns out that copyright was never applied for by the NRC. I love efficiency.
    
    svn path=/bioperl-gui/trunk/; revision=765
    mwilkinson committed Jun 3, 2002
Commits on Apr 23, 2002
  1. changed go database lookup address

    svn path=/bioperl-gui/trunk/; revision=764
    mwilkinson committed Apr 23, 2002
Commits on Mar 28, 2002
  1. Seqcanvas can once again be switched from horizontal to vertical and …

    …back again without messing up the dimensions of the canvases. Canvas dimensions are no longer a class variable, but are calculated on instantiation based on the number of tiers available, which is a class variable.
    
    svn path=/bioperl-gui/trunk/; revision=763
    mwilkinson committed Mar 28, 2002
Commits on Mar 11, 2002
  1. canvas orientation must also be a class variable instead of an instan…

    …ce variable, or you get HUGE canvases when mixing the two
    
    svn path=/bioperl-gui/trunk/; revision=762
    mwilkinson committed Mar 11, 2002
Commits on Mar 6, 2002
  1. removed SeqCanvas filter for objects with the primary tag of CDS. It …

    …appears that EMBL and Genbank have annoyingly different ways to describe genes. EMBL calls them CDS's and associates them with a gene comment tag, wheras Genbank calls them 'gene' features. This is a nusance because when they are parsed by SeqIO the resulting Seq objects have different structures for essentially the same underlying 'thingy'. Arghghgghghghghh
    
    svn path=/bioperl-gui/trunk/; revision=761
    mwilkinson committed Mar 6, 2002
  2. oops. Left some noisy debugging print statements in there

    svn path=/bioperl-gui/trunk/; revision=760
    mwilkinson committed Mar 6, 2002
  3. Canvas dimensions are now a class variable rather than an instance va…

    …riable. This is critical when examining large and disparate data-sources in multiple canvases in order to ensure that all feature sources are included in the area controlled by the scrollbar.
    
    svn path=/bioperl-gui/trunk/; revision=759
    mwilkinson committed Mar 6, 2002
Commits on Feb 28, 2002
  1. SeqCanvas causes errors if it is instantiated in a new TopLevel windo…

    …w from an existing MainWindow. There errors are now suppressed until I can determine the root cause of the problem
    
    svn path=/bioperl-gui/trunk/; revision=758
    mwilkinson committed Feb 28, 2002
Commits on Feb 19, 2002
  1. removing MapViewer which became MuGeN on Bioinformatics.org

    svn path=/bioperl-gui/trunk/; revision=757
    hyphaltip committed Feb 19, 2002
Commits on Feb 5, 2002
  1. make errors in destruction of menus silent because I cant figure out …

    …how to destroy them properly >grin<
    
    svn path=/bioperl-gui/trunk/; revision=756
    mwilkinson committed Feb 5, 2002
Commits on Jan 18, 2002
  1. fixed one more problem with seqcanvas and its features recolouring on…

    … drag-drop. This should be the last change for a long time. Touch wood
    
    svn path=/bioperl-gui/trunk/; revision=755
    mwilkinson committed Jan 18, 2002
  2. added sanity checking to SeqCanvasfeatures, and changed the error mes…

    …sages to dialog boxes for SeqCanvas such that it does not need an open terminal to report errors.
    
    svn path=/bioperl-gui/trunk/; revision=754
    mwilkinson committed Jan 18, 2002
Commits on Jan 17, 2002
  1. oops. I went too far last week with my allowing users to determine th…

    …eir own list of valid feature types. It is a requirement that Genes and their sub-features must implement GeneStructureI, TranscriptI, ExonI, Poly_A_site, Promoter, or UTR, even if they are roll-your-own features types. SeqCanvas now checks the isa to ensure that you aren't trying to fool it into adding an invalid feature, and if you are you are reminded to re-cast the feature into a valid type
    
    svn path=/bioperl-gui/trunk/; revision=753
    mwilkinson committed Jan 17, 2002
Commits on Jan 16, 2002
  1. fixed a small creation of transcripts bug in SeqCanvas, and changed t…

    …he call that looks up the GO database URL to make it more reliable.
    
    svn path=/bioperl-gui/trunk/; revision=752
    mwilkinson committed Jan 16, 2002
Commits on Jan 7, 2002
  1. added a method to retrieve the 'ReCast Feature As' menu to allow edit…

    …ing of the callbacks associated with changing one feature type into another
    
    svn path=/bioperl-gui/trunk/; revision=751
    mwilkinson committed Jan 7, 2002
Commits on Dec 20, 2001
  1. added public method ReCastMenu to allow access to the Re-Cast feature…

    …s menu, as may be required to modify the callbacks for recasting features into different feature types if you are not using the standard BioPerl feature types. This was the case for Genquire, where more than just the feature GFF string is required to create features, so the internal SeqCanvas recasting of features resulted in useless re-cast objects that were not database aware
    
    svn path=/bioperl-gui/trunk/; revision=750
    mwilkinson committed Dec 20, 2001
  2. fixed the broken code that Dave just committed ;-)

    svn path=/bioperl-gui/trunk/; revision=749
    mwilkinson committed Dec 20, 2001
  3. changed Gene creation code to make things more generic

    svn path=/bioperl-gui/trunk/; revision=748
    dblock committed Dec 20, 2001
Commits on Nov 26, 2001
  1. changed authorship to reflect Dave's new address

    svn path=/bioperl-gui/trunk/; revision=747
    mwilkinson committed Nov 26, 2001
Commits on Nov 24, 2001
  1. commit of MapViewer for bioperl scripts project

    svn path=/bioperl-gui/trunk/; revision=746
    hyphaltip committed Nov 24, 2001
Commits on Nov 6, 2001
  1. fixed a small bug in GO_Browser that might have caused problems on a …

    …failed search. SeqCanvas changes were just in formatting of code to fix ugly tabs
    
    svn path=/bioperl-gui/trunk/; revision=745
    mwilkinson committed Nov 6, 2001
Commits on Nov 1, 2001
  1. fixed error in docs,changed package name to Bio::Tk::GO_Browser inste…

    …ad of just GO_Browser
    
    svn path=/bioperl-gui/trunk/; revision=744
    mwilkinson committed Nov 1, 2001
  2. added a filtering option to allow user to override GO::AppHandle defa…

    …ult filtering out of annotations with evidence code of IEA when it is doing a product count or a deep product count
    
    svn path=/bioperl-gui/trunk/; revision=743
    mwilkinson committed Nov 1, 2001
Commits on Oct 25, 2001
  1. SeqCanvas now smart - only deletes features from UpdateableSeqI compl…

    …iant sequences
    
    svn path=/bioperl-gui/trunk/; revision=742
    dblock committed Oct 25, 2001
Commits on Oct 24, 2001
  1. Changes to protect SeqCanvas from unsuccessful deletions in Genquire

    svn path=/bioperl-gui/trunk/; revision=741
    dblock committed Oct 24, 2001
Commits on Oct 23, 2001
  1. Changes to allow bug-free creation/deletion of GeneStructure objects

    svn path=/bioperl-gui/trunk/; revision=740
    dblock committed Oct 23, 2001
  2. committing broken code to fix together with Mark

    svn path=/bioperl-gui/trunk/; revision=739
    dblock committed Oct 23, 2001
Commits on Oct 18, 2001
  1. Doh\!

    svn path=/bioperl-gui/trunk/; revision=738
    mwilkinson committed Oct 18, 2001
  2. added initialization parameters dbuser and dbauth so that you can run…

    … GO browser off of a database that requires username password authentication.
    
    svn path=/bioperl-gui/trunk/; revision=737
    mwilkinson committed Oct 18, 2001