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tag: release-1_45

Jul 15, 2002

  1. This commit was manufactured by cvs2svn to create tag 'release-1_45'.

    Nobody authored
  2. This commit was manufactured by cvs2svn to create branch

    'berkeley-gadfly'.
    Nobody authored
  3. Lincoln Stein

    bumped version number

    lstein authored
  4. Lincoln Stein

    added sequence plugin to manifest

    lstein authored

Jul 10, 2002

  1. Lincoln Stein

    added more documentation to documentation

    lstein authored
  2. Lincoln Stein

    fixed _subseq() to operate properly with Bio::DB::GFF objects; unfort…

    …unately the workaround for split locations is becoming problematic
    lstein authored

Jul 07, 2002

  1. Lincoln Stein

    minor fixes to readme and changelog files

    lstein authored
  2. Lincoln Stein

    This is version 1.45.

    lstein authored
  3. Lincoln Stein

    Got all the plugins debugged and working.

    lstein authored
  4. Lincoln Stein

    ported the fasta dumper to use the Markup module; however there is st…

    …ill a problem with background color mixing -- colors tend to black rather than to white
    lstein authored

Jul 05, 2002

  1. Lincoln Stein

    Made Jason's SequenceDumper check that each format converter

    successfully loads before adding that format to the list.
    
    Added examples of CDS and translation glyphs to wormbase and yeast
    example conf files.
    lstein authored
  2. Lincoln Stein

    Renamed Gudmundur's ncbi_to_gff.pl to process_ncbi_human.pl for

    consistency with the other process_* scripts.
    
    Added appropriate entries in install, manifest and makefile.
    lstein authored

Jul 04, 2002

  1. Lincoln Stein

    a few changes to sequence dumper -- still needs to check for io modul…

    …es and modify popup choices accordingly
    lstein authored
  2. Lincoln Stein

    added NCBI to GFF conversion file - works for human annotations

    lstein authored
  3. Lincoln Stein

    Added support for the "coding" aggregator.

    Added support for using sub {} as the values of options (this only
    works for local features!!!!)
    lstein authored

Jun 30, 2002

  1. Lincoln Stein

    fixed a multiple segment exception

    lstein authored

Jun 28, 2002

  1. Lincoln Stein

    undid changes that caused UTRs not to be drawn correctly

    lstein authored

Jun 26, 2002

  1. Lincoln Stein

    added ability to put predetermined external URLs into a popup menu

    lstein authored
  2. Lincoln Stein

    fixed a soul-eating bug that caused restriction annotator to try to g…

    …enerate restriction map of entire chromosomes at once
    lstein authored
  3. Lincoln Stein

    fixed various aesthetic problems; got bump control working properly o…

    …n plugins; fixed Go! vs Configure problems in plugins
    lstein authored
  4. Lincoln Stein

    Added "global feature" tag to DNA

    lstein authored
  5. Lincoln Stein

    Folded in changes to limit number of features shown.

    This is going to need BioPerl 1.02!!!!
    lstein authored

Jun 19, 2002

  1. Lincoln Stein

    added full-blow restriction annotator from Beth

    lstein authored

Jun 12, 2002

  1. Lincoln Stein

    Fixed a problem that was causing display to stop halfway through

    whenever the restrictionannotator was loaded.
    lstein authored

Jun 11, 2002

  1. Lincoln Stein

    Improved plugin documentation and added a plugin init() method.

    lstein authored

Jun 06, 2002

  1. handle overlapping coloring regions and bold and italics -- fix minor…

    … bug when feature started before the beginning of the region
    Jason Stajich authored

Jun 03, 2002

  1. support dumping of multiple formats (requires an updated Bio-DB-GFF)

    Jason Stajich authored
  2. Lincoln Stein

    added documentation to Bio::Graphics::Browser

    lstein authored

Jun 02, 2002

  1. change defaults to include 100 and 200 bp zooms and change DNA featur…

    …e from sequence -> dna glyph
    Jason Stajich authored

May 24, 2002

  1. Lincoln Stein

    more futzing around with multi-segmented transcripts; probably not qu…

    …ite right still
    lstein authored
  2. Lincoln Stein

    removed heterogeneous_segments glyph and added wormbase_transcript glyph

    lstein authored
  3. Lincoln Stein

    Moved wormbase_transcript into the glyph list (and out of bioperl).

    Modified it so that it hopefully will show nice gray UTRs.
    lstein authored

May 23, 2002

  1. Lincoln Stein

    added emergency reset button for times when it tries to do something …

    …really really big
    lstein authored
  2. Lincoln Stein

    added divide-by-zero check

    lstein authored

May 21, 2002

  1. Lincoln Stein

    cleared bad uploaded files

    lstein authored
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