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Commits on Oct 7, 2004
Commits on Oct 6, 2004
  1. more template cleanup

    Allen Day
    Allen Day committed Oct 6, 2004
  2. further division of template functionality

    Allen Day
    Allen Day committed Oct 6, 2004
  3. more function porting to templates.

    Allen Day
    Allen Day committed Oct 6, 2004
  4. lots of new template files. there is, fortunately, roughly a 1:1

    Allen Day
    Allen Day committed Oct 6, 2004
    correspondence between a tt2 file and a removed method.  there are >5
    subroutines remaining to be cleaned, not counting plugins, etc.
Commits on Oct 4, 2004
  1. this is probably badly broken, but it has cleaned up almost all refer…

    Allen Day
    Allen Day committed Oct 4, 2004
    …ences to
    
    $settings / $page_settings in favor of Bio::Graphics::Browser::Options.
    
    there are definitely still some places where the code was probing inside
    $settings->{features} that ...::Options doesn't support yet.  i'll take care
    of this next.  i think it's the major problem left for the changes in this
    commit.
  2. added two new modules to take over some of the gbrowse.PLS functionality

    Allen Day
    Allen Day committed Oct 4, 2004
    Bio::Graphics::Browser::Constants
    all 'use constant...' statements from gbrowse.PLS moved here.  constants
    are exported with a prefixed 'GBROWSE_' to be easily identifiable
    
    Bio::Graphics::Browser::Options
    replaces $settings (aka $page_settings) with object-oriented access.
    the options object is available via $BROWSER->options().  Likewise
    $CONFIG is available via $BROWSER->config().
Commits on Oct 3, 2004
  1. added stub browser object

    lstein committed Oct 3, 2004
Commits on Sep 18, 2004
  1. added Bio::Das::FeatureTypeI support to the Das/Chado adapter. Class

    Allen Day
    Allen Day committed Sep 18, 2004
    is called Bio::DB::Das::Chado::Type.  Not FeatureType, because the interface
    class namespace is a misnomer, as this class will be used to type objects
    other than features (structure coordinates, quantitative data, &c).
    
    yeah.
  2. block file uploads, etc unless segment is valid

    Allen Day
    Allen Day committed Sep 18, 2004
Commits on Sep 11, 2004
  1. this is needed for das to recognize segments

    Allen Day
    Allen Day committed Sep 11, 2004
Commits on Sep 8, 2004
  1. a version string is necessary for das2

    Allen Day
    Allen Day committed Sep 8, 2004
Commits on Sep 7, 2004
  1. test commit to make sure i'm on branch

    Allen Day
    Allen Day committed Sep 7, 2004
Commits on Sep 6, 2004
  1. This commit was manufactured by cvs2svn to create branch

    Nobody
    Nobody committed Sep 6, 2004
    'gbrowse-template-branch'.
  2. added wording to tutorial to make it easier to figure out what to do …

    lstein committed Sep 6, 2004
    …with the aligner plugin
Commits on Sep 5, 2004
  1. more display code moved to templates

    Allen Day
    Allen Day committed Sep 5, 2004
  2. slider sub no longer needed

    Allen Day
    Allen Day committed Sep 5, 2004
  3. initial stab at templatizing gbrowse. templates live in

    Allen Day
    Allen Day committed Sep 5, 2004
    conf/templates/$appname (e.g. conf/templates/gbrowse/).
    
    i've converted over the navigation table, the scroll/zoom tool, and the
    search box to templates to give people an idea how it works.
    
    the next logical step (aside from templatizing all other html generating
    code), is to templatize the lang .pm files into templates that can just be
    called in with an [% INCLUDE "mylang.tt2" %] directive in the toplevel
    template.  this will simplify the logic code by reducing the number of calls
    that need to be made to $CONF just to ferry the translations into the
    template.
    
    i've also started adding better debug log support that is written to
    $CONF_DIR/gbrowse.log.  see conf/log4perl.conf for details.
    
    this introduces prereqs on the Template toolkit and Log::Log4perl.  you can
    get them e.g.
    
      cpan> install Template Log::Log4perl
Commits on Sep 4, 2004
  1. 1. overhauled conf install script to allow recursive directory installs

    Allen Day
    Allen Day committed Sep 4, 2004
    (skipping CVS dirs).
    
    2. added log4perl.conf file for Log::Log4perl logging API.  great for
    debugging, will start modding modules to log here instead of to apache
    error_log.
    
    3. created conf/templates directory for templatizing gbrowse with
    Template.pm
Commits on Sep 2, 2004
  1. /type responds according to spec now

    Allen Day
    Allen Day committed Sep 2, 2004
  2. added das2 server script

    Allen Day
    Allen Day committed Sep 2, 2004
Commits on Sep 1, 2004
  1. more warning silencing

    Scott Cain
    Scott Cain committed Sep 1, 2004
  2. Added ability to specify multiple landmarks in the URL, and updated d…

    lstein committed Sep 1, 2004
    …ocumentation appropriately
  3. fixing for the case where GFF_source is in dbxref table, but features…

    Scott Cain
    Scott Cain committed Sep 1, 2004
    … don't
    
    have a entry in feature_dbxref
Commits on Aug 30, 2004
  1. some groups are not objects

    Allen Day
    Allen Day committed Aug 30, 2004
Commits on Aug 26, 2004
  1. cleaned up debug output

    Allen Day
    Allen Day committed Aug 26, 2004
  2. this addresses a bug introduced by older -- well, current, but i'm ab…

    Allen Day
    Allen Day committed Aug 26, 2004
    …out to
    
    fix it now -- versions of gmod_load_gff3.pl chado load tool.  this script
    brazenly creates a 'part_of' term for its own use rather than first checking
    to see if one has already been loaded to the cvterm table (and it is
    certainly there, as OBO_REL is a required ontology to load).  we now keep
    track of the 1-many term name -> term ID mappings rather than just a single
    ID mapping.
    
    this change should also have utility for other terms that exist in multiple
    ontologies, e.g. 'protein', which is both a SO term and a GO term.
Commits on Aug 24, 2004
  1. quashing an uninitialized error

    Scott Cain
    Scott Cain committed Aug 24, 2004
  2. putting changes back to make this work with the das cgi script. let's…

    Allen Day
    Allen Day committed Aug 24, 2004
    … move
    
    forward, not back.
    
    it works for me with gbrowse here, but if it is broken for you, please
    either fix it and commit, report it on the list and i will fix it, or use
    the stable tag before i started adding das script compatibility.  the tag
    name is 'stable-but-broken-003'.
Commits on Aug 23, 2004