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Commits on Feb 18, 2002
  1. got all tests to pass

    birney committed Feb 18, 2002
    svn path=/bioperl-run/trunk/; revision=13012
Commits on Feb 14, 2002
  1. Doc clarification, fixed POD error

    bosborne committed Feb 14, 2002
    svn path=/bioperl-run/trunk/; revision=13011
Commits on Feb 6, 2002
  1. params should be appended not overwriting

    hyphaltip committed Feb 6, 2002
    svn path=/bioperl-run/trunk/; revision=13010
Commits on Jan 30, 2002
  1. verbosity=-1 is same as quiet()

    hyphaltip committed Jan 30, 2002
    svn path=/bioperl-run/trunk/; revision=13009
Commits on Jan 14, 2002
  1. test for version()

    heikkil committed Jan 14, 2002
    warns if version < 1.3 (and most tests will fail)
    
    svn path=/bioperl-run/trunk/; revision=13008
  2. added version()

    heikkil committed Jan 14, 2002
    Implementaion might print an annoying string "FATAL error..." on non-UNIX platforms.
    Post 1.37 versions of t_coffee will have an explicit -version argument.
    
    svn path=/bioperl-run/trunk/; revision=13007
Commits on Jan 11, 2002
  1. debug message now uses the debug method

    hyphaltip committed Jan 11, 2002
    svn path=/bioperl-run/trunk/; revision=13005
  2. fixed tests to work when clustalw is not found

    heikkil committed Jan 11, 2002
    svn path=/bioperl-run/trunk/; revision=13004
  3. test for version()

    heikkil committed Jan 11, 2002
    skipping profile align tests on current clustal versions
    
    svn path=/bioperl-run/trunk/; revision=13003
  4. Added method version()

    heikkil committed Jan 11, 2002
    $self->isa('Bio::Factory::ApplicationFactoryI')
    
    svn path=/bioperl-run/trunk/; revision=13002
Commits on Jan 9, 2002
  1. warn about not using old clustalw

    hyphaltip committed Jan 9, 2002
    svn path=/bioperl-run/trunk/; revision=13001
  2. use the updated PROGRAM exe location information to set the PROGRAM v…

    hyphaltip committed Jan 9, 2002
    …ariable
    
    svn path=/bioperl-run/trunk/; revision=13000
  3. check to insure defined object before calling ISA

    hyphaltip committed Jan 9, 2002
    svn path=/bioperl-run/trunk/; revision=12999
Commits on Jan 8, 2002
  1. StandAloneBlast now checks for ecoli.nt (is this right?) and TCoffee …

    birney committed Jan 8, 2002
    …is a little more verbose
    
    svn path=/bioperl-run/trunk/; revision=12998
Commits on Dec 14, 2001
  1. skip msg updated due to clustal 1.81 bug

    hyphaltip committed Dec 14, 2001
    svn path=/bioperl-run/trunk/; revision=12996
  2. nice message printing when blast is not runnable

    hyphaltip committed Dec 14, 2001
    svn path=/bioperl-run/trunk/; revision=12995
  3. more quiet warning so tests are less chatty

    hyphaltip committed Dec 14, 2001
    svn path=/bioperl-run/trunk/; revision=12994
  4. issue nice message when skipping EMBOSS tests

    hyphaltip committed Dec 14, 2001
    svn path=/bioperl-run/trunk/; revision=12993
  5. skip can print a nice message about why it skipped

    hyphaltip committed Dec 14, 2001
    svn path=/bioperl-run/trunk/; revision=12992
  6. emboss factory behaves more quietly when EMBOSS is not installed on s…

    hyphaltip committed Dec 14, 2001
    …ystem
    
    svn path=/bioperl-run/trunk/; revision=12991
Commits on Dec 10, 2001
  1. POD fixes

    heikkil committed Dec 10, 2001
    svn path=/bioperl-run/trunk/; revision=12990
Commits on Nov 20, 2001
  1. Sweeping change:

    lstein committed Nov 20, 2001
    Bio::Root::RootI is now a pure abstract interface and cannot be
    inherited from unless you implement several of its abstract methods.
    Most people will want to inherit from Bio::Root::Root.
    
    This change was necessary in order to support Bioperl objects that
    were not based on hashrefs.
    
    svn path=/bioperl-run/trunk/; revision=12989
Commits on Nov 19, 2001
  1. EMBOSS more runnable and w/ tests

    hyphaltip committed Nov 19, 2001
    svn path=/bioperl-run/trunk/; revision=12988
Commits on Aug 25, 2001
  1. Small fix to shut up File::Spec.

    hlapp committed Aug 25, 2001
    svn path=/bioperl-run/trunk/; revision=12987
  2. Rewrote exists_blast(). Should now work properly on both Unix and MSWin.

    hlapp committed Aug 25, 2001
    svn path=/bioperl-run/trunk/; revision=12982
  3. Changed exists_tcoffee() to use new Bio::Root::IO->exists_exe().

    hlapp committed Aug 25, 2001
    svn path=/bioperl-run/trunk/; revision=12981
  4. Changed exists_clustal() to use new Bio::Root::IO->exists_exe().

    hlapp committed Aug 25, 2001
    svn path=/bioperl-run/trunk/; revision=12980
Commits on Aug 10, 2001
  1. don't have clustalw tests fail for 0.9 release

    hyphaltip committed Aug 10, 2001
    svn path=/bioperl-run/trunk/; revision=12978
Commits on Aug 7, 2001
  1. documentation for retrieve_blast method

    hyphaltip committed Aug 7, 2001
    svn path=/bioperl-run/trunk/; revision=12977
Commits on Jul 24, 2001
  1. claning. Needs code to compare input and ACD options

    heikkil committed Jul 24, 2001
    svn path=/bioperl-run/trunk/; revision=12976
Commits on Jul 23, 2001
  1. Classes for wrapping EMBOSS suite

    heikkil committed Jul 23, 2001
    svn path=/bioperl-run/trunk/; revision=12975
Commits on Jul 4, 2001
  1. *** empty log message ***

    elofsson committed Jul 4, 2001
    svn path=/bioperl-run/trunk/; revision=12974
  2. *** empty log message ***

    elofsson committed Jul 4, 2001
    svn path=/bioperl-run/trunk/; revision=12973
Commits on Jun 20, 2001
  1. The code for setting the path to binary was in BEGIN block making it

    heikkil committed Jun 20, 2001
    impossible to change from a calling perl script. Moved it into new().
    $ENV{TCOFFEEDIR} = '/path/to/clustalwdir/';
     now works.
    
    svn path=/bioperl-run/trunk/; revision=12971
  2. The code for setting the path to binary was in BEGIN block making it

    heikkil committed Jun 20, 2001
    impossible to change from a calling perl script. Moved it into new().
    $ENV{CLUSTALDIR} = '/path/to/clustalwdir/';
     now works.
    
    svn path=/bioperl-run/trunk/; revision=12970