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Commits on Mar 9, 2002
  1. turn of clustalw debugging

    hyphaltip committed Mar 9, 2002
    svn path=/bioperl-run/trunk/; revision=13022
Commits on Mar 8, 2002
  1. tweak to clustalw test for falling over correctly

    birney
    birney committed Mar 8, 2002
    svn path=/bioperl-run/trunk/; revision=13021
  2. Now can take a program path as arg on the new method, aboids need for…

    elia
    elia committed Mar 8, 2002
    … ENV variable (ENV still in not to break other people's scripts,etc)
    
    svn path=/bioperl-run/trunk/; revision=13020
  3. No need for the dir variable

    elia
    elia committed Mar 8, 2002
    svn path=/bioperl-run/trunk/; revision=13019
Commits on Mar 5, 2002
  1. unlink test file output

    hyphaltip committed Mar 5, 2002
    svn path=/bioperl-run/trunk/; revision=13018
Commits on Mar 4, 2002
  1. added ability to dump alignments as well as sequences when running an…

    hyphaltip committed Mar 4, 2002
    … EMBOSS application
    
    svn path=/bioperl-run/trunk/; revision=13017
Commits on Feb 18, 2002
  1. added example documentation to the POD

    hyphaltip committed Feb 18, 2002
    svn path=/bioperl-run/trunk/; revision=13016
  2. test for cmd line argument where value is a Bio::PrimarySeqI or array…

    hyphaltip committed Feb 18, 2002
    … of seqs -- added test for 'water'
    
    svn path=/bioperl-run/trunk/; revision=13015
  3. handle cmd line arguments pointing to a Bio::PrimarySeqI object or ar…

    hyphaltip committed Feb 18, 2002
    …ray or Bio::PrimarySeqI
    
    svn path=/bioperl-run/trunk/; revision=13014
  4. got all tests to pass

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

    bosborne
    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
    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