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Commits on Mar 11, 2002
  1. call cleanup upon _setinput call

    svn path=/bioperl-run/branches/branch-1-0-0/; revision=13029
    hyphaltip committed Mar 11, 2002
  2. parameterized verbose flag

    svn path=/bioperl-run/branches/branch-1-0-0/; revision=13028
    hyphaltip committed Mar 11, 2002
  3. slightly more intelligent checking for clustalw exe

    svn path=/bioperl-run/branches/branch-1-0-0/; revision=13027
    hyphaltip committed Mar 11, 2002
  4. find blast executeable in the PATH if possible -- bl2seq might still …

    …fail if one does not have .ncbirc set correctly
    
    svn path=/bioperl-run/branches/branch-1-0-0/; revision=13025
    hyphaltip committed Mar 11, 2002
Commits on Mar 9, 2002
  1. turn of clustalw debugging

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

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

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

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

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

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

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

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

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

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

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

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

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

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

    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
    heikkil committed Jan 14, 2002
Commits on Jan 11, 2002
  1. debug message now uses the debug method

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

    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
    lstein committed Nov 20, 2001