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

    elofsson
    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
Commits on Jun 15, 2001
  1. minium identity score required instead of hard value to handle differ…

    hyphaltip committed Jun 15, 2001
    …ences between versions of TCoffee
    
    svn path=/bioperl-run/trunk/; revision=12969
Commits on Jun 14, 2001
  1. status set to invalid on a failed retrieval

    hyphaltip committed Jun 14, 2001
    svn path=/bioperl-run/trunk/; revision=12968
Commits on Jun 13, 2001
  1. Error messages for tests #8 & #9 now identifies ClustalW

    heikkil committed Jun 13, 2001
    as the the source of the error.
    
    svn path=/bioperl-run/trunk/; revision=12967
Commits on Jun 12, 2001
  1. uses method get_seq_by_pos()

    heikkil committed Jun 12, 2001
    svn path=/bioperl-run/trunk/; revision=12966
  2. using private state outside of class, must change the key until we go…

    hyphaltip committed Jun 12, 2001
    … to a method name here
    
    svn path=/bioperl-run/trunk/; revision=12964
Commits on Jun 2, 2001
  1. Enabled BPbl2seq to read multiple HSPs. Also various documentation fi…

    peter
    peter committed Jun 2, 2001
    …xes.
    
    svn path=/bioperl-run/trunk/; revision=12963
Commits on May 28, 2001
  1. minor fix (testing sequence count of a wrong alignment)

    heikkil committed May 28, 2001
    svn path=/bioperl-run/trunk/; revision=12962
Commits on May 18, 2001
  1. Fixed a typo in docs and added requirement for the sequence id() to b…

    heikkil committed May 18, 2001
    …e set.
    
    svn path=/bioperl-run/trunk/; revision=12959
  2. The module was requiring input sequences to eq Bio::Seq,

    heikkil committed May 18, 2001
    changed that to isa->Bio::PrimarySeqI.
    
    Clustalw chrashes if the the sequence does not have id() set,
    undef id() now throws an error.
    
    svn path=/bioperl-run/trunk/; revision=12958
Commits on May 16, 2001
  1. t_coffee program orders sequences in an alignment depending on the ve…

    heikkil committed May 16, 2001
    …rsion of the program.
    
    New tests take this into account.
    
    svn path=/bioperl-run/trunk/; revision=12957
  2. typo in docs

    heikkil committed May 16, 2001
    svn path=/bioperl-run/trunk/; revision=12955
  3. merge of branch-07 to head. Mostly POD changes.

    heikkil committed May 16, 2001
    svn path=/bioperl-run/trunk/; revision=12954
  4. changed to reflect the changes in the SimpleAlign

    heikkil committed May 16, 2001
    svn path=/bioperl-run/trunk/; revision=12953
Commits on May 11, 2001
  1. major update to Bio::SimpleAlign. New, bioperl-like method names, doc…

    heikkil committed May 11, 2001
    … fixes, tests. Changes are backward compatible except that Bio::AlignIO is now the ONLY way to read and write SimpleAligns.
    
    svn path=/bioperl-run/trunk/; revision=12952