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Commits on Aug 10, 2001
  1. @hyphaltip

    don't have clustalw tests fail for 0.9 release

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

    documentation for retrieve_blast method

    svn path=/bioperl-run/trunk/; revision=12977
    hyphaltip committed Aug 7, 2001
Commits on Jul 24, 2001
  1. @heikkil

    claning. Needs code to compare input and ACD options

    svn path=/bioperl-run/trunk/; revision=12976
    heikkil committed Jul 24, 2001
Commits on Jul 23, 2001
  1. @heikkil

    Classes for wrapping EMBOSS suite

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

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

    svn path=/bioperl-run/trunk/; revision=12973
    elofsson committed Jul 4, 2001
Commits on Jun 20, 2001
  1. @heikkil

    The code for setting the path to binary was in BEGIN block making it

    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
    heikkil committed Jun 20, 2001
  2. @heikkil

    The code for setting the path to binary was in BEGIN block making it

    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
    heikkil committed Jun 20, 2001
Commits on Jun 15, 2001
  1. @hyphaltip

    minium identity score required instead of hard value to handle differ…

    …ences between versions of TCoffee
    
    svn path=/bioperl-run/trunk/; revision=12969
    hyphaltip committed Jun 15, 2001
Commits on Jun 14, 2001
  1. @hyphaltip

    status set to invalid on a failed retrieval

    svn path=/bioperl-run/trunk/; revision=12968
    hyphaltip committed Jun 14, 2001
Commits on Jun 13, 2001
  1. @heikkil

    Error messages for tests #8 & #9 now identifies ClustalW

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

    uses method get_seq_by_pos()

    svn path=/bioperl-run/trunk/; revision=12966
    heikkil committed Jun 12, 2001
  2. @hyphaltip

    using private state outside of class, must change the key until we go…

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

    …xes.
    
    svn path=/bioperl-run/trunk/; revision=12963
    peter committed Jun 2, 2001
Commits on May 28, 2001
  1. @heikkil

    minor fix (testing sequence count of a wrong alignment)

    svn path=/bioperl-run/trunk/; revision=12962
    heikkil committed May 28, 2001
Commits on May 18, 2001
  1. @heikkil

    Fixed a typo in docs and added requirement for the sequence id() to b…

    …e set.
    
    svn path=/bioperl-run/trunk/; revision=12959
    heikkil committed May 18, 2001
  2. @heikkil

    The module was requiring input sequences to eq Bio::Seq,

    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
    heikkil committed May 18, 2001
Commits on May 16, 2001
  1. @heikkil

    t_coffee program orders sequences in an alignment depending on the ve…

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

    typo in docs

    svn path=/bioperl-run/trunk/; revision=12955
    heikkil committed May 16, 2001
  3. @heikkil

    merge of branch-07 to head. Mostly POD changes.

    svn path=/bioperl-run/trunk/; revision=12954
    heikkil committed May 16, 2001
  4. @heikkil

    changed to reflect the changes in the SimpleAlign

    svn path=/bioperl-run/trunk/; revision=12953
    heikkil committed May 16, 2001
Commits on May 11, 2001
  1. @heikkil

    major update to Bio::SimpleAlign. New, bioperl-like method names, doc…

    … 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
    heikkil committed May 11, 2001
Commits on Apr 30, 2001
  1. @hyphaltip

    migrated test data files to dir t/data

    svn path=/bioperl-run/trunk/; revision=12951
    hyphaltip committed Apr 30, 2001
Commits on Apr 16, 2001
  1. @hyphaltip

    Tests pass even when IO::String is not installed

    svn path=/bioperl-run/trunk/; revision=12950
    hyphaltip committed Apr 16, 2001
Commits on Apr 9, 2001
  1. @hyphaltip

    updated to use ncbi Blast.cgi script rather than blast.cgi

    Text formatting done by cgi rather than HTML tag stripping in module code
    
    svn path=/bioperl-run/trunk/; revision=12949
    hyphaltip committed Apr 9, 2001
Commits on Apr 8, 2001
  1. @hlapp

    Fixed tempfile filehandle handling in retrieve_blast().

    svn path=/bioperl-run/trunk/; revision=12948
    hlapp committed Apr 8, 2001
Commits on Apr 7, 2001
  1. @hyphaltip

    updated num of tests

    svn path=/bioperl-run/trunk/; revision=12947
    hyphaltip committed Apr 7, 2001
  2. @hyphaltip

    quieter tests when verbose == 0, use tempfile for HTML -> text cleanup

    svn path=/bioperl-run/trunk/; revision=12946
    hyphaltip committed Apr 7, 2001
  3. @hyphaltip

    Pure perl (via HTTP) Remote blast submission and retrieval -- see tes…

    …t script for example usage
    
    svn path=/bioperl-run/trunk/; revision=12945
    hyphaltip committed Apr 7, 2001
  4. @hyphaltip

    io was not initialized, meaning tempfiles were not cleaned up - bette…

    …r argument matching
    
    svn path=/bioperl-run/trunk/; revision=12943
    hyphaltip committed Apr 7, 2001
  5. @hyphaltip

    io was not initialized, meaning tempfiles were not cleaned up

    svn path=/bioperl-run/trunk/; revision=12942
    hyphaltip committed Apr 7, 2001
Commits on Feb 28, 2001
  1. @hyphaltip

    properly removing tempfiles

    svn path=/bioperl-run/trunk/; revision=12937
    hyphaltip committed Feb 28, 2001
Commits on Feb 27, 2001
  1. @hlapp

    Hardcoded paths, second pass. Hope to have caught all occurrences now.

    svn path=/bioperl-run/trunk/; revision=12936
    hlapp committed Feb 27, 2001
Commits on Feb 26, 2001
  1. @hlapp

    Fixed hardcoded t directory in filenames to using Bio::Root::IO->catf…

    …ile().
    
    Not complete yet (was an automatic edit).
    
    svn path=/bioperl-run/trunk/; revision=12935
    hlapp committed Feb 26, 2001
  2. @hyphaltip

    fixed TCoffee changes to properly output seqs to temp file when passi…

    …ng in array of seqs
    
    svn path=/bioperl-run/trunk/; revision=12934
    hyphaltip committed Feb 26, 2001
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