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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/branches/branch-07/; 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/branches/branch-07/; 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/branches/branch-07/; revision=12969
Commits on Jun 12, 2001
  1. using private state outside of class

    hyphaltip committed Jun 12, 2001
    svn path=/bioperl-run/branches/branch-07/; revision=12965
Commits on May 28, 2001
  1. SimpleAlign data files and fixes to tests

    heikkil committed May 28, 2001
    svn path=/bioperl-run/branches/branch-07/; revision=12961
Commits on May 22, 2001
  1. checks that seq is a Bio::PrimarySeq and seq->id() is set

    heikkil committed May 22, 2001
    svn path=/bioperl-run/branches/branch-07/; revision=12960
Commits on May 16, 2001
  1. t_coffee program orders sequences in an alignment depending the versi…

    heikkil committed May 16, 2001
    …on of the program.
    
    New tests take this into account.
    
    svn path=/bioperl-run/branches/branch-07/; revision=12956
  2. typo in docs

    heikkil committed May 16, 2001
    svn path=/bioperl-run/branches/branch-07/; revision=12955
Commits on Apr 7, 2001
  1. intitialize io -- facilitate tempfile cleanup

    hyphaltip committed Apr 7, 2001
    svn path=/bioperl-run/branches/branch-07/; revision=12944
Commits on Mar 3, 2001
  1. POD syntax fixes

    heikkil committed Mar 3, 2001
    svn path=/bioperl-run/branches/branch-07/; revision=12940
Commits on Feb 28, 2001
  1. properly removing tempfiles

    hyphaltip committed Feb 28, 2001
    svn path=/bioperl-run/trunk/; revision=12937
Commits on Feb 27, 2001
  1. Hardcoded paths, second pass. Hope to have caught all occurrences now.

    hlapp committed Feb 27, 2001
    svn path=/bioperl-run/trunk/; revision=12936
Commits on Feb 26, 2001
  1. Fixed hardcoded t directory in filenames to using Bio::Root::IO->catf…

    hlapp committed Feb 26, 2001
    …ile().
    
    Not complete yet (was an automatic edit).
    
    svn path=/bioperl-run/trunk/; revision=12935
  2. fixed TCoffee changes to properly output seqs to temp file when passi…

    hyphaltip committed Feb 26, 2001
    …ng in array of seqs
    
    svn path=/bioperl-run/trunk/; revision=12934
  3. Changed to adopt Bio::Root::IO.

    hlapp committed Feb 26, 2001
    svn path=/bioperl-run/trunk/; revision=12933
Commits on Feb 19, 2001
  1. BPlite changes to make BPlite a SeqAnalysisParserI object

    hyphaltip committed Feb 19, 2001
    BPbl2seq now requires named input parameter (no longer can just pass in filehandle reference, must pass in -fh => $filehandle)
    Assundry changes made to related files to handle these changes
    
    svn path=/bioperl-run/trunk/; revision=12932
Commits on Jan 25, 2001
  1. added Test.pm to lococal t dist

    hyphaltip committed Jan 25, 2001
    migrate t tests to fallback on local t copy of Test if it is not installed
    has been tested on perl 5.00404 IRIX and get errors when exit(0) is
    called in the BEGIN block, but otherwise things seem to work okay
    
    svn path=/bioperl-run/trunk/; revision=12931
Commits on Jan 23, 2001
  1. Updated bptutorial and other documentation

    peter
    peter committed Jan 23, 2001
    svn path=/bioperl-run/trunk/; revision=12930
Commits on Jan 8, 2001
  1. correct authors + email for consistency

    hyphaltip committed Jan 8, 2001
    svn path=/bioperl-run/trunk/; revision=12929
  2. Fixed inclusion of 'use Bio::Root::RootI' instead of

    hlapp committed Jan 8, 2001
    Bio::Root::Object. Fixed exists_blast() (didn't work due to missing braces).
    
    svn path=/bioperl-run/trunk/; revision=12928
Commits on Jan 7, 2001
  1. Fixed several doc format bugs.

    hlapp committed Jan 7, 2001
    svn path=/bioperl-run/trunk/; revision=12927
  2. Fixed several doc format bugs. (Why is an unprotected -p in the

    hlapp committed Jan 7, 2001
    DESCRIPTION section disallowed and somewhere else it is not? Anyway,
    perldoc is quiet now.)
    
    svn path=/bioperl-run/trunk/; revision=12926
Commits on Jan 5, 2001
  1. migrated some tests over Test.pm, quieted some that were whining

    hyphaltip committed Jan 5, 2001
    svn path=/bioperl-run/trunk/; revision=12925
Commits on Jan 3, 2001
  1. migrated to new Bio::Root::RootI chained new

    hyphaltip committed Jan 3, 2001
    svn path=/bioperl-run/trunk/; revision=12924
  2. new tests, updated select

    hyphaltip committed Jan 3, 2001
    tests to use the standard Test module (Test.pm)
    
    svn path=/bioperl-run/trunk/; revision=12923
Commits on Dec 29, 2000
  1. Quoted unquoted string literals used as hash keys.

    hlapp committed Dec 29, 2000
    svn path=/bioperl-run/trunk/; revision=12922
Commits on Dec 18, 2000
  1. more intelligent detection of installed modules (File::Spec) and clea…

    hyphaltip committed Dec 18, 2000
    …nup of .dnd files
    
    svn path=/bioperl-run/trunk/; revision=12921
  2. unlinking is not necessary now

    hyphaltip committed Dec 18, 2000
    svn path=/bioperl-run/trunk/; revision=12920
  3. extra documentation

    hyphaltip committed Dec 18, 2000
    svn path=/bioperl-run/trunk/; revision=12919
Commits on Dec 17, 2000
  1. cleanup tmp files until can make TCoffee behave

    hyphaltip committed Dec 17, 2000
    svn path=/bioperl-run/trunk/; revision=12918
  2. Fixed to PROPER usage of tempfile

    hyphaltip committed Dec 17, 2000
    svn path=/bioperl-run/trunk/; revision=12917
  3. renaming packages for new dir structure

    hyphaltip committed Dec 17, 2000
    svn path=/bioperl-run/trunk/; revision=12916
  4. migration of code to Tools::Run

    hyphaltip committed Dec 17, 2000
    svn path=/bioperl-run/trunk/; revision=12915
  5. migrated code that runs tools to Bio::Tools::Run

    hyphaltip committed Dec 17, 2000
    svn path=/bioperl-run/trunk/; revision=12914
Commits on Dec 1, 2000
  1. removing temporary output files

    hyphaltip committed Dec 1, 2000
    svn path=/bioperl-run/trunk/; revision=12913