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Commits on Aug 25, 2001
  1. Fix to avoid bark in File::Spec.

    svn path=/bioperl-run/branches/branch-07/; revision=12984
    hlapp committed Aug 25, 2001
  2. Merged over exists_blast() rewrite and other fixes from the main trunk.

    svn path=/bioperl-run/branches/branch-07/; revision=12983
    hlapp committed Aug 25, 2001
Commits on Jun 20, 2001
  1. 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/branches/branch-07/; revision=12971
    heikkil committed Jun 20, 2001
  2. 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/branches/branch-07/; revision=12970
    heikkil committed Jun 20, 2001
Commits on Jun 15, 2001
  1. minium identity score required instead of hard value to handle differ…

    …ences between versions of TCoffee
    
    svn path=/bioperl-run/branches/branch-07/; revision=12969
    hyphaltip committed Jun 15, 2001
Commits on Jun 12, 2001
  1. using private state outside of class

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

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

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

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

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

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

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

    svn path=/bioperl-run/trunk/; revision=12937
    hyphaltip committed Feb 28, 2001
Commits on Feb 27, 2001
  1. 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. 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. 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
  3. Changed to adopt Bio::Root::IO.

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

    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
    hyphaltip committed Feb 19, 2001
Commits on Jan 25, 2001
  1. added Test.pm to lococal t dist

    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
    hyphaltip committed Jan 25, 2001
Commits on Jan 23, 2001
  1. Updated bptutorial and other documentation

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

    svn path=/bioperl-run/trunk/; revision=12915
    hyphaltip committed Dec 17, 2000