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Commits on Jun 20, 2001
  1. @heikkil

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

    heikkil authored
    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. @heikkil

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

    heikkil authored
    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. @hyphaltip

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

    hyphaltip authored
    …ences between versions of TCoffee
    
    svn path=/bioperl-run/branches/branch-07/; revision=12969
Commits on Jun 12, 2001
  1. @hyphaltip

    using private state outside of class

    hyphaltip authored
    svn path=/bioperl-run/branches/branch-07/; revision=12965
Commits on May 28, 2001
  1. @heikkil

    SimpleAlign data files and fixes to tests

    heikkil authored
    svn path=/bioperl-run/branches/branch-07/; revision=12961
Commits on May 22, 2001
  1. @heikkil

    checks that seq is a Bio::PrimarySeq and seq->id() is set

    heikkil authored
    svn path=/bioperl-run/branches/branch-07/; revision=12960
Commits on May 16, 2001
  1. @heikkil

    t_coffee program orders sequences in an alignment depending the versi…

    heikkil authored
    …on of the program.
    
    New tests take this into account.
    
    svn path=/bioperl-run/branches/branch-07/; revision=12956
  2. @heikkil

    typo in docs

    heikkil authored
    svn path=/bioperl-run/branches/branch-07/; revision=12955
Commits on Apr 7, 2001
  1. @hyphaltip

    intitialize io -- facilitate tempfile cleanup

    hyphaltip authored
    svn path=/bioperl-run/branches/branch-07/; revision=12944
Commits on Mar 3, 2001
  1. @heikkil

    POD syntax fixes

    heikkil authored
    svn path=/bioperl-run/branches/branch-07/; revision=12940
Commits on Feb 28, 2001
  1. @hyphaltip

    properly removing tempfiles

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

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

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

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

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

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

    hyphaltip authored
    …ng in array of seqs
    
    svn path=/bioperl-run/trunk/; revision=12934
  3. @hlapp

    Changed to adopt Bio::Root::IO.

    hlapp authored
    svn path=/bioperl-run/trunk/; revision=12933
Commits on Feb 19, 2001
  1. @hyphaltip

    BPlite changes to make BPlite a SeqAnalysisParserI object

    hyphaltip authored
    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. @hyphaltip

    added Test.pm to lococal t dist

    hyphaltip authored
    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 authored
    svn path=/bioperl-run/trunk/; revision=12930
Commits on Jan 8, 2001
  1. @hyphaltip

    correct authors + email for consistency

    hyphaltip authored
    svn path=/bioperl-run/trunk/; revision=12929
  2. @hlapp

    Fixed inclusion of 'use Bio::Root::RootI' instead of

    hlapp authored
    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. @hlapp

    Fixed several doc format bugs.

    hlapp authored
    svn path=/bioperl-run/trunk/; revision=12927
  2. @hlapp

    Fixed several doc format bugs. (Why is an unprotected -p in the

    hlapp authored
    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. @hyphaltip

    migrated some tests over Test.pm, quieted some that were whining

    hyphaltip authored
    svn path=/bioperl-run/trunk/; revision=12925
Commits on Jan 3, 2001
  1. @hyphaltip

    migrated to new Bio::Root::RootI chained new

    hyphaltip authored
    svn path=/bioperl-run/trunk/; revision=12924
  2. @hyphaltip

    new tests, updated select

    hyphaltip authored
    tests to use the standard Test module (Test.pm)
    
    svn path=/bioperl-run/trunk/; revision=12923
Commits on Dec 29, 2000
  1. @hlapp

    Quoted unquoted string literals used as hash keys.

    hlapp authored
    svn path=/bioperl-run/trunk/; revision=12922
Commits on Dec 18, 2000
  1. @hyphaltip

    more intelligent detection of installed modules (File::Spec) and clea…

    hyphaltip authored
    …nup of .dnd files
    
    svn path=/bioperl-run/trunk/; revision=12921
  2. @hyphaltip

    unlinking is not necessary now

    hyphaltip authored
    svn path=/bioperl-run/trunk/; revision=12920
  3. @hyphaltip

    extra documentation

    hyphaltip authored
    svn path=/bioperl-run/trunk/; revision=12919
Commits on Dec 17, 2000
  1. @hyphaltip

    cleanup tmp files until can make TCoffee behave

    hyphaltip authored
    svn path=/bioperl-run/trunk/; revision=12918
  2. @hyphaltip

    Fixed to PROPER usage of tempfile

    hyphaltip authored
    svn path=/bioperl-run/trunk/; revision=12917
  3. @hyphaltip

    renaming packages for new dir structure

    hyphaltip authored
    svn path=/bioperl-run/trunk/; revision=12916
  4. @hyphaltip

    migration of code to Tools::Run

    hyphaltip authored
    svn path=/bioperl-run/trunk/; revision=12915
  5. @hyphaltip

    migrated code that runs tools to Bio::Tools::Run

    hyphaltip authored
    svn path=/bioperl-run/trunk/; revision=12914
Commits on Dec 1, 2000
  1. @hyphaltip

    removing temporary output files

    hyphaltip authored
    svn path=/bioperl-run/trunk/; revision=12913
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