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Commits on Oct 13, 2005
  1. merge HEAD changes to put EMBOSS require in BEGIN

    hyphaltip committed Oct 13, 2005
    svn path=/bioperl-run/branches/bioperl-run-branch-1-5-1/; revision=13670
Commits on Oct 9, 2005
  1. Merged from HEAD to 1.5.1 branch, changes which remove old bug email …

    hyphaltip committed Oct 9, 2005
    …address and point to bugzilla.bioperl.org website for bug submission
    
    svn path=/bioperl-run/branches/bioperl-run-branch-1-5-1/; revision=13668
Commits on Oct 8, 2005
  1. Changes updated for the release

    hyphaltip committed Oct 8, 2005
    svn path=/bioperl-run/trunk/; revision=13663
  2. teeny code cleanup

    hyphaltip committed Oct 8, 2005
    svn path=/bioperl-run/trunk/; revision=13662
  3. Phrap tests pass

    hyphaltip committed Oct 8, 2005
    svn path=/bioperl-run/trunk/; revision=13661
  4. tests pass, find the right nodes more explicitly

    hyphaltip committed Oct 8, 2005
    svn path=/bioperl-run/trunk/; revision=13660
  5. support new exported Menu variable

    hyphaltip committed Oct 8, 2005
    svn path=/bioperl-run/trunk/; revision=13659
  6. DrawTree Basically works

    hyphaltip committed Oct 8, 2005
    svn path=/bioperl-run/trunk/; revision=13658
Commits on Oct 4, 2005
  1. drawgram works

    hyphaltip committed Oct 4, 2005
    svn path=/bioperl-run/trunk/; revision=13657
Commits on Sep 30, 2005
  1. do the right thing that I wanted you to do (you know that thing)

    hyphaltip committed Sep 30, 2005
    svn path=/bioperl-run/trunk/; revision=13656
  2. indent some code

    hyphaltip committed Sep 30, 2005
    svn path=/bioperl-run/trunk/; revision=13655
  3. test, really what we wanted

    hyphaltip committed Sep 30, 2005
    svn path=/bioperl-run/trunk/; revision=13654
  4. protdist works for me on phylip 3.61

    hyphaltip committed Sep 30, 2005
    svn path=/bioperl-run/trunk/; revision=13653
  5. POD typo

    hyphaltip committed Sep 30, 2005
    svn path=/bioperl-run/trunk/; revision=13652
  6. 2.2.0 testing

    hyphaltip committed Sep 30, 2005
    svn path=/bioperl-run/trunk/; revision=13651
  7. debugging info

    hyphaltip committed Sep 30, 2005
    svn path=/bioperl-run/trunk/; revision=13650
  8. 2.2.3-rc7 values

    hyphaltip committed Sep 30, 2005
    svn path=/bioperl-run/trunk/; revision=13649
Commits on Sep 29, 2005
  1. * generalize the ProtDist test so that it only compares 3 significant

    hartzell
    hartzell committed Sep 29, 2005
      digits worth of the score.  This allows the test to pass with perl
      5.8.7 on FreeBSD 5.4-STABLE i386.
    
      Reviewed by Jason.
    
    	t/ProtDist.t (modified)
    
    svn path=/bioperl-run/trunk/; revision=13648
Commits on Sep 27, 2005
  1. jump out of parser loop when we hit the stats at the bottom of the re…

    hyphaltip committed Sep 27, 2005
    …port (I think this did not used to be there)
    
    svn path=/bioperl-run/trunk/; revision=13647
  2. remove debugging crap

    hyphaltip committed Sep 27, 2005
    svn path=/bioperl-run/trunk/; revision=13646
  3. whoops, inc test count too

    hyphaltip committed Sep 27, 2005
    svn path=/bioperl-run/trunk/; revision=13645
  4. test repeat masker on different versions, this probably also depends …

    hyphaltip committed Sep 27, 2005
    …on your version of the RM libraries, I wonder how to standardize this...
    
    svn path=/bioperl-run/trunk/; revision=13644
  5. cleanup after oneself

    hyphaltip committed Sep 27, 2005
    svn path=/bioperl-run/trunk/; revision=13643
  6. skip where appropriate

    hyphaltip committed Sep 27, 2005
    svn path=/bioperl-run/trunk/; revision=13642
  7. work on diff versions of MUSCLE

    hyphaltip committed Sep 27, 2005
    svn path=/bioperl-run/trunk/; revision=13641
  8. more flexible version matching for percid

    hyphaltip committed Sep 27, 2005
    svn path=/bioperl-run/trunk/; revision=13640
  9. test for wise 2.2.0 and 2.2.3

    hyphaltip committed Sep 27, 2005
    svn path=/bioperl-run/trunk/; revision=13639
  10. simplify java version lookup

    hyphaltip committed Sep 27, 2005
    svn path=/bioperl-run/trunk/; revision=13638
  11. George Hartzell's excellent code fixes

    hyphaltip committed Sep 27, 2005
    svn path=/bioperl-run/trunk/; revision=13637
  12. update test nums and added a test; per George Hartzell

    hyphaltip committed Sep 27, 2005
    svn path=/bioperl-run/trunk/; revision=13636
  13. add some POD, note that this module is probably incomplete

    hyphaltip committed Sep 27, 2005
    svn path=/bioperl-run/trunk/; revision=13635
Commits on Sep 26, 2005
  1. strike that, emboss 2.8.0 is where the cutoff in argument changes mus…

    hyphaltip committed Sep 26, 2005
    …t have happened
    
    svn path=/bioperl-run/trunk/; revision=13634
  2. EMBOSS 3.0.0 testing passes

    hyphaltip committed Sep 26, 2005
    svn path=/bioperl-run/trunk/; revision=13633
Commits on Sep 25, 2005
  1. adhere to the style that makes sense to me

    hyphaltip committed Sep 25, 2005
    svn path=/bioperl-run/trunk/; revision=13632
  2. genewise test files

    hyphaltip committed Sep 25, 2005
    svn path=/bioperl-run/trunk/; revision=13631