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Commits on Oct 13, 2005
  1. @hyphaltip

    merge HEAD changes to put EMBOSS require in BEGIN

    hyphaltip authored
    svn path=/bioperl-run/branches/bioperl-run-branch-1-5-1/; revision=13670
Commits on Oct 9, 2005
  1. @hyphaltip

    Merged from HEAD to 1.5.1 branch, changes which remove old bug email …

    hyphaltip authored
    …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. @hyphaltip

    Changes updated for the release

    hyphaltip authored
    svn path=/bioperl-run/trunk/; revision=13663
  2. @hyphaltip

    teeny code cleanup

    hyphaltip authored
    svn path=/bioperl-run/trunk/; revision=13662
  3. @hyphaltip

    Phrap tests pass

    hyphaltip authored
    svn path=/bioperl-run/trunk/; revision=13661
  4. @hyphaltip

    tests pass, find the right nodes more explicitly

    hyphaltip authored
    svn path=/bioperl-run/trunk/; revision=13660
  5. @hyphaltip

    support new exported Menu variable

    hyphaltip authored
    svn path=/bioperl-run/trunk/; revision=13659
  6. @hyphaltip

    DrawTree Basically works

    hyphaltip authored
    svn path=/bioperl-run/trunk/; revision=13658
Commits on Oct 4, 2005
  1. @hyphaltip

    drawgram works

    hyphaltip authored
    svn path=/bioperl-run/trunk/; revision=13657
Commits on Sep 30, 2005
  1. @hyphaltip

    do the right thing that I wanted you to do (you know that thing)

    hyphaltip authored
    svn path=/bioperl-run/trunk/; revision=13656
  2. @hyphaltip

    indent some code

    hyphaltip authored
    svn path=/bioperl-run/trunk/; revision=13655
  3. @hyphaltip

    test, really what we wanted

    hyphaltip authored
    svn path=/bioperl-run/trunk/; revision=13654
  4. @hyphaltip

    protdist works for me on phylip 3.61

    hyphaltip authored
    svn path=/bioperl-run/trunk/; revision=13653
  5. @hyphaltip

    POD typo

    hyphaltip authored
    svn path=/bioperl-run/trunk/; revision=13652
  6. @hyphaltip

    2.2.0 testing

    hyphaltip authored
    svn path=/bioperl-run/trunk/; revision=13651
  7. @hyphaltip

    debugging info

    hyphaltip authored
    svn path=/bioperl-run/trunk/; revision=13650
  8. @hyphaltip

    2.2.3-rc7 values

    hyphaltip authored
    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 authored
      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. @hyphaltip

    jump out of parser loop when we hit the stats at the bottom of the re…

    hyphaltip authored
    …port (I think this did not used to be there)
    
    svn path=/bioperl-run/trunk/; revision=13647
  2. @hyphaltip

    remove debugging crap

    hyphaltip authored
    svn path=/bioperl-run/trunk/; revision=13646
  3. @hyphaltip

    whoops, inc test count too

    hyphaltip authored
    svn path=/bioperl-run/trunk/; revision=13645
  4. @hyphaltip

    test repeat masker on different versions, this probably also depends …

    hyphaltip authored
    …on your version of the RM libraries, I wonder how to standardize this...
    
    svn path=/bioperl-run/trunk/; revision=13644
  5. @hyphaltip

    cleanup after oneself

    hyphaltip authored
    svn path=/bioperl-run/trunk/; revision=13643
  6. @hyphaltip

    skip where appropriate

    hyphaltip authored
    svn path=/bioperl-run/trunk/; revision=13642
  7. @hyphaltip

    work on diff versions of MUSCLE

    hyphaltip authored
    svn path=/bioperl-run/trunk/; revision=13641
  8. @hyphaltip

    more flexible version matching for percid

    hyphaltip authored
    svn path=/bioperl-run/trunk/; revision=13640
  9. @hyphaltip

    test for wise 2.2.0 and 2.2.3

    hyphaltip authored
    svn path=/bioperl-run/trunk/; revision=13639
  10. @hyphaltip

    simplify java version lookup

    hyphaltip authored
    svn path=/bioperl-run/trunk/; revision=13638
  11. @hyphaltip

    George Hartzell's excellent code fixes

    hyphaltip authored
    svn path=/bioperl-run/trunk/; revision=13637
  12. @hyphaltip

    update test nums and added a test; per George Hartzell

    hyphaltip authored
    svn path=/bioperl-run/trunk/; revision=13636
  13. @hyphaltip

    add some POD, note that this module is probably incomplete

    hyphaltip authored
    svn path=/bioperl-run/trunk/; revision=13635
Commits on Sep 26, 2005
  1. @hyphaltip

    strike that, emboss 2.8.0 is where the cutoff in argument changes mus…

    hyphaltip authored
    …t have happened
    
    svn path=/bioperl-run/trunk/; revision=13634
  2. @hyphaltip

    EMBOSS 3.0.0 testing passes

    hyphaltip authored
    svn path=/bioperl-run/trunk/; revision=13633
Commits on Sep 25, 2005
  1. @hyphaltip

    adhere to the style that makes sense to me

    hyphaltip authored
    svn path=/bioperl-run/trunk/; revision=13632
  2. @hyphaltip

    genewise test files

    hyphaltip authored
    svn path=/bioperl-run/trunk/; revision=13631
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