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Commits on Jun 4, 2002
  1. skipped tests actually report why they are skipped if you put the com…

    …ment as the first parameter to the skip cmd
    
    svn path=/bioperl-run/branches/branch-1-0-0/; revision=13084
    hyphaltip committed Jun 4, 2002
Commits on Apr 21, 2002
  1. merged changes from trunk to branch

    svn path=/bioperl-run/branches/branch-1-0-0/; revision=13070
    hyphaltip committed Apr 21, 2002
Commits on Mar 22, 2002
  1. debug off

    svn path=/bioperl-run/branches/branch-1-0-0/; revision=13063
    hyphaltip committed Mar 22, 2002
  2. less stringent checking because some 'versions' of t_coffee return sl…

    …ighly different alignments (oct 2000 and march 2001)
    
    svn path=/bioperl-run/branches/branch-1-0-0/; revision=13062
    hyphaltip committed Mar 22, 2002
Commits on Mar 18, 2002
  1. update test count

    svn path=/bioperl-run/branches/branch-1-0-0/; revision=13052
    hyphaltip committed Mar 18, 2002
  2. use average and overall percentage identity methods

    svn path=/bioperl-run/branches/branch-1-0-0/; revision=13051
    hyphaltip committed Mar 18, 2002
  3. version determining regexp protected

    svn path=/bioperl-run/branches/branch-1-0-0/; revision=13050
    hyphaltip committed Mar 18, 2002
Commits on Mar 17, 2002
  1. deal with different versions of TCoffee producing different alignment…

    …s and thus different percent id
    
    svn path=/bioperl-run/branches/branch-1-0-0/; revision=13049
    hyphaltip committed Mar 17, 2002
Commits on Mar 16, 2002
  1. Minor documentation fixes

    svn path=/bioperl-run/branches/branch-1-0-0/; revision=13048
    peter committed Mar 16, 2002
Commits on Mar 15, 2002
  1. remove debug code and tests for blastinstalled more efficiently

    svn path=/bioperl-run/branches/branch-1-0-0/; revision=13045
    hyphaltip committed Mar 15, 2002
  2. StandAlone tests will detect that data dir is not set and exit test n…

    …icely
    
    svn path=/bioperl-run/branches/branch-1-0-0/; revision=13044
    hyphaltip committed Mar 15, 2002
  3. test count bumped up by one

    svn path=/bioperl-run/branches/branch-1-0-0/; revision=13043
    hyphaltip committed Mar 15, 2002
  4. more tests for percentid - corrected to use overall percent identity

    svn path=/bioperl-run/branches/branch-1-0-0/; revision=13042
    hyphaltip committed Mar 15, 2002
  5. handle tcoffee 1.22 version too in version test

    svn path=/bioperl-run/branches/branch-1-0-0/; revision=13041
    hyphaltip committed Mar 15, 2002
  6. POD fixes

    svn path=/bioperl-run/branches/branch-1-0-0/; revision=13040
    heikkil committed Mar 15, 2002
  7. merge from main trunk

    svn path=/bioperl-run/branches/branch-1-0-0/; revision=13039
    hyphaltip committed Mar 15, 2002
  8. merge main trunk changes which include using SearchIO by default and …

    …a better SYNOPSIS
    
    svn path=/bioperl-run/branches/branch-1-0-0/; revision=13037
    hyphaltip committed Mar 15, 2002
  9. merge cleanup io from main trunk

    svn path=/bioperl-run/branches/branch-1-0-0/; revision=13036
    hyphaltip committed Mar 15, 2002
Commits on Mar 14, 2002
  1. skip nicely

    svn path=/bioperl-run/branches/branch-1-0-0/; revision=13031
    hyphaltip committed Mar 14, 2002
Commits on Mar 11, 2002
  1. call cleanup upon _setinput call

    svn path=/bioperl-run/branches/branch-1-0-0/; revision=13029
    hyphaltip committed Mar 11, 2002
  2. parameterized verbose flag

    svn path=/bioperl-run/branches/branch-1-0-0/; revision=13028
    hyphaltip committed Mar 11, 2002
  3. slightly more intelligent checking for clustalw exe

    svn path=/bioperl-run/branches/branch-1-0-0/; revision=13027
    hyphaltip committed Mar 11, 2002
  4. find blast executeable in the PATH if possible -- bl2seq might still …

    …fail if one does not have .ncbirc set correctly
    
    svn path=/bioperl-run/branches/branch-1-0-0/; revision=13025
    hyphaltip committed Mar 11, 2002
Commits on Mar 9, 2002
  1. turn of clustalw debugging

    svn path=/bioperl-run/trunk/; revision=13022
    hyphaltip committed Mar 9, 2002
Commits on Mar 8, 2002
  1. tweak to clustalw test for falling over correctly

    svn path=/bioperl-run/trunk/; revision=13021
    birney committed Mar 8, 2002
  2. Now can take a program path as arg on the new method, aboids need for…

    … ENV variable (ENV still in not to break other people's scripts,etc)
    
    svn path=/bioperl-run/trunk/; revision=13020
    elia committed Mar 8, 2002
  3. No need for the dir variable

    svn path=/bioperl-run/trunk/; revision=13019
    elia committed Mar 8, 2002
Commits on Mar 5, 2002
  1. unlink test file output

    svn path=/bioperl-run/trunk/; revision=13018
    hyphaltip committed Mar 5, 2002
Commits on Mar 4, 2002
  1. added ability to dump alignments as well as sequences when running an…

    … EMBOSS application
    
    svn path=/bioperl-run/trunk/; revision=13017
    hyphaltip committed Mar 4, 2002
Commits on Feb 18, 2002
  1. added example documentation to the POD

    svn path=/bioperl-run/trunk/; revision=13016
    hyphaltip committed Feb 18, 2002
  2. test for cmd line argument where value is a Bio::PrimarySeqI or array…

    … of seqs -- added test for 'water'
    
    svn path=/bioperl-run/trunk/; revision=13015
    hyphaltip committed Feb 18, 2002
  3. handle cmd line arguments pointing to a Bio::PrimarySeqI object or ar…

    …ray or Bio::PrimarySeqI
    
    svn path=/bioperl-run/trunk/; revision=13014
    hyphaltip committed Feb 18, 2002
  4. got all tests to pass

    svn path=/bioperl-run/trunk/; revision=13012
    birney committed Feb 18, 2002
Commits on Feb 14, 2002
  1. Doc clarification, fixed POD error

    svn path=/bioperl-run/trunk/; revision=13011
    bosborne committed Feb 14, 2002
Commits on Feb 6, 2002
  1. params should be appended not overwriting

    svn path=/bioperl-run/trunk/; revision=13010
    hyphaltip committed Feb 6, 2002