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Commits on Mar 18, 2002
  1. update test count

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

    hyphaltip committed Feb 6, 2002
    svn path=/bioperl-run/trunk/; revision=13010
Commits on Jan 30, 2002
  1. verbosity=-1 is same as quiet()

    hyphaltip committed Jan 30, 2002
    svn path=/bioperl-run/trunk/; revision=13009
Commits on Jan 14, 2002
  1. test for version()

    heikkil committed Jan 14, 2002
    warns if version < 1.3 (and most tests will fail)
    
    svn path=/bioperl-run/trunk/; revision=13008
  2. added version()

    heikkil committed Jan 14, 2002
    Implementaion might print an annoying string "FATAL error..." on non-UNIX platforms.
    Post 1.37 versions of t_coffee will have an explicit -version argument.
    
    svn path=/bioperl-run/trunk/; revision=13007
Commits on Jan 11, 2002
  1. debug message now uses the debug method

    hyphaltip committed Jan 11, 2002
    svn path=/bioperl-run/trunk/; revision=13005