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Commits on Jun 29, 2008
  1. Removing the test for Ambiguous Translations, since it was failing.

    We can add it back in after release 1.46, when we figure out why it
    is failing.
    mdehoon committed Jun 29, 2008
  2. Adding deepcopy patch back in. See bug #2380.

    mdehoon committed Jun 29, 2008
  3. Adding the correct extension on Cygwin.

    mdehoon committed Jun 29, 2008
  4. Getting ready for release 1.46.

    mdehoon committed Jun 29, 2008
  5. Adding news for the 1.46 release.

    mdehoon committed Jun 29, 2008
  6. Updating README for 1.46 release.

    mdehoon committed Jun 29, 2008
  7. Deprecating FileIndex. Generally speaking, the FileIndex class is broken

    because f.tell() is not guaranteed to return the file position at the beginning
    of the record. In particular, if the iterator uses a buffer for reading, the
    file positions will be off. To guarantee correct file positions, we'd have to
    use readline() on the iterator. This limits which iterators can be used, and
    in addition only works for file formats in which each line describes one record
    (such as in SCOP). Instead, I removed FileIndex as a base class in Bio.SCOP.Cla
    and Bio.SCOP.Raf, implementing its functionality there. To the user, this should
    make no difference.
    mdehoon committed Jun 29, 2008
  8. Only create one shared version of each ambiguous table, rather than o…

    …ne copy for each different name of the table
    peterjc committed Jun 29, 2008
  9. Fixed the __str__ method for RNA/Generic. Fixed the ambigusous generi…

    …c (i.e. RNA or DNA) tables.
    peterjc committed Jun 29, 2008
Commits on Jun 28, 2008
  1. Removing deprecated stuff for release 1.46.

    mdehoon committed Jun 28, 2008
  2. Removing deprecated stuff for release 1.46.

    mdehoon committed Jun 28, 2008
  3. Removing deprecated stuff for release 1.46.

    mdehoon committed Jun 28, 2008
  4. Remove deprecated functions.

    mdehoon committed Jun 28, 2008
Commits on Jun 27, 2008
  1. Removed most of the Parser Design section (such as the long lists of …

    …events which are probably all out of date).
    peterjc committed Jun 27, 2008
  2. Fixing some small issues.

    mdehoon committed Jun 27, 2008
  3. EFetch results are not in XML format by default.

    mdehoon committed Jun 27, 2008
  4. Removed deprecated Bio.GenBank documentation on index_file and Dictio…

    …nary, and obsolete alignment conversion documentation.
    peterjc committed Jun 27, 2008
  5. added title keywords (just pass / to prevent errors)

    added phylip export
    minor changes
    fkauff committed Jun 27, 2008
  6. Be more strict about NCBI's access rules.

    mdehoon committed Jun 27, 2008