Commits on Oct 10, 2003
  1. added rule to include Bio/Cluster/*.c

    they weren't getting included
    jchang committed Oct 10, 2003
  2. updated information for 1.22 release

    jchang committed Oct 10, 2003
Commits on Oct 9, 2003
  1. In Python 2.3.2, the current directory '' is not included in the path.

    Instead the current directory at the time of Python startup is
    included in the path. This breaks setup.py test which relies on the
    first behavior to import the tests.
    grouse committed Oct 9, 2003
  2. Iterator now allows blank lines between files

    Iterator is now a Python 2.0 iterator
    jchang committed Oct 9, 2003
  3. two fixes:

      - now NCBIDictionary returns 1 sequence by default
      - NCBIDictionary is smarter about guessing the format
    jchang committed Oct 9, 2003
  4. now distributes _KDTree.C file

    jchang committed Oct 9, 2003
Commits on Sep 25, 2003
Commits on Sep 23, 2003
  1. Updated water command for new version

    chapmanb committed Sep 23, 2003
Commits on Sep 19, 2003
  1. Check in updates from Yves Bastide. Thanks!

    chapmanb committed Sep 19, 2003
Commits on Sep 16, 2003
  1. committed Michiel de Hoon's fix to get the dtds installed in the right

    place for windows
    jchang committed Sep 16, 2003
Commits on Sep 15, 2003
  1. fixed installation of Bio/EUtils/DTDs

    now packages them in a "data_files"
    jchang committed Sep 15, 2003
Commits on Sep 13, 2003
  1. added release notes for next release

    jchang committed Sep 13, 2003
  2. now installs Martel and doesn't complain about it

    will install Bio.Cluster only if Numeric is present
    jchang committed Sep 13, 2003
  3. updated test for Python 2.3

    jchang committed Sep 13, 2003
Commits on Sep 11, 2003
Commits on Sep 7, 2003
  1. C Clustering Library version 1.23. Bug fix in the palcluster routine in

    src/cluster.c. This is the pairwise average-linkage hierarchical clustering
    code. The last row in the distance matrix was not being copied.
    mdehoon committed Sep 7, 2003
Commits on Sep 4, 2003
  1. added Peter Slickers' patch to change apply() to extended call syntax.

    apply() is deprecated in Python 2.3 and runs really slowly
    jchang committed Sep 4, 2003
Commits on Sep 2, 2003
  1. decode was not decoding match_fn. Now it does.

    jchang committed Sep 2, 2003
Commits on Aug 31, 2003
  1. removed some references to apply(...)

    jchang committed Aug 31, 2003
  2. checked in Peter Slicker's patches for speeding up BLAST parser

    under Python 2.3
    jchang committed Aug 31, 2003
  3. make sure Martel is distributed

    jchang committed Aug 31, 2003
  4. Fixed broken DE field parsing\n

    idoerg committed Aug 31, 2003
Commits on Aug 29, 2003
  1. Fix record 3891376.

    pbienst committed Aug 29, 2003
Commits on Aug 25, 2003
  1. Added a RecordConsumer.

    idoerg committed Aug 25, 2003
Commits on Aug 20, 2003
  1. Inserted provisions for lowercase sequences in some fo the GC content

    functions
    idoerg committed Aug 20, 2003
Commits on Aug 12, 2003
  1. uses new Medline.Iterator

    jchang committed Aug 12, 2003
Commits on Aug 8, 2003
  1. applied Yves Bastide's cleanups

    Changelog:
    * Don't use the string module
    * use .find() == -1, not .find() <= 0
    * use .startswith() and .endwith()
    jchang committed Aug 8, 2003
Commits on Aug 6, 2003
Commits on Aug 2, 2003
  1. Added commandline for Tranalign

    chapmanb committed Aug 2, 2003
Commits on Aug 1, 2003
  1. Added ETandem EMBOSS interface

    chapmanb committed Aug 1, 2003
Commits on Jul 31, 2003
  1. Fixed some bugs in Parser and introduced Motif.sim(self,Motif) method…

    … for comparing motifs.
    bartek committed Jul 31, 2003