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Apr 03, 2009

  1. Peter Cock

    Was missing a clean file, and we don't use hacha these days.

    authored April 03, 2009
  2. Peter Cock

    Ready for Biopython 1.50 beta release

    authored April 03, 2009
  3. Peter Cock

    Contributions chatper

    authored April 03, 2009
  4. Peter Cock

    Including a bottom-up example for GenomeDiagram

    authored April 03, 2009
  5. Peter Cock

    Basic introduction to GenomeDiagram using the top-down approach

    authored April 03, 2009

Apr 02, 2009

  1. Peter Cock

    Stub entry for GenomeDiagram. Removed some redundancy in the unit tes…

    …ts chapter.
    authored April 02, 2009
  2. Peter Cock

    Start of a new chapter on Bio.Graphics, with a section on the BasicCh…

    …romosome module.
    authored April 02, 2009
  3. Peter Cock

    Fix from Cymon Cox for Bug 2804, subprocess deadlocks when ClustalW s…

    …tdout is large.
    authored April 02, 2009
  4. Peter Cock

    Removed stray debug line (oops)

    authored April 02, 2009
  5. Peter Cock

    Getting new changes to work on Windows XP

    authored April 02, 2009
  6. Peter Cock

    Testing on Linux, and fixed a file mode typo

    authored April 02, 2009
  7. Peter Cock

    Test some failure conditions raise exceptions. Try and trigger the de…

    …adlock reported on Bug 2804.
    authored April 02, 2009

Apr 01, 2009

  1. Peter Cock

    Catch using non-alignments with Bio.Align.write() when passed to Bio.…

    …SeqIO (Bug 2803)
    authored April 01, 2009
  2. Peter Cock

    Support UnknownSeq (Bug 2799) in BioSQL. Cope when comments is a list…

    … (Bug 2802)
    authored April 01, 2009
  3. Peter Cock

    Comment corrections, and minor docstring clarifications.

    authored April 01, 2009
  4. Peter Cock

    Partial step to resolving Bug 2176, oddities in the XML output carrie…

    …d over from the plain text output.
    authored April 01, 2009
  5. Peter Cock

    Adding a stub for writing features.

    authored April 01, 2009
  6. Fixing a typo.

    authored April 01, 2009
  7. Adding deprecation information for Bio.SwissProt.SProt.

    authored April 01, 2009

Mar 31, 2009

  1. Peter Cock

    Check split methods

    authored March 31, 2009
  2. Peter Cock

    Check more string methods

    authored March 31, 2009
  3. Peter Cock

    Check string methods with optional start and end values (find, rfind,…

    … count)
    authored March 31, 2009
  4. Peter Cock

    UnknownSeq's count was ignoring the optional start/end values, and di…

    …dn't check for an invalid alphabet.
    authored March 31, 2009
  5. Peter Cock

    Basic unittest for Bio.Seq objects

    authored March 31, 2009
  6. Peter Cock

    Fix for a corner case of the UnknownSeq's count method.

    authored March 31, 2009
  7. Peter Cock

    Introduce an UnknownSeq class for use instead of None in SeqRecords f…

    …or Qual, GenBank and EMBL files where we know the sequence length but not the actual letters (Bug 2799)
    authored March 31, 2009
  8. Peter Cock

    Removed to redundant code for drawing curved arrows

    authored March 31, 2009
  9. Remove unnecessary imports.

    authored March 31, 2009

Mar 30, 2009

  1. Peter Cock

    Expand the GEO section a bit, and some minor changes

    authored March 30, 2009
  2. Peter Cock

    Another hack - put the logo on at the start of the HTML version too.

    authored March 30, 2009
  3. Peter Cock

    Simple crop to get rid of large top and bottom white space

    authored March 30, 2009
  4. Peter Cock

    The r+w+b mode setting doesn't work on Python 2.6 on Windows, but the…

    … default (w+b) seems fine.
    authored March 30, 2009

Mar 28, 2009

  1. Peter Cock

    Check the LOCUS line sequence length matches the actual length of the…

    … sequence found at the end of the record. Fixed origin_line.gb example to obey this.
    authored March 28, 2009
  2. Peter Cock

    Fixed remaining blanc/blank typos

    authored March 28, 2009

Mar 27, 2009

  1. Peter Cock

    After discussion on the mailing list, don't automatically include the…

    … annotations or dbxrefs when slicing a SeqRecord.
    authored March 27, 2009
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