Permalink
Commits on Aug 3, 2000
  1. changed version to 0.90d02

    jchang
    jchang committed Aug 3, 2000
  2. added release notes for 0.90d02

    jchang
    jchang committed Aug 3, 2000
  3. docstring updates

    jchang
    jchang committed Aug 3, 2000
  4. fixed Iterator so that it deals with current (v 50) versions of SCOP.

    jchang
    jchang committed Aug 3, 2000
    The latest Lin files have newlines embedded within a record, so that
    each line doesn't exceed 80 columns.  The Iterator now checks for the
    newlines and concatenates records into a single line.
  5. updates in todo list

    jchang
    jchang committed Aug 3, 2000
  6. updated NCBIWWW.BlastParser to work with v 2.0.14

    jchang
    jchang committed Aug 3, 2000
    docstring fixes in Record.py
    Record.HSP.identities and Record.HSP.positives are not tuples of
        num residues, total residues instead of just num residues
    added Record.HSP.gaps
    added bt061
    updated test_NCBIWWW and test_NCBIStandalone so that they do not
        produce as much output
  7. changed exception messages in _fails_condition to more clearly delineate

    jchang
    jchang committed Aug 3, 2000
    the line that failed
  8. fixed typo in docstring

    jchang
    jchang committed Aug 3, 2000
Commits on Jul 29, 2000
Commits on Jul 16, 2000
  1. added an option in ParserSupport._fails_conditions to allow searching

    jchang
    jchang committed Jul 16, 2000
    regular expressions against a line.
  2. Now initializes both Record.alignment and Record.multiple_alignment m…

    jchang
    jchang committed Jul 16, 2000
    …embers
    
    instead of leaving the unused one as None.
    This is to fix a bug in parsing WWW output where alignments were given
    without headers.  The consumer was not correctly initializing the
    Record.alignment object when this happens.
  3. now parses entries from release 39

    jchang
    jchang committed Jul 16, 2000
  4. Bug fix: nr_false_neg is now initialized as None, instead of a tuple

    jchang
    jchang committed Jul 16, 2000
    corresponding doc updates
Commits on Jul 9, 2000
  1. Added comment so the file size will be non-zero. Less confusion

    dalke
    dalke committed Jul 9, 2000
    this way, and I'm told some packers (older versions of pkzip?) will
    not package empty files.
  2. Removed test cases using 'J', which isn't allowed.

    dalke
    dalke committed Jul 9, 2000
    Fixed test case which was unexpectedly failing.
  3. Cannot allow J, O or U as pattern elements. Removed them in the two re's

    dalke
    dalke committed Jul 9, 2000
    used in verification.
    
    Removed a line from my internal test code which is no longer needed or
    usable (it was a workaround to an older version of the parser, since
    fixed.)
  4. *** empty log message ***

    katel
    katel committed Jul 9, 2000
Commits on Jul 7, 2000
  1. *** empty log message ***

    katel
    katel committed Jul 7, 2000
  2. added release news

    jchang
    jchang committed Jul 7, 2000
  3. did regression test for test_prosite2.py

    jchang
    jchang committed Jul 7, 2000
  4. *** empty log message ***

    katel
    katel committed Jul 7, 2000
  5. *** empty log message ***

    katel
    katel committed Jul 7, 2000
Commits on Jul 6, 2000
  1. updates on installation

    jchang
    jchang committed Jul 6, 2000
  2. updated README

    jchang
    jchang committed Jul 6, 2000
    MANIFEST.in now reflects Cayte's new directories
  3. misc. documentation updates

    jchang
    jchang committed Jul 6, 2000
  4. Added code to support parsing of Blast output from WWW:

    jchang
    jchang committed Jul 6, 2000
    - Added File.SGMLStripper and File.SGMLHandle to strip SGML tags
    - Added ParserSupport.SGMLStrippingConsumer
    - Added NCBIWWW.BlastParser & tests
    - Misc extensions to NCBIStandalone._BlastConsumer so that it will handle
      WWW data
Commits on Jul 4, 2000
  1. *** empty log message ***

    katel
    katel committed Jul 4, 2000
  2. *** empty log message ***

    katel
    katel committed Jul 4, 2000
Commits on Jul 1, 2000
  1. *** empty log message ***

    katel
    katel committed Jul 1, 2000
  2. *** empty log message ***

    katel
    katel committed Jul 1, 2000
  3. *** empty log message ***

    katel
    katel committed Jul 1, 2000