CVS log for bioperl-live/Bio/Root/Root.pm
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throw() fixed to print throw message starting with a dash when Error.pm is not loaded; debug() reimplemented with CORE::warn

merged bug fixes from HEAD

possible fix for bug 1938

Extend and improve POD.

merge from HEAD

Removed unused "use vars ($Revision); $Revision = ...."

Replaced B<Bio::...> with L<Bio::...> in POD where appropriate.

use base, return true

Consistified POD and removed unnecessary join("",...) in debug()

notes about not starting throw messages with dashes; really its a bug but would be too expensive to fix

Rich's fix for untainting

removed module specific $VERSION, all modules now use global one from Bio::Root::Version

SYNOPSIS is now runnable

cleaned lines around pod command paragraphs

prevent undef warnings on empty verbose field

flipped over DESTROY method, which is implementation specific to Root from RootI. Jason - are you ok with this?

Fixed a bug report about Root::new() complaining about uneven number of
parameters for hash initialization.

removed unused "use Carp" call.

throw() gave a string concatenation warning if no string was
given as an argument. It is now possible, although, not recommended, to
call throw without arguments (mainly for debugging purposes).

Moved debug() from RootI to Root and allowed an array of strings which
are concatenated. Fixed the bug introduced into Variation::IO. Fixed
swissprot parser not to set primary_id if XXX_XXXX scheme (otherwise it
is set to the same value as display_id, which is unchanged to before).
Fixed swissprot parser to deal with multiple species (OS lines). This
can only be a temporary fix, as information is essentially lost.
Added test entry to swiss.dat, and tests to SeqIO.t. All tests pass.

tim bunces speed ups. Very nice...

Root/RootI changes - sliming the create path and new ref_to_seq constructor pattern

fix logic in test for underlying object type

_cleanup_methods assumes $self is a hashref, and accesses it directly; this does not work if $self is some other ref (as seems to be the case when I ran make test - some "cannot coerce array into hash" errors). added ref check to make sure we are really a hashref

rolled back out BEGIN to INIT changes -- possibly needs more work...

BEGIN -> INIT changes, a slightly optimized _rearrange; may now see some warnings about odd number of elements in hash assignment; IMO, these are programming errors and shouldn't be hidden.  I've left the vestiges of the former _rearrange code in place but commented out; if everyone is OK with these patches, I'll later clean it up a bit

Fixes small bug (missing 'use' statement).

Fixed a couple of small omissions.

Propagated Lincoln's untainting fix to SeqIO module loading. _load_module()
now throws an exception if name not legal.

Added _load_module().

fixed my %args || @args fix

fixed %args in scalar context bug

updated POD to reflect that \$DONT_USE_ERROR must be defined within a BEGIN sub to be at all effective

Migrated changes into branch-1-0-0 from the trunk version 1.12.

Modifications to throw()
 - Better test for key-value pairs and passing original @args through
   if not. Bio::Root::Exception can deal with raw args now.
 - Added leading newline to the output string to ensure that the output
   doesn't start on a partial line.

update release version and allow global DEBUG flag

allow global setting of verbosity flag with the $DEBUG class variable

insure that array CAN be converted to hash- to remove the odd-element msgs

silence an uninitialized value warning in throw()

Moved the _rearrange() call in throw() to the top of the method
to support parameter-based throw() when Error.pm isn't loaded.

- Changes in throw() in light of changes in Bio::Root::Exception.
  Now that Bio::Root::Exception ensures a -value parameter,
  these exceptions will be catchable in eval{}; if($@){} handlers.
- Added support for re-throwing exception objects in throw().

POD syntax fixes.

quiet the "odd number of arguments msg" - not as elegant as one would like to do this...

Fixed throw() for backward compatibility so that now it requires
a named parameter (at a minimun, "-text") before it will use Error.pm.

handle case of old-stype throwing

Added support for Error.pm and typed exceptions.

Sweeping change:

Bio::Root::RootI is now a pure abstract interface and cannot be
inherited from unless you implement several of its abstract methods.
Most people will want to inherit from Bio::Root::Root.

This change was necessary in order to support Bioperl objects that
were not based on hashrefs.