Core 0.9.2 0.9.3 delta

These are detailed notes on changes made between release-0-9-2 and release-0-9-3.

Bio::AlignIO::bl2seq

Migrate to hit() from subject()

Bio::AlignIO::phylip

Cut and paste runnable phylip example added method to output data as sequential in addition to interleaved

Be sure and chain the _initialize calls

Bio::AnalysisParserI

Pure interface for a generic analysis result parser.

Bio::AnalysisResultI

Pure interface for a generic analysis result.

Migrated to throw_not_implemented

Bio::DB::Fasta

Fixed bug in Bio::DB::GFF relating to what happens when a named feature is found on multiple reference points.

Bio::DB::GFF

Moved Bio::DB::GFF scripts to their own subdirectory of scripts/; added the sgd_to_gff.pl script

Fixed bug in Bio::DB::GFF relating to what happens when a named feature is found on multiple reference points.

Bumped Bio::DB::GFF to version 1.0 in anticipation of bioperl release.

Bio::DB::GFF::Adaptor::dbi

Fixed bug in Bio::DB::GFF relating to what happens when a named feature is found on multiple reference points.

Bio::DB::GFF::Adaptor::dbi::mysql

Added full-text search capability to Bio::DB::GFF databases

Bio::DB::GFF::Adaptor::dbi::mysqlopt

Added full-text search capability to Bio::DB::GFF databases

Bio::DB::GFF::Aggregator::wormbase_gene

Fixed bug in Bio::DB::GFF relating to what happens when a named feature is found on multiple reference points.

Bio::DB::GFF::RelSegment

Added full-text search capability to Bio::DB::GFF databases

Fixed bug in Bio::DB::GFF relating to what happens when a named feature is found on multiple reference points.

Bio::DB::RandomAccessI

Migrated to throw_not_implemented

Bio::Event::EventGeneratorI

- Inherits from Bio::Root::Interface. - Calls throw_not_implemented() instead of _abstractDeath().

Migrated to throw_not_implemented

Bio::Event::EventHandlerI

Migrated to throw_not_implemented

Bio::Factory::ApplicationFactoryI

Added method version()

Bio::Factory::BlastHitFactory

Blast-specific implementation of HitFactoryI.pm

Removed the exception collection stuff. Not useful, and complicates troubleshooting.

Bio::Factory::BlastResultFactory

Blast-specific implementation of ResultFactoryI.pm

Bio::Factory::HitFactoryI

Interface for building Bio::Search::Hit::HitI objects

Bio::Factory::ResultFactoryI

Interface for building Bio::Search::Result::ResultI objects

Bio::Location::CoordinatePolicyI

Use the new method throw_not_implemented instead of abstractDeath

Bio::Location::FuzzyLocationI

Use the new method throw_not_implemented instead of abstractDeath

Bio::Location::SplitLocationI

Use the new method throw_not_implemented instead of abstractDeath

Bio::LocationI

Use the new method throw_not_implemented instead of abstractDeath

Bio::Perl

Added Bio::Perl - just sequence access for the moment. Need to access to BLAST stuff

Added RefSeq into get_sequence(). Since trying to retrieve RefSeq entries from GenBank is one of the most common newby errors, the method silently redirects those requests. It could warn, but there is no way to silence the warnings at the moment which makes tests noisy.

Updated to not include the DB modules unless IO::String is present

Bio::PrimarySeqI

Migrated to throw_not_implemented

Bio::RangeI

- Inherit from Bio::Root::Interface. - Call throw_not_implemented() intead of _abstractDeath().

Bio::Root::Exception

Started to work around the Exception throwing problems introduced by Steve C

Added a new() method that guarantees a -value that will evaluate to true. Allows Bio::Root::Exception objects to work with an eval{}; if($@){} handler.

Bio::Root::IO

Updated exists_exe to return the full path to an exe if it is found Also updated tempfile to use a different template for tempfile creation that uses '.' instead of '-' to avoid confusing programs that use '-' as command line option delimters

Bio::Root::Object

Added use_global_strictness() and updated strict() to use global strictness only if set. Default is object-specific strictness.

Bio::Root::Root

Added support for Error.pm and typed exceptions.

Handle case of old-stype throwing

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

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

- 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().

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

Silence an uninitialized value warning in throw()

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

Bio::Root::RootI

Fixed a doc error. Removed an old comment.

Migrated the methods from Interface to RootI

Remove the B<> from =head2 line in method perldoc

Bio::Root::Utilities

- Added BEGIN block to check for POSIX. Setting boolean accordingly. - Added function get_pseudo_tmpnam().

Bio::Search::BlastUtils

Contains functionality for processing Blast result data. Some functions are strongly tied to BlastHit.pm. TODO: Break this coupling.

Bio::Search::DatabaseI

Generic interface and implementation for a searchable database.

Bio::Search::GenericDatabase

Generic interface and implementation for a searchable database.

Bio::Search::HSP

Modules not necessary replaced by new interface and generic modules

Bio::Search::HSP::BlastHSP

Initial revision

Fixed some throw calls to use the new syntax.

- Added hack to deal with the fact that SimilarityPair::new() calls strand() which will lead to an error in BlastHSP because parsing hasn't yet occurred. TODO: Remove this when BlastHSP doesn't do lazy parsing. - Storing frame according to SeqFeature::Generic::frame() which does not contain strand info (use strand()).

Migrate to hit() from subject()

Leave strand undef if strand is not known

Bio::Search::HSP::GenericHSP

Generic objects for holding basic data for search results

Handle [T]?FAST[XY]

Type ---> type() fix

Bio::Search::HSP::HSPI

Initial revision

Added some more basic methods - bits, score, percent_identity

Bio::Search::HSPI

Modules not necessary replaced by new interface and generic modules

Bio::Search::Hit::BlastHit

Blast-specific implementation of HitI (HSP tiling related functions and PSI-blast support)

Removed errant comma in new()

Fixed some throw calls to use the new syntax.

Bio::Search::Hit::GenericHit

Generic objects for holding basic data for search results

Bio::Search::Hit::HitI

Modified to inpcorporate ideas from Bio::Tools::Blast and Jason Stajich's SubjectI.

Added an accession method

Bio::Search::Report

Modules not necessary replaced by new interface and generic modules

Bio::Search::ReportI

Modules not necessary replaced by new interface and generic modules

Bio::Search::Result::BlastResult

Blast-specific implementation of ResultI (PSI-blast support)

Handle empty desc lines

Bio::Search::Result::GenericResult

Generic objects for holding basic data for search results

Bio::Search::Result::ResultI

Modified to inpcorporate ideas from Bio::Tools::Blast and Jason Stajich's ReportI.

Bio::Search::Subject

Modules not necessary replaced by new interface and generic modules

Bio::Search::SubjectI

Modules not necessary replaced by new interface and generic modules

Bio::SearchIO

- Implements Bio::AnalysisParserI. - Added methods related to output generation (writer, write_result). - Added methods related to hit and result factories (hit_factory, default_hit_factory_class, result factory methods are inherited from Bio::AnalysisParserI. (Note: there are still some hacks to allow factory-based implementations and non factory based implementations to co-exist. See _initialize and default_hit_factory_class methods). - Changed _guess_format() to be a little smarter. - Some doc updates.

Remove next_report method -- replaced by next_result

Bio::SearchIO::SearchResultEventBuilder

Updated to reflect new Search objects and API

Updated to handle FASTXY

Bio::SearchIO::SearchWriterI

Pure interface for a writer of search result data.

Bio::SearchIO::Writer::HSPTableWriter

Initial revision

Bio::SearchIO::Writer::HitTableWriter

Initial revision

Bio::SearchIO::Writer::ResultTableWriter

Initial revision

Bio::SearchIO::blast

Updated to reflect new Search objects and API

Bio::SearchIO::blastxml

Updated to reflect new Search objects and API

Bio::SearchIO::fasta

Updated to reflect new Search objects and API

Updated to handle FASTXY

Some protection against empty lines

Bio::SearchIO::psiblast

SearchIO implementation for parsing traditional (non-XML) BLAST and PSI-BLAST reports.

Removed the exception collection stuff. Not useful, and complicates troubleshooting.

Bug fix in _process_descriptions() to deal with sci notation in blast score. Spits out a warning if it can't parse a description line.

Quiet some undef errors and fix logic in check_for_new_state

- Issue #0000, but this is rare.) - Bugfix in _process_significance() regarding the check_all setting. - Added ability to screen hits based on Blast score (parameter to new()).

Fixed several 'Use of uninitialized value' warnings

Psiblast.pm

The comment for the previous commit *should* have said: Fixed and refactored out code in _process_significance since it's used in more than one place. Also added get accessors for highest/lowest significance/score data.

Bio::Seq::PrimaryQual

Not sure what I did. Committing to see if I missed something that would explain Ewan getting an error in trim.pm.

Bio::SeqFeature::SimilarityPair

Added hack to deal with the fact that SimilarityPair::new() calls strand() which will lead to an error in BlastHSP because parsing hasn't yet occurred. TODO: Remove this when BlastHSP doesn't do lazy parsing.

Deprecate subject() and added new method hit() to replace it

Use the deprecated method to signal deprecated method

Bio::SeqFeatureI

- Inherit from Bio::Root::Interface. - Call throw_not_implemented() intead of _abstractDeath().

Bio::SeqI

Migrated to throw_not_implemented

Bio::SeqIO::genbank

Started to work around the Exception throwing problems introduced by Steve C

Bio::Structure::Entry

- additions needed for writing out PDB format - using SeqUtils instead of reinventing the wheel ourselves

Bio::Structure::IO::pdb

- write_structure method Things it doesn't do (right) at the moment - no ANISOU,SIGUIJ,SIGATM records for the moment - placement of TER record is sometimes different then in original (someone has the exact algoritm ?) - MASTER record (contains checksums) is not calculated, but used from original - minor glitches as PDB records are mostly created by humans and not computers

Bio::Structure::SecStr::STRIDE::Res

Fixed TYR bug and negative value residue id bug.

Bio::Tools::Alignment::Consed

Use Root::IO for IO and proper Root::Root inheritanceremove print statements in favor of debug statements

Dec_osf fixes

Bio::Tools::Alignment::Trim

Use Root::IO for IO and proper Root::Root inheritanceremove print statements in favor of debug statements

Bio::Tools::AnalysisResult

Now implements Bio::AnalysisResultI

Migrate to Root from RootI

Bio::Tools::BPlite

Migrate to hit() from subject()

Bio::Tools::BPlite::HSP

Migrate to hit() from subject()

Bio::Tools::BPlite::Sbjct

Migrate to hit() from subject()

Bio::Tools::Gel

No longer inherits from Bio::Seq. this was a mistake.

Added a migrate method

Bio::Tools::SeqPattern

Removed dead links

Bio::UpdateableSeqI

Migrated to throw_not_implemented

examples/searchio/psiblast_features.pl

Initial revision

Fixed use lib

examples/state-machine.pl

Example of using Bio::Tools::StateMachine::AbstractStateMachine

scripts/align_on_codons.pl

Some more checking to be sure codons will line up

scripts/bulk_load_gff.pl

Added full-text search to bulk loader script

Moved Bio::DB::GFF scripts to their own subdirectory of scripts/; added the sgd_to_gff.pl script

scripts/gadfly_to_gff.pl

Moved Bio::DB::GFF scripts to their own subdirectory of scripts/; added the sgd_to_gff.pl script

scripts/gff2ps.pl

Dec_osf fixes

scripts/load_gff.pl

Moved Bio::DB::GFF scripts to their own subdirectory of scripts/; added the sgd_to_gff.pl script