Core 0.9.2 0.9.3 delta

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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
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