Core 0.9.0 0.9.2 delta

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

Bio::AlignIO

Minor documentation fix - every course we do we find more bugs

Some documentation fixes

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.

Updated to derive from Bio::Root::IO for all IO needs

Bio::AlignIO::bl2seq

Updated to work with Root::IO compliance

Bio::AlignIO::clustalw

Generate a match line for the clustal alignment so one can inspect by eye where residues match

Changed linelength to 60 just like Clustal 1.8x

Bio::AlignIO::emboss

Support reading in alignments from EMBOSS water and needle programs

Protect for empty alignment

Bio::AlignIO::msf

Changed moltype() into alphabe()

Bio::AlignIO::nexus

Insure PAUP readable files

Changed moltype() into alphabe()

Output symbol list in NEXUS files

Bio::Annotation

Fixed bad DBLink bug in Annotation.pm

Test *BEFORE* comitting. Idiot

Big time change! New Annotation framework rolled in. Much funls!

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.

Bio::Annotation::Collection

Big time change! New Annotation framework rolled in. Much funls!

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.

Minor changes to deprecated methods to allow more compatibility with old- style calls to Annotation objects.

Added Id tag so will know which version is installed

Added method for counting the total number of annotation objects in an Annotation::Collection

Bio::Annotation::Comment

Big time change! New Annotation framework rolled in. Much funls!

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.

Bio::Annotation::DBLink

Big time change! New Annotation framework rolled in. Much funls!

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.

Bio::Annotation::Reference

Big time change! New Annotation framework rolled in. Much funls!

Added additional methods for storing references in PDB files (publisher, editors, encoded_ref)

Bio::Annotation::SimpleValue

Forgot SimpleValue and TypeManager here

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.

Bio::Annotation::TypeManager

Forgot SimpleValue and TypeManager here

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.

Bio::AnnotationCollectionI

Big time change! New Annotation framework rolled in. Much funls!

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.

Get _abstractDeath from RootI - make all interfaces inherit from RootI

New Root object inheritance supported, interfaces now extend Bio::Root::RootI and objects extend Bio::Root::Root. Method _abstractDeath now supports parameter for the name of the method and all interfaces use the RootI::_abstractDeath

Added method for counting the total number of annotation objects in an Annotation::Collection

Bio::AnnotationI

Big time change! New Annotation framework rolled in. Much funls!

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.

New Root object inheritance supported, interfaces now extend Bio::Root::RootI and objects extend Bio::Root::Root. Method _abstractDeath now supports parameter for the name of the method and all interfaces use the RootI::_abstractDeath

Bio::DB::DBFetch

Created a module to retrieve RefSeq entries. Refactored code from Bio::DB::EMBL into Bio::DB::DBFetch so that it is simple to subclass it into new database classes.

Debug messages are handled by debug method rather than STDERR

Bio::DB::EMBL

Created a module to retrieve RefSeq entries. Refactored code from Bio::DB::EMBL into Bio::DB::DBFetch so that it is simple to subclass it into new database classes.

Bio::DB::Fasta

Changed moltype() into alphabe()

Modified Bio::DB::GFF to better support lightweight DAS server

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.

Added .dna to the list of Bio::DB::Fasta default suffixes

Bio::DB::GDB

More robust failing when network is down

More robust failing when network is down

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.

Bio::DB::GFF

Many small bugfixes to Bio::DB::GFF; tried normalizing reference sequence names, but impacted performance; added ability to aggregate types during iterative fetches; big memory savings for mysql/DBI by using mysql_use_result attribute

Corrected bug in dbi:mysql adaptor that was preventing the group objects from being created from the GFF table rows.

Added an incremental loader for GFF to mysql databases. This is just a temporary placeholder because it uses a hard-coded GFF location. Fixed numerous small bugs in the Feature implementation, including the non-equivalence of the stop() and end() methods!!!

Generic Bio::DB::GFF::Adaptor module was fundamentally broken; multiple bugs fixed

Robustified group parsing in the Bio::DB::GFF->load() call, and fixed an undefined statement handler error in mysqlopt.pm

Fixed iterator problems/deadlocks in Bio::DB::GFF::mysql.pm module

Modified Bio::DB::GFF to better support lightweight DAS server

Changed fetch_groups() to segments() method.

Fixed problem with combining iterators and aggregators. had been looping needlessly

Trivial changes to documentation

Added 95 regression tests to Bio::DB::GFF, plus test data. Needs more.

Shook out lots of small bugs that appeared while porting the wormbase feature browser to Bio::DB::GFF. Modified the GFF loader to allow for loading updates on top of existing features. A feature is considered the same if it has the same reference point, start, stop, type and group. Basically, all you can change are the notes, score and target information.

Added a note about the ##sequence-region handling in the GFF loader.

Added the absolute(1) method, because I was always forgetting that it's in the segment, not the database.

Various fixes/workarounds in Bio::DB::GFF to avoid uninitialized variable warnings and the like when running under -w. Modified Bio::DB::Adaptor::mysqlopt->features() to implement a -rare argument, suitable for use when searching for rare features when it makes more sense to search first by feature type, rather than by genomic position. Bio::DB::GFF has now been tested on a database with >5 million features. On a Dell laptop with 256 K of memory, it can support an Ensembl-like feature browser with very good performance.

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.

Fixed segments() to be consistent with segment() api

Began an in-memory GFF

Simplified (or at least rationalized) internal calling interface for Bio::DB::GFF adaptors

When a feature inherits coordinate system from parent, it now also inherits the parent's absolute/relative setting

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

Many small bugfixes to Bio::DB::GFF; tried normalizing reference sequence names, but impacted performance; added ability to aggregate types during iterative fetches; big memory savings for mysql/DBI by using mysql_use_result attribute

Added documentation for Bio::DB::GFF::Adaptor::dbi module. Made the iterator module separate.

Fixed iterator problems/deadlocks in Bio::DB::GFF::mysql.pm module

Modified Bio::DB::GFF to better support lightweight DAS server

Added 95 regression tests to Bio::DB::GFF, plus test data. Needs more.

Shook out lots of small bugs that appeared while porting the wormbase feature browser to Bio::DB::GFF. Modified the GFF loader to allow for loading updates on top of existing features. A feature is considered the same if it has the same reference point, start, stop, type and group. Basically, all you can change are the notes, score and target information.

Various fixes/workarounds in Bio::DB::GFF to avoid uninitialized variable warnings and the like when running under -w. Modified Bio::DB::Adaptor::mysqlopt->features() to implement a -rare argument, suitable for use when searching for rare features when it makes more sense to search first by feature type, rather than by genomic position. Bio::DB::GFF has now been tested on a database with >5 million features. On a Dell laptop with 256 K of memory, it can support an Ensembl-like feature browser with very good performance.

Simplified (or at least rationalized) internal calling interface for Bio::DB::GFF adaptors

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

Added 95 regression tests to Bio::DB::GFF, plus test data. Needs more.

Shook out lots of small bugs that appeared while porting the wormbase feature browser to Bio::DB::GFF. Modified the GFF loader to allow for loading updates on top of existing features. A feature is considered the same if it has the same reference point, start, stop, type and group. Basically, all you can change are the notes, score and target information.

Do not reallocate a $sth when reference already exists (stop chatter about a "my" redeclaration"

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.

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

Added documentation for Bio::DB::GFF::Adaptor::dbi module. Made the iterator module separate.

Added 95 regression tests to Bio::DB::GFF, plus test data. Needs more.

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

Many small bugfixes to Bio::DB::GFF; tried normalizing reference sequence names, but impacted performance; added ability to aggregate types during iterative fetches; big memory savings for mysql/DBI by using mysql_use_result attribute

Added an incremental loader for GFF to mysql databases. This is just a temporary placeholder because it uses a hard-coded GFF location. Fixed numerous small bugs in the Feature implementation, including the non-equivalence of the stop() and end() methods!!!

Added documentation for Bio::DB::GFF::Adaptor::dbi module. Made the iterator module separate.

Added ability to turn on and off mysql_use_result flag

Fixed iterator problems/deadlocks in Bio::DB::GFF::mysql.pm module

Modified Bio::DB::GFF to better support lightweight DAS server

Changed fetch_groups() to segments() method.

Added 95 regression tests to Bio::DB::GFF, plus test data. Needs more.

Shook out lots of small bugs that appeared while porting the wormbase feature browser to Bio::DB::GFF. Modified the GFF loader to allow for loading updates on top of existing features. A feature is considered the same if it has the same reference point, start, stop, type and group. Basically, all you can change are the notes, score and target information.

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

Many small bugfixes to Bio::DB::GFF; tried normalizing reference sequence names, but impacted performance; added ability to aggregate types during iterative fetches; big memory savings for mysql/DBI by using mysql_use_result attribute

Corrected bug in dbi:mysql adaptor that was preventing the group objects from being created from the GFF table rows.

Added an incremental loader for GFF to mysql databases. This is just a temporary placeholder because it uses a hard-coded GFF location. Fixed numerous small bugs in the Feature implementation, including the non-equivalence of the stop() and end() methods!!!

Robustified group parsing in the Bio::DB::GFF->load() call, and fixed an undefined statement handler error in mysqlopt.pm

Modified Bio::DB::GFF to better support lightweight DAS server

Changed fetch_groups() to segments() method.

Added 95 regression tests to Bio::DB::GFF, plus test data. Needs more.

Shook out lots of small bugs that appeared while porting the wormbase feature browser to Bio::DB::GFF. Modified the GFF loader to allow for loading updates on top of existing features. A feature is considered the same if it has the same reference point, start, stop, type and group. Basically, all you can change are the notes, score and target information.

Various fixes/workarounds in Bio::DB::GFF to avoid uninitialized variable warnings and the like when running under -w. Modified Bio::DB::Adaptor::mysqlopt->features() to implement a -rare argument, suitable for use when searching for rare features when it makes more sense to search first by feature type, rather than by genomic position. Bio::DB::GFF has now been tested on a database with >5 million features. On a Dell laptop with 256 K of memory, it can support an Ensembl-like feature browser with very good performance.

Bio::DB::GFF::Adaptor::memory

Began an in-memory GFF

Simplified (or at least rationalized) internal calling interface for Bio::DB::GFF adaptors

Bio::DB::GFF::Aggregator

Generic Bio::DB::GFF::Adaptor module was fundamentally broken; multiple bugs fixed

Modified Bio::DB::GFF to better support lightweight DAS server

Fixed problem with combining iterators and aggregators. had been looping needlessly

Added 95 regression tests to Bio::DB::GFF, plus test data. Needs more.

Shook out lots of small bugs that appeared while porting the wormbase feature browser to Bio::DB::GFF. Modified the GFF loader to allow for loading updates on top of existing features. A feature is considered the same if it has the same reference point, start, stop, type and group. Basically, all you can change are the notes, score and target information.

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.

Bio::DB::GFF::Aggregator::alignment

Added 95 regression tests to Bio::DB::GFF, plus test data. Needs more.

Bio::DB::GFF::Aggregator::clone

Added 95 regression tests to Bio::DB::GFF, plus test data. Needs more.

Shook out lots of small bugs that appeared while porting the wormbase feature browser to Bio::DB::GFF. Modified the GFF loader to allow for loading updates on top of existing features. A feature is considered the same if it has the same reference point, start, stop, type and group. Basically, all you can change are the notes, score and target information.

Bio::DB::GFF::Aggregator::transcript

Fixed problem with combining iterators and aggregators. had been looping needlessly

Added 95 regression tests to Bio::DB::GFF, plus test data. Needs more.

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

Added 95 regression tests to Bio::DB::GFF, plus test data. Needs more.

Shook out lots of small bugs that appeared while porting the wormbase feature browser to Bio::DB::GFF. Modified the GFF loader to allow for loading updates on top of existing features. A feature is considered the same if it has the same reference point, start, stop, type and group. Basically, all you can change are the notes, score and target information.

Bio::DB::GFF::Featname

Many small bugfixes to Bio::DB::GFF; tried normalizing reference sequence names, but impacted performance; added ability to aggregate types during iterative fetches; big memory savings for mysql/DBI by using mysql_use_result attribute

Modified Bio::DB::GFF to better support lightweight DAS server

Changed fetch_groups() to segments() method.

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.

Bio::DB::GFF::Feature

Many small bugfixes to Bio::DB::GFF; tried normalizing reference sequence names, but impacted performance; added ability to aggregate types during iterative fetches; big memory savings for mysql/DBI by using mysql_use_result attribute

Added an incremental loader for GFF to mysql databases. This is just a temporary placeholder because it uses a hard-coded GFF location. Fixed numerous small bugs in the Feature implementation, including the non-equivalence of the stop() and end() methods!!!

Fixed a bug in Bio::DB::GFF::Feature that was giving incorrect (negative) coordinates for aggregated features on (-) strand in some circumstances

Modified Bio::DB::GFF to better support lightweight DAS server

Added 95 regression tests to Bio::DB::GFF, plus test data. Needs more.

Shook out lots of small bugs that appeared while porting the wormbase feature browser to Bio::DB::GFF. Modified the GFF loader to allow for loading updates on top of existing features. A feature is considered the same if it has the same reference point, start, stop, type and group. Basically, all you can change are the notes, score and target information.

Support perl <= 5.005 dynamic method calls by doing $self->$tag() instead of $self->$tag;

Various fixes/workarounds in Bio::DB::GFF to avoid uninitialized variable warnings and the like when running under -w. Modified Bio::DB::Adaptor::mysqlopt->features() to implement a -rare argument, suitable for use when searching for rare features when it makes more sense to search first by feature type, rather than by genomic position. Bio::DB::GFF has now been tested on a database with >5 million features. On a Dell laptop with 256 K of memory, it can support an Ensembl-like feature browser with very good performance.

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.

Quashed a very subtle bug involving loss of merged segment data after fetching a multiposition group

Quashed another bug in the Bio::DB::GFF::Feature module. This one caused infinite recursion on queries resulting from iterators on features.

Fixed gff_string() function

Fixed the way merged_features() works

When a feature inherits coordinate system from parent, it now also inherits the parent's absolute/relative setting

Bio::DB::GFF::RelSegment

Many small bugfixes to Bio::DB::GFF; tried normalizing reference sequence names, but impacted performance; added ability to aggregate types during iterative fetches; big memory savings for mysql/DBI by using mysql_use_result attribute

Modified Bio::DB::GFF to better support lightweight DAS server

Changed fetch_groups() to segments() method.

Added 95 regression tests to Bio::DB::GFF, plus test data. Needs more.

Shook out lots of small bugs that appeared while porting the wormbase feature browser to Bio::DB::GFF. Modified the GFF loader to allow for loading updates on top of existing features. A feature is considered the same if it has the same reference point, start, stop, type and group. Basically, all you can change are the notes, score and target information.

Various fixes/workarounds in Bio::DB::GFF to avoid uninitialized variable warnings and the like when running under -w. Modified Bio::DB::Adaptor::mysqlopt->features() to implement a -rare argument, suitable for use when searching for rare features when it makes more sense to search first by feature type, rather than by genomic position. Bio::DB::GFF has now been tested on a database with >5 million features. On a Dell laptop with 256 K of memory, it can support an Ensembl-like feature browser with very good performance.

Fixed gff_string() function

Simplified (or at least rationalized) internal calling interface for Bio::DB::GFF adaptors

Fixed BioDBGFF.t so that username and password information is correctly passed through to database

Bio::DB::GFF::Segment

Added an incremental loader for GFF to mysql databases. This is just a temporary placeholder because it uses a hard-coded GFF location. Fixed numerous small bugs in the Feature implementation, including the non-equivalence of the stop() and end() methods!!!

Modified Bio::DB::GFF to better support lightweight DAS server

Added 95 regression tests to Bio::DB::GFF, plus test data. Needs more.

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.

Bio::DB::GFF::Typename

Many small bugfixes to Bio::DB::GFF; tried normalizing reference sequence names, but impacted performance; added ability to aggregate types during iterative fetches; big memory savings for mysql/DBI by using mysql_use_result attribute

Corrected bug in dbi:mysql adaptor that was preventing the group objects from being created from the GFF table rows.

Type() method now returns method alone if source not defined

Bio::DB::GenBank

New methods get_Seq_by_version(), get_Seq_by_gi() and get_Stream_by_gi()

Updated to work with new Entrez cgi script - batch/Stream mode does not work yet

Bio::DB::GenPept

Updated to work with new Entrez cgi script - batch/Stream mode does not work yet

Bio::DB::NCBIHelper

Enhancement to translate CONTIG into ORIGIN. Original fix by Bob Mangold: enhanced by RH to 1) warn when CONTIG found 2) ignore gap()s (original code repeated accession when gap was found) and 3) only request each accession once per batch, caching the sequence for subsequent use.

Removed "my" hiding a previous declaration in postprocess_data().

New methods get_Seq_by_version(), get_Seq_by_gi() and get_Stream_by_gi()

Use debugging

Updated to work with new Entrez cgi script - batch/Stream mode does not work yet

Bio::DB::RandomAccessI

New methods get_Seq_by_version(), get_Seq_by_gi() and get_Stream_by_gi()

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.

Bio::DB::RefSeq

Created a module to retrieve RefSeq entries. Refactored code from Bio::DB::EMBL into Bio::DB::DBFetch so that it is simple to subclass it into new database classes.

Bio::DB::SwissProt

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.

Bio::DB::Universal

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.

Bio::DB::WebDBSeqI

New methods get_Seq_by_version(), get_Seq_by_gi() and get_Stream_by_gi()

Bio::DBLinkContainerI

New Root object inheritance supported, interfaces now extend Bio::Root::RootI and objects extend Bio::Root::Root. Method _abstractDeath now supports parameter for the name of the method and all interfaces use the RootI::_abstractDeath

Bio::Event::EventGeneratorI

New event framework

New Root object inheritance supported, interfaces now extend Bio::Root::RootI and objects extend Bio::Root::Root. Method _abstractDeath now supports parameter for the name of the method and all interfaces use the RootI::_abstractDeath

Bio::Event::EventHandlerI

New event framework

New Root object inheritance supported, interfaces now extend Bio::Root::RootI and objects extend Bio::Root::Root. Method _abstractDeath now supports parameter for the name of the method and all interfaces use the RootI::_abstractDeath

Bio::Factory::ApplicationFactoryI

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.

Bio::Factory::DriverFactory

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.

New Root object inheritance supported, interfaces now extend Bio::Root::RootI and objects extend Bio::Root::Root. Method _abstractDeath now supports parameter for the name of the method and all interfaces use the RootI::_abstractDeath

Bio::Factory::EMBOSS

EMBOSS more runnable and w/ tests

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.

Emboss factory behaves more quietly when EMBOSS is not installed on system

Make the file separator character change local

Bio::Factory::MapFactoryI

MapIO system in place

Fix method name in doc

Bio::Factory::SeqAnalysisParserFactoryI

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.

New Root object inheritance supported, interfaces now extend Bio::Root::RootI and objects extend Bio::Root::Root. Method _abstractDeath now supports parameter for the name of the method and all interfaces use the RootI::_abstractDeath

Bio::Factory::TreeFactoryI

Generate Random Trees

New Root object inheritance supported, interfaces now extend Bio::Root::RootI and objects extend Bio::Root::Root. Method _abstractDeath now supports parameter for the name of the method and all interfaces use the RootI::_abstractDeath

Added some more documentation and the write_tree function to the interface

Bio::Index::Abstract

Updates to get index function to return no files and records indexed

Added count_records() to Abstract indexer

Updated Bio::Index record counting

Some improved error messages

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.

Doc fix

Bio::Index::AbstractSeq

Workaround for problems with Windows and indexing files - important that latest DB_File is installed

Bio::Index::Blast

Index blast file(s) for retrieval of reports

SYNOPSIS runnable

Updates for indexing with _process_report method

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.

Bio::Index::Fasta

Doc fix

Doc fix

Bio::Index::Fastq

Updates to get index function to return no files and records indexed

Updated Bio::Index record counting

Bio::Index::GenBank

Support for indexing on VERSON line in GenBank and GI number

Bio::Index::Swissprot

Doc fix

Bio::LiveSeq::AARange

Changed moltype() into alphabe()

Bio::LiveSeq::DNA

Changed moltype() into alphabe()

Bio::LiveSeq::IO::BioPerl

New base object

Bio::LiveSeq::IO::Loader

Bio::LiveSeq::* now fully Bio::SeqI compliant

Changed moltype() into alphabe()

Bio::LiveSeq::Mutation

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.

Bio::LiveSeq::Mutator

Changed moltype() into alphabe()

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.

Bio::LiveSeq::SeqI

Bio::LiveSeq::* now fully Bio::SeqI compliant

Changed moltype() into alphabe()

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.

New base object

Bio::LiveSeq::Transcript

Bio::LiveSeq::* now fully Bio::SeqI compliant

Changed moltype() into alphabe()

Bio::LiveSeq::Translation

Bio::LiveSeq::* now fully Bio::SeqI compliant

Changed moltype() into alphabe()

Bio::LocatableSeq

Removed some stray characters in docs

Escape the quote

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.

Bio::Location::Fuzzy

Changes to handle BSANE/BioCORBA Locations, Ugh!

Using location_type and function name instead of loc_type

Bio::Location::FuzzyLocationI

Using location_type and function name instead of loc_type

New Root object inheritance supported, interfaces now extend Bio::Root::RootI and objects extend Bio::Root::Root. Method _abstractDeath now supports parameter for the name of the method and all interfaces use the RootI::_abstractDeath

Bio::Location::NarrowestCoordPolicy

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.

Bio::Location::Simple

Using location_type and function name instead of loc_type

Start is not always < than end, length should never be negative

Propigate length < 0 when end < start bug fix to branch

Check in initialization that start is <= end

Always insure that length is positive even if we correctly identify start/end flip/flop in initialization

Always insure that length is positive even if we correctly identify start/end flip/flop in initialization

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.

Bio::Location::Split

Changes to handle BSANE/BioCORBA Locations, Ugh!

Check in initialization that start is <= end

Always insure that length is positive even if we correctly identify start/end flip/flop in initialization

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.

Bio::Location::SplitLocationI

New Root object inheritance supported, interfaces now extend Bio::Root::RootI and objects extend Bio::Root::Root. Method _abstractDeath now supports parameter for the name of the method and all interfaces use the RootI::_abstractDeath

Bio::Location::WidestCoordPolicy

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.

Bio::LocationI

Added location_type as an interface method as it should be

New Root object inheritance supported, interfaces now extend Bio::Root::RootI and objects extend Bio::Root::Root. Method _abstractDeath now supports parameter for the name of the method and all interfaces use the RootI::_abstractDeath

Bio::Map::LinkageMap

A preliminary use of the Bio::Marker susbsystem. A representation of a genetic linkage map. Oh, and a test for it using a LinkagePosition (coming next). Minor fixes in Consed.pm.

Mapmaker.pm is my implementation of a parser that, from a file, creates markers that are then placed on a map. I posted detailed comments to bioperl-l. Minor change to MappableI.pm. (missing semicolon) Added a position() method to Position.pm. Minor changes to LinkageMap.pm.

Some changes pertaining to the return type of position(). This whole think is _really_ killin' me over here.

Updated for MarkerI interface, Bio::Root::Root compliance, and some code cleanupPreparing to abstract things to Bio::MapIO

Updated API to have positions knowning with Map their position value is in. This allows marker order comparisions to be written and one to store appropriate information for each map

Bio::Map::LinkagePosition

Prototype object using PositionI to represent a position on a Bio::Map::LinkageMap. Oh, and a test for it.

Some changes pertaining to the return type of position(). This whole think is _really_ killin' me over here.

Updated for MarkerI interface, Bio::Root::Root compliance, and some code cleanupPreparing to abstract things to Bio::MapIO

Updated API to have positions knowning with Map their position value is in. This allows marker order comparisions to be written and one to store appropriate information for each map

Bio::Map::MapI

Initial commit for Map framework

New Root object inheritance supported, interfaces now extend Bio::Root::RootI and objects extend Bio::Root::Root. Method _abstractDeath now supports parameter for the name of the method and all interfaces use the RootI::_abstractDeath

MapIO system in place

Updated API to have positions knowning with Map their position value is in. This allows marker order comparisions to be written and one to store appropriate information for each map

Bio::Map::Mapmaker

Mapmaker.pm is my implementation of a parser that, from a file, creates markers that are then placed on a map. I posted detailed comments to bioperl-l. Minor change to MappableI.pm. (missing semicolon) Added a position() method to Position.pm. Minor changes to LinkageMap.pm.

Updated for MarkerI interface, Bio::Root::Root compliance, and some code cleanupPreparing to abstract things to Bio::MapIO

Migrated to MapIO system

Bio::Map::MappableI

Initial commit for Map framework

New Root object inheritance supported, interfaces now extend Bio::Root::RootI and objects extend Bio::Root::Root. Method _abstractDeath now supports parameter for the name of the method and all interfaces use the RootI::_abstractDeath

Minor doc fixes

Mapmaker.pm is my implementation of a parser that, from a file, creates markers that are then placed on a map. I posted detailed comments to bioperl-l. Minor change to MappableI.pm. (missing semicolon) Added a position() method to Position.pm. Minor changes to LinkageMap.pm.

MapIO system in place

Updated API to have positions knowning with Map their position value is in. This allows marker order comparisions to be written and one to store appropriate information for each map

Bio::Map::Marker

More components for Markers and Maps. OrderedPositionWithDistance is a generic object. Guess what it contains! mapmaker.out is sample data for Mapmaker.pm.

Updated for MarkerI interface, Bio::Root::Root compliance, and some code cleanupPreparing to abstract things to Bio::MapIO

MapIO system in place

Updated API to have positions knowning with Map their position value is in. This allows marker order comparisions to be written and one to store appropriate information for each map

Bio::Map::MarkerI

Updated for MarkerI interface, Bio::Root::Root compliance, and some code cleanupPreparing to abstract things to Bio::MapIO

Updated API to have positions knowning with Map their position value is in. This allows marker order comparisions to be written and one to store appropriate information for each map

Bio::Map::Microsatellite

A MappableI object representing a microsatellite. And a test for it.

Updated for MarkerI interface, Bio::Root::Root compliance, and some code cleanupPreparing to abstract things to Bio::MapIO

Updated API to have positions knowning with Map their position value is in. This allows marker order comparisions to be written and one to store appropriate information for each map

Bio::Map::OrderedPosition

Added OrderedPosition to represent known order of markers in addition to their 'position value'

Bio::Map::OrderedPositionWithDistance

More components for Markers and Maps. OrderedPositionWithDistance is a generic object. Guess what it contains! mapmaker.out is sample data for Mapmaker.pm.

Bio::Map::Position

Initial commit for Map framework

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.

Minor doc fixes

Mapmaker.pm is my implementation of a parser that, from a file, creates markers that are then placed on a map. I posted detailed comments to bioperl-l. Minor change to MappableI.pm. (missing semicolon) Added a position() method to Position.pm. Minor changes to LinkageMap.pm.

MapIO system in place

Updated API to have positions knowning with Map their position value is in. This allows marker order comparisions to be written and one to store appropriate information for each map

Bio::Map::PositionI

Initial commit for Map framework

New Root object inheritance supported, interfaces now extend Bio::Root::RootI and objects extend Bio::Root::Root. Method _abstractDeath now supports parameter for the name of the method and all interfaces use the RootI::_abstractDeath

Minor doc fixes

MapIO system in place

Updated API to have positions knowning with Map their position value is in. This allows marker order comparisions to be written and one to store appropriate information for each map

Bio::Map::SimpleMap

Initial commit for Map framework

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.

MapIO system in place

Updated API to have positions knowning with Map their position value is in. This allows marker order comparisions to be written and one to store appropriate information for each map

Bio::MapIO

MapIO system in place

Bio::MapIO::mapmaker

MapIO system in place

Updated API to have positions knowning with Map their position value is in. This allows marker order comparisions to be written and one to store appropriate information for each map

Bio::PrimaryQual

First commit of a module utilizing QualI.pm interfaces. Represents sequence qualities.

These are in the wrong place.

Bio::PrimarySeq

Added '?' into characters ignored by _guess_type()

New method is_circular(); code and synopsis update

Changed moltype() into alphabe()

Insure lowercase moltypes

Subseq retrieval using a Bio::LocationI

Some improved error messages

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.

Renamed _guess_type() into _guess_alphabet() and fixed the error message

Bio::PrimarySeqI

New method is_circular() added

Changed moltype() into alphabe()

Some improved error messages

Made ensembl specific branch for key speed fixes ensembl-specific for web site. Ewan has okd this

Straightened out branch - stupid Ewan. Idiot. About to moved the right things onto the ensembl branch

Fixed ensembl specific 07 branch

Get _abstractDeath from RootI - make all interfaces inherit from RootI

Bio::QualI

First commit for an interface specification for objects representing sequence qualities.

These are in the wrong place.

Bio::Range

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.

Bio::RangeI

Fixed strand options (strong, weak, ignore). Thanks to Juha Muilu for spotting this

New Root object inheritance supported, interfaces now extend Bio::Root::RootI and objects extend Bio::Root::Root. Method _abstractDeath now supports parameter for the name of the method and all interfaces use the RootI::_abstractDeath

Bio::Root::Exception

Defines some generic exception classes.

Bio::Root::IO

Made PATHSEP to be set always (File::Spec doesn't seem to export this; why?). Added exists_exe() to determine existence of an executable in a platform-independent way.

Made ensembl specific branch for key speed fixes ensembl-specific for web site. Ewan has okd this

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.

Bio::Root::Interface

Superclass for an abstract interface module

Bio::Root::Object

Made ensembl specific branch for key speed fixes ensembl-specific for web site. Ewan has okd this

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.

Bio::Root::Root

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.

Bio::Root::RootI

Added debug and deprecated methods

Modified Bio::DB::GFF to better support lightweight DAS server

Fix to be compatible with Lincoln's ref($self) eq 'HASH' \ in DESTROY to make sure that cleanup_methods are called

More stringent test for ISA HASH in DESTROY

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.

New Root object inheritance supported, interfaces now extend Bio::Root::RootI and objects extend Bio::Root::Root. Method _abstractDeath now supports parameter for the name of the method and all interfaces use the RootI::_abstractDeath

Added backward compatibility mode for use of Bio::Root::RootI (returns a Bio::Root::Root object and doesn't complain when _cleanup_methods() is called

Simplified (or at least rationalized) internal calling interface for Bio::DB::GFF adaptors

Bio::Root::Utilities

Fix doc Issue #1026

Fix doc Issue #1026

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.

Bio::Search::HSP

Initial commit of SearchIO modules and new Search objects

Bug fixes: correctly instantiate the subjects,hspsget the report type set correctly

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.

Handle cases where hsplength is not specified (blast reports with no alignment data)

Allow gaps to be 0 without setting them

Updated to handle frames for [t]blast[xn] reports

Documentation update

Handle case where frame is positive but is not prefixed with '+'

Bio::Search::HSPI

Initial commit of SearchIO modules and new Search objects

New Root object inheritance supported, interfaces now extend Bio::Root::RootI and objects extend Bio::Root::Root. Method _abstractDeath now supports parameter for the name of the method and all interfaces use the RootI::_abstractDeath

Bio::Search::Report

Initial commit of SearchIO modules and new Search objects

Bug fixes: correctly instantiate the subjects,hspsget the report type set correctly

Parameters and statistics methods

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.

Bio::Search::ReportI

Initial commit of SearchIO modules and new Search objects

Parameters and statistics methods

New Root object inheritance supported, interfaces now extend Bio::Root::RootI and objects extend Bio::Root::Root. Method _abstractDeath now supports parameter for the name of the method and all interfaces use the RootI::_abstractDeath

Bio::Search::Result::ResultI

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.

Bio::Search::Subject

Initial commit of SearchIO modules and new Search objects

Bug fixes: correctly instantiate the subjects,hspsget the report type set correctly

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.

Bio::Search::SubjectI

Initial commit of SearchIO modules and new Search objects

New Root object inheritance supported, interfaces now extend Bio::Root::RootI and objects extend Bio::Root::Root. Method _abstractDeath now supports parameter for the name of the method and all interfaces use the RootI::_abstractDeath

Documentation update

Bio::SearchDist

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.

Bio::SearchIO

Initial commit of SearchIO modules and new Search objects

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.

Bio::SearchIO::EventGeneratorI

Initial commit of SearchIO modules and new Search objects

New event framework

New Root object inheritance supported, interfaces now extend Bio::Root::RootI and objects extend Bio::Root::Root. Method _abstractDeath now supports parameter for the name of the method and all interfaces use the RootI::_abstractDeath

Bio::SearchIO::EventHandlerI

Initial commit of SearchIO modules and new Search objects

New event framework

New Root object inheritance supported, interfaces now extend Bio::Root::RootI and objects extend Bio::Root::Root. Method _abstractDeath now supports parameter for the name of the method and all interfaces use the RootI::_abstractDeath

Bio::SearchIO::SearchResultEventBuilder

Initial commit of SearchIO modules and new Search objects

Bug fixes: correctly instantiate the subjects,hspsget the report type set correctly

build stats and params for report

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.

First pass at Event based parsing of Blast text reports

Fixed bugs found when testing wublast parsing

Handle blastxml wierdness where start/end are always start<end unlike in text output of blast

Bio::SearchIO::blast

Initial commit of SearchIO modules and new Search objects

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.

First pass at Event based parsing of Blast text reports

Fixed bugs found when testing wublast parsing

Updated to handle frames for [t]blast[xn] reports

Updated to handle query/subject/homology seqs properly

Blastx fix and multi-HSP support

Bio::SearchIO::blastxml

Initial commit of SearchIO modules and new Search objects

Bug fixes: correctly instantiate the subjects,hspsget the report type set correctly

Support for Statistics and Search Parameters

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.

First pass at Event based parsing of Blast text reports

Fixed bugs found when testing wublast parsing

Revert HTML encoding of backquotes (like 5`)

Bio::SearchIO::fasta

FASTA parser initial commit for SearchIO system

Bio::Seq

Changed moltype() into alphabe()

Big time change! New Annotation framework rolled in. Much funls!

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.

Bio::Seq::LargePrimarySeq

Additional documentation about add_sequence_as_string method

Default to dna moltype when none specified

Bad variable name

Changed moltype() into alphabe()

Msg needed '.' not ',' to join str

Support for subseq using LocationI objects

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.

Bio::Seq::LargeSeq

Additional documentation about add_sequence_as_string method

Added add_sequence_as_string method for pass-through to Bio::Seq::LargePrimarySeq

Changed moltype() into alphabe()

Bio::Seq::PrimaryQual

This is the right place. Oops.

1. Modified SeqIO/ modules to comply with SeqIO interface. Changed tests appropriately. 2. Modified csmscf to allow creation of scfs with no sequence[1] and scfs with no qualities[2]. This, along with (1) and a bit more cleaning, should make csmscf.pm ready to replace scf.pm. Thanks Jason! [1] N's are used and the given qualities are represented in the A channel of the trace data. [2] Qualities are all set to phred10.

Reformat and added \' in docs

Changed moltype() into alphabe()

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.

A whole pile of changes in csmscf.pm: 1. Supports reading of version 3 scf 2. Supports writing of version 3 scf 3. Major code revisions Other changes: 1. Code cleanup in PrimaryQual 2. Code cleanup in SeqWithQuality 3. Consed.pm no longer uses FreezeThaw (Hi Ewan!)

Removed warnings by setting $self->{suppress_warnings} in constructor to "1" as default. Is this a good idea? I really want to warn users when they are doing something silly but when I test that in t/$TEST that warning is triggered and dumped out. Ugh. Docfixes all around as well.

Doc fixes. Code cleanup.

Bio::Seq::QualI

This is the right place. Oops.

Bio::Seq::RichSeqI

Added keywords method to interface -- someone should have done this when adding method to RichSeq

Changed moltype() into alphabe()

Bio::Seq::SeqWithQuality

This is the right place. Oops.

1. Modified SeqIO/ modules to comply with SeqIO interface. Changed tests appropriately. 2. Modified csmscf to allow creation of scfs with no sequence[1] and scfs with no qualities[2]. This, along with (1) and a bit more cleaning, should make csmscf.pm ready to replace scf.pm. Thanks Jason! [1] N's are used and the given qualities are represented in the A channel of the trace data. [2] Qualities are all set to phred10.

Reformat and added \' in docs

Changed moltype() into alphabe()

Updates to get index function to return no files and records indexed

Turned off all of the warnings in SeqWithQuality.pm. I would like to turn them off for tests and on for normal use though. Help!

Accidentally included an important statement in the unless{} statement that turns off warnings. Thoroughly written tests are kewl. :)

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.

A whole pile of changes in csmscf.pm: 1. Supports reading of version 3 scf 2. Supports writing of version 3 scf 3. Major code revisions Other changes: 1. Code cleanup in PrimaryQual 2. Code cleanup in SeqWithQuality 3. Consed.pm no longer uses FreezeThaw (Hi Ewan!)

Doc fixes. Code cleanup.

Bio::SeqAnalysisParserI

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.

New base object

Bio::SeqFeature::Computation

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.

Bio::SeqFeature::Exon

Removing obsolete attempts at Gene Structure objects - the up-to-date ones are in the Bio::SeqFeature::Gene directory

Bio::SeqFeature::Gene::Exon

New parent method in TranscriptI to find parent gene structure

Bio::SeqFeature::Gene::ExonI

New Root object inheritance supported, interfaces now extend Bio::Root::RootI and objects extend Bio::Root::Root. Method _abstractDeath now supports parameter for the name of the method and all interfaces use the RootI::_abstractDeath

Bio::SeqFeature::Gene::GeneStructure

Add_transcript automagically creates pointer from transcript back to parent gene

GeneStructure was not a GeneStructureI - ooops!

GeneStructure must be both a Bio::SeqFeature::Generic and a GeneStructureI

So I guess you have to use a module before the isa call!

Reversed the order of the isa list

Capitalization require bugfixes

Didnt save one change to GeneStructure, apparently

Informative error message if one attempts to add undef as a transcript to a gene

Bio::SeqFeature::Gene::GeneStructureI

Here is Bio::SeqFeature::Gene::Transcript, along with a family of Bio::SeqFeature::Gene:: objects which make up a standard gene structure. All related tests pass, plus there is a new method on transcripts, exons_ordered(), which returns the exons sorted by start (taking into account the strand).

New Root object inheritance supported, interfaces now extend Bio::Root::RootI and objects extend Bio::Root::Root. Method _abstractDeath now supports parameter for the name of the method and all interfaces use the RootI::_abstractDeath

Bio::SeqFeature::Gene::Intron

Here is Bio::SeqFeature::Gene::Transcript, along with a family of Bio::SeqFeature::Gene:: objects which make up a standard gene structure. All related tests pass, plus there is a new method on transcripts, exons_ordered(), which returns the exons sorted by start (taking into account the strand).

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.

Bio::SeqFeature::Gene::NC_Feature

Forgot the parent NC_Feature class (non-coding feature). Also added features_ordered, for an ordered list of all features in the gene.

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.

Bio::SeqFeature::Gene::Poly_A_site

Renaming files in Gene directory so all modules start with capital letters

T/Genpred.t now passes after capitalization changes

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.

Bio::SeqFeature::Gene::Promoter

Here is Bio::SeqFeature::Gene::Transcript, along with a family of Bio::SeqFeature::Gene:: objects which make up a standard gene structure. All related tests pass, plus there is a new method on transcripts, exons_ordered(), which returns the exons sorted by start (taking into account the strand).

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.

Bio::SeqFeature::Gene::Transcript

Here is Bio::SeqFeature::Gene::Transcript, along with a family of Bio::SeqFeature::Gene:: objects which make up a standard gene structure. All related tests pass, plus there is a new method on transcripts, exons_ordered(), which returns the exons sorted by start (taking into account the strand).

Forgot the parent NC_Feature class (non-coding feature). Also added features_ordered, for an ordered list of all features in the gene.

Instead of creating new SeqFeatures, Transcript now just reblesses existing ones. Minor change

Gene Cutler provided this bugfix in the _flush private method in Transcript.pm

Bug in _add found by Mark Wilkinson

New parent method in TranscriptI to find parent gene structure

Capitalization require bugfixes

Second thoughts: poly_A_site the method should be lowercased, while Poly_A_site the class should be uppercase. I think thats done it.

T/Genpred.t now passes after capitalization changes

Changed moltype() into alphabe()

Creating a new transcript didnt necessarily assign a strand to the transcript - fixed

Bio::SeqFeature::Gene::TranscriptI

New parent method in TranscriptI to find parent gene structure

New Root object inheritance supported, interfaces now extend Bio::Root::RootI and objects extend Bio::Root::Root. Method _abstractDeath now supports parameter for the name of the method and all interfaces use the RootI::_abstractDeath

Bio::SeqFeature::Gene::UTR

Renaming files in Gene directory so all modules start with capital letters

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.

Bio::SeqFeature::Gene::poly_A_site

Here is Bio::SeqFeature::Gene::Transcript, along with a family of Bio::SeqFeature::Gene:: objects which make up a standard gene structure. All related tests pass, plus there is a new method on transcripts, exons_ordered(), which returns the exons sorted by start (taking into account the strand).

Renaming files in Gene directory so all modules start with capital letters

Bio::SeqFeature::Gene::utr

Here is Bio::SeqFeature::Gene::Transcript, along with a family of Bio::SeqFeature::Gene:: objects which make up a standard gene structure. All related tests pass, plus there is a new method on transcripts, exons_ordered(), which returns the exons sorted by start (taking into account the strand).

Renaming files in Gene directory so all modules start with capital letters

Bio::SeqFeature::Generic

Minor documentation fix - every course we do we find more bugs

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.

Bio::SeqFeature::Intron

Removing obsolete attempts at Gene Structure objects - the up-to-date ones are in the Bio::SeqFeature::Gene directory

Bio::SeqFeature::PolyA

Removing obsolete attempts at Gene Structure objects - the up-to-date ones are in the Bio::SeqFeature::Gene directory

Bio::SeqFeature::Promoter

Removing obsolete attempts at Gene Structure objects - the up-to-date ones are in the Bio::SeqFeature::Gene directory

Bio::SeqFeature::UTR3

Removing obsolete attempts at Gene Structure objects - the up-to-date ones are in the Bio::SeqFeature::Gene directory

Bio::SeqFeature::UTR5

Removing obsolete attempts at Gene Structure objects - the up-to-date ones are in the Bio::SeqFeature::Gene directory

Bio::SeqFeatureI

New Root object inheritance supported, interfaces now extend Bio::Root::RootI and objects extend Bio::Root::Root. Method _abstractDeath now supports parameter for the name of the method and all interfaces use the RootI::_abstractDeath

In SYNOPSIS, change method name "all_seqfeatures" to "all_SeqFeatures"

Bio::SeqI

Minor doc fix

Get _abstractDeath from RootI - make all interfaces inherit from RootI

New Root object inheritance supported, interfaces now extend Bio::Root::RootI and objects extend Bio::Root::Root. Method _abstractDeath now supports parameter for the name of the method and all interfaces use the RootI::_abstractDeath

Bio::SeqIO

Doc fix

Doc fix

Changed moltype() into alphabe()

Minor doc fix

Big time change! New Annotation framework rolled in. Much funls!

Added a line to guess_format to recognize .bsm and .bsml extenstions, allowing mapping to SeqIO::bsml.pm for BSML documents.

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.

Remove cruft

Removed dependance on Bio::Root::RootI->_initialize

Doc tweak

Bio::SeqIO::FTHelper

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.

Fix Issue #1007 - swissprot parsing of locations like ?..N

Fixed Issue #1007 - swissprot parsing for locations like ?..N, with tests

Handle accession names with '_'

Bio::SeqIO::ace

Changed moltype() into alphabe()

Bio::SeqIO::bsml

First commit for bsml.pm -- WILL NOT WORK with Annotation::Collection.pm -- I'm putting this here to be fully compatible with the old Annotation module, I plan to upgrade the code to conform to the new Collection system. We've used this module a lot at BMS, but I'm sure Issue #2002 and will incorporate many more features. I will upgrade the module to cope with any new data structures in BSML 3. -CAT

Minor improvement to parsing of species classification line. This will be my last commit that uses the old Annotation method - my next commit will take advantage of the new Annotation::Collection system.

Minor change to logical test for assigning Site-pos children to features.

Bio::SeqIO::csmscf

Oops. I put csmscf.pm into t/ rather then into Bio/SeqIO/.

Chad's modules do not emit any print statements and code is cleaned up to bioperl standards -- hash strings are quoted - code is made more readable by fitting in 80 char window in many cases Updated bioperl-mailing list to be bioperl-l@bioperl.org

1. Modified SeqIO/ modules to comply with SeqIO interface. Changed tests appropriately. 2. Modified csmscf to allow creation of scfs with no sequence[1] and scfs with no qualities[2]. This, along with (1) and a bit more cleaning, should make csmscf.pm ready to replace scf.pm. Thanks Jason! [1] N's are used and the given qualities are represented in the A channel of the trace data. [2] Qualities are all set to phred10.

More cleanup of csmscf.pm. Removed a metric boatload of debugging information.

Changes to write_seq/next_seq instead of write_scf/next_scfallowed use of Root::IO::_print rather than directly to FH

Missing 'T' elsif and added a default quality parameter to be used (and customized by user if needed)

Removed some unnecessary warnings. The remaining warnings... Well I would like them to stay for normal use but go away when somebody does: $ make test_csmscf Is there a way to make warnings not appear under certain conditions? Looking into this...

A whole pile of changes in csmscf.pm: 1. Supports reading of version 3 scf 2. Supports writing of version 3 scf 3. Major code revisions Other changes: 1. Code cleanup in PrimaryQual 2. Code cleanup in SeqWithQuality 3. Consed.pm no longer uses FreezeThaw (Hi Ewan!)

Doc fixes. Code cleanup.

Chad's module replacing the old scf module

Bio::SeqIO::embl

Moltype() returns DNA even with RNA on ID line. moleule() is the method to call for source molecule.

Fixes into ID line parsing: - moltype() returns 'DNA' even on RNA entries - parses and writes 'circular' - writing translates molecule from GenBank conventions (mRNA -> RNA)

Changed moltype() into alphabe()

Big time change! New Annotation framework rolled in. Much funls!

Fix for EMBL files with missing "^FH " line

Applied Malcolm Cook's fix to read/write secondary accessions for EMBL.

Bio::SeqIO::fasta

Changed moltype() into alphabe()

Bio::SeqIO::fastq

Updates to get index function to return no files and records indexed

Bio::SeqIO::game

Changed moltype() into alphabe()

Bio::SeqIO::game::idHandler

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.

Bio::SeqIO::game::seqHandler

Changed moltype() into alphabe()

Bio::SeqIO::gcg

Changed moltype() into alphabe()

Bio::SeqIO::genbank

Properly write protein sequences out in genbank format

Print protein sequences properly in genbank format

Moltype is set to 'rna' if the LOCUS line contains substring 'RNA' in the right place.

Reverts to 1.39 code. 1.40 'fixes' to moltype removed parses and writes 'circular' from LOCUS line.

Changed moltype() into alphabe()

Simpler logic for alphabet/molecule assignment

More precise use of molecule and moltype in 07 branch

Big time change! New Annotation framework rolled in. Much funls!

Genbank dumping fix for ensembl

Bio::SeqIO::largefasta

Fixed bug that would return an empty Bio::Seq::LargePrimarySeq when it should return null s.t. \ while( $seq = $seqio->next_seq ) { } \ misbehaved and was an infinite loop \ That was very bad. Should fix probably as reported by Josep Abril

Fixed bug as reported by Josep Abril which was causing infinite loops with next_seq

Slightly more intelligent fix that allows for zero length sequences (why you would have a zero length seq while reading in with largefasta is beyond me though...)

Bio::SeqIO::phd

The first committed version of a SeqIO module for phred datafiles. Passes _my_ tests and returns SeqWithQuality objects (coming next).

Chad's modules do not emit any print statements and code is cleaned up to bioperl standards -- hash strings are quoted - code is made more readable by fitting in 80 char window in many cases Updated bioperl-mailing list to be bioperl-l@bioperl.org

1. Modified SeqIO/ modules to comply with SeqIO interface. Changed tests appropriately. 2. Modified csmscf to allow creation of scfs with no sequence[1] and scfs with no qualities[2]. This, along with (1) and a bit more cleaning, should make csmscf.pm ready to replace scf.pm. Thanks Jason! [1] N's are used and the given qualities are represented in the A channel of the trace data. [2] Qualities are all set to phred10.

Simplify argument scheme and allow use of Root::IO print/read facilities

Bio::SeqIO::pir

Changed moltype() into alphabe()

Bio::SeqIO::qual

The first committed version of a SeqIO module for working with quality files that resemble fasta files: >chads kewl sequence quality 10 20 30 20 30 10 ..... Returns PrimaryQual objects (committing those next).

Chad's modules do not emit any print statements and code is cleaned up to bioperl standards -- hash strings are quoted - code is made more readable by fitting in 80 char window in many cases Updated bioperl-mailing list to be bioperl-l@bioperl.org

1. Modified SeqIO/ modules to comply with SeqIO interface. Changed tests appropriately. 2. Modified csmscf to allow creation of scfs with no sequence[1] and scfs with no qualities[2]. This, along with (1) and a bit more cleaning, should make csmscf.pm ready to replace scf.pm. Thanks Jason! [1] N's are used and the given qualities are represented in the A channel of the trace data. [2] Qualities are all set to phred10.

Qual handles write_seq instead of write_qual

Use Root::IO for printing rather than direct to FH

Changed moltype() into alphabe()

Removed warnings by setting $self->{suppress_warnings} in constructor to "1" as default. Is this a good idea? I really want to warn users when they are doing something silly but when I test that in t/$TEST that warning is triggered and dumped out. Ugh. Docfixes all around as well.

Bio::SeqIO::raw

Updates to get index function to return no files and records indexed

Bio::SeqIO::scf

Chad's module replacing the old scf module

Bio::SeqIO::swiss

Swiss prot requires feature tag length to be 8

Swiss prot requires feature tag length to be 8

Hard code moltype to protein for swissprot always

Hard code moltype to protein for swissprot always

Changed moltype() into alphabe()

Big time change! New Annotation framework rolled in. Much funls!

Issue #1028 fixed - swissprot writing of ambigous locations

Issue #1028 swissprot writing of ambiguous locations

Bio::SeqUtils

Changed moltype() into alphabe()

Added translate_3frames() and translate_6frames()

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.

Migrated valid_aa from CodonTable to SeqUtils

Seq3in() converts ALL unknown triplets into 'X'. doc fix.

Bio::SeqWithQuality

First commit of an object representing a sequence and its qualities.

These are in the wrong place.

Bio::SimpleAlign

New method: consensus_iupac() Code mostly from David.Evans@vir.gla.ac.uk Some loop optimisations to consensus_string().

Generate a line for matching residues - only registers a match or non-match, no conservate change coding at this time

Added code to handle weak/strong base conservation output in match_line. The base combos are based on Clustalw 1.82 documentation which are from PAM 250 matrix - perhaps the hash for this data should be put in a more universal place?

Remove debugging

Changed moltype() into alphabe()

Fixes 100% consensus problem reported in Issue #1023

Fixes 100% consensus problem reported in Issue #1023

Support for reporting available symbols in an alignment

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.

Handle dashes and dots the same when determining the match_line

Match line will print empty when first seq char is '.' in an alignment

Bio::Species

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.

Bio::Structure::Atom

First draft for Bio::Structure objects

Added explicit GC as per Chris Mungall suggestion. Call all children DESTROY method explicitely and then remove references from parent to child

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.

Version which has all the parent/child stuff in the Entry object. All parent/child access should now go via an Entry object This version is believed to not contain reference cycles

Further development triggered by finishing PDB parser - additional methods - fixing of stupid bugs - removed reference cycle (finally I hope)

Bio::Structure::Chain

First draft for Bio::Structure objects

Added explicit GC as per Chris Mungall suggestion. Call all children DESTROY method explicitely and then remove references from parent to child

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.

Version which has all the parent/child stuff in the Entry object. All parent/child access should now go via an Entry object This version is believed to not contain reference cycles

Bio::Structure::Entry

First draft for Bio::Structure objects

Added explicit GC as per Chris Mungall suggestion. Call all children DESTROY method explicitely and then remove references from parent to child

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.

Version which has all the parent/child stuff in the Entry object. All parent/child access should now go via an Entry object This version is believed to not contain reference cycles

Further development triggered by finishing PDB parser - additional methods - fixing of stupid bugs - removed reference cycle (finally I hope)

Bug fixes and enhancements after finalising PDB parser

Added seqres method (returns PrimarySeq object found in SEQRES record) minor bug fixes

Perl 5.005 compliance

Handle undefined keys better

Bio::Structure::IO

First commit of classes needed for PDB parsing IO.pm: adaptation of Bio::SeqIO pdb.pm: reading of PDB records (no writing)

Bio::Structure::IO::pdb

First commit of classes needed for PDB parsing IO.pm: adaptation of Bio::SeqIO pdb.pm: reading of PDB records (no writing)

Added -noatom and -noheader attributes unpack: changed bug in template

Bio::Structure::Model

First draft for Bio::Structure objects

Added explicit GC as per Chris Mungall suggestion. Call all children DESTROY method explicitely and then remove references from parent to child

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.

Version which has all the parent/child stuff in the Entry object. All parent/child access should now go via an Entry object This version is believed to not contain reference cycles

Bio::Structure::Residue

First draft for Bio::Structure objects

Added explicit GC as per Chris Mungall suggestion. Call all children DESTROY method explicitely and then remove references from parent to child

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.

Version which has all the parent/child stuff in the Entry object. All parent/child access should now go via an Entry object This version is believed to not contain reference cycles

Bio::Structure::SecStr::DSSP::Res

Modules for using STRIDE and DSSP

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

Modules for using STRIDE and DSSP

Bio::StructureI

Placeholder for now. Come back later

Bio::Symbol::Alphabet

Symbols and alphabets to meet the BioCORBA 0.3 spec

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.

Changes to make Alphabets that are usable with Biocorba

Bio::Symbol::AlphabetI

Symbols and alphabets to meet the BioCORBA 0.3 spec

Bio::Symbol::DNAAlphabet

A DNA alphabet shortcut

Changes to make Alphabets that are usable with Biocorba

Bio::Symbol::ProteinAlphabet

Alphabet for protein residues

Migrated valid_aa from CodonTable to SeqUtils

Bio::Symbol::Symbol

Symbols and alphabets to meet the BioCORBA 0.3 spec

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.

Changes to make Alphabets that are usable with Biocorba

Bio::Symbol::SymbolI

Symbols and alphabets to meet the BioCORBA 0.3 spec

Fixed doc

Bio::Tools::AlignFactory

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.

Bio::Tools::Alignment::Consed

Committed the module for parsing phrap and cap3 .ace files. The module is quite old and requires substantial revision to use Bioperl objects like PrimarySeq, PrimaryQual, and SeqWithQuality. It does, however, work well and I have been using it forever. Next time I am required to work on the code for my EST pipeline I will rewrite this substantially.

Code reformatting

Made module more compliant. - io uses Root:IO - additional methods being added to return preconstructed SeqWithQuality objects where it is useful to do so. - removed cruft

A preliminary use of the Bio::Marker susbsystem. A representation of a genetic linkage map. Oh, and a test for it using a LinkagePosition (coming next). Minor fixes in Consed.pm.

A whole pile of changes in csmscf.pm: 1. Supports reading of version 3 scf 2. Supports writing of version 3 scf 3. Major code revisions Other changes: 1. Code cleanup in PrimaryQual 2. Code cleanup in SeqWithQuality 3. Consed.pm no longer uses FreezeThaw (Hi Ewan!)

General code cleanup. Removed old debug messages.

More cleaning. Removed profanity and contractions.

Bio::Tools::Alignment::Trim

Committed a module containing functions for implementing a sliding-window-look-forward-average smoothing algorithm. This was created because existing trimming programs didn't do _exactly_ what we needed. I wouldn't really advise that people use this much. It operates, in my context, as a part of Consed.pm and works well but it is a bit... special. :) The rest of the files comprise a consed project and are used to test Trim.pm. I really should rewrite t/consed.t to use this as well but t/data/consed_project represents a minimal project and t/acefile.ace.1, along with t/acefile.singlets is a much larger project. I did not include the chromats (too big) _BUT_ the phreds in t/data/consed_project/phd_dir could be used as fodder for SeqIO/csmscf.pm to create synthetic chromats to put in that directory. In fact, that is _exactly_ why I wrote csmscf.pm. It really is good for _something_!

Code reformatting

More cleaning. Removed profanity and contractions.

Bio::Tools::AnalysisResult

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.

Bio::Tools::BPbl2seq

Migrate to Bio::Root::IO system for all IO rather than passing FH/LASTLINE in to Sbjct/HSP/Iteration

Parsing of empty reports

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.

Return an undef when no more data found in the parser

Bio::Tools::BPlite

Add code to check for beginning and ending limits.

BPLite enhancement to properly parse frame(s). Frame can be called in scalar or array context. In scalar context, the query frame is returned if defined, else, the subject frame is returned if defined. In array context ($qframe, $sframe), undef is returned if the frame is undefined.

Changed [\w-\.] into [\w\.-] which is not interpreted as a range.

Migrate to Bio::Root::IO system for all IO rather than passing FH/LASTLINE in to Sbjct/HSP/Iteration

Convert comment to debuging

Minor doc fix

Minor synopsis doc fix

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.

Removed overloaded double-quotes examples from the doc.

Bio::Tools::BPlite::HSP

BPLite enhancement to properly parse frame(s). Frame can be called in scalar or array context. In scalar context, the query frame is returned if defined, else, the subject frame is returned if defined. In array context ($qframe, $sframe), undef is returned if the frame is undefined.

Rewrote report type interpretation in new(). Default is now frame pertains to query. Blast types are handled properly if defined (caveat: bl2seq does not define the program, hence tblastn will NOT recognized properly in this case!). Added report_type().

Migrate to Bio::Root::IO system for all IO rather than passing FH/LASTLINE in to Sbjct/HSP/Iteration

Fix to make strand get set properly when parsing BLASTN report

Bio::Tools::BPlite::Iteration

Migrate to Bio::Root::IO system for all IO rather than passing FH/LASTLINE in to Sbjct/HSP/Iteration

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.

Bio::Tools::BPlite::Sbjct

BPLite enhancement to properly parse frame(s). Frame can be called in scalar or array context. In scalar context, the query frame is returned if defined, else, the subject frame is returned if defined. In array context ($qframe, $sframe), undef is returned if the frame is undefined.

Added report_type(). Rearranged report type interpretation such that the default is frame pertains to query. Blast types are handled properly if defined (caveat: bl2seq does not define the program, hence tblastn will NOT recognized properly in this case!).

Handle scoreline of Expect(2) = 1e-10 rather than Expect = 1e-10 As reported on bioperl list by Leonardo Marino-Ramirez <marino@tofu.tamu.edu>

Migrate to Bio::Root::IO system for all IO rather than passing FH/LASTLINE in to Sbjct/HSP/Iteration

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.

Scoreline fix from David Martin (already in HEAD).

Bio::Tools::BPpsilite

Migrate to Bio::Root::IO system for all IO rather than passing FH/LASTLINE in to Sbjct/HSP/Iteration

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.

Bio::Tools::Blast

Fixed Issue #1019 by the fix suggested by carl virtanen <carl@chugai-pharm.co.jp> (multiple WUBlast report format broken due to format change).

Bio::Tools::CodonTable

Deleted translate_old(), previous version of translate()

Made ensembl specific branch for key speed fixes ensembl-specific for web site. Ewan has okd this

Straightened out branch - stupid Ewan. Idiot. About to moved the right things onto the ensembl branch

Fixed ensembl specific 07 branch

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.

Valid_aa method added

Migrated valid_aa from CodonTable to SeqUtils

Bio::Tools::EPCR

Added documentation

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.

New base object

Bio::Tools::ESTScan

Changed moltype() into alphabe()

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.

Bio::Tools::FASTAParser

create FASTAParser.pm Nov/19/2001 Added Files: FASTAParser.pm

Bio::Tools::GFF

Added gff2ps - will need editing wherever it is used, but good starting script and tweaked gff parsing to work with acedb

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.

Bio::Tools::Gel

For calculating electrophoretic migration distances of Bio::Seq objects

Bio::Tools::Genemark

Changed moltype() into alphabe()

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.

Bio::Tools::Genscan

Changed moltype() into alphabe()

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.

Fixed bug reported by Brian Osborne (module dies if no predicted sequences at all).

Merged bug fix on main trunk over to branch.

Bio::Tools::Grail

Changed moltype() into alphabe()

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.

Bio::Tools::HMMER::Results

Fixed to handle hmmer 2.2g

Changes to support hmmer 2.2g

Added hmmfile and seqfile methods to provide access to these data values in hmmer output

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.

Bio::Tools::HMMER::Set

Added accession and desc methods for a query sequence as hmmer 2.2 supports more robust information about a sequence

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.

Bio::Tools::IUPAC

Changed moltype() into alphabe()

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.

Static method access to alphabets

Bio::Tools::Lucy

Initial commit of Lucy module for handling output from TIGR's lucy program

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.

Bio::Tools::OddCodes

Changed moltype() into alphabe()

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.

Bio::Tools::RestrictionEnzyme

Add code to check for beginning and ending limits.

Add code to check for beginning and ending limits.

Changed moltype() into alphabe()

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.

Bio::Tools::Run::EMBOSSApplication

EMBOSS more runnable and w/ tests

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.

Bio::Tools::Run::RemoteBlast

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.

Bio::Tools::Run::StandAloneBlast

Rewrote exists_blast(). Should now work properly on both Unix and MSWin.

Merged over exists_blast() rewrite and other fixes from the main trunk.

Fix to avoid bark in File::Spec.

Small fix to shut up File::Spec.

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.

Nice message printing when blast is not runnable

Bio::Tools::SeqPattern

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.

Bio::Tools::SeqStats

Changed moltype() into alphabe()

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.

Bio::Tools::SeqWords

Changed moltype() into alphabe()

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.

Bio::Tools::Sim4::Results

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.

Bio::Tools::WWW

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.

Bio::Tools::pSW

Fix jitterIssue #1044 and added code to set sequence ids to seq1/seq2 when ids are empty\ added code to make output filehandle default to STDOUT if it is not set in method align_and_show

SYNOPSIS updated and some more protection for empty sequences in the alignment methods

Initialize a little more safely

Bio::Tree::AlleleNode

Corrections when building tree

Migrate to multi-child tree structure so that polytomy works

Bug fixes for adding mutations

Bio::Tree::Node

Nodes for Building Trees

Changes to handle adding nodes

Corrections when building tree

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.

Migrate to multi-child tree structure so that polytomy works

Moved some methods to the interface, made NodeI interface decorated

Set the ancestor when descendent is added

New Root object inheritance supported, interfaces now extend Bio::Root::RootI and objects extend Bio::Root::Root. Method _abstractDeath now supports parameter for the name of the method and all interfaces use the RootI::_abstractDeath

Bug fixes for adding mutations

Bio::Tree::NodeI

Nodes for Building Trees

Changes to handle adding nodes

Corrections when building tree

Migrate to multi-child tree structure so that polytomy works

Moved some methods to the interface, made NodeI interface decorated

New Root object inheritance supported, interfaces now extend Bio::Root::RootI and objects extend Bio::Root::Root. Method _abstractDeath now supports parameter for the name of the method and all interfaces use the RootI::_abstractDeath

Bio::Tree::PhyloNode

Nodes for Building Trees

Branch length field

Corrections when building tree

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.

Bio::Tree::RandomFactory

Generate Random Trees

Poisson distribution for branch lengthsMigrated to new Non-Binary tree structure to handle polytomy (grr)

RandomTrees generated in a uniform fashion

Respect maxcount only if it is nonzero

Random mutations can be added to a tree based on branch length (coalescent process)

Bio::Tree::Statistics

Calculate Fu and Li's D for a Tree

Documentation update

Bio::Tree::Tree

Preliminary Tree object - very basic and not implemented yet

Changes to handle adding nodes

Corrections when building tree

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.

Test for branch length

Bio::Tree::TreeI

Preliminary Tree object - very basic and not implemented yet

Changes to handle adding nodes

Corrections when building tree

Test for branch length

Bug fixes for adding mutations

Bio::TreeIO

Initial TreeIO framework

Make TreeIO a TreeFactory

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.

Doc update

Removed dependance on Bio::Root::RootI->_initialize and added write_tree as part of new method to factory interface

Bio::TreeIO::TreeEventBuilder

Initial TreeIO framework

Branch lens not bootstraps in newick data from clustal

Real parsing of newick/phylip format still probably don't handle the notion of polytomy very wellI assume that all trees are bifurcating and can be represented by a binary treehowever this is not always the case with polytomy produced by some analysis

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.

Handle multi-child node tree structure

Better parsing support for tree building

Bio::TreeIO::newick

Initial TreeIO framework

Branch lens not bootstraps in newick data from clustal

Real parsing of newick/phylip format still probably don't handle the notion of polytomy very wellI assume that all trees are bifurcating and can be represented by a binary treehowever this is not always the case with polytomy produced by some analysis

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.

Handle multi-child node tree structure

Correctly output phylip/newick formation

Bio::UpdateableSeqI

Added Bio::UpdateableSeqI with method delete_feature

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.

Bio::Variation::AAChange

Fixes to labels and mutated alleles in several types of mutations: 1.) AA level: deletion, complex 2.) AA level: complex, inframe 3.) RNA level: silent

Fixes to labels and mutated alleles in several types of mutations: 1.) AA level: deletion, complex 2.) AA level: complex, inframe 3.) RNA level: silent

Bio::Variation::AAReverseMutate

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.

Bio::Variation::Allele

Changed moltype() into alphabe()

Bio::Variation::DNAMutation

Changed moltype() into alphabe()

Bio::Variation::IO

Tiny doc fixes already committed to HEAD

Bio::Variation::IO::flat

Changed moltype() into alphabe()

Bio::Variation::IO::xml

Changed moltype() into alphabe()

Bio::Variation::RNAChange

Fixes to labels and mutated alleles in several types of mutations: 1.) AA level: deletion, complex 2.) AA level: complex, inframe 3.) RNA level: silent

Fixes to labels and mutated alleles in several types of mutations: 1.) AA level: deletion, complex 2.) AA level: complex, inframe 3.) RNA level: silent

Bio::Variation::SeqDiff

Changed moltype() into alphabe()

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.

Bio::Variation::VariantI

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.

Makefile.PL

Added Bio::Index::Blast as another module dependant on IO::String

Added 95 regression tests to Bio::DB::GFF, plus test data. Needs more.

Bumped version number for release

Support for PPD

bioperl.lisp

Cleaned away a couple of extra lines from CONTRIBUTORS section

Minor documentation fix - every course we do we find more bugs

Add documentation to the new function by default

Interface template as a bp emacs menu item

Missing newlines added

Added a space in the abstract interface creation

New root object

New Root object inheritance supported, interfaces now extend Bio::Root::RootI and objects extend Bio::Root::Root. Method _abstractDeath now supports parameter for the name of the method and all interfaces use the RootI::_abstractDeath

biostart.pod

Added L<> tags, missing Bio::Seq methods and objects, links to bptutorial.pl

bptutorial.pl

Changed moltype() into alphabe()

Numerous mods to bptutorial.pl

Changes for 0.7.2 release

Remove reference to tutorial.pl

examples/aligntutorial.pl

Example code on how to use EMBOSS, pSW, and the MSA interfaces in bioperl to align 2 sequences within bioperl

Corrected syntax for clustalw/tcoffee

examples/change_gene.pl

Changed moltype() into alphabe()

examples/hitdisplay.pl

Need Tk reference

load_gff.pl

Added an incremental loader for GFF to mysql databases. This is just a temporary placeholder because it uses a hard-coded GFF location. Fixed numerous small bugs in the Feature implementation, including the non-equivalence of the stop() and end() methods!!!

Moved load_gff.pl to examples/; this should be deleted eventually

models/map_proposal.txt

Proposals about how to handle new types of data

models/population_proposal.txt

Proposals about how to handle new types of data

scripts/align_on_codons.pl

Align cDNA sequences in protein space and see alignment in DNA space

Emable help command

scripts/blast_fetch.pl

Changed moltype() into alphabe()

scripts/bulk_load_gff.pl

Added a bulk loader for GFF to mysql databases. Fast, but only suitable for initial loading, not incrementals.

Robustified group parsing in the Bio::DB::GFF->load() call, and fixed an undefined statement handler error in mysqlopt.pm

Minor change to bulkloader messages

Modified Bio::DB::GFF to better support lightweight DAS server

Shook out lots of small bugs that appeared while porting the wormbase feature browser to Bio::DB::GFF. Modified the GFF loader to allow for loading updates on top of existing features. A feature is considered the same if it has the same reference point, start, stop, type and group. Basically, all you can change are the notes, score and target information.

Added error checking and status reporting to bulk loader

scripts/chaos_plot.pl

Added script for chaos plotting of dna sequence data

Fixed usage to print out the current script name made script not to die on EMBL sequences of type RNA and made 'U' residue interpreted as 'T'

Arg fix

Changed moltype() into alphabe()

Commit for bioperl scripts project

scripts/das/das_server

Simple DAS server on top of Bio::DB::GFF - needs configuration file still

scripts/est_tissue_query.pl

Better reporting of tissue type

Better caching and handling of zipped gbest files

scripts/gadfly_to_gff.pl

Added script to massage Gadfly files into "correct" GFF format

scripts/generate_random_seq.pl

I am stupid RNA has not 'T'

Cmdline arg update

Changed moltype() into alphabe()

scripts/gff2ps.pl

Added gff2ps - will need editing wherever it is used, but good starting script and tweaked gff parsing to work with acedb

scripts/load_gff.pl

Moved load_gff.pl to examples/; this should be deleted eventually

Modified Bio::DB::GFF to better support lightweight DAS server

Shook out lots of small bugs that appeared while porting the wormbase feature browser to Bio::DB::GFF. Modified the GFF loader to allow for loading updates on top of existing features. A feature is considered the same if it has the same reference point, start, stop, type and group. Basically, all you can change are the notes, score and target information.

scripts/make_mrna_protein.pl

Cmd line convert mrna/cdna to protein sequence

scripts/make_primers.pl

Commit for bioperl scripts project

scripts/prosite2perl.pl

Commit for bioperl scripts project

scripts/run_genscan.pl

Script to run GENSCAN, parse, save predicted sequences as fasta.

scripts/seqstats/aacomp.pl

Script to calculate aa stats - just like EMBOSS app

scripts/seqstats/chaos_plot.pl

Commit for bioperl scripts project

scripts/seqstats/gccalc.pl

Commit for bioperl scripts project

scripts/seqstats/oligo_count.pl

Commit for bioperl scripts project

scripts/tree/paup2phylip.pl

Convert tree block to phylip tree

Truncate taxon name