Core 0.9.0 0.9.2 delta

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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
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