Core 1.5.1 1.5.2 delta

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These are detailed notes on changes made between bioperl-release-1-5-1 and bioperl-release-1-5-2. The main new features are explained in more friendly prose here.

Bio::Align::DNAStatistics
Fix Issue #1991: lower case nucleotides do not work
Email obscuring
Changed die() to __PACKAGE__->throw()
Dnds_pattern_number basically counts the number of codons that have no gaps in the sequence -- patterns in the PAML lingo
Bio::AlignIO
Forgot to commit this; added metafasta to _guess_format
Add xmfa write_aln() method, stk and xmfa file extensions for guessing format
Bio::AlignIO::arp
Simple ARP parser
Bio::AlignIO::bl2seq
Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"
Bio::AlignIO::clustalw
Issue #2000; need to change AlignIO::fasta next_aln to make it more like AlignIO::clustalw, but works for now
Issue #2042; added warnings for duplicate sequences
Issue #2042; fixed unit'd value in numeric == bug
Fix extra Issue #2042
Throw when unable to deal with file, not just warn
Bio::AlignIO::fasta
Start and End refer to length of sequence without gaps
Specify a width in an alignment writing and use regexp to format instead of while loop
Per Albert
Issue #1958; made '?' ambiguous to prevent removal from sequences (was adding trailing gaps)
Issue #2000; need to change AlignIO::fasta next_aln to make it more like AlignIO::clustalw, but works for now
Issue #2000; got rid of sequence validation and substitution (which caused nasty unwarned deletions); sequence validation done in PrimarySeq!
Bio::AlignIO::meme
Version numbers can be non-numeric, corrected throw detection
Meme converts ambiguity codes and its own inserted gaps to X, and allows dash gaps, regex fixed to handle
Bio::AlignIO::metafasta
Need to 'use' module for using module
Issue #2016 : several fixes to accomodate changes in handling meta data. Reverted redundant fix in SimpleAlign; removed relevant tests in SimpleAlign.t
Remove extraneous use statement
Bio::AlignIO::nexus
Don't single quote wrap every id, only those which need it. MrBayes doesn't like it
Bio::AlignIO::phylip
Allow linewrap for phylip sequential
Space
Simplify covoluted logic
Bio::AlignIO::psi
Print last column
Bio::AlignIO::stockholm
Add experimental stockholm write_aln() support
Add sequence-based meta output
Remove old initialization parameter; will add builder later
Add alignment meta string output
Additional fun stuff; write_aln() test added; may move tests to separate test suite (lots of them)
Using DBLinks for database refs
Remove extraneous debugging staatements
Small fixes for AnnotationFactory
Bio::AlignIO::xmfa
First pass at xmfa parser (next_aln() implemented only)
Add xmfa write_aln() method, stk and xmfa file extensions for guessing format
Bio::AnnotatableI
Correct
Bio::Annotation::AnnotationFactory
Add Bio::Annotation::Target to guessed types. Doc fixes: type is guessed, there is no default value
Ticky-tack changes
Bio::Annotation::Collection
Issue #1923
Issue #1922
Bio::Annotation::DBLink
Improved NAME, SYNOPSIS, DESCRIPTION docs
Bio::Annotation::OntologyTerm
Don't use the identifier for as_text() - it's optional, and not in the same alternate key as name. Instead, let's add is_obsolete(), which is in the same alternate key as name, and hence contributes to distinguishing one term from another.
Ticky-tack changes
Bio::Annotation::Reference
Add support for consortiums (CONSRTM) - Issue #2006
Issue #2020
Made pubmed more of an equal alternative to medline
Bio::Annotation::SimpleValue
Fix to allow 0 values despite operator overload (Paul Mooney)
Bio::Annotation::Target
Adding short description
Bio::Assembly::Contig
Issue #2064
Bio::Assembly::IO::ace
Issue #2031; added ace format tests to Assembly.t
Use throw_not_implemented() instead
Bio::Assembly::IO::phrap
Use throw_not_implemented() instead
Bio::Assembly::Scaffold
Issue #2048; need to take a closer look at test suite, skips a lot of tests
Bio::Cluster::SequenceFamily
Replaced Bio::Root::IO->catfile/rmtree/$TEMPDIR with File::Spec and File::Path native Perl 5.6.1 equivalents.
Bio::ClusterIO::dbsnp
Issue #2018, patched parser to accept new dbSNP XML, a lot of tags are not recognised and processed
Bio::CodonUsage::IO
More detail
Strip trailing space from species name, fixes t/DBCUTG.t
Bio::DB::Biblio::biofetch
Issue #2083. Add default retrieval type and use it during initialization.
Predeclared $TMP so it doesn't masks earlier use in same sub
Bio::DB::BioFetch
Handle ebi database name change for swall to uniprot
Improve error message by reporting $base
Bio::DB::CUTG
More detail
Throw on server error, skip on test
Bio::DB::DBFetch
Issue #2083. Add format= to URL.
Predeclared $F so it doesn't masks earlier declaration in same scope
Bio::DB::EUtilities
Initial EUtilities commit; test and test modules on the way...
Make get_db_refs a little more forgiving for arrays
Cleaning up; need to make the cookie and elinkset data accessors better, but for now...
More error fixes
Changed the way get_db_ids works
EInfo stuff
Fixed problems with cookies
Fixed retmode issue; added keep_cookies method (for repeated queries using same cookie); minor fixes
Small issue fixed for retmode; separate methods from parameters
Removed extra debugging statement, Doh!
Small fixes
Small update, weirdness with elink.
Small fixes; working on tests and HOWTO
Cleaning up the API a bit
Small fixes picked up during tests
Update, bugs fixes for tests
EUtilties fixes, additional tests
Change use var to our; comment out Dumper lines
Setting DB from cookie is bad for elink; it should be dbfrom
Fixes to get EGQuery working correctly
Bio::DB::EUtilities::Cookie
Cookie not cookie (this is not a plugin)
Updates to elink, methods and so on
Cleaning up; need to make the cookie and elinkset data accessors better, but for now...
Cleaning up the API a bit
EUtilties fixes, additional tests
Adding short description
Bio::DB::EUtilities::DocSum
Add simple docsum container object for esummary
Adding methods to DocSum and esummary (still experimental)
Fixes for tests
Bio::DB::EUtilities::ElinkData
Updates to elink, methods and so on
Cleaning up; need to make the cookie and elinkset data accessors better, but for now...
Oops! Found a few mistakes...
EInfo stuff
Small fix for odd linksets with no return data
A bt more lenient for empty linksets
Small fixes
Small update, weirdness with elink.
Cleaning up the API a bit
Update, bugs fixes for tests
EUtilties fixes, additional tests
Change use var to our; comment out Dumper lines
Bio::DB::EUtilities::ElinkScores
Object to deal with relevancy scores (storing internally was getting too complicated(
Remove ElinkScores (name changed to ElinkData)
Bio::DB::EUtilities::cookie
Initial EUtilities commit; test and test modules on the way...
Renaming cookie
Bio::DB::EUtilities::efetch
Initial EUtilities commit; test and test modules on the way...
Small issue fixed for retmode; separate methods from parameters
Change use var to our; comment out Dumper lines
Bio::DB::EUtilities::egquery
Initial EUtilities commit; test and test modules on the way...
Minor updates
Change use var to our; comment out Dumper lines
Bio::DB::EUtilities::einfo
Initial EUtilities commit; test and test modules on the way...
EInfo stuff
Cleaning up the API a bit
Update, bugs fixes for tests
Change use var to our; comment out Dumper lines
Bio::DB::EUtilities::elink
Initial EUtilities commit; test and test modules on the way...
Minor updates
Updates to elink, methods and so on
Cleaning up; need to make the cookie and elinkset data accessors better, but for now...
Oops! Found a few mistakes...
More error fixes
Fixed problems with cookies
Fixed retmode issue; added keep_cookies method (for repeated queries using same cookie); minor fixes
Small fix for odd linksets with no return data
Small update, weirdness with elink.
Small fixes; working on tests and HOWTO
EUtilties fixes, additional tests
Change use var to our; comment out Dumper lines
Changed or removed VERSION
Oops!
Bio::DB::EUtilities::epost
Initial EUtilities commit; test and test modules on the way...
Fixed problems with cookies
Fixed retmode issue; added keep_cookies method (for repeated queries using same cookie); minor fixes
Change use var to our; comment out Dumper lines
Oops!
Bio::DB::EUtilities::esearch
Initial EUtilities commit; test and test modules on the way...
More error fixes
Changed the way get_db_ids works
Fixed retmode issue; added keep_cookies method (for repeated queries using same cookie); minor fixes
Cleaning up the API a bit
Small fixes picked up during tests
Not description, term
Change use var to our; comment out Dumper lines
Force IDs to be an array at all times
Fixes to get EGQuery working correctly
Bio::DB::EUtilities::esummary
Initial EUtilities commit; test and test modules on the way...
Change use var to our; comment out Dumper lines
Add simple docsum container object for esummary
Adding methods to DocSum and esummary (still experimental)
Fixes for tests
Bio::DB::EntrezGene
Add EntrezGene.pm
Seems that this is required by SeqIO/entrezgene
Doc corrections
More detail on ids
More detail
Email changed
Bio::DB::Expression
Adding support to screenscrape ncbi GEO
Bio::DB::Expression::geo
Adding support to screenscrape ncbi GEO
Updates to parsing code and lazy loading of object attributes
Removed redundant "if $self->verbose" suffix from "$self->debug()" calls
No setting of own $VERSION
Bio::DB::Fasta
Edits
Add to example
Additional suffixes
Add is_circular()
Fixed Issue #2045
Accepted Charles Tilford's patch for fasta files > 4 GB in length
Bio::DB::Flat
Replaced Bio::Root::IO->catfile/rmtree/$TEMPDIR with File::Spec and File::Path native Perl 5.6.1 equivalents.
Bio::DB::Flat::BinarySearch
Issue #1840
Issue #1917
Adding short description
Replaced Bio::Root::IO->catfile/rmtree/$TEMPDIR with File::Spec and File::Path native Perl 5.6.1 equivalents.
Bio::DB::GDB
Throw, not die
Made (env_proxy => 1) the default for LWP::UserAgent instantiations
Throw on server error
Bio::DB::GFF
Bio::DB::GFF was *unable* to parse GFF3 files; fixed this bad bug
Added regression tests for gff3 support
Lincoln's fix of bug that was introduced prior to 1.5.1 release (fix onto branch)
Removed unsigned from the fdata table so that start and end coordinates can take on negative values
Set gff3_flag properly
Fix gff3_flag full variable name
Fixed gff3 name munging flag
GFF3 processing is a little better now
Remove extra quote
Fix the file handles
Added the method, delete_fattribute_to_feature().
Bio::DB::GFF::Adaptor::berkeleydb
Fixed problem related to aliases not being searched in get_feature_by_name()
Throw, not die
Make synopsis runnable, since this is needed on initial creation
Changing search_notes method to allow wild cards to be passed in
Fixed misalignment of reversec dna glyph and rescued missing grid lines that occur near ends of panel
Bio::DB::GFF::Adaptor::dbi
Fixed problem related to aliases not being searched in get_feature_by_name()
Changing search_notes method to allow wild cards to be passed in
Escaped embedded _ and % characters in strings that will be used with the LIKE operator
Goal: delete fattribute_to_feature rows when deleting features. Modified _delete_feature() to use _delete_fattribute_to_feature() to delete fattribute_to_feature values which had been ignored up to this point. Added _delete_fattribute_to_feature() which will remove values from the fattribute_to_feature table. Modified _delete_group() to use the delete_feature method rather than implement that functionality again. This might take a little more time but makes sense for code upkeep. The _delete_fattribute_to_feature() method could potentially check for orphaned fattribute rows and remove them.
Bio::DB::GFF::Adaptor::dbi::mysql
Removed unsigned from the fdata table so that start and end coordinates can take on negative values
Throw, not die
Moving result filtering from gbrowse to mysql adaptor (where it belongs, so that anybody who uses this method will actually get the results they are expecting).
A few more tweaks to the search_notes methods
Changes to make storable in GFF3 databases
Bio::DB::GFF::Adaptor::dbi::mysqlcmap
Changing search_notes method to allow wild cards to be passed in
Bio::DB::GFF::Adaptor::dbi::oracle
Throw, not die
Changing search_notes method to allow wild cards to be passed in
Meant to strip the wild cards
Bio::DB::GFF::Adaptor::dbi::pg
Throw, not die
Sped up case insensitive name searching in postgres
Added documentation and a commented out version of the search_notes method; this is in preparation of commiting another pg adaptor that implements a fast full text search
Making feature name (gname) and ref seq (fref) searching case insensitive. Class names are not case insensitive though; should they be?
A few more case insensitive fixes
Bio::DB::GFF::Adaptor::dbi::pg_fts
New postgres GFF adaptor: makes use of TSearch2 for fast, full text searching of note attributes
Adding a few doc items
Bio::DB::GFF::Adaptor::memory
Bio::DB::GFF was *unable* to parse GFF3 files; fixed this bad bug
Lincoln's fix of bug that was introduced prior to 1.5.1 release (fix onto branch)
Fixed inconsistent behavior wrt "attributes()" and "abs_stop()" both of which are deprecated
Changing search_notes method to allow wild cards to be passed in
A few more tweaks to the search_notes methods
Fixed logic bug in dna retrieval
Bio::DB::GFF::Feature
Fixed an issue in which the gff string will print out "." when the start or end coordinates are zero
Bio::DB::SeqFeature works with gbrowse, but a couple of esthetic problems to track down
Fixed problem with segments glyph not showing target DNA / multiple alignments due to Bio::DB::GFF::Feature API change
Bio::DB::GFF::RelSegment
Fixed inconsistent behavior wrt "attributes()" and "abs_stop()" both of which are deprecated
Bio::DB::SeqFeature works with gbrowse, but a couple of esthetic problems to track down
Bio::DB::GFF::Segment
Added draw_dna and draw_protein options to the generic glyph
Bio::DB::GenBank
Issue #1405
Added more (better!) warnings, docs on complexity
Added batch retrieval via epost; only accessible using get_seq_stream using GI's at the moment
Make 'gbwithparts' the default format; added default_format (wasn't picking up $DEFAULTFORMAT from the BEGIN block for some reason).
Bio::DB::GenPept
Added batch retrieval via epost; only accessible using get_seq_stream using GI's at the moment
Bio::DB::GenericWebDBI
Initial EUtilities commit; test and test modules on the way...
Fixed retmode issue; added keep_cookies method (for repeated queries using same cookie); minor fixes
Pass to SUPER::proxy (Issue #2109)
Bio::DB::LocationI
Add Location and Reference RandomAccessI-like interfaces, SeqFeatureI-like one to be added
Bio::DB::MANIFEST
No purpose
No purpose
Bio::DB::Makefile.PL
No purpose
No purpose
Bio::DB::MeSH
Fix for multi-line
Convert 'print' to $self->debug/warn as appropriate. Refactored duplicate hard-coded URLs into a subroutine.
Bio::DB::NCBIHelper
Issue #1405
Add format 'gbwithparts' for contig retrieval, and postprocess_data fix for contig assembly (now directly from NCBI instead of bioperl-ish build)
Get rid of potential circular ref from last fix
Issue #1405 (fixed 'strand' issue)
Moved Bio::DB::GenBank-specific params (seq_start, seq_stop, strand, complexity, no_redirect) to NCBIHelper for now; disabled complexity parameter for the time being
Added complexity tag for Bio::DB::GenBank
Added more (better!) warnings, docs on complexity
Added batch retrieval via epost; only accessible using get_seq_stream using GI's at the moment
Make postprocess_data NOOP (removed warnings); use format 'gbwithparts' to get contig files with features or 'fasta' for full sequences alone
Use $self->warn, not warn, for GenBank warnings
Changed or removed VERSION
Bio::DB::Query::GenBank
Use $self->warn, not warn, for GenBank warnings
Bio::DB::ReferenceI
Add Location and Reference RandomAccessI-like interfaces, SeqFeatureI-like one to be added
Bio::DB::Registry
Wiki address
Issue #2012 patch applied, tests pass
This warning shouldn't require a verbosity > 0, otherwise code can fail with no feedback at all
Make it clear we're using globals, declare them up top, and break up overly large main function into logical parts
Allow non-alphabetic chars in database names
Don't lc() the values taken from OBDA registry files
Corrected warning to not include the thing it was warning did not exist!
Bio::DB::SeqFeature
Renamed Bio::DB::SeqFeature::LazyTableFeature to Bio::DB::SeqFeature
More documentation
Fix for Issue #1830
Added more documentation to the GFF3 loader
Added methods to SeqFeature::Segment so that it acts more like a SeqFeature; fixed normalized subfeatures so that they remember what Store they come from, allowing them to fetch their underlying dna/protein and other cute tricks
Accelerate loading performance for humungous multisegmented features
Added a temporary "broken" adaptor to test radical modifications to the DBI::mysql adaptor
Fixed a bug in bio::db::seqfeature which prevented it from producing correct split locations
Fixed boundaries of parent target (in an alignment) to span boundaries of child targets
Fixed bugs: 1) load_id() again returns the load ID as documented; 2) get_SeqFeatures(@typelist) works with children that are inline, not just stored in normalized fashion
Bio::DB::SeqFeature::LazyFeature
Incomplete implementation of a GFF3-compatible store for Bio::SeqFeature objects
Refactored redundant code; ready to doc
Began documentation for Bio::DB::SeqFeature::Store
Renamed Bio::DB::SeqFeature::LazyTableFeature to Bio::DB::SeqFeature
Renamed Bio::DB::SeqFeature::LazyFeature to Bio::DB::SeqFeature::NormalizedFeature
Bio::DB::SeqFeature::LazyTableFeature
Incomplete implementation of a GFF3-compatible store for Bio::SeqFeature objects
Bio::DB::SeqFeature works with gbrowse, but a couple of esthetic problems to track down
Refactored redundant code; ready to doc
Finished documentation for Bio::DB::SeqFeature::Store; Removed Bio::DB::SeqFeature::Store::Cacher because its functionality has been folded into Bio::DB::SeqFeature::Store
Renamed Bio::DB::SeqFeature::LazyTableFeature to Bio::DB::SeqFeature
Bio::DB::SeqFeature::NormalizedFeature
Renamed Bio::DB::SeqFeature::LazyFeature to Bio::DB::SeqFeature::NormalizedFeature
More documentation
Fix for Issue #1830
Added documentation to Bio::DB::SeqFeature; fixed minor bugs in Bio::Graphics
Added more documentation to the GFF3 loader
Fixed syntax errors introduced by recent documentation!
Added a GFF3/SO-compatible gene glyph and made it possible to move labels to the left-hand side of the feature
Tweaking interface to work properly with gbrowse
Added methods to SeqFeature::Segment so that it acts more like a SeqFeature; fixed normalized subfeatures so that they remember what Store they come from, allowing them to fetch their underlying dna/protein and other cute tricks
Updated segments glyph so that it does not assume that features use aggregators
A number of bug fixes and features enhancements to support forthcoming gbrowse release
Various small fixes
Hacky workaround to compensate for the fact that some Bio::DasI adaptors reutrn a string for seq() and others return Bio::PrimarySeq
Added regression tests for Bio::DB::SeqFeature::Store (memory,bdb + mysql)
Fixed boundaries of parent target (in an alignment) to span boundaries of child targets
Fixed bugs: 1) load_id() again returns the load ID as documented; 2) get_SeqFeatures(@typelist) works with children that are inline, not just stored in normalized fashion
Output of gff3_string() method now matches input to GFF3 loader
##Index-subfeatures meta command now case-insensitive; fixed issue with gff3 dumping not matching ID and Parent fields correctly
Never dump load_id and parent_id attributes -- these will cause confusion down the line
Fixed mixing of numeric and symbolic strand notations
Fixed handling of GFF3 printing so that the GFF3 output file matches the input file.
Bio::DB::SeqFeature::NormalizedFeatureI
Incomplete implementation of a GFF3-compatible store for Bio::SeqFeature objects
Added more documentation to the GFF3 loader
Bio::DB::SeqFeature::NormalizedTableFeatureI
Incomplete implementation of a GFF3-compatible store for Bio::SeqFeature objects
Added more documentation to the GFF3 loader
Bio::DB::SeqFeature::Segment
Oops, need this file to work
Refactored redundant code; ready to doc
Renamed Bio::DB::SeqFeature::LazyTableFeature to Bio::DB::SeqFeature
Added a GFF3/SO-compatible gene glyph and made it possible to move labels to the left-hand side of the feature
Tweaking interface to work properly with gbrowse
Added methods to SeqFeature::Segment so that it acts more like a SeqFeature; fixed normalized subfeatures so that they remember what Store they come from, allowing them to fetch their underlying dna/protein and other cute tricks
Updated segments glyph so that it does not assume that features use aggregators
A number of bug fixes and features enhancements to support forthcoming gbrowse release
Various small fixes
Added in-memory adaptor - seems to work fine with gbrowse
Segment->features() now behaves properly when given a list (not an array ref) of feature types
Fixed problem that was causing Bio::DB::SeqFeature::Store->segments() to return multiple segments of identical length
Added methods needed by BatchDumper.pm module of gbrowse
Created a fallback overload to avoid cmp functions failing mysteriously
Created a fallback overload to avoid cmp functions failing mysteriously
Bio::DB::SeqFeature::Store
Incomplete implementation of a GFF3-compatible store for Bio::SeqFeature objects
Bio::DB::SeqFeature works with gbrowse, but a couple of esthetic problems to track down
Refactored redundant code; ready to doc
Began documentation for Bio::DB::SeqFeature::Store
Fixed a problem with combined attribute/location queries, but made query ugly
Added more documentation
Added LRU caching to the scheme
Finished documentation for Bio::DB::SeqFeature::Store; Removed Bio::DB::SeqFeature::Store::Cacher because its functionality has been folded into Bio::DB::SeqFeature::Store
Renamed Bio::DB::SeqFeature::LazyTableFeature to Bio::DB::SeqFeature
More documentation
Fix for Issue #1830
Added more documentation to the GFF3 loader
Added a GFF3/SO-compatible gene glyph and made it possible to move labels to the left-hand side of the feature
Tweaking interface to work properly with gbrowse
Added methods to SeqFeature::Segment so that it acts more like a SeqFeature; fixed normalized subfeatures so that they remember what Store they come from, allowing them to fetch their underlying dna/protein and other cute tricks
Fixed a bug which prevented the search_notes() feature from returning any results
Added in-memory adaptor - seems to work fine with gbrowse
Berkeleydb adaptor is functional; added compress option to reduce database size
Full tie() interface supported
Added a temporary "broken" adaptor to test radical modifications to the DBI::mysql adaptor
Fixed problem that was causing Bio::DB::SeqFeature::Store->segments() to return multiple segments of identical length
Added regression tests for Bio::DB::SeqFeature::Store (memory,bdb + mysql)
Added Bio::DB::SeqFeature::Store can now create Bio::PrimarySeq objects directly when requested
Use Storable::nfreeze rather than Storable::freeze for saving feature data to allow freeze/thaw across platforms (e.g. x86 / SPARC / PPC). [malcook]
Should now be able to serialize & deserialize features that contain CODE references, such as Bio::Root::Root cleanup procedures
Bio::Graphics::Glyph::Segments -- improved realignment and display of gaps; Bio::DB::SeqFeature::Store -- handle features that contain CODE references
Bio::DB::SeqFeature::Store::Cacher
Incomplete implementation of a GFF3-compatible store for Bio::SeqFeature objects
Finished documentation for Bio::DB::SeqFeature::Store; Removed Bio::DB::SeqFeature::Store::Cacher because its functionality has been folded into Bio::DB::SeqFeature::Store
Bio::DB::SeqFeature::Store::DBI::Iterator
Incomplete implementation of a GFF3-compatible store for Bio::SeqFeature objects
Bio::DB::SeqFeature::Store::DBI::broken
Added a temporary "broken" adaptor to test radical modifications to the DBI::mysql adaptor
Removed DBI::broken adaptor because it is now working and code transferred to DBI::mysql
Bio::DB::SeqFeature::Store::DBI::mysql
Incomplete implementation of a GFF3-compatible store for Bio::SeqFeature objects
Bio::DB::SeqFeature works with gbrowse, but a couple of esthetic problems to track down
Began documentation for Bio::DB::SeqFeature::Store
Fixed a problem with combined attribute/location queries, but made query ugly
Added more documentation
Finished documentation for Bio::DB::SeqFeature::Store; Removed Bio::DB::SeqFeature::Store::Cacher because its functionality has been folded into Bio::DB::SeqFeature::Store
Fix for Issue #1830
Some, but not all, documentation for mysql adaptor
Fixed syntax errors introduced by recent documentation!
Added a GFF3/SO-compatible gene glyph and made it possible to move labels to the left-hand side of the feature
Tweaking interface to work properly with gbrowse
Fixed a bug which prevented the search_notes() feature from returning any results
Various small fixes
Added in-memory adaptor - seems to work fine with gbrowse
Berkeleydb implementation now working; not extensively tested
Accelerate loading performance for humungous multisegmented features
Fixed exception that occured when loading a FASTA file only
Setting -vertical_spacing to zero now suppresses span lines
Performance improvements to DBI::mysql adaptor; ALL PREVIOUS DATABASE LOADS ARE INVALID AND WILL HAVE TO BE RELOADED
Removed annoying debugging messages
Added regression tests for Bio::DB::SeqFeature::Store (memory,bdb + mysql)
Target attributes now automatically become display names; replaced "or die" with "throw"
Insure that STH is finish-ed before returing from these functions
Accepted Jason's changes to quelch statement handler still active warnings
Bio::DB::SeqFeature::Store::GFF3Loader
Incomplete implementation of a GFF3-compatible store for Bio::SeqFeature objects
Bio::DB::SeqFeature works with gbrowse, but a couple of esthetic problems to track down
Refactored redundant code; ready to doc
Began documentation for Bio::DB::SeqFeature::Store
Renamed Bio::DB::SeqFeature::LazyTableFeature to Bio::DB::SeqFeature
Added more documentation to the GFF3 loader
Some, but not all, documentation for mysql adaptor
Tweaking interface to work properly with gbrowse
Added draw_dna and draw_protein options to the generic glyph
Added documentation to the gene glyph and made "gray" a synonym for "grey" in the Bio::Graphics::Panel color list
Added in-memory adaptor - seems to work fine with gbrowse
Implementation of Bio::DB::SeqFeature::Store in BerkeleyDB databases; syntax checked but not tested in any other way
Full tie() interface supported
Accelerate loading performance for humungous multisegmented features
Setting -vertical_spacing to zero now suppresses span lines
Added regression tests for Bio::DB::SeqFeature::Store (memory,bdb + mysql)
Test GFF3 file now passes validation tests at http://dev.wormbase.org/db/validate_gff3/validate_gff3_online
Target attributes now automatically become display names; replaced "or die" with "throw"
Fixed boundaries of parent target (in an alignment) to span boundaries of child targets
Target coordinates work properly now
Fixed bugs: 1) load_id() again returns the load ID as documented; 2) get_SeqFeatures(@typelist) works with children that are inline, not just stored in normalized fashion
##Index-subfeatures meta command now case-insensitive; fixed issue with gff3 dumping not matching ID and Parent fields correctly
Replaced complex CGI::Util::escape routine with a simpler one that respects + characters
Bio::DB::SeqFeature::Store::bdb
Incomplete implementation of a GFF3-compatible store for Bio::SeqFeature objects
Finished documentation for Bio::DB::SeqFeature::Store; Removed Bio::DB::SeqFeature::Store::Cacher because its functionality has been folded into Bio::DB::SeqFeature::Store
Added in-memory adaptor - seems to work fine with gbrowse
Adding short description
Bio::DB::SeqFeature::Store::berkeleydb
Implementation of Bio::DB::SeqFeature::Store in BerkeleyDB databases; syntax checked but not tested in any other way
Berkeleydb adaptor is functional; added compress option to reduce database size
Berkeleydb implementation now working; not extensively tested
Added missing search_by_attribute() functionality
Full tie() interface supported
Added regression tests for Bio::DB::SeqFeature::Store (memory,bdb + mysql)
Target attributes now automatically become display names; replaced "or die" with "throw"
Fix BioDBSeqfeature bug; passes tests, but still have temp file problems...
Saved too early; added regex for win32
Fixed bug which caused the Bio::DB::SeqFeature::berkeleydb regression test to fail with a "./features.idx not found" error
Fixed bug which caused the Bio::DB::SeqFeature::berkeleydb regression test to fail with a "./features.idx not found" error
Bio::DB::SeqFeature::Store::memory
Added in-memory adaptor - seems to work fine with gbrowse
Implementation of Bio::DB::SeqFeature::Store in BerkeleyDB databases; syntax checked but not tested in any other way
Berkeleydb implementation now working; not extensively tested
Added missing search_by_attribute() functionality
Full tie() interface supported
Added regression tests for Bio::DB::SeqFeature::Store (memory,bdb + mysql)
Target attributes now automatically become display names; replaced "or die" with "throw"
Target coordinates work properly now
Bio::DB::SeqHound
Made (env_proxy => 1) the default for LWP::UserAgent instantiations
_init_SeqHound returns FALSE on failure, removed uninformative warning and plain print statement, added informative warning
Converted hidden 'log file name' to class variable and use $self->debug instead of 'print STDERR';
Do not alter users verbosity
Bio::DB::SeqI
Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"
Bio::DB::SeqVersion
Add DB::SeqVersion files. These serve to query NCBI's Revision History page but they could probably be modified to accomodate other databases without too much difficulty.
Email changed
Remove unused regexp capture
Use clearer lc() instead of "\L"
Remove unused global variable $MODVERSION
Migrated to Bio::WebAgent from Bio::HTTPGet and added more error checking; now works with authenticating proxies. Partial fix to Issue #2110.
Bio::DB::SeqVersion::gi
How was this deleted from CVS?
Remove unused global variable $ua.
Remove unused global variable $MODVERSION
Removed redundant "if $self->verbose" suffix from "$self->debug()" calls
Migrated to Bio::WebAgent from Bio::HTTPGet and added more error checking; now works with authenticating proxies. Partial fix to Issue #2110.
Bio::DB::SwissProt
Changed EBI default database to UniProtKB
Bio::DB::Taxonomy
Taxa->taxon
Doc fixes, and as per addendum to Issue #2047
Documentation clarification, significantly, get_Taxonomy_Node returns a Bio::Taxonomy::Node, not a Taxon
Bio::Taxonomy overhaul, see Issue #2061
Can now recursively fetch all descendents
Bio::DB::Taxonomy::entrez
As per Issue #2047
Doc fixes, and as per addendum to Issue #2047
Documentation clarification, significantly, get_Taxonomy_Node returns a Bio::Taxonomy::Node, not a Taxon
Bio::Taxonomy overhaul, see Issue #2061
Now a Bio::WebAgent instead of a Bio::Root::HTTPget, allowing proxys to work
Possible fix for Issue #1938: ncbi_taxid() is no longer a direct synonym of id(), only returning if ncbi_taxid had been set
Bio::DB::Taxonomy::flatfile
As per Issue #2047
Doc fixes, and as per addendum to Issue #2047
Documentation clarification, significantly, get_Taxonomy_Node returns a Bio::Taxonomy::Node, not a Taxon
Bio::Taxonomy overhaul, see Issue #2061
Return immediately from get_taxon if supplied a taxonid no in db
Return immediately from get_taxon if supplied a taxonid no in db
Possible fix for Issue #1938: ncbi_taxid() is no longer a direct synonym of id(), only returning if ncbi_taxid had been set
Bio::DB::Taxonomy::list
Bio::Taxonomy overhaul, see Issue #2061
Improved throw messages, can handle consecutive nodes with the same name in the same supplied lineage
Corrected detection of most appropriate throw message
Put the bad lineage and throw in the correct place. there is still a memory leak problem
Possible fix for Issue #1938: ncbi_taxid() is no longer a direct synonym of id(), only returning if ncbi_taxid had been set
Bio::DB::WebDBSeqI
Issue #1405
Removed old email bug reporting address.
Made (env_proxy => 1) the default for LWP::UserAgent instantiations
Issue #1405 (fixed 'strand' issue)
Moved Bio::DB::GenBank-specific params (seq_start, seq_stop, strand, complexity, no_redirect) to NCBIHelper for now; disabled complexity parameter for the time being
Added complexity tag for Bio::DB::GenBank
Added more (better!) warnings, docs on complexity
Use $self->isa, not m//
STREAM could fall out of scope, closing filehandle in returned SeqIO, preventing sequence reads; should be fixed
Issue #2104, may be rolled back if tests on other OS's do not pass
Replaced '/dev/null' with File::Spec->devnull
Bio::Expression::Contact
Adding support to screenscrape ncbi GEO
Updates to parsing code and lazy loading of object attributes
Fixed broken _initialize() docs.
Bio::Expression::DataSet
Adding support to screenscrape ncbi GEO
Fixed broken _initialize() docs.
Bio::Expression::Platform
Adding support to screenscrape ncbi GEO
Updates to parsing code and lazy loading of object attributes
Fixed _initialize() docs
Bio::Expression::Sample
Adding support to screenscrape ncbi GEO
Fixed broken _initialize() docs.
Bio::Factory::DriverFactory
Replaced Bio::Root::IO->catfile/rmtree/$TEMPDIR with File::Spec and File::Path native Perl 5.6.1 equivalents.
Bio::Factory::FTLocationFactory
Issue #1754, Florian enhancement to include UNCERTAIN values. Patch did not go in cleanly, needed to hand-coded. Documentation changed
Fixed spacing for future bugfix
Refactored from_string() for full recursion, get rid of $`, $&, $' (bad!!!)
Reverting this back to 1.22, and turning off debugging
Refactored code now passes all tests; let others try it out
Bio::FeatureIO
Syntactic changes to code and documentation needed to compsenate for what seemed to be quick cutting and pasting from the SeqIO module.
Fixed the (presumably untested) tied hash interface which was using code cut&pasted from SeqIO, calling next_seq and write_seq instead of next_feature and write_feature
Added .ptt to _guess_format()
Bio::FeatureIO::bed
Use $feature->end instead of $feature->stop to avoid error: Can't locate object method "stop" via package "Bio::SeqFeature::Annotated" at ..//Bio/FeatureIO/bed.pm line 163.
Improved NAME, SYNOPSIS, DESCRIPTION docs
Bio::FeatureIO::gff
Adding support for Derives_from tag, which is relatively new to the GFF3 spec
Allow Bio::FeatureIO::gff to return the cigar string as a SimpleValue; modified tests to bring in a gff line with a Gap attribute to test that it successfully parses that attribute.
Fixing Target attribute string parsing. Previously, valid postitive strand '+'s were being dropped. Valid strings include: Target=AB1234+1+199 and Target=AB1234 1 199 + but not Target=AB1234+1+199++ because that just plain looks silly. If anyone (ie, Lincoln) complains, I may reconsider this position.
Minor fixes for writing gff3
Cleaning up a mess cause by me editting and commit an old version of this file
Issue #2071
Added a nasty message and a throw if someone violates the GFF3 spec with their tags (before the data was being silently thrown away; which would you prefer?)
Improved NAME, SYNOPSIS, DESCRIPTION docs
Thought I committed this a few months ago; minor addition to add Index tag to the list a acceptable reserved tags
Comment fix
Bio::FeatureIO::interpro
Improved NAME, SYNOPSIS, DESCRIPTION docs
Bio::FeatureIO::ptt
Added read support for NCBI "PTT" protein table feature files.
Return from next_feature early if not in reading mode
Bio::Graph::Edge
Remove duplicate files
Add back Graph files after clean-up
Bio::Graph::IO
Remove duplicate files
Add back Graph files after clean-up
Bio::Graph::IO::dip
Remove duplicate files
Add back Graph files after clean-up
Bio::Graph::IO::psi_xml
HPRD PSI XML has no fullName, use shortLabel for description instead
Remove debugging code
psi_xml graph now destroyed properly
Duplicate lines
Remove duplicate files
Add back Graph files after clean-up
Make friendlier with new Bio::Species
Adding short description
Removed 'Bio::Root::Object' from base class list; all t/protgraph.t tests pass.
Bio::Graph::ProteinGraph
Remove duplicate files
Add back Graph files after clean-up
Bio::Graph::SimpleGraph
Remove duplicate files
Add back Graph files after clean-up
Adding short description
Bio::Graph::SimpleGraph::Traversal
Remove duplicate files
Add back Graph files after clean-up
Adding short description
Bio::Graphics
Fixed synopsis so that it works!
Bio::Graphics::Feature
Made Bio::Graphics::Feature more SeqFeature-compliant
Documented that maxfeature must be a power of 10
Fixed inconsistent behavior wrt "attributes()" and "abs_stop()" both of which are deprecated
Changes to make storable in GFF3 databases
Bio::DB::SeqFeature works with gbrowse, but a couple of esthetic problems to track down
Refactored redundant code; ready to doc
Bio::Graphics::FeatureBase
Refactored redundant code; ready to doc
Began documentation for Bio::DB::SeqFeature::Store
Fixed dna and cds glyphs so that letters are correctly aligned to right side of base tick when in flip orientation
Tweaking interface to work properly with gbrowse
Updated segments glyph so that it does not assume that features use aggregators
A number of bug fixes and features enhancements to support forthcoming gbrowse release
Major performance increases on xyplot; fixed(?) the cds/translation glyph disconnect
Added documentation to the gene glyph and made "gray" a synonym for "grey" in the Bio::Graphics::Panel color list
Various small fixes
Added in-memory adaptor - seems to work fine with gbrowse
Fix possible uninitialized value in numeric comparisons
Added methods needed by BatchDumper.pm module of gbrowse
Target coordinates work properly now
Output of gff3_string() method now matches input to GFF3 loader
Sigh; yet another problem with GFF3 dumping squashed
Added version flag for gff3 dumping
Fixed handling of GFF3 printing so that the GFF3 output file matches the input file.
Fixed handling of GFF3 writing so that the formatting of features tied together by a single shared ID is not transformed into a object with a parent and multiple children
Quenched "masks earlier declaration" warning
Created a fallback overload to avoid cmp functions failing mysteriously
Bio::Graphics::FeatureFile
Fixed bad interactions between FeatureFile and Bio::DB::GFF
Made FeatureFile work better with gff3 inputs
Changing search_notes method to allow wild cards to be passed in
Added sanity checks to featurefile parsing
Made featurefile robust against bad input data
Added documentation to Bio::DB::SeqFeature; fixed minor bugs in Bio::Graphics
Fix possible uninitialized value in numeric comparisons
Made the API to get the box around the track keys more like the regular boxes() API
Supressed "uninitialized value in hash element" warning
Changed parser to avoid breaking when lines have trailing comments: bgcolor = blue # my favorite color
Cganhed regex to spare hex colors from comment deletion
Bio::Graphics::Glyph
Fixed problem related to aliases not being searched in get_feature_by_name()
Changes to make storable in GFF3 databases
Bio::DB::SeqFeature works with gbrowse, but a couple of esthetic problems to track down
Removing a stray warn
Removed merged_segments() detection from glyph class because this was causing problems drawing ideograms
Adding an option to limit the number of subfeatures to get (useful when using chado and there are many levels and you only want one)
Added a GFF3/SO-compatible gene glyph and made it possible to move labels to the left-hand side of the feature
Updated segments glyph so that it does not assume that features use aggregators
Cleaned up interaction between padding and label position; however, three-part features (e.g. gene) are still adding an extra "additional_arrow_width" amount of left padding, which causes slightly inefficient padding.
A number of bug fixes and features enhancements to support forthcoming gbrowse release
Added draw_dna and draw_protein options to the generic glyph
Removed code that was causing noticeable performance losses
Major performance increases on xyplot; fixed(?) the cds/translation glyph disconnect
Adding an option to allow ignoring a subpart when drawing a glyph
Fixed more bugs in the cds glyph
Added documentation to the gene glyph and made "gray" a synonym for "grey" in the Bio::Graphics::Panel color list
Modifying the ignore subpart option to allow a space delimited list
Performance increases (maybe 1.5x) for gene glyph
Found and fixed place where padding of subparts were being counted twice
Setting -vertical_spacing to zero now suppresses span lines
Slight performance improvement on box calculations
Removed a restriction that was causing introns not to be drawn correctly when transcript too close to edge of panel
If the left and right borders of a box are on the same pixels, then move right border one pixel to right -- this fixes problems with imagemaps under IE
Restored the previous behavior of -box_subparts=>1 so that the subparts AND the whole feature are appropriately boxed
Generalized -box_subparts so that you can control the level of recursion exactly
Removed stray debugging statement
Allow codon table option to be either "codontable" or "geneticcode" for compatibility with the gbrowse Protein dumper
Test GFF3 file now passes validation tests at http://dev.wormbase.org/db/validate_gff3/validate_gff3_online
Fixed a bug in bio::db::seqfeature which prevented it from producing correct split locations
Added documentation about the new maxdepth() method to bio::graphics::glyph and friends
Replaced die() with throw()
If aligned segment is off at start or end, dash characters now added
If aligned segment is off at start or end, dash characters now added
Fixed aggregation issue
Fixed aggregation issue
Bio::Graphics::Glyph: fixed handling of aggregated features so that subfeatures will be recursed into by default; redgreen_box: made behave more like heterogeneous segments when color_subparts option turned on; xyplot.pm: fixed coordinates issue that caused the contents of all plots to be drawn at the same y offset
Bio::Graphics::Glyph: fixed handling of aggregated features so that subfeatures will be recursed into by default; redgreen_box: made behave more like heterogeneous segments when color_subparts option turned on; xyplot.pm: fixed coordinates issue that caused the contents of all plots to be drawn at the same y offset
Added a -filter callback to selectively display features
Added a -filter callback to selectively display features
Fixed minor bug which caused some features drawn with the "box" glyph to have an unexpected height
Fixed minor bug which caused some features drawn with the "box" glyph to have an unexpected height
Speculative change to fix behavior when zoomed way in on introns
Removed debugging warning
Removed debugging warning
Bio::Graphics::Glyph::Factory
Major performance increases on xyplot; fixed(?) the cds/translation glyph disconnect
Performance increases (maybe 1.5x) for gene glyph
Replaced die() with throw()
Bio::Graphics::Glyph::anchored_arrow
Exceedingly small logic error that blocked display of arrow for features extending off left of panel
Bio::Graphics::Glyph::arrow
Changed draw() to draw_component() for several glyphs in order to make them more easily subclassable
Removed unsigned from the fdata table so that start and end coordinates can take on negative values
Added a -label_intervals option to the arrow glyph
Workaround for roundoff errors in tick position calculation that cause major and minor ticks to sometimes not match by a pixel
Adding short description
Bio::Graphics::Glyph::box
Speculative change to fix behavior when zoomed way in on introns
Removed debugging warning
Bio::Graphics::Glyph::cds
Fixed dna and cds glyphs so that letters are correctly aligned to right side of base tick when in flip orientation
Fixed inconsistent representations of reading frame in dna, cds and translation glyphs
Added draw_dna and draw_protein options to the generic glyph
Cds and translation glyph working correctly forward and reverse strand, flipped and unflipped; all colors, translations and frame positions now consistent
Fixed more bugs in the cds glyph
Fixed bug that caused stray lines to be displayed when applying the filled arrow to a very narrow feature
Removing a redundant line
Added documentation to the gene glyph and made "gray" a synonym for "grey" in the Bio::Graphics::Panel color list
Hacky workaround to compensate for the fact that some Bio::DasI adaptors reutrn a string for seq() and others return Bio::PrimarySeq
Added a temporary "broken" adaptor to test radical modifications to the DBI::mysql adaptor
No setting of own $VERSION
Bio::Graphics::Glyph::dna
Bio::DB::SeqFeature works with gbrowse, but a couple of esthetic problems to track down
Dramatically simplified the logic of drawing minus strand DNA. LS must have been crazy when he wrote the original version
Fixed misalignment of reversec dna glyph and rescued missing grid lines that occur near ends of panel
Added draw_dna and draw_protein options to the generic glyph
Dna glyph wasn't observing flip flag when strand==0
Avoid gc window division by zero on small regions; fixed alignment glyph so that special case is for bio::db::gff::feature, not other way around
Bio::Graphics::Glyph::ex
Adding short description
Bio::Graphics::Glyph::flag
Adding short description
Bio::Graphics::Glyph::gene
Added a GFF3/SO-compatible gene glyph and made it possible to move labels to the left-hand side of the feature
Cleaned up interaction between padding and label position; however, three-part features (e.g. gene) are still adding an extra "additional_arrow_width" amount of left padding, which causes slightly inefficient padding.
Added draw_dna and draw_protein options to the generic glyph
Fixed bug that caused stray lines to be displayed when applying the filled arrow to a very narrow feature
Added documentation to the gene glyph and made "gray" a synonym for "grey" in the Bio::Graphics::Panel color list
Added in-memory adaptor - seems to work fine with gbrowse
Adding a sub_part option to the gene glyph, to allow specifying exons be used to build transcripts.
Performance increases (maybe 1.5x) for gene glyph
Found and fixed place where padding of subparts were being counted twice
Setting -vertical_spacing to zero now suppresses span lines
Bio::Graphics::Glyph::generic
Dramatically simplified the logic of drawing minus strand DNA. LS must have been crazy when he wrote the original version
Added a GFF3/SO-compatible gene glyph and made it possible to move labels to the left-hand side of the feature
Cleaned up interaction between padding and label position; however, three-part features (e.g. gene) are still adding an extra "additional_arrow_width" amount of left padding, which causes slightly inefficient padding.
A number of bug fixes and features enhancements to support forthcoming gbrowse release
Added draw_dna and draw_protein options to the generic glyph
Hacky workaround to compensate for the fact that some Bio::DasI adaptors reutrn a string for seq() and others return Bio::PrimarySeq
Found and fixed place where padding of subparts were being counted twice
Added a temporary "broken" adaptor to test radical modifications to the DBI::mysql adaptor
Fixed problem with segments glyph not showing target DNA / multiple alignments due to Bio::DB::GFF::Feature API change
Sorted out confusion between -canonical_strand and -true_target
Added documentation about the new maxdepth() method to bio::graphics::glyph and friends
Fixed minor bug which caused some features drawn with the "box" glyph to have an unexpected height
Fixed minor bug which caused some features drawn with the "box" glyph to have an unexpected height
Speculative change to fix behavior when zoomed way in on introns
Removed debugging warning
Bio::Graphics::Glyph::group
Cleaned up interaction between padding and label position; however, three-part features (e.g. gene) are still adding an extra "additional_arrow_width" amount of left padding, which causes slightly inefficient padding.
Bio::Graphics::Glyph::heterogeneous_segments
Heterogeneous segments glyph was invoking the graded_segments draw() method, thereby wiping out its calculation of part colors
The -merge_parts option was preventing heterogeneous segments from drawing properly
Bio::Graphics::Glyph::image
Added a glyph that will paste photographic images onto the sequence display
Made (env_proxy => 1) the default for LWP::UserAgent instantiations
Setting -vertical_spacing to zero now suppresses span lines
Replaced die() with throw()
Bio::Graphics::Glyph::lightning
Added an option to make the lightning bolt point upward
Bio::Graphics::Glyph::line
Changed draw() to draw_component() for several glyphs in order to make them more easily subclassable
Bio::Graphics::Glyph::merge_parts
Adding short description
Bio::Graphics::Glyph::primers
Changed draw() to draw_component() for several glyphs in order to make them more easily subclassable
Added option to control line thickness
Bio::Graphics::Glyph::processed_transcript
Folded in Don Gilbert\'s patch that prevents exons from getting clipped to oblivion
Added documentation to the gene glyph and made "gray" a synonym for "grey" in the Bio::Graphics::Panel color list
Setting -vertical_spacing to zero now suppresses span lines
Bio::Graphics::Glyph::protein
Initial Kyte-Doolittle hydropathy plot glyph
Now it works, enjoy
Bio::Graphics::Glyph::redgreen_box
Bio::Graphics::Glyph: fixed handling of aggregated features so that subfeatures will be recursed into by default; redgreen_box: made behave more like heterogeneous segments when color_subparts option turned on; xyplot.pm: fixed coordinates issue that caused the contents of all plots to be drawn at the same y offset
Bio::Graphics::Glyph: fixed handling of aggregated features so that subfeatures will be recursed into by default; redgreen_box: made behave more like heterogeneous segments when color_subparts option turned on; xyplot.pm: fixed coordinates issue that caused the contents of all plots to be drawn at the same y offset
Bio::Graphics::Glyph::ruler_arrow
Adding short description
Bio::Graphics::Glyph::segments
Cleaned up interaction between padding and label position; however, three-part features (e.g. gene) are still adding an extra "additional_arrow_width" amount of left padding, which causes slightly inefficient padding.
A number of bug fixes and features enhancements to support forthcoming gbrowse release
Added draw_dna and draw_protein options to the generic glyph
Fixed problem with segments glyph not showing target DNA / multiple alignments due to Bio::DB::GFF::Feature API change
Sorted out confusion between -canonical_strand and -true_target
Workaround for chado adaptor
Added documentation about the new maxdepth() method to bio::graphics::glyph and friends
Improved the way that mismatched bases are drawn. New option -mismatch_color
Fixed boundaries of parent target (in an alignment) to span boundaries of child targets
Avoid gc window division by zero on small regions; fixed alignment glyph so that special case is for bio::db::gff::feature, not other way around
Added protein alignments to segments glyph (experimental)
Realign=1 now forces realignment with dynamic programming aligner; slows it down some, but results are more satisfactory
Bio::Graphics::Glyph::Segments -- improved realignment and display of gaps; Bio::DB::SeqFeature::Store -- handle features that contain CODE references
If aligned segment is off at start or end, dash characters now added
If aligned segment is off at start or end, dash characters now added
Created a fallback overload to avoid cmp functions failing mysteriously
Multiple alignments now accomodate a data bug in which target start < end
Multiple alignments now accomodate a data bug in which target start < end
Bio::Graphics::Glyph::so_transcript
No setting of own $VERSION
Bio::Graphics::Glyph::three_letters
Adding short description
Bio::Graphics::Glyph::transcript
Added a GFF3/SO-compatible gene glyph and made it possible to move labels to the left-hand side of the feature
Cleaned up interaction between padding and label position; however, three-part features (e.g. gene) are still adding an extra "additional_arrow_width" amount of left padding, which causes slightly inefficient padding.
Added draw_dna and draw_protein options to the generic glyph
Setting -vertical_spacing to zero now suppresses span lines
Bio::Graphics::Glyph::transcript2
Fixed problem related to aliases not being searched in get_feature_by_name()
Removed stray debugging statement
Added a GFF3/SO-compatible gene glyph and made it possible to move labels to the left-hand side of the feature
Cleaned up interaction between padding and label position; however, three-part features (e.g. gene) are still adding an extra "additional_arrow_width" amount of left padding, which causes slightly inefficient padding.
Added draw_dna and draw_protein options to the generic glyph
Setting -vertical_spacing to zero now suppresses span lines
Bio::Graphics::Glyph::translation
Fixed dna and cds glyphs so that letters are correctly aligned to right side of base tick when in flip orientation
Fixed inconsistent representations of reading frame in dna, cds and translation glyphs
Added methods to SeqFeature::Segment so that it acts more like a SeqFeature; fixed normalized subfeatures so that they remember what Store they come from, allowing them to fetch their underlying dna/protein and other cute tricks
Removed stray debugging message in translation glyph
Added draw_dna and draw_protein options to the generic glyph
Removed code that was causing noticeable performance losses
Major performance increases on xyplot; fixed(?) the cds/translation glyph disconnect
Fixed logic bug in dna retrieval
Removing a stray debugging statement
Maybe fixed reverse complement - needs testing
Cds and translation glyph working correctly forward and reverse strand, flipped and unflipped; all colors, translations and frame positions now consistent
Fixed more bugs in the cds glyph
Hacky workaround to compensate for the fact that some Bio::DasI adaptors reutrn a string for seq() and others return Bio::PrimarySeq
Fix to stop drawing translation key glyphs 'beneath' from crashing the panel
Allow codon table option to be either "codontable" or "geneticcode" for compatibility with the gbrowse Protein dumper
No setting of own $VERSION
Bio::Graphics::Glyph::xyplot
Fix for Issue #1830
Cleaned up interaction between padding and label position; however, three-part features (e.g. gene) are still adding an extra "additional_arrow_width" amount of left padding, which causes slightly inefficient padding.
Removed code that was causing noticeable performance losses
Major performance increases on xyplot; fixed(?) the cds/translation glyph disconnect
Bio::Graphics::Glyph: fixed handling of aggregated features so that subfeatures will be recursed into by default; redgreen_box: made behave more like heterogeneous segments when color_subparts option turned on; xyplot.pm: fixed coordinates issue that caused the contents of all plots to be drawn at the same y offset
Bio::Graphics::Glyph: fixed handling of aggregated features so that subfeatures will be recursed into by default; redgreen_box: made behave more like heterogeneous segments when color_subparts option turned on; xyplot.pm: fixed coordinates issue that caused the contents of all plots to be drawn at the same y offset
Bio::Graphics::Panel
Fixed sort_order documentation
Bio::DB::GFF was *unable* to parse GFF3 files; fixed this bad bug
Removed unsigned from the fdata table so that start and end coordinates can take on negative values
Updating version in Panel for GBrowse patch awareness
Bumping api version for gbrowse
Bio::DB::SeqFeature works with gbrowse, but a couple of esthetic problems to track down
Fixed misalignment of reversec dna glyph and rescued missing grid lines that occur near ends of panel
Ripped out thread sharing stuff, which isn't working
Fixed inconsistent representations of reading frame in dna, cds and translation glyphs
Fixed more bugs in the cds glyph
Added documentation to the gene glyph and made "gray" a synonym for "grey" in the Bio::Graphics::Panel color list
Fixed problem in which full color range was not utilized in truecolor images
Bumping biographics api version in prep for a gbrowse release
Added a method for getting the rectangles around the track labels
Made the API to get the box around the track keys more like the regular boxes() API
Generalized -box_subparts so that you can control the level of recursion exactly
Replaced die() with throw()
Added option to extend grid into pad top and pad bottom regions; this is useful when placing images top to bottom
Added option to extend grid into pad top and pad bottom regions; this is useful when placing images top to bottom
Added a -filter callback to selectively display features
Added a -filter callback to selectively display features
Bio::Graphics::Pictogram
Adding short description
Bio::Graphics::Util
Fixed inconsistent representations of reading frame in dna, cds and translation glyphs
Adding short description
Bio::Index::Abstract
Switched to 3-arg open(), removed GLOB filehandles, and replaced /\/\// with m{//}
Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"
Removed redundant "if $self->verbose" suffix from "$self->debug()" calls
Replaced warn "" with $self->warn("")
Changed warn() to debug() as more appropriate.
Bio::Index::AbstractSeq
Issue #1989 - don't reset the primary_id if it is a GI number
Issue #2049; committed patches from Robert Buels - need to add warnings for nonexistent IDs
Doc fix
Bio::Index::Blast
Throw, not die
Switched to 3-arg open(), removed GLOB filehandles, and replaced /\/\// with m{//}
Fixed uninitialized value in join or string emerging from test script
No setting of own $VERSION
Bio::Index::EMBL
Switched to 3-arg open(), removed GLOB filehandles, and replaced /\/\// with m{//}
Bio::Index::Fasta
Refer to online Bioperl Tutorial
Switched to 3-arg open(), removed GLOB filehandles, and replaced /\/\// with m{//}
Bio::Index::Fastq
Switched to 3-arg open(), removed GLOB filehandles, and replaced /\/\// with m{//}
Bio::Index::GenBank
Remove redundancy in collection accession numbers
Prevents indexing of the same sequence by the same id more than once
Switched to 3-arg open(), removed GLOB filehandles, and replaced /\/\// with m{//}
Bio::Index::Hmmer
Throw, not die
Switched to 3-arg open(), removed GLOB filehandles, and replaced /\/\// with m{//}
No setting of own $VERSION
Bio::Index::Qual
Refer to online Bioperl Tutorial
Switched to 3-arg open(), removed GLOB filehandles, and replaced /\/\// with m{//}
Bio::Index::SwissPfam
Switched to 3-arg open(), removed GLOB filehandles, and replaced /\/\// with m{//}
Bio::Index::Swissprot
New address
Make it a bit clearer that there are 2 scripts here
Prevents indexing of the same sequence by the same id more than once
Switched to 3-arg open(), removed GLOB filehandles, and replaced /\/\// with m{//}
Email changed
Bio::LiveSeq::IO::Loader
Removed unused and outdated Bio::LiveSeq::IO::SRS class from the distribution
Bio::LiveSeq::IO::README
Removed unused and outdated Bio::LiveSeq::IO::SRS class from the distribution
Bio::LiveSeq::IO::SRS
Removed unused and outdated Bio::LiveSeq::IO::SRS class from the distribution
Bio::LiveSeq::Mutator
Issue #1701
Bio::Location::Atomic
Convert use vars to our; small Issue #2101- can't treat remote locations differently with strand()
Bio::Location::Fuzzy
Issue #1754, Florian enhancement to include UNCERTAIN values. Patch went in cleanly, documentation changed
Realign synopsis code
Bug 992
Convert use vars to our; small Issue #2101- can't treat remote locations differently with strand()
Bio::Location::FuzzyLocationI
Convert use vars to our; small Issue #2101- can't treat remote locations differently with strand()
Bio::Location::Simple
Convert use vars to our; small Issue #2101- can't treat remote locations differently with strand()
Bio::Location::Split
Change to_FTstring to work even if the split location contain only a single sublocation. Previously, it did not correctly complement in this case. In general practice split locations won't only contain a single sublocation, unless you write code that treats all features added to a sequence 'equally' and thus adds them all as Split features.
Obfuscation is fun
Issue #2008
Added comments pertaining to Issue #1952; need to work out what's going wrong here
Convert use vars to our; small Issue #2101- can't treat remote locations differently with strand()
Issue #2101 (tentative fix)
Updating from HEAD (Issue #2101)
Remove redundant sub_Location_by_order()
Bio::Map::Clone
Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules
Bio::Map::Contig
Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules
Bio::Map::CytoMap
First pass at making Positions central to the object model; will probably be completely done shortly, but at least this works
Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules
Bio::Map::CytoMarker
As per Issue #2028
Doc update and use tidy; CytoPosition no longer a Bio::Variation::VariantI
First pass at making Positions central to the object model; will probably be completely done shortly, but at least this works
Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules
Bio::Map::CytoPosition
Removed questionable 'undef' r-value on my() array assignment.
Replaced die() with throw()
As per Issue #2028
Doc update and use tidy; CytoPosition no longer a Bio::Variation::VariantI
Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules
You can no longer set numeric
Bio::Map::EntityI
Bio::Map objects are now EntityIs
Corrected inheritance and new() args for PositionHandler and Mappable
The core Map modules can now cope with relative positions
Bio::Map::FPCMarker
Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules
New tests and bugfixes from Will Nelson
Bio::Map::LinkageMap
First pass at making Positions central to the object model; will probably be completely done shortly, but at least this works
Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules
Bio::Map::LinkagePosition
First pass at making Positions central to the object model; will probably be completely done shortly, but at least this works
Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules
Bio::Map::MapI
First pass at making Positions central to the object model; will probably be completely done shortly, but at least this works
Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules
Corrected inheritance and new() args for PositionHandler and Mappable
The core Map modules can now cope with relative positions
Minor tweaks. Mappables are now AnnotatableIs
Do not directly return a sort
Precompute sort values when they involve subroutine calls for efficiency and to avoid bugs
Major bug fixes and API change for overlap-related methods
Bio::Map::Mappable
First pass at making Positions central to the object model; will probably be completely done shortly, but at least this works
Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules
Corrected inheritance and new() args for PositionHandler and Mappable
The core Map modules can now cope with relative positions
Minor tweaks. Mappables are now AnnotatableIs
Accept and handle -name and -id
Precompute sort values when they involve subroutine calls for efficiency and to avoid bugs
Major bug fixes and API change for overlap-related methods
Speed up and bugfixes for disconnected_*
Bio::Map::MappableI
First pass at making Positions central to the object model; will probably be completely done shortly, but at least this works
Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules
Corrected inheritance and new() args for PositionHandler and Mappable
The core Map modules can now cope with relative positions
Minor tweaks. Mappables are now AnnotatableIs
Do not directly return a sort, option for unsorted position retrieval
Precompute sort values when they involve subroutine calls for efficiency and to avoid bugs
Bio::Map::Marker
Issue #1998 : Added Sendu Bala's Bio::Map modifications and tests
Added CVS tag
As per Issue #2028
First pass at making Positions central to the object model; will probably be completely done shortly, but at least this works
Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules
The core Map modules can now cope with relative positions
Minor tweaks. Mappables are now AnnotatableIs
Bio::Map::MarkerI
First pass at making Positions central to the object model; will probably be completely done shortly, but at least this works
Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules
The core Map modules can now cope with relative positions
Minor tweaks. Mappables are now AnnotatableIs
Bio::Map::Microsatellite
First pass at making Positions central to the object model; will probably be completely done shortly, but at least this works
Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules
Bio::Map::OrderedPosition
First pass at making Positions central to the object model; will probably be completely done shortly, but at least this works
Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules
Corrected inheritance and new() args for PositionHandler and Mappable
The core Map modules can now cope with relative positions
Bio::Map::OrderedPositionWithDistance
First pass at making Positions central to the object model; will probably be completely done shortly, but at least this works
Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules
Bio::Map::Physical
Cleanup doc versus implementation consistency
Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules
New tests and bugfixes from Will Nelson
Bio::Map::Position
Issue #1998 : Added Sendu Bala's Bio::Map modifications and tests
As per Issue #2028
First pass at making Positions central to the object model; will probably be completely done shortly, but at least this works
Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules
The core Map modules can now cope with relative positions
Length() now settable, new absolute_relative method, tweaks and bug fixes
Major bug fixes and API change for overlap-related methods
Bio::Map::PositionHandler
Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules
Corrected inheritance and new() args for PositionHandler and Mappable
The core Map modules can now cope with relative positions
Bug fix for purging when position supplied
Bio::Map::PositionHandlerI
Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules
The core Map modules can now cope with relative positions
Bio::Map::PositionI
Issue #1998 : Added Sendu Bala's Bio::Map modifications and tests
First pass at making Positions central to the object model; will probably be completely done shortly, but at least this works
Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules
Corrected inheritance and new() args for PositionHandler and Mappable
The core Map modules can now cope with relative positions
Precompute sort values when they involve subroutine calls for efficiency and to avoid bugs
Major bug fixes and API change for overlap-related methods
Speed up and bugfixes for disconnected_*
Bio::Map::Relative
The core Map modules can now cope with relative positions
Minor tweaks. Mappables are now AnnotatableIs
Bio::Map::RelativeI
The core Map modules can now cope with relative positions
Minor tweaks. Mappables are now AnnotatableIs
Bio::Map::SimpleMap
First pass at making Positions central to the object model; will probably be completely done shortly, but at least this works
Reimplementation to use PositionHandlers, Positions are central to the object model. Also, tidyup of various modules
Corrected inheritance and new() args for PositionHandler and Mappable
The core Map modules can now cope with relative positions
Minor tweaks. Mappables are now AnnotatableIs
Do not directly return a sort
Precompute sort values when they involve subroutine calls for efficiency and to avoid bugs
Bio::MapIO::fpc
Issue #1952
New tests and bugfixes from Will Nelson
Bio::MapIO::mapmaker
Fixed missing marker, Issue #1890, but additional work may be necessary, depending on how the module is used
Multiple maps
Bio::Matrix::Generic
Fix remove_column
Correct name
Synopsis snafu
Bio::Matrix::PSM::IO::mast
Gao Ge Issue #1900
Gao Ge Issue #1901
Issue #1905 + plus additional checks
Edits
Handle nuc DB and protein motif query+frames
Bio::Matrix::PSM::IO::masta
Correction for 0 in SiteMatrix not required and invalid; resulted in wrong frequencies, IUPAC, consensus and regex. Now all fixed, and tests corrected to expect the correct answers
Bio::Matrix::PSM::IO::transfac
Actually get the dbid when parsing references
Bio::Matrix::PSM::InstanceSite
Gao Ge Issue #1901
Added frame, which may be necessary if the motif was protein, but the DB is nucleic acid
Bio::Matrix::PSM::ProtMatrix
Throw, not die
Bio::Matrix::PSM::SiteMatrix
Throw, not die
Bug: chop chokes so split is better here, bug found by Elodie Portales, UBC
Correction for 0 in SiteMatrix not required and invalid; resulted in wrong frequencies, IUPAC, consensus and regex. Now all fixed, and tests corrected to expect the correct answers
Option to do pseudocount correction, threshold for IUPAC, test expectations updated with new behaviour in mind
Improved docs to explain the consensus-related methods, changed default significance level of IUPAC method to 95%, allowed changing of the thresholds of consensus() and IUPAC() to be independant of each other
Added sites(), a method to get/set one of the attributes you can set in new()
Regexp methods now output regexps that will match sequences with ambiguity codes in them, and also now works when the regexp is supposed to include an N; sequence_match_weight now works with mixed-case input sequences and warns about inputs with ambiguity codes
Bio::Matrix::PSM::SiteMatrixI
Made (more) consistent with SiteMatrix.pm
Bio::Ontology::DocumentRegistry
Fixing URL for so ontology files due to SourceForge's server reorg
Bio::Ontology::OBOEngine
Adding OBO-format ontology parser by Sohel Merchant.
MIgrated all the methods from SimpleGOEngine to this module.
New method: find_similar_terms() that finds term instances where name or synonym or part of one matches the query
Find_similar_terms(): documentaion updated. Note that the argument is a term, not names parameters
New method find_identically_named_terms(), there are now three methods for searching on ontology with a term object
Bio::Ontology::OBOterm
Adding OBO-format ontology parser by Sohel Merchant.
Moved the has_dblink method to Term object
Bio::Ontology::Ontology
Must have get_relationship_type - API demands it.
Adding OBO-format ontology parser by Sohel Merchant.
Made synopsis runnable: Bio::Ontology::Term needs an identifier or you can add only one term inot an ontology (with an empty but unique identifier!)
Find_similar_terms(): documentaion updated. Note that the argument is a term, not names parameters
New method find_identically_named_terms(), there are now three methods for searching an ontology with a term object
Bio::Ontology::SimpleGOEngine
Moved all the methods to Bio::Ontology::OBOEngine
Bio::Ontology::SimpleOntologyEngine
Find_similar_terms(): documentaion updated. Note that the argument is a term, not names parameters
Bio::Ontology::Term
Added the method has_dblink() from OBOterm object
Removed 'use Bio::Root::Object' artifact.
Bio::Ontology::Xref
Adding OBO-format ontology parser by Sohel Merchant.
No message
Bio::OntologyIO
Adding OBO-format ontology parser by Sohel Merchant.
Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler
Adding short description
Bio::OntologyIO::dagflat
Susbtituted all the references to SimpleGOEngine by OBOEngine
Do not cross-reference a term back to itself
Bio::OntologyIO::obo
Adding OBO-format ontology parser by Sohel Merchant.
Removed unnecessary 'undef' assignments.
Fix warnings popping up on 'make test'
Bio::OntologyIO::simplehierarchy
Susbtituted all the references to SimpleGOEngine by OBOEngine
Bio::Phenotype::Correlate
Removed "use Bio::Root::Object" artifact; all tests pass.
Bio::Phenotype::Measure
Removed "use Bio::Root::Object" relic; all tests pass.
Bio::Phenotype::OMIM::MiniMIMentry
Removed "use Bio::Root::Object" artifact; all tests pass.
Bio::Phenotype::OMIM::OMIMentryAllelicVariant
Removed "use Bio::Root::Object" artifact; all tests pass.
Bio::Phenotype::OMIM::OMIMparser
Issue #1951
$self->throw, not die
Bio::PopGen::IO::hapmap
Switch to $self->throw_not_implemented();
Replace warn() with explicit $self->warn()
Bio::PopGen::Marker
Corrected confusing grammar/tense in throw() message for parameter type-checking.
Bio::PopGen::Simulation::Coalescent
Throw, not die
Bio::PopGen::Statistics
Make sure haploid pop is called when calculating sample size for theta
Jason gets bad marks in spelling.
Added F* which was present but not listed here
Bio::PrimarySeq
When reporting the pattern mismatch, list it out with commas separating, previously just reporting the length of the array (number of mismatched bases)
Issue #2000; need to change AlignIO::fasta next_aln to make it more like AlignIO::clustalw, but works for now
Issue #2000; got rid of sequence validation and substitution (which caused nasty unwarned deletions); sequence validation done in PrimarySeq!
Seq() does not take named parameters
For wrong input to subseq(), no undefined variables in warn message, return undef
Bio::PrimarySeqI
Better way to pass alternative initation codon to translate()
Add -offset parameter to translate() for fuzzy locations
Bio::PullParserI
New PullParserI and hmmer parser
Documentation clarification, warn that rewind does not work in sequential_read mode, make that mode default
Compatable with perls older than 5.8
Nicer perl version test
Filehandle was already lexically scoped; avoid redeclaration
Bio::RangeI
Intersection now can take an array ref: slight API change
Mention both args for equals() in its docs
Bio::Restriction::Analysis
Edits
Border condition where a RE cuts at the end of the sequence.
Oops. Forgot to remove the print.
Bio::Restriction::Enzyme
Fixed error when asking for the isoschizomers() of an enzyme that has none.
Border condition where a RE cuts at the end of the sequence.
Issue #2139
Bio::Restriction::EnzymeCollection
Conrad's patch
Bio::Restriction::IO::bairoch
A little rearranging, though bairoch.pm is still broken
Added warning for multicut/multisite enzyme issue (Issue #2010); will resolve hopefully soon
Convert print STDERR to $self->debug and new Class to Class->new
Bio::Restriction::IO::base
A little rearranging, though bairoch.pm is still broken
Bio::Restriction::IO::withrefm
A little rearranging, though bairoch.pm is still broken
Bio::Root::Err
Deprecated and removed these relics
Bio::Root::Global
Deprecated and removed these relics
Bio::Root::HTTPget
As per Issue #2037
Proxy default to environment variable
Proxy fixes
Bio::Root::IO
Issue #2022; speed improvements for Windows parsing; shouldn't affect other OS's
Fix for mode(): do not push back random lines into the buffer, do not leave the filehandle at a random point under Mac OS X
Rewrote mode(), prevents spurious warnings, works on all platforms (?) and with piped input
Bio::Root::IOManager
Deprecated and removed these relics
Bio::Root::Object
Removed references to deprecated/removed Bio::Tools::Blast
Deprecated and removed these relics
Bio::Root::Root
Notes about not starting throw messages with dashes; really its a bug but would be too expensive to fix
Possible fix for Issue #1938
Bio::Root::RootI
Remove cruft from warn(); passes all tests
Notes about not starting throw messages with dashes; really its a bug but would be too expensive to fix
Bio::Root::Storable
Throw, not die
Get rid of $'
Replaced Bio::Root::IO->catfile/rmtree/$TEMPDIR with File::Spec and File::Path native Perl 5.6.1 equivalents.
Bio::Root::Utilities
Fixed num2month() returning wrong months, 0/1 array base problem
Made mean_stdev() more robust when data list has less than 2 elements
Bug in std.dev. calculation, was X^2/N-1 should be X^2/(N-1)
* Added file_flavor() -- a simple wrapper around get_newline() that returns the 'flavor' given a filename (unix, dos, mac). * Added require FileHandle at the appropriate spot in create_filehandle() for convenience.
Deprecated and removed these relics
Bio::Root::Vector
Deprecated and removed these relics
Bio::Root::Version
CPAN-compatible version
Our $VERSION (perl 5.6.1-ish)
Quenched "masks earlier declaration" warning
Good style for $VERSION
Version increase for 1.5.2rc4
Version increase for RC5
Bio::Root::Xref
Deprecated and removed these relics
Bio::Search::GenericStatistics
Added available_* methods so GenericResult can delegate, made GenericResult use objects properly
Bio::Search::HSP::GenericHSP
Missing :
General SearchIO speed-up
Issue #2075; I will add tests for these as soon as I can to SearchIO.t
Simplify Issue #2075 fixes; now reports RPS-BLAST type (BLASTP or BLASTX), similar to blastxml; revert changes in BlastResult
Merge Bio::SearchIO speedup from experimental
Fix for Issue #2075
Merge Bio::SearchIO speedup changes from branch-1-5-2
Lazily evaluate feature1 and feature2, not just query and hit
Bio::Search::HSP::HMMERHSP
Spelling correction
Bio::Search::HSP::HSPI
Syncing documents with code for matches method
Off by one error; previously all matches returned could have been wrong!
Complete fix for out by 1 error
Bio::Search::HSP::HmmpfamHSP
New PullParserI and hmmer parser
Use base, not @ISA
Bio::Search::HSP::PullHSPI
New PullParserI and hmmer parser
Bio::Search::Hit::BlastHit
Changed 'require Class' to 'use Class'
Bio::Search::Hit::Fasta
Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"
Bio::Search::Hit::GenericHit
General SearchIO speed-up
Merge Bio::SearchIO speedup from experimental
Merge Bio::SearchIO speedup changes from branch-1-5-2
Changed 'require Class' to 'use Class'
Bio::Search::Hit::HmmpfamHit
New PullParserI and hmmer parser
Bio::Search::Hit::PsiBlastHit
Changed 'require Class' to 'use Class'
Bio::Search::Hit::PullHitI
New PullParserI and hmmer parser
Bio::Search::Iteration::GenericIteration
General SearchIO speed-up
Merge Bio::SearchIO speedup from experimental
Merge Bio::SearchIO speedup changes from branch-1-5-2
Bio::Search::Result::BlastResult
Issue #2075; I will add tests for these as soon as I can to SearchIO.t
Simplify Issue #2075 fixes; now reports RPS-BLAST type (BLASTP or BLASTX), similar to blastxml; revert changes in BlastResult
Bio::Search::Result::GenericResult
General SearchIO speed-up
Added available_* methods so GenericResult can delegate, made GenericResult use objects properly
Merge Bio::SearchIO speedup from experimental
Merge Bio::SearchIO speedup changes from branch-1-5-2
Next_hit, not next_hits
Bio::Search::Result::HmmpfamResult
New PullParserI and hmmer parser
Make evalues play nice under WinXP
Bio::Search::Result::PullResultI
New PullParserI and hmmer parser
Bio::Search::Result::ResultI
Fix error message to accurately report failed condition
Bio::Search::SearchUtils
Tile_hsps() now returns HSP contig data in a two-element array. 0=query contigs, 1=sbjct contigs
Tiling of hsps was broken; now HitI methods frac_aligned_query and frac_aligned_hit will return more sane answers (perhaps even correct ones!)
Fixed uninitialized values introduced in last commit
Spelling error
Calculate identities and conserveds correctly when merging hsps into tiles
Hsp tiling and indentitiy calculation algorithm should now be correct (though there are much simpler, saner ways of doing the same thing...)
Removed debug line
Bio::SearchIO
Wiki address
Bio::SearchIO::EventHandlerI
Moved start_iteration, end_iteration to EventHandlerI; modified SearchIO::blast to play nice when using other event handlers
Bio::SearchIO::FastHitEventBuilder
Allow event handler to work with SearchIO::blast
Moved start_iteration, end_iteration to EventHandlerI; modified SearchIO::blast to play nice when using other event handlers
Make this a bit more flexible. This handler doesn't use HSP's!
Bio::SearchIO::IteratedSearchResultEventBuilder
General SearchIO speed-up
Merge Bio::SearchIO speedup from experimental
Merge Bio::SearchIO speedup changes from branch-1-5-2
Bio::SearchIO::SearchResultEventBuilder
Issue #1986 and allow SREB to be swapped back into IteratedREB
Moved start_iteration, end_iteration to EventHandlerI; modified SearchIO::blast to play nice when using other event handlers
General SearchIO speed-up
Merge Bio::SearchIO speedup from experimental
Merge Bio::SearchIO speedup changes from branch-1-5-2
Bio::SearchIO::Writer::BSMLResultWriter
Improved NAME, SYNOPSIS, DESCRIPTION docs
Bio::SearchIO::Writer::GbrowseGFF
Sped up case insensitive name searching in postgres
Silenced a warning about warn() given an uninitialised argument
Bio::SearchIO::Writer::HTMLResultWriter
Replaced 'print STDERR' with '$self->warn', plus minor formatting.
Add back in $Revision assignment line; this module actually prints it out in the footer of the HTML it produces.
Bio::SearchIO::Writer::HitTableWriter
Add 'rank' and 'num_hits' to column_map
Bio::SearchIO::Writer::ResultTableWriter
Support new column in result table: num_hits
Bio::SearchIO::axt
Issue #1748, set $/ to "\n" and local $_
Add extra comment via Cathy
Bio::SearchIO::blast
Issue #1748, set $/ to "\n" and local $_
Issue #1934; perltidy'd code, workarounds for added/changed text output
Fix for Issue #1985 - difference in blastpgp output from Linux and Windows breaks parsing
Added CVS tag line (wasn't updating)
Issue #1986 and allow SREB to be swapped back into IteratedREB
Moved start_iteration, end_iteration to EventHandlerI; modified SearchIO::blast to play nice when using other event handlers
Small fix to catch optional frame info for RPS-BLAST (BLASTX-like); working on rest of Issue #2075
Issue #2075; I will add tests for these as soon as I can to SearchIO.t
Simplify Issue #2075 fixes; now reports RPS-BLAST type (BLASTP or BLASTX), similar to blastxml; revert changes in BlastResult
Issue #2091 (second bug)
Added comments relevant to Issue #1986
Issue #2108
Deal with WU-BLAST weird case
Removed redundant "if $self->verbose" suffix from "$self->debug()" calls
Issue #2121
Bio::SearchIO::blasttable
Issue #1748, set $/ to "\n" and local $_
Removed ambiguous undef assignment to array
Bio::SearchIO::blastxml
Issue #1748, set $/ to "\n" and local $_
Added SAX2 parsing (switch over to XML::SAX)
Added a bit about using XML::SAX and XML::SAX::ExpatXS
Added warnings for XML::SAX::Expat, which has DTD issues. Still won't play nice!
Oops! Made XML::SAX::Expat the default during testing...
Simplify Issue #2075 fixes; now reports RPS-BLAST type (BLASTP or BLASTX), similar to blastxml; revert changes in BlastResult
Commented out timing debugs to give clean test output
Throw, not warn, since this dies 99% of the time anyway. Make error message more explicit.
Bio::SearchIO::exonerate
Issue #1748, set $/ to "\n" and local $_
Bio::SearchIO::fasta
Issue #1748, set $/ to "\n" and local $_
Wiki address
Bio::SearchIO::hmmer
Issue #1748, set $/ to "\n" and local $_
Repair broken regexp (duplicated \s+ prevented domains with more than 99 instances from being seen); also handle PVM-restartable hmmpfam format (e.g. Query sequence 15:); other tidying
Perltidy'd for personal sanity; working on Issue #2036...
Fix Issue #2036
Removed redundant "if $self->verbose" suffix from "$self->debug()" calls
Bio::SearchIO::hmmer_pull
New PullParserI and hmmer parser
Documentation clarification, warn that rewind does not work in sequential_read mode, make that mode default
Default hmmer_pull piped_behaviour mode now sequential_read
Bio::SearchIO::megablast
Issue #1748, set $/ to "\n" and local $_
Corrected confusing grammar/tense in throw() message for parameter type-checking.
Bio::SearchIO::psl
Issue #1748, set $/ to "\n" and local $_
Fix Issue #1977
Removed ambiguous undef assignment to array.
Bio::SearchIO::sim4
Issue #1748, set $/ to "\n" and local $_
Bio::SearchIO::waba
Issue #1748, set $/ to "\n" and local $_
Bio::SearchIO::wise
Issue #1748, set $/ to "\n" and local $_
Bio::Seq
The API has changed... binomial_name --> binomial
Bio::Seq::BaseSeqProcessor
Corrected write_seq() to it should be (IMHO anyway).
Bio::Seq::Meta
Copy-paste error in synopsis code
Bio::Seq::RichSeq
Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"
Bio::SeqFeature::Annotated
Remove id, test passes.
Emmanuel's suggestion on names
Issue #2026; Robert's enhancements
Fixing a bug that silently converted phases of 0 to null
Bio::SeqFeature::Collection
Replaced Bio::Root::IO->catfile/rmtree/$TEMPDIR with File::Spec and File::Path native Perl 5.6.1 equivalents.
Bio::SeqFeature::Gene::NC_Feature
Improved NAME, SYNOPSIS, DESCRIPTION docs
Bio::SeqFeature::Gene::Poly_A_site
Improved NAME, SYNOPSIS, DESCRIPTION docs
Bio::SeqFeature::Gene::Transcript
Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"
Bio::SeqFeature::Generic
Format
Throw, not die
Documented that -primary and -primary_tag contructor keys are synonyms.
Changes to make storable in GFF3 databases
Bio::SeqFeature::SimilarityPair
General SearchIO speed-up
Bio::SeqFeature::Tools::Unflattener
Fixed unflattener for unusual form of genbank record - see new test for details
Issue #1810
Bio::SeqFeatureI
Format
Issue #2039 : changed spliced_seq API, added warning about old API (but having it still work)
Issue #1780 (try to catch mismatched location end/seq length)
Bio::SeqIO
Add suffix for entrezgene
Wiki address
Add a couple more suffixes to fasta
Extend _guess_format to know about 'strider' files
Bio::SeqIO::abi
Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"
Bio::SeqIO::agave
Throw, not die
Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"
Bio::SeqIO::alf
Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"
Bio::SeqIO::bsml
Throw, not die
Bio::SeqIO::bsml_sax
Bio::Taxonomy overhaul, see Issue #2061
Bio::SeqIO::chadoxml
Clarify that this is write-only
Throw, not die
Bio::SeqIO::chaos
Throw, not die
Fixed syntax error (is anybody using this module?).
Replace print STDERR with $self->warn
Bio::SeqIO::ctf
Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"
Bio::SeqIO::embl
Throw, not die
Issue #2056 : Update embl.pm for EMBL sequence format changes
Bio::Taxonomy overhaul, see Issue #2061
Improved species handling; now more likely that output of input OS, OC lines matches input
Removed print line
Issue #2077; make organism name parsing more consistent between GenBank and EMBL formats (Bio::Taxon methods only)
Issue #2077 : split and store dates from versioning info, rebuild on write_seq()
Add warning to check seq quality
Not map(), join(); not unless, if (!defined()). Damian Conway would be proud...
Issue #2087
Throw informative message for OS and OC line problems, prior to handing off to Bio::Species
Do not throw when the next sequence is just a blank line
Improved genus capturing, new-style organism parsing for swiss.pm
Return with no species on failure to parse even the scientific name
Issue #2089
Indenting code and init DBlink all at once
Indent madness merged to trunk
Issue #2130
Issue #2130
Bio::SeqIO::entrezgene
Capture locus synonym data was missing annotation when not an array for gene->db
Speed up parser and suppress some warnings by initializing debug to 'off'
Capture KEGG pathway name
Bit more on what's returned
Handles multiple taxon id/db entries
Some refseqs uncaptured when multiple comment->product levels exist
Revert back to previous revision to avoid bug
Bio::SeqIO::excel
Added SeqIO parsers for column-delimited tables, and as a specialization for Excel workbooks. Includes test files and script.
Id line
Bio::SeqIO::exp
Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"
Bio::SeqIO::fasta
Issue #2022; speed improvements for Windows parsing; shouldn't affect other OS's
Oops; fixed wrong line! Odd that tests didn't pick that up...
Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"
Bio::SeqIO::fastq
Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"
Bio::SeqIO::game::gameWriter
Issue #1954 : patch from Robert Buels, adds <computational_analysis> to output
Get rid of $&
Bio::SeqIO::gcg
Checksum on uppercase sequence; Do not filter sequence, remove only explicitly specified characters
Bio::SeqIO::genbank
Fix Issue #1647
New address
Wiki address
Issue #1925. I fix this thing and it just looks worse and worse, someday...
Added WGS_SCAFLD support for WGS files (was not parsing these)
Fix suggested by Scott Markel (issue with writing GenBank files)
Back out the last changes (fixes for Scott) as they are redundant; Heikki's fix to Bio::Annotation::SimpleValue (1.15) already addressed this issue
Changed the way CONTIG line is handled; passes tests and should fix infinite loop bug
Make it a little easier to get CONTIG info, if needed for Bio::Location objects
Drop debug and reformat indents
Add support for consortiums (CONSRTM) - Issue #2006
Extra check for empty CONSRTM line (per M. Rogoff)
Issue #2020
Do not exceed 80 character line width when printing out long SOURCE lines
Correct handling of genus, species and subspecies in in/out
Bio::Taxonomy overhaul, see Issue #2061
Fixed handling of organism lines split over 2 lines and creation of classification array when multi-word name is split over 2 lines
Parse out organelle, common name, abbr. name (bypassed for now)
Some small common name changes (more to come?)
Issue #2077; make organism name parsing more consistent between GenBank and EMBL formats (Bio::Taxon methods only)
Issue #2062
Improved genus capturing, new-style organism parsing for swiss.pm
Return with no species on failure to parse even the scientific name
Email changed
Replaced /^\Q...\E$/ and /\Q...\E/ code with clearer more efficient 'eq' and 'index()'
Dblink fix to keep version and accession separate
Indentation madness
Indentation madness merged to 1.5.2 branch
Issue #2146
Issue #2124
Issue #2152
Change for block to a map
Bio::SeqIO::interpro
Issue #1908. Also removed use statements for Data::Dumper and XML::DOM::XPath, these modules appear to be unused.
Improved NAME, SYNOPSIS, DESCRIPTION docs
Bio::SeqIO::kegg
Guido's new version
Format
On Fri, 18 Nov 2005, "Greenberg, Simon [PRDUS Non-J&J]" <SGreenb1@prdus.jnj.com> wrote: > Hi Allen, > > I'm trying to implement KEGG parser and found your latest release. > I made some minor changes because not all input files containing some of the > 'key' values:
Fix to return the value rather than a boolean
Bio::SeqIO::largefasta
Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"
Bio::SeqIO::lasergene
Support strider and lasergene formats in seqio. NB: new dependency in strider.pm - Convert::Binary::C
Fixed to actually pass "perl -c", removed cruft, converted die to throw
Repaired module and wrote tests for "Lasergene" sequence format.
Bio::SeqIO::locuslink
Improved NAME, SYNOPSIS, DESCRIPTION docs
Bio::SeqIO::metafasta
Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"
Bio::SeqIO::phd
Added support for reading comments in a phd file. This really needs a "phred_comments" object of some sort so that it will be serializable. Then when java clients get this object they will be able to deserialize it.
Issue #2120
Bio::SeqIO::pln
Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"
Bio::SeqIO::scf
Nancy's patch and some formatting, removing debugging statements
Nancy's patch
Bio::SeqIO::strider
Support strider and lasergene formats in seqio. NB: new dependency in strider.pm - Convert::Binary::C
Replaced die() with $self->throw()
Documentation fix
Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"
Bio::SeqIO::swiss
Issue #2003 : added support for seq_version; see bug report for details
Improved genus capturing, new-style organism parsing for swiss.pm
Return with no species on failure to parse even the scientific name
STANDARD/PRELIMINARY based on SwissProt/TrEMBL
Replaced /^\Q...\E$/ and /\Q...\E/ code with clearer more efficient 'eq' and 'index()'
Simplified dblink parsing and setting, code indenting
Issue #2134
Issue #2134 (change output to conform with rel. 9 ID changes)
Use Comment object
Bio::SeqIO::table
Added SeqIO parsers for column-delimited tables, and as a specialization for Excel workbooks. Includes test files and script.
Id line
Bio::SeqIO::tinyseq
No setting of own $VERSION
Bio::SeqIO::tinyseq::tinyseqHandler
No setting of own $VERSION
Bio::SeqIO::ztr
Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"
Bio::SeqUtils
Added and modified Roy Chaudhuri's cat method for concatenating sequences with features
Fix for some omissions in last commit
Interim procedural solution to sequence evolution simulation
Added trunc_with_features and relevant tests (Roy Chaudhuri, from Issue #2019)
Allow any sort of uc or lc triplet in seq3in()
Issue #2052
Issue #2053
Added additional IUPAC amino acids GenBank is adding starting in October (per Neil Saunders on the mail list)
Replaced print STDERR with $self->debug()
Issue #2145
Bio::SimpleAlign
Modified remove_columns(). Now columns can be removed by property (['weak','mismatch']) or by position ([0,0],[5,10]).
Must sort args, can't assume user enters them in correct order
Edits
Fix cigar_line (it had never been completed in fact), add tests. This is the old-style cigar line, not the exonerate/ENSEMBL-style cigar line.
Edits
New function to get a matrix of where the gaps are in the alignment. test and example code to be added later; also respect gapchar
Fix wrong coordinate
Fix slice() when the slice is a single column, this wasn't working
Add slice() example
Resolving metafasta/SimpleAlign::consensus_string() issues in Issue #2016
Issue #2016 : several fixes to accomodate changes in handling meta data. Reverted redundant fix in SimpleAlign; removed relevant tests in SimpleAlign.t
Issue #1984
Issue #2106
Issue #2099
Email changed
Replaced /^\Q...\E$/ and /\Q...\E/ code with clearer more efficient 'eq' and 'index()'
Implement AnnotatableI (for alignment-specific annotation)
Add experimental stockholm write_aln() support
Add alignment meta string output
Additional fun stuff; write_aln() test added; may move tests to separate test suite (lots of them)
No symbols if no seq
Bio::Species
Additional 'rule' in validate_species_name - not entirely sure that it's possible to validate some of these virus names
Bio::Taxonomy overhaul, see Issue #2061
Put the bad lineage and throw in the correct place. there is still a memory leak problem
Fixes for binomial, species when creating a Bio::Species from a db; merges scientific_name now
Remove debug comments
This fixes Issue #2092. What I don't know is whether this is also the correct behaviour. It turns out that when you're working within bioperl-db you're comparing the node_name to elements of an array where the species name and the genus name are in adjacent elements.
Do not try and shortcut in binomial() to better emulate old usage
Do not call classification() in new unless a classification actually supplied
Possible fix for Issue #1938: ncbi_taxid() is no longer a direct synonym of id(), only returning if ncbi_taxid had been set
Weaken refs to avoid circular references
Get rid of cleanup methods for serialize success
Bio::Structure::Entry
Issue #1893
Add alias for conect()
Issue #1894
Bio::Structure::IO
Removed text which didn't make much sense
Bio::Structure::IO::pdb
Issue #1895
Initialize to suppress a warning
Bio::Structure::SecStr::DSSP::Res
Spelling error
Issue #1966
Bio::Structure::StructureI
Remove duplicated lines
Bio::Symbol::Alphabet
Improved NAME, SYNOPSIS, DESCRIPTION docs
Bio::Symbol::ProteinAlphabet
Yet mores fixes for additional amino acid codes 'U', 'O', 'J'
Bio::Taxon
Bio::Taxonomy overhaul, see Issue #2061
Fixes for binomial, species when creating a Bio::Species from a db; merges scientific_name now
Corrected confusing grammar/tense in throw() message for parameter type-checking.
Possible fix for Issue #1938: ncbi_taxid() is no longer a direct synonym of id(), only returning if ncbi_taxid had been set
Bio::Taxonomy
Bio::Taxonomy overhaul, see Issue #2061
Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"
Bio::Taxonomy::FactoryI
Bio::Taxonomy overhaul, see Issue #2061
Bio::Taxonomy::Node
Added get_Lineage_Nodes
Added get_LCA_Node
As per Issue #2047
Doc fixes, and as per addendum to Issue #2047
Bio::Taxonomy overhaul, see Issue #2061
Bio::Taxonomy::Taxon
Minor code and doc fixes
Bio::Taxonomy doesnt export rank information; dont try and use it to validate in rank()
Bio::Taxonomy overhaul, see Issue #2061
Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"
Bio::Taxonomy::Tree
Minor code and doc fixes
Bio::Taxonomy overhaul, see Issue #2061
Bio::Tools::Alignment::Consed
Throw, not die
Corrected comment URL reference to 'tcgrep'
Replaced UNIX-specific "/" stuff with File::Spec->splitpath
Replaced Bio::Root::IO->catfile/rmtree/$TEMPDIR with File::Spec and File::Path native Perl 5.6.1 equivalents.
Bio::Tools::Analysis::DNA::ESEfinder
Made (env_proxy => 1) the default for LWP::UserAgent instantiations
Throw on server error, skip on tests
Throw on all server errors
New WebAgent, not UserAgent
Bio::Tools::Analysis::Protein::ELM
Adding short description
Bio::Tools::Analysis::Protein::GOR4
Behave well on server error
Behave well on server error
Bio::Tools::Analysis::Protein::HNN
Behave well on server error
Behave well on server error
Bio::Tools::Analysis::Protein::Scansite
Corrected URL for MIT's ScanSite web site
Fixed previously mis-deduced part of documentation (via author's other modules)
Bio::Tools::BPbl2seq
Add deprecation warnings
Warn, not warning (duh....)
Bio::Tools::BPlite
Add deprecation warnings
Warn, not warning (duh....)
Fixed formatting of deprecation message.
Bio::Tools::BPlite::Iteration
Replaced /^\Q...\E$/ and /\Q...\E/ code with clearer more efficient 'eq' and 'index()'
Bio::Tools::BPpsilite
Fixed localization problem
Add deprecation warnings
Warn, not warning (duh....)
Replaced Bio::Root::IO->catfile/rmtree/$TEMPDIR with File::Spec and File::Path native Perl 5.6.1 equivalents.
Replaced /^\Q...\E$/ and /\Q...\E/ code with clearer more efficient 'eq' and 'index()'
Bio::Tools::Blast
Removing files from CVS HEAD which were scheduled for removal in version 1.1 but were still hanging around.
Bio::Tools::Blat
Adding short description
Bio::Tools::CodonTable
Added Bio::Tools::CodonTable->tables() method and corresponding tests.
Added additional IUPAC amino acids GenBank is adding starting in October (per Neil Saunders on the mail list)
Bio::Tools::Coil
Adding short description
Bio::Tools::ECnumber
Removed "use Bio::Root::Object" relic; all tests pass. It already ISA Bio::Root::Root.
Bio::Tools::EPCR
Support decoding strand supplied when calling e-PCR with decode -option
Avoid adding empty 'Note' tag to feature when $rest only contained e-PCR strand info
Bio::Tools::ERPIN
Initial commit; adding tests to rnamotif.test
Get rid of newline at end of sequence
Minor changes; plan on makeover for these soon (maybe move to SearchIO?)
Minor changes (deal with evalue perliness)
Now with 'our'
Bio::Tools::Fgenesh
Fixed (selected) vestigal cruft wrought by Genscan.pm copy/paste origins of this module: * start/end coordinate swapping is NOT needed for fgenesh (at least in fgenesh v 2.4 in my hands). * analysis_method still 'thought' it was genscan. Not! I'm expect there is other such cruft...
Fixed spelling in comment.
1) small corrections to field to tag mapping from 'PolA' to 'PolyAsite' and 'TSS' to 'Promoter' (which remains incorrect, but at least now maps the correct field) 2) comment out a debugging/trace message
allows >999 predictions to be parsed without error
Bio::Tools::FootPrinter
Improved NAME, SYNOPSIS, DESCRIPTION docs
V2.1 now has header lines - added compatability
Bio::Tools::GFF
Updating the lists of reserved tags (it was REALLY out of date).
Fixing the handling of Targets for GFF3
Adding items to escape in GFF3 attributes per Robert Buels patch
Fix for segments to have a defined length
Bio::Tools::Gel
Updated the synopsis
Bio::Tools::Geneid
Removed redundant "if $self->verbose" suffix from "$self->debug()" calls
Bio::Tools::Genewise
Issue #1980
Issue #1973
Removed redundant "if $self->verbose" suffix from "$self->debug()" calls
Bio::Tools::Genomewise
Removed redundant "if $self->verbose" suffix from "$self->debug()" calls
Bio::Tools::Glimmer
Added support for GlimmerHMM and clarified that module does not support Glimmer2 and Glimmer3.
Bio::Tools::GuessSeqFormat
Throw, not die
Deleting debugging comments
Bio::Tools::HMM
No setting of own $VERSION
Bio::Tools::HMMER::Results
Fixed wrong bugzilla URL.
Replaced Carp::carp with $self->warn()
Bio::Tools::HMMER::Set
Checking URLs
Bio::Tools::Hmmpfam
Adding short description
Bio::Tools::IUPAC
Fixes for new amino acid codes 'J', 'O'
Bio::Tools::Lucy
Removed references to deprecated/removed Bio::Tools::Blast
Bio::Tools::OddCodes
Cleaned up documentation and improved method examples
Throw, not die
Corrected URL for bugzilla (removed "www." prefix)
Bio::Tools::Phylo::Molphy
Improved NAME, SYNOPSIS, DESCRIPTION docs
Bio::Tools::Phylo::Molphy::Result
Improved NAME, SYNOPSIS, DESCRIPTION docs
Corrected confusing grammar/tense in throw() message for parameter type-checking.
Bio::Tools::Phylo::PAML
Capturing number of parameters as tree id
Added parsing for beta_w1
Uops -- there was a type in the last commit
Sometimes the omega is too big and there is no space
Treefile is seqfile instead in paml (this is only cosmetic)
PAML 3.15 parsing supported
Issue #1983, parse NEB and BEB sites from PAML 3.15 properly now so that all model reports are parsed
Ryan's version
Ryan Golhar's fixes for 3.15 parsing
Issue #2054
Issue #1883
Issue #2055; committing these in steps in case of rollbacks
Bio::Taxonomy overhaul, see Issue #2061
Issue #2080
Replaced Bio::Root::IO->catfile/rmtree/$TEMPDIR with File::Spec and File::Path native Perl 5.6.1 equivalents.
Move get_posteriors comments to TO DO section
More API doc in the SYNOPSIS
Bio::Tools::Phylo::PAML::ModelResult
Issue #1983, parse NEB and BEB sites from PAML 3.15 properly now so that all model reports are parsed
Corrected confusing grammar/tense in throw() message for parameter type-checking.
Bio::Tools::Phylo::PAML::Result
Adding seqfile method -- it may not make sense for this to set, but it makes to get
Corrected confusing grammar/tense in throw() message for parameter type-checking.
Bio::Tools::Phylo::Phylip::ProtDist
Improved NAME, SYNOPSIS, DESCRIPTION docs
Bio::Tools::Primer3
Some hashes were used for temporary storage in next_primer(), removed them for simplicity
Issue #1833
Email changed
Bio::Tools::Promoterwise
Improved NAME, SYNOPSIS, DESCRIPTION docs
Bio::Tools::QRNA
Throw, not die
Bio::Tools::RNAMotif
Initial commit
Changed line endings from Windows to UNIX
Add clean_features method; returns hits based on score, location as Bio::Seqfeature::Collection object
Fixed silly mistake in clean_features.
Fix error in clean_features where last SeqFeature may be left off
Forgot to take out debugging before committing.
Make seqfeature tags more like Bio::Tools::ERPIN
Minor changes; plan on makeover for these soon (maybe move to SearchIO?)
Remove debugging stuff
Now with 'our'
Bio::Tools::RandomDistFunctions
Throw, not die
Bio::Tools::RepeatMasker
Emmanuel Quevillon's reported bug in creating feature2, I also simplified code into 2 new calls
Add Id line
Use internal warn instead of STDERR
Fix RepeatMasking - features were flipped 1/2
Adding short description
Bio::Tools::RestrictionEnzyme
Add DEPRECATED
Module cleanup. Shame I didn't realise it was deprecated until afterwards!
Add deprecation warnings
Warn, not warning (duh....)
Bio::Tools::Run::GenericParameters
Added available_* methods so GenericResult can delegate, made GenericResult use objects properly
Bio::Tools::Run::RemoteBlast
Throw, not die
Further removing myself from direct responsibility... =)
Issue #1935; save XML output
Applied Sendu Bala's patch (Issue #2015)
Issue #2007
Add option to change default URL (highly experimental, emphasis on the 'mental')
Perltidy'd for future work
Save tabular blast output
Avoid UTF-8 warnings
Bio::Tools::Run::StandAloneBlast
Torsten's patch
Documentation and formatting cleanup
Updated valid command line switches for NCBI BLAST tools.
Minor logic and formatting changes.
Added support for "-param" options as well as "param" as per Bioperl Issue #1912
Named parameters in docs
Replaced '/dev/null' with File::Spec->devnull
Replaced Bio::Root::IO->catfile/rmtree/$TEMPDIR with File::Spec and File::Path native Perl 5.6.1 equivalents.
Bio::Tools::Run::WrapperBase
Replaced Bio::Root::IO->catfile/rmtree/$TEMPDIR with File::Spec and File::Path native Perl 5.6.1 equivalents.
Is an abstract base class, not an interface - use Bio::Root::Root
Bio::Tools::Seg
Issue #1898
Completely re-wrote and documented Seg.pm parser and added sample input and tests.
Bio::Tools::SeqAnal
Removing files from CVS HEAD which were scheduled for removal in version 1.1 but were still hanging around.
Bio::Tools::SeqPattern
Get rid of $`,$&
Bio::Tools::SeqStats
Throw, not die
Added hydropathicity() calculation.
Silence a warning
Bio::Tools::SiRNA::Ruleset::saigo
Repaired mis-use of $self->debug ; all tests pass.
Bio::Tools::SiRNA::Ruleset::tuschl
Get rid of $`,$&
Bio::Tools::Signalp
Adding short description
Bio::Tools::Sim4::Results
Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"
Bio::Tools::Spidey::Results
Throw, not die
Removed false/redundant comment "# Object preamble - inherits from Bio::Root::Object"
Bio::Tools::Tmhmm
Totally reimplemented TMHMM parser and added previously non-existent tests.
Bio::Tools::WWW
Removing files from CVS HEAD which were scheduled for removal in version 1.1 but were still hanging around.
Bio::Tools::WebBlat
HTTP::Response, not LWP
Made (env_proxy => 1) the default for LWP::UserAgent instantiations
No setting of own $VERSION
Bio::Tools::dpAlign
Added Ends-Free Alignment support
Fixed a bug that complains when you specify ends-free alignment
Sorry another minor fix
No setting of own $VERSION
Bio::Tools::pICalculator
Throw, not die
Correct URL for description of EMBOSS "iep" program
Adding short description
Bio::Tools::tRNAscanSE
Fix return type - thanks to Ryan Morin @ BCGSC.ca
Bio::Tree::Compatible
Postorder is postorder_traversal
Fixed sub topological_restriction
Bio::Tree::Draw::Cladogram
Added branch coloring
Added label coloring
Revised drawing colored branches
Fixed drawing colored branches
Bio::Tree::Node
Support alpha sorting for node order in each_Descendent
Allow arbitrary code to passed in for sorting
Oops - need to keep mapping, undo stupid change
Undo change to sub height
Bio::Taxonomy overhaul, see Issue #2061
When branch length changes, so does the tree height
Weaken refs to avoid circular references
Bio::Tree::NodeI
Clarify documentation
Rejigger sort order so it doesn't require query to get the height (by default)
Bio::Tree::NodeNHX
Only write NHX block when there is something to write
Bio::Tree::Tree
ID and SCORE are settable at init time
Rejigger sort order so it doesn't require query to get the height (by default)
Bio::Taxonomy overhaul, see Issue #2061
Bio::Tree::TreeFunctionsI
Create nodes of the same type as the existing nodes when re-rooting
Bio::Taxonomy overhaul, see Issue #2061
Issue #2082
Bio::Tree::TreeI
Rejigger sort order so it doesn't require query to get the height (by default)
Bio::Taxonomy overhaul, see Issue #2061
Bio::TreeIO
Allow newline separated clustalW dendogram style output
Bio::TreeIO::cluster
Corrected confusing grammar/tense in throw() message for parameter type-checking.
Issue #2151
Bio::TreeIO::newick
Sort node order so that it can be consistently printed out for same node set
Allow newline separated clustalW dendogram style output
Hackily parse score and associate it with a tree
Bio::TreeIO::nexus
Proper nexus writing, map the names to numbers in the tree writing
Proper nexus writing, map the names to numbers in the tree writing; merge to branch for fun
Bio::TreeIO::nhx
Issue #1823; write internal node ids in nhx format
Allow newline separated clustalW dendogram style output
Bio::Variation::IO::flat
Changed "if not" to "if not defined" for numeric regexp captures
Bio::Variation::VariantI
Use $self->throw_not_implemented();
Bio::WebAgent
Made (env_proxy=>1) the default in the constructor while maintaining ability for user to over-ride it by passing (env_proxy=>0).
Replaced warn() with $self->warn()
New() no longer expects all args are method names, allowing complex inheritance
Fix for last commit
Warning in sleep was only supposed to happen when verbose; changed to debug()
Build.PL
Moved to Module::Build installation system
Removed extraneous comment
Added bioperl.lisp to MANIFEST.SKIP
MANIFEST.SKIP deprecated module Bio/Tools/WebBlat.pm
Corrected comment
New Build.PL system added to branch
Made required pre_reqs from bioperl 1.5.1 requirments in 1.5.2 as well
Nicer BioDBGFF questions
Added dynamic_config, clarified BioDBGFF feedback
Additions to get `perl Build.PL` to complete successfully on Windows with ActivePerl 819 and no DBD::mysql
Fixed bug which caused the Bio::DB::SeqFeature::berkeleydb regression test to fail with a "./features.idx not found" error
Fixed bug which caused the Bio::DB::SeqFeature::berkeleydb regression test to fail with a "./features.idx not found" error
Better auto-feature checking for BioDBGFF test
Better auto-feature checking for BioDBGFF test
No printing undef
Added URI::Escape as an optional pre-req
FAQ
Remove FAQ
Makefile.PL
Removed unused and outdated Bio::LiveSeq::IO::SRS class from the distribution
Note that Set::Scalar is needed by Bio::Tree::Compatible
Comments on Set::Scalar
Added dependency on Convert::Binary::C needed by Bio::SeqIO::strider
Added dependency HTML::Parser > 3.0 for Bio::DB::GDB
Commented out unnecessary 'IO::Scalar' dependency for now non-existent Bio::Tools::Blast::Run::Webblast
Removed the deleted documentation files
Added new dependencies: t/chaosxml...................Data::Stag::Writer t/interpro...................XML::DOM::XPath t/table......................Spreadsheet::ParseExcel
OBOEngine.pm replaces SimpleGOEngine.pm
Rearranged dependencies
Getting rid of tabs!
More ordering
Fixed small formatting error that disabled Makefile
Add XML::Simple
Added regression tests for Bio::DB::SeqFeature::Store (memory,bdb + mysql)
Now uses %packages to create a hash for PREREQ_PM. "perl Makefile.PL" uses this to check for prerequisites and reports any that are missing. In addition, "nmake ppd" will now result in PPD containing all the prerequisites listed in %packages.
Overhauled: use strict; use File::Spec; pre-reqs corrected; bugs fixed; clearer output; delete created files on make clean; reordered for sanity
Removed unnecessary comments
IO::String pre-reqs correction
Another pre-req correction
Corrected install path
Added comment to clarify external dependencies are optional
We need at least v1.01 of Class::AutoClass
Exclusion system to avoid circular dependencies
Nicer messaging for excluded prereqs, forced to ask for 1.0 of Class::AutoClass, not 1.01
Removed unneccessary use
Clearer version checking
Correct strict problem
Some modules don't define VERSION, default to 0
Use single quotes for system calls to prevent interpolation
Need 'use IO::File' statement
Moved to Module::Build installation system
Added Makefile.PL back as a stub that just issues a warning
Warning that Build.PL is preferred
Improved warning message, pre_reqs do not include optional modules
Improved warning message, pre_reqs do not include optional modules
Reverted back to stub for HEAD
ModuleBuildBioperl.pm
Moved to Module::Build installation system
When have ll pre-reqs, dont complain
Nice, CPAN-aware dist names
Nice, CPAN-aware dist names, correction
Nice, CPAN-aware dist names, further correction
New Build.PL system added to branch
CPAN doesn't like RC in middle of version number?
CPAN doesn't like RC in middle of version number?
Dist runs manifest and creates all archive forms
Dist runs manifest and creates all archive forms
CPAN doesn't support optional_features syntax? Include recommends as well...
CPAN doesn't support optional_features syntax? Include recommends as well...
Removed duplicated methods
Offer to install optional deps
Comment clarification
Improved module install question, corrected comments, added bootstrap to install Module::Build
No need for print_build_script() override, add self to INC just in case
Generalized checking types, added excludes_os type
Fixed interactive script installation, allowed install of .pl files
Fix strange stringify bug
Update fix from HEAD
Explicitly require v0.2805 of Module::Build since some earlier versions do not have Module::Build::Notes
bptutorial.pl
Correct URL
Correct URL
Correct translate() docs
Better way to pass alternative initation codon to translate()
Wiki addresses
No more BPLite
Created a dummy entry for run_test number 7, modified list of all tests to ignore test no 7
Fixed formatting and URL's
Fixed remote blast tutorial (was using BPLite, maybe?)
RemoteBlasts are not performed with StandAloneBlast!
Change input file for Structure tutorial
Remove bptutorial.pl, the tutorial is now in the Wiki.
Was removed from HEAD
doc/Deobfuscator/Build.PL
Deobfuscator 1st check-in
doc/Deobfuscator/Changes
Deobfuscator 1st check-in
Committing BioPerl Deobfuscator v0.0.3. See CHANGES file for details.
NEW: -s <version_string> option now can be passed to deob_index.pl to store a version string in packages.db which deob_interface.cgi can read and show.
doc/Deobfuscator/LICENSE
Deobfuscator 1st check-in
doc/Deobfuscator/MANIFEST
Deobfuscator 1st check-in
Committing BioPerl Deobfuscator v0.0.3. See CHANGES file for details.
doc/Deobfuscator/META.yml
Deobfuscator 1st check-in
Committing BioPerl Deobfuscator v0.0.3. See CHANGES file for details.
doc/Deobfuscator/Makefile.PL
Deobfuscator 1st check-in
doc/Deobfuscator/README
Deobfuscator 1st check-in
Committing BioPerl Deobfuscator v0.0.3. See CHANGES file for details.
doc/Deobfuscator/bin/deob_index.pl
Deobfuscator 1st check-in
Committing BioPerl Deobfuscator v0.0.3. See CHANGES file for details.
Deob_index.pl now accepts relative paths for BioPerl lib dir and output dir
NEW: -s <version_string> option now can be passed to deob_index.pl to store a version string in packages.db which deob_interface.cgi can read and show.
Updating USAGE
doc/Deobfuscator/cgi-bin/deob_detail.cgi
Deobfuscator 1st check-in
Committing BioPerl Deobfuscator v0.0.3. See CHANGES file for details.
doc/Deobfuscator/cgi-bin/deob_flowchart.png
Deobfuscator 1st check-in
doc/Deobfuscator/cgi-bin/deob_help.html
Deobfuscator 1st check-in
Committing BioPerl Deobfuscator v0.0.3. See CHANGES file for details.
doc/Deobfuscator/cgi-bin/deob_interface.cgi
Deobfuscator 1st check-in
Committing BioPerl Deobfuscator v0.0.3. See CHANGES file for details.
NEW: -s <version_string> option now can be passed to deob_index.pl to store a version string in packages.db which deob_interface.cgi can read and show.
doc/Deobfuscator/excluded_modules.txt
Committing BioPerl Deobfuscator v0.0.3. See CHANGES file for details.
doc/Deobfuscator/lib/Deobfuscator.pm
Deobfuscator 1st check-in
Committing BioPerl Deobfuscator v0.0.3. See CHANGES file for details.
doc/Deobfuscator/t/00.load.t
Deobfuscator 1st check-in
doc/Deobfuscator/t/pod.t
Deobfuscator 1st check-in
doc/README
Add README
examples/Bio-DB-GFF/load_ucsc.pl
Issue #2060
examples/root/README
Inclusion of Error.pm causes CPAN indexing failure, removed
Inclusion of Error.pm causes CPAN indexing failure, removed
examples/root/lib/Error.pm
Inclusion of Error.pm causes CPAN indexing failure, removed
Inclusion of Error.pm causes CPAN indexing failure, removed
examples/tools/extract_genes.pl
Add script that extracts genes
Better docs
A bit more
examples/tools/run_primer3.pl
Add example script
Change email
examples/tools/standaloneblast.pl
Removed code referring to BPLite, but script still does not work
maintenance/README
Added list of dependencies
maintenance/check_NAME.pl
Removed cut-paste cruft and added count summary.
maintenance/check_URLs.pl
Fix regexp to also clean URLs ending with ")."
Improved removal of non-URL punctuation at end of embedded URLs
maintenance/cvs2cl_by_file.pl
Hack version of cvs2cl.pl that is file-centric, useful for doing Change Log updates
Highlight bug fixes, skip trivial commits
maintenance/modules.pl
Throw, not die
Better "untested" functionality
Improve untested() to take into account syntax to import methods, e.g. use Bio::Align::Utilities qw(aa_to_dna_aln bootstrap_replicates);
maintenance/ncbi_blast_switches.pl
Maintenance Perl script to summarize the command line switches of the NCBI BLAST tools, so updating the @PARAMS in StandAloneBlast.pm is easier and more accurate.
maintenance/symlink_script.pl
Moved to Module::Build installation system
Newline after printing message
Newline after printing message
New Build.PL system added to branch
maintenance/symlink_scripts.PLS
Moved to Module::Build installation system
scripts/Bio-DB-GFF/bulk_load_gff.PLS
Documented that maxfeature must be a power of 10
Added an "analyze" step after loading data - should make queries faster
Added albert smith's fix to mixed gff2/gff3 file loading
Made the bulk and fast loaders reset gff3 tag each time a ##gff-version comment is found
Fixed case-sensitive confusion in the two bulk loaders
Got rid of extraneous debugging message
Added a setting for temporary directory
Fixed syntax error and added temporary directory error reporting to fast loader
Removing postgres password flag (-W doesn't work the way I thought it does)
Fast and bulk loaders no longer leave temporary fasta files lying around
scripts/Bio-DB-GFF/fast_load_gff.PLS
Documented that maxfeature must be a power of 10
Added an "analyze" step after loading data - should make queries faster
Added albert smith's fix to mixed gff2/gff3 file loading
Fixed invalid check for mysql version
Made the bulk and fast loaders reset gff3 tag each time a ##gff-version comment is found
Fixed case-sensitive confusion in the two bulk loaders
Fixed syntax error and added temporary directory error reporting to fast loader
Fast and bulk loaders no longer leave temporary fasta files lying around
I believe I've fixed a bug in the fast loader that caused it to miss some existing types in the database, and possibly fixed an similar bug with groups.
scripts/Bio-DB-GFF/load_gff.PLS
Documented that maxfeature must be a power of 10
Allow shorthand u and p
scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS
Incomplete implementation of a GFF3-compatible store for Bio::SeqFeature objects
Finished documentation for Bio::DB::SeqFeature::Store; Removed Bio::DB::SeqFeature::Store::Cacher because its functionality has been folded into Bio::DB::SeqFeature::Store
Fixed dna and cds glyphs so that letters are correctly aligned to right side of base tick when in flip orientation
Some, but not all, documentation for mysql adaptor
Tweaking interface to work properly with gbrowse
Berkeleydb adaptor is functional; added compress option to reduce database size
Setting -vertical_spacing to zero now suppresses span lines
Remove unecessary use lib
scripts/DB/biofetch_genbank_proxy.PLS
Scripts are installed as .pl files, instructions made to match
scripts/DB/bioflat_index.PLS
Scripts are installed as .pl files, instructions made to match
scripts/README
Removed ^M chars
scripts/install_bioperl_scripts.pl
Redundant
No purpose
scripts/searchio/parse_hmmsearch.PLS
Add Mauricio's script
scripts/seq/seqconvert.PLS
Added some newer SeqIO formats to known_formats array
scripts/taxa/local_taxonomydb_query.PLS
API changed and this is no longer a Taxonomy::Node but a Bio::Taxon object with different methods
scripts/taxa/taxonomy2tree.PLS
Add Gabriel's script
Added contraction of simple paths
Bio::Taxonomy overhaul, see Issue #2061
scripts/utilities/bp_sreformat.PLS
Issue #2073
scripts/utilities/mutate.PLS
New address
Change email
scripts/utilities/pairwise_kaks.PLS
Ryan's fix to deal with inclusion of internal stops in target sequences
scripts/utilities/remote_blast.PLS
New method names
Evan's version
scripts/utilities/search2gff.PLS
Added a whole number of additions, like --addid, --parent, --onehsp, and options for controlling the score, location, and method of a feature.
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