diff --git a/DEPRECATED.md b/DEPRECATED.md
index 411b7249a31bc708a0b8c91a25c90362b6eb0a5e..e8a2629363f3a5c8182c64c3ea920cf310f879a3 100644
--- a/DEPRECATED.md
+++ b/DEPRECATED.md
@@ -8,6 +8,11 @@ When a method is deprecated, a deprecation warning is thrown whenever the method
The warning also contains instructions on replacing the deprecated method and when it will be removed.
A year after deprecation (4 Ensembl releases), the method is removed from the API.
+### Removed in Ensembl Release 91 ###
+
+ - Bio::EnsEMBL::DBSQL::**BaseAdaptor**::*dump_data()*
+ - Bio::EnsEMBL::DBSQL::**BaseAdaptor**::*get_dumped_data()*
+
### Removed in Ensembl Release 88 ###
- Bio::EnsEMBL::**Slice**::*get_all_VariationFeatures()*
@@ -163,7 +168,6 @@ A year after deprecation (4 Ensembl releases), the method is removed from the AP
- Bio::EnsEMBL::**Root**::*stack_trace()*
- Bio::EnsEMBL::**Slice**::*get_all_SNPs()*
- Bio::EnsEMBL::**Slice**::*get_all_genotyped_SNPs()*
- - Bio::EnsEMBL::**Slice**::*get_all_OligoFeatures_by_type()*
- Bio::EnsEMBL::**Slice**::*get_all_supercontig_Slices()*
- Bio::EnsEMBL::**Slice**::*get_Chromosome()*
- Bio::EnsEMBL::**Slice**::*chr_name()*
diff --git a/docs/ensembl_changes_spec.txt b/docs/ensembl_changes_spec.txt
deleted file mode 100644
index 0670adfca6619ea3f06a7e09266987dc986d7b09..0000000000000000000000000000000000000000
--- a/docs/ensembl_changes_spec.txt
+++ /dev/null
@@ -1,955 +0,0 @@
-ENSEMBL - API Change Specification
-==================================
-
-CONTENTS
---------
-
-Introduction
-Goals
-Schema Modifications
- Proposed New/Modified Tables
- seq_region
- coord_system
- seq_region_annotation
- dna
- assembly
- gene
- transcript
- translation
- all feature tables
- meta_coord
- misc_feature
- misc_set
- misc_feature_misc_set
- misc_attrib
- Removed Tables
- contig
- clone
- chromosome
-Meta Information
-API Changes
- Slice
- Tile
- SliceAdaptor
- RawContig
- RawContigAdaptor
- Clone
- CloneAdaptor
- Chromosome
- ChromosomeAdaptor
- Root
- Storable Base Class
- Features
- transform
- transfer
- move
- project
- StickyExon
- AssemblyMapper
- FeatureAdaptors
- CoordSystemAdaptor
-New Features
- Assembly Exceptions
- Haplotypes
- Pseudo Autosomal Regions
- Multiple Assemblies
-Other Considerations
- Loci
-
-
-INTRODUCTION
-------------
-
-This document describes the changes that are being made to the EnsEMBL core
-schema and Perl/Java/C APIs.
-
-GOALS
------
--A cleaner, more intuitive API
--A more general schema able to better capture divergent assembly types
--More flexibility with regards to assembly related data such as haplotypes,
- PARs, WGS assemblies etc.
-
-SCHEMA MODIFICATIONS
---------------------
-
-Proposed New/Modified Tables:
------------------------------
-
- seq_region
- ----------
- The seq_region table is a generic replacement for the clone, contig,
- and chromosome tables. Additionally supercontigs which were formerly in the
- assembly table are also present in this table. The name column can contain
- chromosome names, clone accessions, supercontig names or anything that is
- appropriate for the seq_region it describes. The coord_system_id is a
- foreign key to the new coordinate system and is used to distinguish
- between the divergent types of sequence regions in the table.
-
- seq_region_id int
- name varchar
- coord_system_id int references coord_system table
- length int
-
-
- coord_system
- ------------
- The coordinate system table lists the available coordinate systems in the
- database. The attrib is mysql set and is used to denote the default version
- of each named coordinate system. E.g. there may be two 'chromosome' coordiate
- systems and the default may be version 'NCBI34'. The 'top_level' and
- sequence level attribs denote the coordinate system from which sequence is
- retrieved and the coordinate system which has the largest assembled pieces.
- The top_level coordinate system will usually be 'chromosome' but for some
- shrapnel assemblied this may be something like 'supercontig' or 'clone'.
-
- There may be multiple toplevel coordinate systems providing that they share
- the same name (but different version) and providing one of them is the
- default. There may only be a single sequence level coordinate system.
-
- Note that the version in the coordinate system can be viewed as applying
- to every seq_region of a given coordinate system. It is analagous to
- a CVS tag, not a CVS version. E.g. The version would 'NCBI33' apply to
- every chromosome seq_region so it is a valid version. A clone accession of
- '8' would not be a valid version because it only describes a particular
- seq_region of the coordinate system - not all of them.
-
- coord_system_id int
- name varchar
- version varchar
- attrib set ('top_level', 'default_version', 'sequence_level')
-
-
- seq_region_annotation
- ---------------------
- This table allows for extra arbitrary information to be attached to
- seq_regions. For example the htg_phase was formerly part of the clone table
- but now is stored in this table.
-
- seq_region_id int
- attrib_type_id smallint references attrib_type table
- value varchar
-
-
- dna
- ---
- Formerly the contig table referenced the dna table. Now the dna table
- refrences the seq_region_table. Every seq_region which has a coordinate
- system with the 'sequence_level' attrib should be referenced by an entry in
- the dna table.
-
- seq_region_id int
- sequence varchar
-
-
- assembly
- --------
- The assembly table has been made more generic. Columns that previously
- were names chr_* and contig_* have been renamed asm_* and cmp_* (assembled
- and component) respectively. The superctg_name column has been removed.
- Supercontigs are now defined in the seq_region table.
-
- The makeup of all seq_regions from smaller seq_regions can be described in
- this table. The relationships which are explicitly defined must be listed
- in the meta table. For example, the clone <-> contig mapping used to be
- defined in the contig table with an embl_offset column. This information is
- now found in this table instead.
-
- asm_seq_region_id int
- asm_start int
- asm_end int
- cmp_seq_region_id int
- cmp_start int
- cmp_end int
- ori tinyint
-
- gene
- ----
- For faster retrieval and retrieval independently of transcripts and
- exons, genes have a seq_region_id, seq_region_start and seq_region_end
- which defines the span of their transcript.
-
- The transcript_count column has been removed as it was never used.
-
- gene_id int
- type varchar
- analysis_id int
- seq_region_id int
- seq_region_start int
- seq_region_end int
- seq_region_strand tinyint
- display_xref_id int
-
-
- transcript
- ----------
- For faster retrieval and retrieval independently of genes and exons
- transcripts also have a seq_region_id, seq_region_start and
- seq_region_end. The translation_id has been removed; translations will point
- to transcripts instead (and pseudogenes will have no translation).
-
- The exon_count column has been removed as it was never used.
-
- transcript_id int
- gene_id int
- seq_region_id int
- seq_region_start int
- seq_region_end int
- seq_region_strand tinyint
- display_xref_id int
-
-
- translation
- -----------
- Translations now reference transcripts rather than transcripts referencing
- a single (or no) translation. This allows for more elegant handling of
- pseudogenes (where there is no translation) and also can be used to supply
- multiple translations for a single transcript (e.g. polycistronic genes).
-
- translation_id int
- transcript_id int
- start_exon_id int
- end_exon_id int
- seq_start int
- seq_end int
-
-
- all feature tables
- ------------------
- All feature tables would now have seq_region_id, seq_region_start,
- seq_region_end, seq_region_strand instead of contig_id, contig_start,
- contig_end. This includes the repeat_feature, simple_feature,
- dna_align_feature, protein_align_feature, exon, marker_feature,
- karyotype and qtl_feature tables.
-
- meta_coord
- ----------
- The meta coord table defines what coordinate systems are used to store each
- type of feature. A given type of feature may be stored in multiple
- coordinate systems, but these will not be retrieved by the API unless there
- is an entry in the meta_coord table.
-
- table_name varchar
- coord_system_id int
-
-
- misc_feature
- ------------
- This is a renaming of the mapfrag table. The renaming reflects the fact that
- this table can be used to store any type of feature.
-
- misc_feature_id
- seq_region_id
- seq_region_start
- seq_region_end
- seq_region_strand
-
- misc_set
- --------
- This table was formerly names mapset. It defines 'sets' that can be used
- to group misc_features together.
-
- misc_set_id smallint
- code varchar
- name description
- description text
- max_length int
-
- misc_feature_misc_set
- ---------------------
- This is a link table defining the many-to-many relationship between the
- misc_set and misc_feature tables.
-
- misc_feature_id int
- misc_set_id smallint
-
-
- misc_attrib
- -----------
- This table was formerly named mapfrag_annotation. It contains arbitrary
- annotations of misc_features and links to the same attrib_type table that
- the seq_region_attrib table uses.
-
- misc_feature_id int
- attrib_type_id smallint
- value varchar
-
-
-
-Removed Tables
---------------
-
- contig
- ------
- Contigs are no longer needed. They are stored as entries in the seq_region
- table with type 'contig'. The embl_offset and clone_id will not be
- necessary as their relationship to clones can be described by the
- assembly table.
-
- clone
- -----
- Clones are no longer needed. Clones are stored as entries in the seq_region
- table with coord_system 'clone'. The modified timestamp will be discarded
- as it is no longer maintained anyway. The embl_acc, version, and
- embl_version columns are redundant and will also be discarded. Versions
- are simply appended onto the end of the name with a delimiting '.'.
-
- Any additional information that needs to be present (such as htg_phase) can
- be added to the seq_region_attrib table.
-
- chromosome
- ----------
- This table is no longer needed. Chromosomes can be stored in the
- seq_region table with a 'chromosome' coord_system.
-
-
-
-META INFORMATION
-----------------
-
-Considerable more meta information is stored in the core
-databases in order for the general approach to be maintained.
-This information is stored in the new coord_system table and in the
-meta, and meta_coord tables.
-
-Meta information includes the following:
-
- * The coordinate system that features of a given type are stored in. This
- information is stored in the meta_coord table and is used when constructing
- queries for a particular feature table.
-
- * The top-level coordinate system. For human
- this would be 'chromosome'. For briggsae this may be something like
- 'scaffold' or 'super contig'. This information would be used to construct
- the web display and would possibly be the default coordinate system when
- a coordinate system is unspecified by a user. This is stored as a flag
- in the coord_system table.
-
- * The default version of each coordinate system. This is stored as a flag
- in the coord_system table.
-
- * The coord_system where sequence is stored. This will be stored as a
- flag in the coord_system table. Initially it will only be possible
- to have a single coord_system in which sequence is stored. This
- may be extended in the future to allow sequence to be stored for multiple
- coord_systems.
-
- * The coordinate system relationships between that are explicitly defined
- in the assembly table. The new API is capable of 2 step (implicit) mapping
- between coordinate systems, but these relationships can be determined
- through the direct relationship information.
-
- For example the clone, chromosome and nt_contig coordinate systems may all
- be constructed from the contig coordinate system:
- contig -> clone
- contig -> chromosome
- contig -> nt_contig
- Or there may be a more hierarchical approach:
- contig -> clone
- clone -> nt_contig
- nt_contig -> chromosome
- This information is stored in the meta table under the key
- 'assembly.mapping' with the following format (versions are optional):
- assembled_coord_system_name[:version]|component_coord_system_name[:version]
-
- For example the meta table for human might contain the following entries:
- mysql> select * from meta where meta_key = 'assembly.mapping';
- +---------+------------------+--------------------------+
- | meta_id | meta_key | meta_value |
- +---------+------------------+--------------------------+
- | 43 | assembly.mapping | chromosome:NCBI33|contig |
- | 44 | assembly.mapping | clone|contig |
- | 45 | assembly.mapping | supercontig|contig |
- +---------+------------------+--------------------------+
-
- * The names of the allowable coordinate systems. This would allow for
- quick validation of API requests and provide a list that could be used
- by the website for coordinate system selection. This information will be
- stored in the coord_system table.
-
- * The coordinate system(s) that each feature type is stored in. This is
- stored in the meta_coord table.
-
-
-API CHANGES
------------
-
-Slice
------
- Slice methods chr_start, chr_end, chr_name will be renamed start, end,
- seq_region_name. For backwards compatibility the old methods are
- chained to the new methods with deprecated warnings.
-
- A new slice method 'coord_system' will be added and will return a
- Bio::EnsEMBL::CoordSystem object.
-
- Slices will represent a region on a seq_region as opposed to a region on a
- chromosome. Slices will be immutable (i.e. their attributes will not be
- changeable). A new slice will have to be created if the attributes are to
- be changed.
-
- The following attributes will therefore define a unique slice:
- coord_system (e.g. object with name and version)
- seq_region_name (e.g. 'X' or 'AL035554.1')
- start (e.g. 1000000 or 1)
- end (e.g. 2000001 or 800)
- strand (e.g. 1 or -1)
-
- The name method will return the above values joined by a ':' delimiter, and
- will not be settable:
- e.g. 'chromosome:NCBI33:X:1000000:2000001:1' or 'clone::AL035554.1:1:800:-1'
- This value can be used as a hashvalue that uniquely defines a slice.
-
- The concept of an 'empty' slice will no longer exist.
-
- The get_tiling_path method will be deprecated in favour of a more general
- method project(). Whereas get_tiling_path() implies a relationship between
- an assembly and the coordinate system which makes up the assembly the
- project method will allow conversion accross any two coordinate systems.
- It will take a coord_system string as an argument and rather
- than returning a list of Tile objects it will return a listref of triplets
- containing a start int, and end int, and a 'to' slice object. The following
- is an example of how this method would be used ($clone is a reference to a
- slice object in the clone coordinate system):
-
- my $clone_path = $slice->project('clone');
-
- foreach my $segment (@$clone_path) {
- my ($start, $end, $clone) = @$segment;
- print $slice->seq_region_name, ':', $start, '-', $end , ' -> ',
- $clone->seq_region_name, ':', $clone->start, '-', $clone->end,
- $clone->strand, "\n";
- }
-
- An optional second argument to project() will be the coordinate
- system version. E.g.:
- $ncbi34_path = $slice->project('chromosome','NCBI34').
-
-
-Tile
-----
- The tile object will no longer be necessary. However for backwards
- compatibility it will remain in the system for some time before being phased
- out along with the get_tiling_path method.
-
-
-SliceAdaptor
-------------
- The Slice adaptor must provide a method to fetch a slice via its coordinate
- system, seq_region_name, start, end, and strand.
- The old, commonly used method fetch_by_chr_start_end has been altered to
- simply chain to this new method (with a warning) as do most other
- SliceAdaptor methods.
-
- Another method which is necessary with the disapearence of the Clone,
- RawContig and Chromosome adaptors is one which allows for all slices
- of a certain type to be retrieved. For example it is often necessary to
- retrieve all chromosomes, or clones for a species. This method is simply
- named fetch_all. The old fetch_all methods on the ChromosomeAdaptor,
- RawContigAdaptor, CloneAdaptor, etc. chain to the new method for backwards
- compatibility.
-
- Method Names and Signatures
- ---------------------------
- Slice fetch_by_region(coord_system, name)
- Slice fetch_by_region(coord_system, name, start)
- Slice fetch_by_region(coord_system, name, start, end)
- Slice fetch_by_region(coord_system, name, start, end, strand)
- Slice fetch_by_region(coord_system, name, start, end, strand, version)
- listref of Slices fetch_all(coord_system)
- listref of Slices fetch_all(coord_system, version)
-
-RawContig
----------
- The RawContig object is no longer necessary with the new system. RawContigs
- are replaced by Slices with coord_system = 'contig'. In the interests of
- backwards compatibility the RawContig class will still be present for
- sometime as a minimal implmentation inheriting from the Slice class.
-
-
-RawContigAdaptor
-----------------
- The RawContigAdaptor is no longer necessary. The RawContigAdaptor is
- replaced by the SliceAdaptor. For backwards compatibility a minimal
- implementation of the RawContigAdaptor will remain which inherits from the
- SliceAdaptor.
-
-Clone
------
- The Clone object is no longer necessary in the new system. Clones are
- replaced by Slices with coord_system = 'clone'. For backwards compatibility
- a minimal implementation will remain which inherits from the Slice object.
-
-CloneAdaptor
-------------
- The CloneAdaptor object is no longer necessary in the new system. The
- CloneAdaptor is replaced by the SliceAdaptor. For backwards compatibility
- a minimal implementation will remain which inherits from the SliceAdaptor.
-
-Chromosome
-----------
- The Chromosome object is no longer necessary in the new system. The
- Chromosome is replaced by Slices with coord system 'chromosome' (or
- whatever the top level seq_region type is for that species). For backwards
- compatibility a minimal implementation will remain which inherits from the
- Slice object.
-
- Statistical information (e.g. known genes, genes, snps) that
- was on chromosomes may be stored in the seq_region_attrib table or
- in some sort of density table.
-
-ChromosomeAdaptor
------------------
- The Chromosome object is no longer necessary in the new system. The
- ChromosomeAdaptor is replaced by the SliceAdaptor. For backwards
- compatibility a minimal implementation which inherits from the SliceAdaptor
- will remain.
-
-
-Root
-----
- Every class in the current EnsEMBL perl API inherits directly or indirectly
- from Bio::EnsEMBL::Root. This inheritance is almost exclusively for the
- following following three methods:
- throw
- warn
- _rearrange
-
- Nothing is gained by implementing this relationship as inheritance, and there
- are several disadvantages:
- (1) Everything must inherit from this class to use those 3 object methods.
- This can result in patterns of multiple inheritance which are generally
- considered to be a bad thing.
-
- (2) It is not possible to use the throw, warn or rearrange method within
- the constructor until the object is blessed. Blessing the object first
- and then calling rearrange to extract named arguments is slower because
- the blessed hash needs to be expanded as more keys are added and several
- key access/value assignements may need to be performed.
-
- (3) Objects become larger and object construction becomes slightly slower
- because constructors traverse an additional level of inheritance.
-
- A better approach, which we have used, is to make the methods static and
- create a static utility class that exports the methods. The warn method has
- been renamed warning so as not to conflict with the builtin perl function
- warn and the _rearrange method has be renamed rearrange.
-
- The following is an example of the old styl Root inheritance and the new
- style static utility methods:
-
- #
- # OLD STYLE
- #
- package Old;
-
- use Bio::EnsEMBL::Root;
-
- @ISA = qw(Bio::EnsEMBL::Root);
-
- sub new {
- my $caller = shift;
- my $class = ref($caller) || $caller;
-
- $self = $class->SUPER::new(@_);
-
- my ($start, $end) = $self->_rearrange(['START', 'END'], @_);
-
- if(!defined($start) || !$defined($end)) {
- $self->throw('-START and -END arguments are required');
- }
-
- $self->{'start'} = $start;
- $self->{'end'} = $end;
-
- return $self;
- }
-
- #
- # NEW STYLE
- #
- package New;
-
- use Bio::EnsEMBL::Utils::Exception qw(throw warning);
- use Bio::EnsEMBL::Utils::Argument qw(rearrange);
-
- sub new {
- my $caller = shift;
-
- my $class = ref($caller) || $caller;
-
- my ($start, $end) = rearrange(['START', 'END'], @_);
-
- if(!defined($start) || !defined($end)) {
- throw('-START and -END arguments are required');
- }
-
- return bless {'start' => $start, 'end' => $end}, $class;
- }
-
- The calls to $self->rearrange $self->warn and $self->throw have been
- replaced by class method calls to warning() and throw() inside the core API.
- However, for backwards compatibility the existance inheritance to
- Bio::EnsEMBL::Root will remain in many cases (and be removed at a later date)
-
-
-Storable Base Class
--------------------
- Almost all business objects in the EnsEMBL system are storable in the db
- and the ones which are always require 2 methods: dbID() and adaptor(). These
- methods have been moved to a Storable base class which most of the
- business objects now inherit from. This module has an additional method
- is_stored() which takes a database argument and returns true if the object
- appears to already have been stored in the provided database.
-
-Features
---------
- All features should inherit from a base class that implements common feature
- functionality. Formerly this role was filled by the bloated SeqFeature class
- which inherits from Bio::SeqFeature and Bio::SeqFeatureI etc.
- This class has been replaced by a smaller, less complicated
- implementation named Feature. To make classes more polymorphic in general,
- the gene, and transcript objects should now also inherit from the Feature
- class. This class implements the following core methods common to all
- features:
-
- start
- end
- strand
- slice (formerly named contig/entire_seq/etc.)
- transform
- transfer
- project
- analysis
-
- The feature class inherits from the Storable base class and thereby inherits
- the following methods:
-
- adaptor
- dbID
- is_stored
-
- The signature and behaviour of the transform method has been changed. The
- existing method works differently depending on the arguments passed as
- described below.
-
- OLD transform(no arguments)
- -----------------------
- Transforms from slice coordinates to contig coordinates. The feature
- is changed in place and returned. If the feature already is in contig
- coordinates an exception is thrown. The feature may be split into two
- features in which case both features are returned (not sure if one of
- them is transformed in place). Some features are not permitted to be
- split in two in which case an exception is thrown? (not sure) if it is
- to be split accross contigs.
-
- OLD transform(slice)
- ----------------
- If the feature is already in slice coordinates and the slice is on the
- same chromosome the features coordinates are simply shifted. If the
- feature is already in slice coordinates but on a different chromosome
- an exception is thrown.
- It the feature is in contig coordinates and the slice is not empty then
- it is transformed onto the new slice (or an exception is thrown if the
- transform would cause the feature to end up on a different chromosome
- than the slice). If the feature is in contig coordinates and the
- slice is an empty slice the feature is transformed into chromosomal
- coordinates and placed on a newly created slice of the entire chromosome.
-
- The new transformation has only a single valid signature and splits its
- responsibilities with the new transfer method. The transfer
- method transfers a feature onto another slice, whereas the transform
- method simply converts coordinate systems. Transform does
- NOT transform features in place but rather returns the newly
- transformed feature as a new object:
-
- transform(coord_system, [version])
- -----------------------
- Takes a single string specifying the new coord system. If the coord
- system is not valid an exception is thrown. If the coord system is the
- same coord system as the feature is currently in a new feature that is
- a copy of the old one is still be returned. This also retrieves
- a slice which is the entire span of the region of the coordinate system
- that this feature is being transformed to. For example transforming
- an exon in contig coordinates to chromosomal coodinates will place a
- copied exon on a slice of an entire chromosome. If a feature spans a
- boundary in the coordinate system, undef is returned by the method
- instead.
-
- transfer(slice)
- ----------------
- Shifts a feature from one slice to another. If the new slice is in the
- same coordinate system but different seq_region_name (e.g. both
- chromosomal but different chromosomes) an exception is thrown.
- If the new slice is in a different coordinate system then the
- transform method is internally called first. If the feature would be
- split across a boundary undef is returned instead. After the transform
- there follows a potential move, if the slice does not cover the full
- seq_region. If there is no transform call necessary, the feature is
- copied and then moved.
-
- move( start, end, strand )
- --------------------------
- In place change of the coordinates of the feature. It will stay on the
- same slice.
-
- project(coord_system, [version])
- -----------------
- This method is analagous to the project method on Bio::EnsEMBL::Slice.
- It 'projects' a feature onto another coordinate system and returns the
- results formatted as a listref of [$start, $end, $feature] triplets.
- The $features returned are copies of the feature on which the method was
- called, but with coordinates in the coordinate system that was projected
- to. If the feature maps entirely to a gap then an empty list ref [] will
- be returned. If the feature is mapped to multiple locations a listref
- containing split features will be returned.
-
-StickyExon
-----------
- The sticky exon object is not be present in the new system. It does not
- make sense to define features in a coordinate system where they are simply
- not present. Exons are calculated in chromosomal coordinates and they
- will generally be retrieved in the same coordinates system. It will
- of course be possible to still retrieve exons in contig coordinates but only
- is they are fully defined on the contigs of interest.
- The split coordinates can be obtained through a call to the project
- method.
-
-
-AssemblyMapper
---------------
- The assembly mapper and assembly mapper adaptor classes have become more
- general and sophisticated.Not only is it possible to map between two
- coordinates systems whose relationship is explicitly defined in the assembly
- table, but it is also possible to perform implicit, 2-step mapping
- using 'coordinate system chaining'.
-
- For example if no explicit relationship is defined between the supercontig
- and clone coordinate systems but relationships between the clone and contig
- and the supercontig and contig coordinate systems is present the mapper has
- the faculty to perform the mapping between the clone and supercontig systems.
- In this case the contig cooridinate system is used as an intermediary:
-
- NTContig <-> Contig <-> Clone
-
- In the above example the assembly mapper adaptor internally does the
- following:
-
- (1) Create a mapper object between the NTContig and Contig region
- (2) Create a mapper object between the Contig and Clone region
- (3) Create and return a third mapper constructed from the sets of mappings
- generated by the intermediate mappers.
-
-
-FeatureAdaptors
----------------
- Most FeatureAdaptors inherit from the BaseFeature adaptor. As a
- minimum feature adaptors provide fetch_all_by_Slice and fetch_by_dbID
- methods. The fetch by slice method provides the same return types and
- requires the same arguments as before, but required some internal changes.
-
- The simplified algorithm for fetching features via a slice is:
-
- (1) Check with coord system is requested or that slice is in.
- (2) Check which coord system features are in
- (3) Obtain mapper between coord systems
- (5) Retrieve features in their native coord system.
- (6) Remap features to the requested coord system using the mapper
- (7) Return the features
-
- The method fetch_all_by_RawContig is obsolete (it is equivalent to
- fetching by a slice of a contig) but has be left in as an alias for the
- fetch all by slice method for backwards compatibility.
-
- When performing a non-locational fetch (e.g. by dbID) features are still
- returned in the coordinate system that they are calculated in. This is to
- ensure that the feature can always be retrieved in this manner of fetching
- and so that features which are not in the database can be distinguished from
- features which are simply not in the requested coordinate sytem. When a
- single feature which is not in the database is requested via a non-locational
- fetch undef is returned instead. If multiple features are requested but none
- are present in the database a reference to an empty list is returned. If the
- features are required in a specific coordinate system the transfer, project
- or transform method can always be used.
-
-
-CoordSystemAdaptor
-------------------
- A CoordSystemAdaptor provides access to the information in the
- coord_system, meta and meta_coord tables. This adaptor provides
- Bio::EnsEMBL::CoordSystem objects.
-
-
-NEW FEATURES
-------------
-
-Assembly Exceptions (Symbolic Sequence Links)
----------------------------------------------
-
- It is sometimes desirable to have multiple regions refer to the same
- sequence.
-
- In much the same way a symlinked file acts as a pointer to a real file,
- a symlinked region can point to another region of sequence.
-
- This can be described in the database through the addition of a table which
- has a structure that mirrors that of the assembly table. The assembly table
- does not define the structure underlying this seq_region, and it does not
- have sequence of its own. By means of the assembly_exception table this
- seq_region points to another seq_region where the underlying sequence is
- defined:
-
- assembly_exception
- ------------------
- seq_region_id int
- seq_region_start int
- seq_region_end int
- exc_type enum('HAP', 'PAR')
- exc_seq_region_id int
- exc_seq_region_start int
- exc_seq_region_end int
- ori int (may not be needed, may implicitly be 1)
-
- When fetching features and sequence from a slice that overlaps a symlinked
- region, the features and sequence from the symlinked region are returned.
- This may be implemented by altering fetch by slice calls and adding a
- SliceAdaptor method with splits a slice into non-symlinked components.
- The following algorithm would apply to sequence and feature fetches:
- (1) Split the slice into non-symlinked component slices
- (2) Recursively call the method with the component slices
- (3) Adjust the start and end of the returned features and place them
- back on the original slice (or splice the sequence together if this
- is a sequence fetch)
- (4) Return the features or sequence
-
- Consider a slice which overlaps regions (A), (B), and (C) on chromosome Y:
-
- =============== (chrX)
- ^^^^^^^^^^^
- ======== symlink ========= (chrY)
- (A) (B) (C)
-
- Regions (A) and (C) are described by the assembly table, but region (B)
- is described in the assembly_exception table and points to a region of
- chromosome Y. When features or sequence are retrieved the slice is split
- into 3 component slices which have no symlinks: region (A) and (C) are
- slices on chromosome Y but region (B) is made into a slice on chromsome (X).
- All of the features are fetched from the individual slices adjusted by
- some addition and placed on back on the original Slice before being
- returned.
-
-
-
-Haplotypes (and the MHC region)
--------------------------------
- There are several requirements related to haplotypes:
- - Must be able to determine which haplotypes overlap a slice
- - Must be able to run genebuild/raw computes over the haplotypes
- - Must be able to retrieve a slice on a haplotype and its flanking
- regions (i.e. the regions of the default assembly bordering the
- haplotype).
- - It may be desireable to interpolate features from the default sequence
- onto the haplotype
-
- Proposal:
- The haplotype will be present as a full length 'chromosome' in the
- seq_region table (or other appropriate coordinate system) but only the
- region which differs from the the default assembly will be described in
- the chromosome table. The regions which are identical will be described
- by the assembly_exception table.
-
- It is possible to retrieve a slice on a haplotype just as any other slice
- is retrieved from the SliceAdaptor. For example:
- $slice = $slice_adaptor->fetch_by_region('chromosome', '6_DR52');
-
- A slice created on a haplotype will have coordinates relative to the
- start of the chromosome NOT relative to the start of the haplotype
- region. For all intents and purposes a haplotype slice will behave as
- a normal slice.
-
- For example, the assembly table could define the composition of the
- divergent region of chromosome 6_DR52 (C), but leave the remainder of the
- chromosomal composition undefined. The remainder of the
- chromosome composition would be accounted for by 2 rows in the
- assembly_exception table which described the synonymous regions in terms
- of chromosome 6:
-
- ============== 6 ============== 6
- ^ ^
- _____|________ _______|______
- C ========== 6_DR52
-
-
-
-
-
-Pseudo Autosomal Regions (PARs)
--------------------------------
- There are several requirements related to PARs:
- - The same sequence and features must be present on a region of
- both chromosome X and chromosome Y
- - The region and features should be returned when retreiving features
- from either chromosome.
- - It must still be possible to retrieve one of the features via its
- identifier
- - It must still be possible to transform features in the region from
- chromosomal coordinates to contig coords and vice-versa.
- - The genebuild should run over the region, but only once.
-
- Proposal:
- Use the assembly_exception table in a similar fashion as it is used
- for the haplotypes described above. Chromosome X can be the 'default'
- chromosome for the PAR and Chromosome Y can be described by the assembly
- table except in the PAR. The PAR on chromosome Y can be defined by the
- assembly_exception table and refer to the corresponding sequence on
- chromosome X. The same algorithm as used for haplotypes can then be used
- when retrieving sequence or features from slices which overlap this
- exception on chromosome Y.
-
- The following diagram illustrates how chromsome X and chromosome Y could
- be defined:
-
- ========================================== X
- ^ ^
- _|_ ____|____
- ====== ============ ============= Y
-
-
-Multiple Assemblies
--------------------
-
-In theory it is possible to load multiple assemblies into the same database.
-For example two coordinate systems with two versions chromosome:NCBI33 and
-chromosome:NCBI34 could be loaded into the database. Leveraging the fact that
-two step mapping is possible and that these coordinate systems share a
-coincident mapping with the contig coorinate system it is possible to pull
-across annotation from one assembly to the other. The following example
-illustrates the transfer of genes from the chromosome X on the NCBI33 assembly
-to the NCBI34 assembly:
-
- $slice = $slice_adaptor->fetch_by_region('chromosome', 'X', undef,
- undef,undef, 'NCBI33');
- @genes = @{$gene_adaptor->fetch_all_by_Slice($slice)};
-
- foreach my $gene (@genes) {
- $gene->transform('chromosome', 'NCBI34');
- #...
- }
-
-
-OTHER CONSIDERATIONS
---------------------
-
-Loci
-----
-
-Similar genes which are defined across haplotypes need
-to be somehow linked into loci. The intent is that
-a user would be able to see that a gene has a counterpart
-on an equivalent haplotypic sequence.
-
-This is work in progress. The current opinion among us is to implement
-it via a relationship table that specifies which genes on default
-haplotypes are considered equivalent to other genes on
-(overlapping) haplotypes.
-
diff --git a/modules/Bio/EnsEMBL/Analysis/PairAlign.pm b/modules/Bio/EnsEMBL/Analysis/PairAlign.pm
index 404364bb3e917b4034676314430491332b461123..9a4d2f947bcff6cce99f4eccffc95dc9b27ddebe 100755
--- a/modules/Bio/EnsEMBL/Analysis/PairAlign.pm
+++ b/modules/Bio/EnsEMBL/Analysis/PairAlign.pm
@@ -67,8 +67,6 @@ use vars qw(@ISA);
use strict;
-@ISA = qw(Bio::EnsEMBL::Root);
-
sub new {
my($class,@args) = @_;
my $self = {};
diff --git a/modules/Bio/EnsEMBL/ArchiveStableId.pm b/modules/Bio/EnsEMBL/ArchiveStableId.pm
index 566518381102c0549f01e576d6b48c15c1923298..6601a512fb3beb6ebea5862a837b3ed15e79716b 100644
--- a/modules/Bio/EnsEMBL/ArchiveStableId.pm
+++ b/modules/Bio/EnsEMBL/ArchiveStableId.pm
@@ -63,9 +63,6 @@ use strict;
use warnings;
no warnings qw(uninitialized);
-use Bio::EnsEMBL::Root;
-our @ISA = qw(Bio::EnsEMBL::Root);
-
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Scalar::Util qw(weaken isweak);
diff --git a/modules/Bio/EnsEMBL/AssemblyMapper.pm b/modules/Bio/EnsEMBL/AssemblyMapper.pm
index 10c90513f58b5e54f299bdfb4c30dd471fbf148e..6c97d0d318660f58728243504b4565ca62f8eacd 100644
--- a/modules/Bio/EnsEMBL/AssemblyMapper.pm
+++ b/modules/Bio/EnsEMBL/AssemblyMapper.pm
@@ -737,98 +737,4 @@ sub adaptor {
return $self->{'adaptor'};
}
-=head2 in_assembly
-
- Description: DEPRECATED, use map() or list_ids() instead.
-
-=cut
-
-sub in_assembly {
- my ( $self, $object ) = @_;
-
- deprecate('in_assembly is deprecated and will be removed in e87. Use map() or list_ids() instead.');
-
- my $csa = $self->db->get_CoordSystemAdaptor();
-
- my $top_level = $csa->fetch_top_level();
-
- my $asma =
- $self->adaptor->fetch_by_CoordSystems( $object->coord_system(),
- $top_level );
-
- my @list = $asma->list_ids( $object->seq_region(),
- $object->start(),
- $object->end(),
- $object->coord_system() );
-
- return ( @list > 0 );
-}
-
-=head2 map_coordinates_to_assembly
-
- Description: DEPRECATED, use map() instead.
-
-=cut
-
-sub map_coordinates_to_assembly {
- my ( $self, $contig_id, $start, $end, $strand ) = @_;
-
- deprecate('map_coordinates_to_assembly is deprecated and will be removed in e87. Use map() instead.');
-
- # Not sure if contig_id is seq_region_id or name...
- return
- $self->map( $contig_id, $start, $end, $strand,
- $self->contig_CoordSystem() );
-
-}
-
-=head2 fast_to_assembly
-
- Description: DEPRECATED, use map() instead.
-
-=cut
-
-sub fast_to_assembly {
- my ( $self, $contig_id, $start, $end, $strand ) = @_;
-
- deprecate('fast_to_assembly is deprecated and will be removed in e87. Use map() instead.');
-
- # Not sure if contig_id is seq_region_id or name...
- return
- $self->map( $contig_id, $start, $end, $strand,
- $self->contig_CoordSystem() );
-}
-
-=head2 map_coordinates_to_rawcontig
-
- Description: DEPRECATED, use map() instead.
-
-=cut
-
-sub map_coordinates_to_rawcontig {
- my ( $self, $chr_name, $start, $end, $strand ) = @_;
-
- deprecate('map_coordinates_to_rawcontig is deprecated and will be removed in e87. Use map() instead.');
-
- return
- $self->map( $chr_name, $start, $end, $strand,
- $self->assembled_CoordSystem() );
-}
-
-=head2 list_contig_ids
-
- Description: DEPRECATED, use list_ids() instead.
-
-=cut
-
-sub list_contig_ids {
- my ( $self, $chr_name, $start, $end ) = @_;
-
- deprecate('list_contig_ids is deprecated and will be removed in e87. Use list_ids() instead.');
-
- return
- $self->list_ids( $chr_name, $start, $end,
- $self->assembled_CoordSystem() );
-}
-
1;
diff --git a/modules/Bio/EnsEMBL/ChainedAssemblyMapper.pm b/modules/Bio/EnsEMBL/ChainedAssemblyMapper.pm
index 43d0cc3271e21d38208ca7e40b685abd8a4dc5a2..e6422226d856b7eb941f2789b27ec29a3271141b 100644
--- a/modules/Bio/EnsEMBL/ChainedAssemblyMapper.pm
+++ b/modules/Bio/EnsEMBL/ChainedAssemblyMapper.pm
@@ -733,96 +733,4 @@ sub adaptor {
}
-=head2 in_assembly
-
- Deprecated. Use map() or list_ids() instead
-
-=cut
-
-sub in_assembly {
- my ($self, $object) = @_;
-
- deprecate('in_assembly is deprecated and will be removed in e87. Use map() or list_ids() instead.');
-
- my $csa = $self->db->get_CoordSystemAdaptor();
-
- my $top_level = $csa->fetch_top_level();
-
- my $asma = $self->adaptor->fetch_by_CoordSystems($object->coord_system(),
- $top_level);
-
- my @list = $asma->list_ids($object->seq_region(), $object->start(),
- $object->end(), $object->coord_system());
-
- return (@list > 0);
-}
-
-
-=head2 map_coordinates_to_assembly
-
- DEPRECATED use map() instead
-
-=cut
-
-sub map_coordinates_to_assembly {
- my ($self, $contig_id, $start, $end, $strand) = @_;
-
- deprecate('map_coordinates_to_assembly is deprecated and will be removed in e87. Use map() instead.');
-
- #not sure if contig_id is seq_region_id or name...
- return $self->map($contig_id, $start, $end, $strand,
- $self->contig_CoordSystem());
-
-}
-
-
-=head2 fast_to_assembly
-
- DEPRECATED use map() instead
-
-=cut
-
-sub fast_to_assembly {
- my ($self, $contig_id, $start, $end, $strand) = @_;
-
- deprecate('fast_to_assembly is deprecated and will be removed in e87. Use map() instead.');
-
- #not sure if contig_id is seq_region_id or name...
- return $self->map($contig_id, $start, $end, $strand,
- $self->contig_CoordSystem());
-}
-
-
-=head2 map_coordinates_to_rawcontig
-
- DEPRECATED use map() instead
-
-=cut
-
-sub map_coordinates_to_rawcontig {
- my ($self, $chr_name, $start, $end, $strand) = @_;
-
- deprecate('map_coordinates_to_rawcontig is deprecated and will be removed in e87. Use map() instead.');
-
- return $self->map($chr_name, $start, $end, $strand,
- $self->assembled_CoordSystem());
-
-}
-
-=head2 list_contig_ids
- DEPRECATED Use list_ids instead
-
-=cut
-
-sub list_contig_ids {
- my ($self, $chr_name, $start, $end) = @_;
-
- deprecate('list_contig_ids is deprecated and will be removed in e87. Use list_ids() instead.');
-
- return $self->list_ids($chr_name, $start, $end,
- $self->assembled_CoordSystem());
-}
-
-
-
1;
diff --git a/modules/Bio/EnsEMBL/DBEntry.pm b/modules/Bio/EnsEMBL/DBEntry.pm
index 939ad7eac44a08e5e99b8fef75da08a6aefe24dd..50f2dec99311fe7a1f9f7124ed07f69883e31430 100644
--- a/modules/Bio/EnsEMBL/DBEntry.pm
+++ b/modules/Bio/EnsEMBL/DBEntry.pm
@@ -666,22 +666,5 @@ sub status{
return $self->{status};
}
-=head1 DEPRECATED METHODS
-
-=cut
-
-=head2 get_synonyms
-
- DEPRECATED use get_all_synonyms instead
-
-=cut
-
-sub get_synonyms {
- my $self = shift;
-
- deprecate("get_synonyms is deprecated and will be removed in e87. Use get_all_synonyms instead.");
- return $self->get_all_synonyms;
-}
-
1;
diff --git a/modules/Bio/EnsEMBL/DBSQL/AltAlleleGroupAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/AltAlleleGroupAdaptor.pm
index 556c805374f51be79f318e88ac1373775a61e6b6..04b8ac545698d352796dd2b77ce24a100260c0f0 100644
--- a/modules/Bio/EnsEMBL/DBSQL/AltAlleleGroupAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/AltAlleleGroupAdaptor.pm
@@ -73,20 +73,6 @@ use Bio::EnsEMBL::Utils::Exception qw/throw deprecate warning/;
use Bio::EnsEMBL::Utils::Scalar qw/assert_ref/;
use DBI qw( :sql_types );
-=head2 fetch_all_Groups
-
- Arg[1] : (optional) String - type of group
- Description : DEPRECATED. Please use fetch_all()
- Returntype : ArrayRef of Bio::EnsEMBL::AltAlleleGroup
-
-=cut
-
-sub fetch_all_Groups {
- my ($self, $type) = @_;
- deprecate('fetch_all_Groups is deprecate and will be removed in e87. Please use fetch_all()');
- return $self->fetch_all($type);
-}
-
=head2 fetch_all
Arg[1] : (optional) String - type of group
@@ -176,35 +162,6 @@ sub fetch_all {
return \@group_list;
}
-=head2 fetch_all_Groups_by_type
-
- Arg[1] : String - type of group
- Description : DEPRECATED. Please use fetch_all()
- Returntype : ArrayRef of Bio::EnsEMBL::AltAlleleGroup
-
-=cut
-
-sub fetch_all_Groups_by_type {
- my ($self, $type) = @_;
- deprecate('fetch_all_Groups_by_type is deprecated and will be removed in e87. Please use fetch_all()');
- my $group_list = $self->fetch_all($type);
- return $group_list;
-}
-
-=head2 fetch_Group_by_id
-
- Arg[1] : AltAlleleGroup dbID.
- Description : DEPRECATED. Please use fetch_by_dbID
- Returntype : Bio::EnsEMBL::AltAlleleGroup
-
-=cut
-
-sub fetch_Group_by_id {
- my ($self, $group_id) = @_;
- deprecate('fetch_Group_by_id is deprecated and will be removed in e87. Please use fetch_by_dbID()');
- return $self->fetch_by_dbID($group_id);
-}
-
=head2 fetch_by_dbID
Arg[1] : AltAlleleGroup dbID.
@@ -262,21 +219,6 @@ sub fetch_by_dbID {
return;
}
-=head2 fetch_Group_by_Gene_dbID
-
- Arg[1] : Integer Gene ID of the member to query by
- Description : DEPRECATED. Please use fetch_by_gene_id
- Returntype : Bio::EnsEMBL::AltAlleleGroup
-
-=cut
-
-
-sub fetch_Group_by_Gene_dbID {
- my ($self, $gene_id) = @_;
- deprecate('fetch_Group_by_Gene_dbID is deprecated and will be removed in e87. Please use fetch_by_gene_id()');
- return $self->fetch_by_gene_id($gene_id);
-}
-
=head2 fetch_by_gene_id
Arg[1] : Integer Gene ID of the member to query by
diff --git a/modules/Bio/EnsEMBL/DBSQL/AnalysisAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/AnalysisAdaptor.pm
index c9cebdeeac4bc50cc0515cb6b7a7ac6370127c00..7b92e224de6d1e34136b245332ebde8c88bd134a 100755
--- a/modules/Bio/EnsEMBL/DBSQL/AnalysisAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/AnalysisAdaptor.pm
@@ -203,36 +203,6 @@ SELECT DISTINCT analysis_id FROM %s |;
return [@analyses];
}
-
-=head2 feature_classes
-
- Arg [1] : NONE
- Example : my @fclasses = $analysis_adaptor->feature_classes;
- Description: Returns a list of the different classes of Ensembl feature
- object that have an analysis
- Returntype : List of feature classes
- Exceptions : none
- Caller : general
- Status : Stable
-
-=cut
-
-sub feature_classes{
- deprecate("feature_classes is deprecated and will be removed in e87. Hard-coded logic is not supported");
- # Can't think of a way to do this programatically, so hard-coded
- return qw(
- DensityFeature
- DnaAlignFeature
- Gene
- MarkerFeature
- PredictionTranscript
- ProteinAlignFeature
- ProteinFeature
- RepeatFeature
- SimpleFeature
- );
-}
-
=head2 fetch_by_dbID
Arg [1] : int $internal_analysis_id - the database id of the analysis
diff --git a/modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm
index 39b0d248429408a0eefa57eafd6d8479f5e273b7..f63af928a076bc0a1dd6a6aef8b9a4b8a8c744f0 100644
--- a/modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm
@@ -1804,60 +1804,4 @@ sub delete_cache{
}
-=head2 register_region
-
- Description: DEPRECATED use register_assembled instead
-
-=cut
-
-sub register_region{
- my ($self, $assmapper, $type, $chr_name, $start, $end) = @_;
-
- deprecate('register_region is deprecated and will be removed in e87. Use register_assembled instead');
-
- $self->register_assembled($assmapper, $chr_name, $start, $end);
-}
-
-
-=head2 register_contig
-
- Description: DEPRECATED use register_component instead
-
-=cut
-
-sub register_contig {
- my ($self, $assmapper, $type, $contig_id ) = @_;
-
- deprecate('register_contig is deprecated and will be removed in e87. Use register_component instead');
-
- #not sure if the use is passing in a seq_region_name or a
- #seq_region_id...
- register_component($assmapper, $contig_id);
-}
-
-
-=head2 fetch_by_type
-
- Description: DEPRECATED use fetch_by_CoordSystems instead
-
-=cut
-
-sub fetch_by_type{
- my ($self,$type) = @_;
-
- deprecate('fetch_by_type is deprecated and will be removed in e87. Use fetch_by_CoordSystems instead');
-
- #assume that what the user wanted was a mapper between the sequence coord
- #level and the top coord level
-
- my $csa = $self->db()->get_CoordSystemAdaptor();
-
- my $cs1 = $csa->fetch_top_level($type);
- my $cs2 = $csa->fetch_sequence_level();
-
- return $self->fetch_by_CoordSystems($cs1,$cs2);
-}
-
-
-
1;
diff --git a/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm
index ea86076702edd860aea3d611b7ba049ab98e1afe..471949c5d70db3d7da4f29ac03528cf83974c3f4 100755
--- a/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm
@@ -92,8 +92,6 @@ case the convention is to go list_XXXX, such as
(note: this method is poorly named)
-=head1 METHODS
-
=cut
package Bio::EnsEMBL::DBSQL::BaseAdaptor;
@@ -101,7 +99,7 @@ require Exporter;
use vars qw(@ISA @EXPORT);
use strict;
-use Bio::EnsEMBL::Utils::Exception qw(throw);
+use Bio::EnsEMBL::Utils::Exception qw(throw deprecate);
use Bio::EnsEMBL::Utils::Scalar qw(assert_ref assert_integer wrap_array);
use DBI qw(:sql_types);
use Data::Dumper;
@@ -1096,7 +1094,7 @@ sub _build_id_cache {
sub dump_data {
my $self = shift;
my $data = shift;
-
+ deprecate('This method is deprecated and will be removed in e91. Please use the get_all_attributes() and add_attributes() methods of DnaDnaAlignFeature instead. In the more general case, many feature types allow attributes to be stored as well');
my $dumper = Data::Dumper->new([$data]);
$dumper->Indent(0);
$dumper->Terse(1);
@@ -1109,7 +1107,7 @@ sub dump_data {
sub get_dumped_data {
my $self = shift;
my $data = shift;
-
+ deprecate('This method is deprecated and will be removed in e91. Please use the get_all_attributes() and add_attributes() methods of DnaDnaAlignFeature instead. In the more general case, many feature types allow attributes to be stored as well');
$data =~ s/\n|\r|\f|(\\\\)//g;
return eval ($data); ## no critic
}
diff --git a/modules/Bio/EnsEMBL/DBSQL/BaseAlignFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/BaseAlignFeatureAdaptor.pm
index 9fade068415e99960bcb1014f6c27b46e1651a1c..e5816bb3823ec58cc8305d9963d0f0bea9a6d4ab 100644
--- a/modules/Bio/EnsEMBL/DBSQL/BaseAlignFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/BaseAlignFeatureAdaptor.pm
@@ -297,35 +297,6 @@ sub fetch_all_by_hit_name_unversioned {
}
-
-=head2 fetch_all_by_RawContig_and_pid
-
- Description: DEPRECATED use fetch_all_by_Slice_and_pid instead
-
-=cut
-
-sub fetch_all_by_RawContig_and_pid {
- my($self, $contig, $pid, $logic_name) = @_;
- deprecate('fetch_all_by_RawContig_and_pid is deprecated and will be removed in e87. Use fetch_all_by_Slice_and_pid instead.');
-
- my $constraint;
-
- #get the primary table alias
- my @tabs = $self->_tables;
- my $alias = $tabs[0]->[1];
-
- if(defined $pid) {
- $constraint = "${alias}.perc_ident > $pid";
- }
-
- return $self->fetch_all_by_RawContig_constraint($contig,
- $constraint,
- $logic_name);
-}
-
-
-
-
##implemented by subclasses:
# store
# _tables
diff --git a/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
index 33330c7828fb982f93d4bdd972ecfd30733ceb7a..1e48340c167199823a7602696d02b60ad11dbae9 100755
--- a/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
@@ -1331,60 +1331,6 @@ sub _list_seq_region_ids {
}
-=head1 DEPRECATED METHODS
-
-=cut
-
-
-=head2 fetch_all_by_RawContig_constraint
-
- Description: DEPRECATED use fetch_all_by_RawContig_constraint instead
-
-=cut
-
-sub fetch_all_by_RawContig_constraint {
- my $self = shift;
- deprecate('fetch_all_by_RawContig_constraint is deprecated and will be removed in e87. Use fetch_all_by_Slice_constraint() instead.');
- return $self->fetch_all_by_slice_constraint(@_);
-}
-
-=head2 fetch_all_by_RawContig
-
- Description: DEPRECATED use fetch_all_by_Slice instead
-
-=cut
-
-sub fetch_all_by_RawContig {
- my $self = shift;
- deprecate('fetch_all_by_RawContig is deprecated and will be removed in e87. Use fetch_all_by_Slice() instead.');
- return $self->fetch_all_by_Slice(@_);
-}
-
-=head2 fetch_all_by_RawContig_and_score
-
- Description: DEPRECATED use fetch_all_by_Slice_and_score instead
-
-=cut
-
-sub fetch_all_by_RawContig_and_score{
- my $self = shift;
- deprecate('fetch_all_by_RawContig_and_score is deprecated and will be removed in e87. Use fetch_all_by_Slice_and_score() instead.');
- return $self->fetch_all_by_Slice_and_score(@_);
-}
-
-=head2 remove_by_RawContig
-
- Description: DEPRECATED use remove_by_Slice instead
-
-=cut
-
-sub remove_by_RawContig {
- my $self = shift;
- deprecate("fetch_by_RawContig is deprecated and will be removed in e87. Use remove_by_Slice instead");
- return $self->remove_by_Slice(@_);
-}
-
-
sub remove_by_analysis_id {
my ($self, $analysis_id) = @_;
diff --git a/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
index d5bcf42f1bd1346d3b693bee0fa9ce7f9cfe6489..5475d8d0cae7fced9dace0ba9718f4aa203af38b 100755
--- a/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
@@ -1109,129 +1109,5 @@ sub revert_adaptor {
return $deleted_adaptor;
}
-#########################
-# sub DEPRECATED METHODS
-#########################
-=head2 db
-
- Description: DEPRECATED
-
-=cut
-
-sub db{
- my ($self, $arg ) = @_;
- deprecate("DBAdaptor->db is deprecated and will be removed in e87. Please use DBConnection->db instead.");
- return $self->dbc($arg);
-}
-
-
-=head2 assembly_type
-
- Description: DEPRECATED - Use CoordSystemAdaptor to obtain default coordinate
- system instead.
-
-=cut
-
-sub assembly_type{
- my $self = shift;
-
- deprecate('assembly_type is deprecated and will be removed in e87. Please use CoordSystemAdaptor $csa->fetch_all->[0]->version() instead');
-
- my $csa = $self->get_CoordSystemAdaptor();
- my ($cs) = @{$csa->fetch_all()};
- return ($cs) ? $cs->version() : undef;
-}
-
-
-
-=head2 list_supported_assemblies
-
- Description: DEPRECATED - Use CoordSystemAdaptor to obtain list of top-level
- coordinate systems instead
-
-=cut
-
-sub list_supported_assemblies {
- my($self) = @_;
- deprecate('list_supported_assemblies is deprecated and will be removed in e87. Please use CoordSystemAdaptor::fetch_all instead');
-
- my $csa = $self->get_CoordSystemAdaptor();
- my %versions;
- foreach my $cs (@{$csa->fetch_all()}) {
- $versions{$cs->version()} = 1;
- }
-
- return keys %versions;
-}
-
-
-sub prepare{
- my ($self, @args) = @_;
-
- deprecate("DBAdaptor->prepare is deprecated and will be removed in e87. Please use DBConnection->prepare instead.");
- $self->dbc->prepare(@args);
-}
-
-sub dbname{
- my ($self, @args) = @_;
-
- deprecate("DBAdaptor->dbname is deprecated and will be removed in e87. Please use DBConnection->dbname instead.");
- $self->dbc->dbname(@args);
-}
-
-sub disconnect_when_inactive{
- my ($self, @args) = @_;
-
- deprecate("DBAdaptor->disconnect_when_inactive is deprecated and will be removed in e87. Please use DBConnection->disconnect_when_inactive instead.");
- $self->dbc->disconnect_when_inactive(@args);
-}
-
-sub reconnect_when_lost{
- my ($self, @args) = @_;
-
- deprecate("DBAdaptor->reconnect_when_lost is deprecated and will be removed in e87. Please use DBConnection->reconnect_when_lost instead.");
- $self->dbc->reconnect_when_lost(@args);
-}
-
-
-sub host{
- my ($self, @args) = @_;
-
- deprecate("DBAdaptor->host is deprecated and will be removed in e87. Please use DBConnection->host instead.");
- $self->dbc->host(@args);
-}
-sub username{
- my ($self, @args) = @_;
-
- deprecate("DBAdaptor->username is deprecated and will be removed in e87. Please use DBConnection->username instead.");
- $self->dbc->username(@args);
-}
-sub password{
- my ($self, @args) = @_;
-
- deprecate("DBAdaptor->password is deprecated and will be removed in e87. Please use DBConnection->password instead.");
- $self->dbc->password(@args);
-}
-sub driver{
- my ($self, @args) = @_;
-
- deprecate("DBAdaptor->driver is deprecated and will be removed in e87. Please use DBConnection->driver instead.");
- $self->dbc->driver(@args);
-}
-sub port{
- my ($self, @args) = @_;
-
- deprecate("DBAdaptor->port is deprecated and will be removed in e87. Please use DBConnection->port instead.");
- $self->dbc->port(@args);
-}
-
-sub db_handle{
- my ($self, @args) = @_;
-
-
- deprecate("DBAdaptor->db_handle is deprecated and will be removed in e87. Please use DBConnection->db_handle instead.");
- $self->dbc->db_handle(@args);
-}
-
1;
diff --git a/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm b/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm
index 99caa4c7475bd80c33bd65578c3e7f52f6064f65..63156658eca4c57cea22996aabe7658a9604113f 100644
--- a/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm
@@ -71,7 +71,6 @@ package Bio::EnsEMBL::DBSQL::DBConnection;
use vars qw(@ISA);
use strict;
-use Bio::EnsEMBL::Root;
use DBI;
use Bio::EnsEMBL::DBSQL::StatementHandle;
@@ -81,8 +80,6 @@ use Bio::EnsEMBL::Utils::Argument qw/rearrange/;
use Bio::EnsEMBL::Utils::Scalar qw/assert_ref wrap_array/;
use Bio::EnsEMBL::Utils::SqlHelper;
-@ISA = qw(Bio::EnsEMBL::Root); # for backwards compatibility
-
=head2 new
Arg [DBNAME] : (optional) string
@@ -1075,40 +1072,6 @@ sub to_hash {
return $hash;
}
-####
-#deprecated functions
-####
-
-=head2 group
-
- group is no longer available in DBConnection and should be accessed if needed
- from an adaptor.
-
-=cut
-
-sub group {
- my ($self, $arg ) = @_;
- ( defined $arg ) &&
- ( $self->{_group} = $arg );
- deprecate("DBConnection->group is deprecated and will be removed in e87. Please use adaptor->group instead.");
- return $self->{_group};
-}
-
-=head2 species
-
- species is no longer available in DBConnection and should be accessed if needed
- from an adaptor.
-
-=cut
-
-sub species {
- my ($self, $arg ) = @_;
- ( defined $arg ) &&
- ( $self->{_species} = $arg );
- deprecate("DBConnection->species is deprecated and will be removed in e87. Please use adaptor->species instead.");
- return $self->{_species};
-}
-
=head2 _driver_object
=cut
diff --git a/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
index b934ab6f8b112cb4033499bd2c2fc506d718750e..d69e9767ab12072d55dadcf919b31bf322f0e63f 100644
--- a/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
@@ -2376,44 +2376,5 @@ sub get_db_name_from_external_db_id{
}
-=head2 geneids_by_extids
-
- Description: DEPRECATED use list_gene_ids_by_extids instead
-
-=cut
-
-sub geneids_by_extids{
- my ($self,$name) = @_;
- deprecate("gene_ids_by_extids is deprecated and will be removed in e87. Please use 'list_gene_ids_by_extids instead");
- return $self->list_gene_ids_by_extids( $name );
-}
-
-
-=head2 translationids_by_extids
-
- DEPRECATED use list_translation_ids_by_extids instead
-
-=cut
-
-sub translationids_by_extids{
- my ($self,$name) = @_;
- deprecate("translationids_by_extids is deprecated and will be removed in e87. Please use list_translation_ids_by_extids instead");
- return $self->list_translation_ids_by_extids( $name );
-}
-
-
-=head2 transcriptids_by_extids
-
- DEPRECATED use transcriptids_by_extids instead
-
-=cut
-
-sub transcriptids_by_extids{
- my ($self,$name) = @_;
- deprecate("transcriptids_by_extids is deprecated and will be removed in e87. Please use list_transcript_ids_by_extids instead.");
- return $self->list_transcript_ids_by_extids( $name );
-}
-
-
1;
diff --git a/modules/Bio/EnsEMBL/DBSQL/DataFileAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/DataFileAdaptor.pm
index b9ec20cccd92aa16b47b9037872c1f67c8e91d0a..252cbac8139a16cc930cf2ceaa46805f57a6911a 100644
--- a/modules/Bio/EnsEMBL/DBSQL/DataFileAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/DataFileAdaptor.pm
@@ -109,24 +109,6 @@ sub get_base_path {
throw "No base path discovered. Either provide a path, set a global using global_base_path() or specify 'data_file.base_path' in meta";
}
-=head2 DataFile_to_extension
-
- Deprecated
- Arg[1] : Bio::EnsEMBL::DataFile
- Example : my $ext = $dfa->DataFile_to_extension($bam_df);
- Description : Returns an expected extension for the given DataFile type
- Returntype : Scalar of the expected file extension
- Exceptions : Raised if the given file type is not understood
-
-=cut
-
-sub DataFile_to_extension {
- my ($self, $df) = @_;
- deprecate("DataFile_to_extension is deprecated and will be removed in e87. Please use DataFile_to_extensions() instead");
- my $extensions = $self->DataFile_to_extensions($df);
- return $extensions->[0];
-}
-
=head2 DataFile_to_extensions
Arg[1] : Bio::EnsEMBL::DataFile
diff --git a/modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm
index d220acd8ca6556ca6118d2988bb54d721831d359..9c2ea825a01c743d2427578b7c797b9346ca4faf 100644
--- a/modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm
@@ -773,118 +773,6 @@ sub _objs_from_sth {
return \@exons;
} ## end sub _objs_from_sth
-=head1 DEPRECATED METHODS
-
-=cut
-
-
-=head2 get_stable_entry_info
-
- Description: DEPRECATED. This method is no longer necessary. Exons are
- always fetched with their stable identifiers (if they exist) and
- no lazy loading is necessary.
-
-=cut
-
-sub get_stable_entry_info {
- my ($self,$exon) = @_;
-
- deprecate( "get_stable_entry_info is deprecated and will be removed in e87. Please use object->stable_id instead." );
-
- if( !$exon || !ref $exon || !$exon->isa('Bio::EnsEMBL::Exon') ) {
- $self->throw("Needs a exon object, not a $exon");
- }
- if(!$exon->dbID){
- #$self->throw("can't fetch stable info with no dbID");
- return;
- }
-
- my $created_date = $self->db->dbc->from_date_to_seconds("created_date");
- my $modified_date = $self->db->dbc->from_date_to_seconds("modified_date");
- my $sth = $self->prepare("SELECT stable_id, " . $created_date . ",
- " . $modified_date . ", version
- FROM exon
- WHERE exon_id = ");
-
- $sth->bind_param(1, $exon->dbID, SQL_INTEGER);
- $sth->execute();
-
- # my @array = $sth->fetchrow_array();
- if( my $aref = $sth->fetchrow_arrayref() ) {
- $exon->{'_stable_id'} = $aref->[0];
- $exon->{'_created'} = $aref->[1];
- $exon->{'_modified'} = $aref->[2];
- $exon->{'_version'} = $aref->[3];
- }
-
- return 1;
-}
-
-
-=head2 fetch_all_by_gene_id
-
- Description: DEPRECATED. This method should not be needed - Exons can
- be fetched by Transcript.
-
-=cut
-
-sub fetch_all_by_gene_id {
- my ( $self, $gene_id ) = @_;
- my %exons;
- my $hashRef;
- my ( $currentId, $currentTranscript );
-
- deprecate("exon_adaptor->fetch_all_by_gene_id is deprecated and will be removed in e87. Please use transcript->get_all_Exons instead." );
-
- if( !$gene_id ) {
- $self->throw("Gene dbID not defined");
- }
-
- $self->{rchash} = {};
-
- my $straight_join = $self->_can_straight_join ? 'STRAIGHT_JOIN' : '';
- my $query = qq {
- SELECT
- ${straight_join}
- e.exon_id
- , e.contig_id
- , e.contig_start
- , e.contig_end
- , e.contig_strand
- , e.phase
- , e.end_phase
- , e.sticky_rank
- FROM transcript t
- , exon_transcript et
- , exon e
- WHERE t.gene_id = ?
- AND et.transcript_id = t.transcript_id
- AND e.exon_id = et.exon_id
- ORDER BY t.transcript_id,e.exon_id
- , e.sticky_rank DESC
- };
-
- my $sth = $self->prepare( $query );
- $sth->bind_param(1,$gene_id,SQL_INTEGER);
- $sth->execute();
-
- while( $hashRef = $sth->fetchrow_hashref() ) {
- if( ! exists $exons{ $hashRef->{exon_id} } ) {
-
- my $exon = $self->_exon_from_sth( $sth, $hashRef );
-
- $exons{$exon->dbID} = $exon;
- }
- }
- delete $self->{rchash};
-
- my @out = ();
-
- push @out, values %exons;
-
- return \@out;
-}
-
1;
diff --git a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
index 8bee80799dbeb191aa38e5de0a4001bab1cee110..09dc6445d6cb551ee26a99d538f444f7005e4746 100644
--- a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
@@ -2063,188 +2063,5 @@ sub fetch_all_by_transcript_supporting_evidence {
return \@genes;
} ## end sub fetch_all_by_transcript_supporting_evidence
-##########################
-# #
-# DEPRECATED METHODS #
-# #
-##########################
-
-=head2 fetch_nearest_Gene_by_Feature
-
- Description: DEPRECATED - use fetch_nearest_Genes_by_Feature
-
-=cut
-
-sub fetch_nearest_Gene_by_Feature{
- my ($self, $feat, $stranded, $stream) = @_;
- #This had no prime spec and was returning all overlaps regardless of strand
- #else the first 10 from the stream with the first closest gene
-
- deprecate( "fetch_neared_Gene_by_Feature is deprecated and will be removed in e87. Please use fetch_nearest_Genes_by_Feature instead");
- #need to change params order here to account for new prime arg
- return $_[0]->fetch_nearest_Genes_by_Feature($feat, undef, $stranded, $stream);
-}
-
-
-=head2 fetch_by_maximum_DBLink
-
- DEPRECATED - use fetch_all_by_external_name instead
-
-=cut
-
-sub fetch_by_maximum_DBLink {
- my ($self, $external_id) = @_;
-
- deprecate("fetch_by_maximum_DBLink is deprecated and will be removed in e87. Pleaseuse fetch_all_by_external_name instead");
-
- my $genes = $self->fetch_all_by_external_name($external_id);
-
- my $biggest;
- my $max = 0;
- my $size = scalar(@$genes);
- if ($size > 0) {
- foreach my $gene (@$genes) {
- my $size = scalar(@{$gene->get_all_Exons});
- if ($size > $max) {
- $biggest = $gene;
- $max = $size;
- }
- }
- return $biggest;
- }
- return;
-}
-
-=head2 get_display_xref
-
- DEPRECATED use $gene->display_xref
-
-=cut
-
-sub get_display_xref {
- my ($self, $gene) = @_;
-
- deprecate("gene_adaptor->get_display_xref is deprecated and will be removed in e87. Please use gene->display_xref instead");
-
- if (!defined $gene) {
- throw("Must call with a Gene object");
- }
-
- my $sth = $self->prepare(
- qq(
- SELECT e.db_name,
- x.display_label,
- x.xref_id
- FROM gene g,
- xref x,
- external_db e
- WHERE g.gene_id = ?
- AND g.display_xref_id = x.xref_id
- AND x.external_db_id = e.external_db_id
- ));
-
- $sth->bind_param(1, $gene->dbID, SQL_INTEGER);
- $sth->execute();
-
- my ($db_name, $display_label, $xref_id) = $sth->fetchrow_array();
- if (!defined $xref_id) {
- return undef;
- }
-
- my $db_entry = Bio::EnsEMBL::DBEntry->new(-dbid => $xref_id,
- -adaptor => $self->db->get_DBEntryAdaptor(),
- -dbname => $db_name,
- -display_id => $display_label);
-
- return $db_entry;
-} ## end sub get_display_xref
-
-=head2 get_description
-
- DEPRECATED, use gene->get_description
-
-=cut
-
-sub get_description {
- my ($self, $dbID) = @_;
-
- deprecate("gene_adaptor->get_description is deprecated and will be removed in e87. Please use gene->get_description() instead");
-
- if (!defined $dbID) {
- throw("must call with dbID");
- }
-
- my $sth = $self->prepare(
- "SELECT description
- FROM gene_description
- WHERE gene_id = ?");
-
- $sth->bind_param(1, $dbID, SQL_INTEGER);
- $sth->execute();
-
- my @array = $sth->fetchrow_array();
- return $array[0];
-}
-
-=head2 fetch_by_Peptide_id
-
- DEPRECATED, use fetch_by_translation_stable_id()
-
-=cut
-
-sub fetch_by_Peptide_id {
- my ($self, $translation_stable_id) = @_;
-
- deprecate("fetch_by_Peptide_id is deprecated and will be removed in e87. Please use fetch_by_translation_stable_id instead");
-
- $self->fetch_by_translation_stable_id($translation_stable_id);
-}
-
-=head2 get_stable_entry_info
-
- DEPRECATED use $gene->stable_id instead
-
-=cut
-
-sub get_stable_entry_info {
- my ($self, $gene) = @_;
-
- deprecate("gene_adaptor->get_stable_entry_info is deprecated and will be removed in e87. Please use gene->stable_id instead.");
-
- if (!defined $gene || !ref $gene || !$gene->isa('Bio::EnsEMBL::Gene')) {
- throw("Needs a gene object, not a $gene");
- }
-
- my $created_date = $self->db->dbc->from_date_to_seconds("created_date");
- my $modified_date = $self->db->dbc->from_date_to_seconds("modified_date");
-
- my $sth = $self->prepare("SELECT stable_id, " . $created_date . "," . $modified_date . ", version FROM gene WHERE gene_id = ?");
-
- $sth->bind_param(1, $gene->dbID, SQL_INTEGER);
- $sth->execute();
-
- my @array = $sth->fetchrow_array();
- $gene->{'stable_id'} = $array[0];
- $gene->{'created'} = $array[1];
- $gene->{'modified'} = $array[2];
- $gene->{'version'} = $array[3];
-
- return 1;
-} ## end sub get_stable_entry_info
-
-=head2 fetch_all_by_DBEntry
-
- DEPRECATED - Use fetch_all_by_external_name instead
-
-=cut
-
-sub fetch_all_by_DBEntry {
- my $self = shift;
-
- deprecate('fetch_all_by_DBEntry is deprecated and will be removed in e87. Please use fetch_all_by_external_name instead.');
-
- return $self->fetch_all_by_external_name(@_);
-}
-
1;
diff --git a/modules/Bio/EnsEMBL/DBSQL/KaryotypeBandAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/KaryotypeBandAdaptor.pm
index f7e8727ec3d739c4ec90a17b2f2c4b3b8da68c27..16deefa142485d41d71c0bc9c497ae062b922513 100644
--- a/modules/Bio/EnsEMBL/DBSQL/KaryotypeBandAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/KaryotypeBandAdaptor.pm
@@ -254,34 +254,6 @@ sub fetch_all_by_chr_band {
}
-=head2 fetch_by_chr_band
-
- Arg [1] : string $chr_name
- Name of the chromosome from which to retrieve the band
- Arg [2] : string $band
- The name of the band to retrieve from the specified chromosome
- Example : @bands = @{$kary_adaptor->fetch_all_by_chr_band('4', 'q23')};
- Description: Fetches the karyotype band object from the database
- for the given chromosome and band name. If no such band
- exists, undef is returned instead. This function uses fuzzy
- matching of the band name. For example the bands 'q23.1' and
- 'q23.4' could be matched by fetch_all_by_chr_band('20', 'q23');
- Returntype : Bio::EnsEMBL::KaryotypeBand in chromosomal coordinates.
- Exceptions : throws if chr or band is missing in arguments
- Caller : general
- Status : Stable
-
-=cut
-
-sub fetch_by_chr_band {
- my $self = shift;
- deprecate('fetch_by_chr_band is deprecated and will be removed in e87. Use fetch_all_by_chr_band instead.');
-
- my ($band) = @{$self->fetch_all_by_chr_band(@_)};
- return $band;
-}
-
-
=head2 list_dbIDs
Arg [1] : none
diff --git a/modules/Bio/EnsEMBL/DBSQL/MetaContainer.pm b/modules/Bio/EnsEMBL/DBSQL/MetaContainer.pm
index 4dfe7bec19372cff230bd9e0c4dd391c85ad006d..a74eaa0959e9fe00002335d3ac5068287fd28bb3 100644
--- a/modules/Bio/EnsEMBL/DBSQL/MetaContainer.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/MetaContainer.pm
@@ -144,47 +144,6 @@ sub get_division {
return $self->single_value_by_key('species.division');
}
-=head2 get_Species
-
- Arg [1] : none
- Example : $species = $meta_container->get_Species();
- Description: Obtains the species from this databases meta table. Call is
- deprecated; please use other subroutines in this package
- Returntype : Bio::Species
- Exceptions : none
- Caller : ?
- Status : Deprecated
-
-=cut
-
-sub get_Species {
- my ($self) = @_;
-
- deprecate('get_Species is deprecated and will be removed in e87. Please use $self->get_common_name() / $self->get_classification() / $self->get_scientific_name() instead');
-
- my $common_name = $self->get_common_name();
- my $classification =
- $self->list_value_by_key('species.classification');
- if ( !@$classification ) {
- return undef;
- }
-
- #Re-create the old classification data structure by adding the scientific
- #name back onto the classification but with species before genus e.g.
- # sapiens -> Homo -> Hominade
- my $scientific_name = $self->get_scientific_name();
- my ($genus, @sp) = split(/ /, $scientific_name);
- unshift(@{$classification}, join(q{ }, @sp), $genus);
-
- my $species = Bio::Species->new();
- $species->common_name($common_name);
-
- $species->classification($classification, 1); #always force it
-
- return $species;
-}
-
-
=head2 get_taxonomy_id
Arg [1] : none
@@ -202,30 +161,6 @@ sub get_taxonomy_id {
return $self->single_value_by_key('species.taxonomy_id', 1);
}
-
-
-=head2 get_default_assembly
-
- Description: DEPRECATED. Use the version of the coordinate system you are
- interested in instead.
-
- Example: #use this instead
- my ($highest_cs) = @{$db->get_CoordSystemAdaptor->fetch_all()};
- my $assembly = $highest_cs->version();
-
-=cut
-
-sub get_default_assembly {
- my $self = shift;
-
- deprecate("get_default_assembly is deprecated and will be removed in e87. Please use cs_adaptor->get_default_version instead.");
-
- my ($cs) = @{$self->db->get_CoordSystemAdaptor->fetch_all()};
-
- return $cs->version();
-}
-
-
=head2 get_genebuild
Arg [1] : none
diff --git a/modules/Bio/EnsEMBL/DBSQL/ProteinFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/ProteinFeatureAdaptor.pm
index f1059ac9b30c27d809149cf36fe74c16272a3279..81686ab1e61a4b8e357daf9cfe5133f89dec717b 100755
--- a/modules/Bio/EnsEMBL/DBSQL/ProteinFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/ProteinFeatureAdaptor.pm
@@ -143,13 +143,20 @@ sub fetch_all_by_logic_name {
sub fetch_by_dbID {
my ($self, $protfeat_id) = @_;
- my $sth = $self->prepare("SELECT p.seq_start, p.seq_end, p.analysis_id, " . " p.score, p.perc_ident, p.evalue, " . " p.hit_start, p.hit_end, p.hit_name, " . " x.description, x.display_label, i.interpro_ac " . "FROM protein_feature p " . "LEFT JOIN interpro AS i ON p.hit_name = i.id " . "LEFT JOIN xref AS x ON x.dbprimary_acc = i.interpro_ac " . "WHERE p.protein_feature_id = ?");
+ my $sth = $self->prepare("SELECT p.translation_id, p.seq_start, p.seq_end, p.analysis_id, "
+ . "p.score, p.perc_ident, p.evalue, "
+ . "p.hit_start, p.hit_end, p.hit_name, p.hit_description, "
+ . "x.description, x.display_label, i.interpro_ac "
+ . "FROM protein_feature p "
+ . "LEFT JOIN interpro AS i ON p.hit_name = i.id "
+ . "LEFT JOIN xref AS x ON x.dbprimary_acc = i.interpro_ac "
+ . "WHERE p.protein_feature_id = ?");
$sth->bind_param(1, $protfeat_id, SQL_INTEGER);
my $res = $sth->execute();
- my ($start, $end, $analysis_id, $score, $perc_ident, $pvalue, $hstart,
- $hend, $hseqname, $idesc, $ilabel, $interpro_ac) = $sth->fetchrow_array();
+ my ($translation_id, $start, $end, $analysis_id, $score, $perc_ident, $pvalue, $hstart,
+ $hend, $hseqname, $hdesc, $idesc, $ilabel, $interpro_ac) = $sth->fetchrow_array();
if($sth->rows == 0) {
$sth->finish();
@@ -168,13 +175,15 @@ sub fetch_by_dbID {
-HSTART => $hstart,
-HEND => $hend,
-HSEQNAME => $hseqname,
+ -HDESCRIPTION => $hdesc,
-ANALYSIS => $analysis,
-SCORE => $score,
-P_VALUE => $pvalue,
-PERCENT_ID => $perc_ident,
-IDESC => $idesc,
- -ILABEL => $ilabel,
- -INTERPRO_AC => $interpro_ac);
+ -ILABEL => $ilabel,
+ -INTERPRO_AC => $interpro_ac,
+ -TRANSLATION_ID => $translation_id);
} ## end sub fetch_by_dbID
=head2 store
@@ -260,31 +269,6 @@ sub store {
return $dbID;
} ## end sub store
-sub fetch_by_translation_id {
- deprecate("fetch_by_translation_id is deprecated. Please use fetch_all_by_translation_id instead.");
- fetch_all_by_translation_id(@_);
-}
-
-sub fetch_all_by_feature_and_dbID {
- my $self = shift;
- my $feature = shift;
- my $translation_id = shift;
- deprecate("fetch_all_by_feature_and_dbID is deprecated. Please use fetch_all_by_translation_id instead.");
-
- print STDERR "translation_id = $translation_id feature = $feature\n";
-
- my $features = $self->fetch_all_by_translation_id($translation_id);
-
- my @out;
- foreach my $f (@$features) {
- my $logic_name = lc($f->analysis->logic_name());
- print STDERR "LOGIC_NAME = $logic_name | FEATURE = $feature\n";
- push(@out, $f) if ($logic_name eq lc($feature));
- }
-
- return \@out;
-}
-
sub save {
my ($self, $features) = @_;
diff --git a/modules/Bio/EnsEMBL/DBSQL/RepeatConsensusAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/RepeatConsensusAdaptor.pm
index a6eb8380fc3573eb02964c3b39c74e0002e062be..5275b132276d0e3fdb5e71803f974837f739cebd 100644
--- a/modules/Bio/EnsEMBL/DBSQL/RepeatConsensusAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/RepeatConsensusAdaptor.pm
@@ -180,12 +180,6 @@ sub fetch_all_by_class_seq {
}
-sub fetch_by_class_seq {
- deprecate('fetch_by_class_seq is deprecated. Please use fetch_all_by_class_seq instead');
- fetch_all_by_class_seq(@_);
-}
-
-
=head2 _generic_fetch
Arg [1] : string $where_clause
diff --git a/modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm
index 15b7d9b7da4ff03d41694382879ae758c7ff563d..e34ec91c549fce06de7b6af79c5abf643baa6f7d 100644
--- a/modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm
@@ -501,42 +501,6 @@ sub remove {
return;
}
-
-=head2 fetch_by_assembly_location
-
- Description: DEPRECATED use fetch_by_Slice_start_end_strand() instead.
-
-=cut
-
-sub fetch_by_assembly_location {
- my ( $self, $chrStart, $chrEnd,
- $strand, $chrName, $assemblyType ) = @_;
-
- deprecate('fetch_by_assembly_location is deprecated and will be removed in e87. Please use fetch_by_Slice_start_end_strand() instead');
-
- my $csa = $self->db->get_CoordSystem();
- my $top_cs = @{$csa->fetch_all};
-
- my $slice_adaptor = $self->db->get_SliceAdaptor();
- my $slice = $slice_adaptor->fetch_by_region($top_cs->name(), $chrName,
- $chrStart, $chrEnd,
- $strand, $top_cs->version);
-
- return $self->fetch_by_Slice_start_end_strand($slice,1, $slice->length,1);
-}
-
-
-=head2 fetch_by_RawContig_start_end_strand
-
- Description: DEPRECATED use fetch_by_Slice_start_end_strand instead
-
-=cut
-
-sub fetch_by_RawContig_start_end_strand {
- deprecate('fetch_by_RawContig_start_end_strand is deprecated and will be removed in e87. Please use fetch_by_Slice_start_end_strand instead.');
- fetch_by_Slice_start_end_strand(@_);
-}
-
=head2 _populate_seq_region_edits
Description: Query the database for any _rna_edit attributes attached to a seq region
diff --git a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
index a8cecfecc90265979899428b39ac9bf4ad4b9253..5529b1237d9954c5716f09ed3aed6e3752b2e2f1 100644
--- a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
@@ -941,8 +941,8 @@ sub get_seq_region_id {
The version of the coordinate system to retrieve slices of
Arg [3] : bool $include_non_reference (optional)
If this argument is not provided then only reference slices
- will be returned. If set, both reference and non refeference
- slices will be rerurned.
+ will be returned. If set, both reference and non reference
+ slices will be returned.
Arg [4] : int $include_duplicates (optional)
If set duplicate regions will be returned.
@@ -2705,221 +2705,4 @@ sub _build_circular_slice_cache {
} ## end _build_circular_slice_cache
-#####################################
-# sub DEPRECATED METHODs
-#####################################
-
-=head2 fetch_by_mapfrag
-
- Function: DEPRECATED use fetch_by_misc_feature_attribute('synonym',$mapfrag)
-
-=cut
-
-sub fetch_by_mapfrag{
- my ($self,$mymapfrag,$flag,$size) = @_;
- deprecate('fetch_by_mapfrag is deprecated and will be removed in e87. Please use fetch_by_misc_feature_attribute instead');
- $flag ||= 'fixed-width'; # alt.. 'context'
- $size ||= $flag eq 'fixed-width' ? 100000 : 0;
- return $self->fetch_by_misc_feature_attribute('synonym',$mymapfrag,$size);
-}
-
-
-
-=head2 fetch_by_chr_start_end
-
- Description: DEPRECATED use fetch_by_region instead
-
-=cut
-
-sub fetch_by_chr_start_end {
- my ($self,$chr,$start,$end) = @_;
- deprecate('fetch_by_chr_start_end is deprecated and will be removed in e87. Please use fetch_by_region() instead');
-
- #assume that by chromosome the user actually meant top-level coord
- #system since this is the old behaviour of this deprecated method
- my $csa = $self->db->get_CoordSystemAdaptor();
- my ($cs) = @{$csa->fetch_all()}; # get the highest coord system
-
- return $self->fetch_by_region($cs->name,$chr,$start,$end,1,$cs->version);
-}
-
-
-
-=head2 fetch_by_contig_name
-
- Description: Deprecated. Use fetch_by_region(), Slice::project(),
- Slice::expand() instead
-
-=cut
-
-sub fetch_by_contig_name {
- my ($self, $name, $size) = @_;
-
- deprecate('fetch_by_contig_name is deprecated and will be removed in e87. Please use fetch_by_region(), Slice::project() and Slice::expand().');
-
- #previously wanted chromosomal slice on a given contig. Assume this means
- #a top-level slice on a given seq_region in the seq_level coord system
- my $csa = $self->db()->get_CoordSystemAdaptor();
- my $seq_level = $csa->fetch_sequence_level();
-
- my $seq_lvl_slice = $self->fetch_by_region($seq_level->name(), $name);
-
- if(!$seq_lvl_slice) {
- return undef;
- }
-
- my @projection = @{$seq_lvl_slice->project('toplevel')};
-
- if(@projection != 1) {
- warning("$name is mapped to multiple toplevel locations.");
- }
-
- return $projection[0]->[2]->expand($size, $size);
-}
-
-
-=head2 fetch_by_clone_accession
-
- Description: DEPRECATED. Use fetch_by_region, Slice::project, Slice::expand
- instead.
-
-=cut
-
-sub fetch_by_clone_accession{
- my ($self,$name,$size) = @_;
-
- deprecate('fetch_by_clone_accession is deprecated and will be removed in e87. Please use fetch_by_region(), Slice::project() and Slice::expand().');
-
- my $csa = $self->db()->get_CoordSystemAdaptor();
- my $clone_cs = $csa->fetch_by_name('clone');
-
- if(!$clone_cs) {
- warning('Clone coordinate system does not exist for this species');
- return undef;
- }
-
- #this unfortunately needs a version on the end to work
- if(! ($name =~ /\./)) {
- my $sth =
- $self->prepare( "SELECT sr.name "
- . "FROM seq_region sr, coord_system cs "
- . "WHERE cs.name = 'clone' "
- . "AND cs.coord_system_id = sr.coord_system_id "
- . "AND sr.name LIKE '$name.%'"
- . "AND cs.species_id = ?" );
-
- $sth->bind_param( 1, $self->species_id(), SQL_INTEGER );
- $sth->execute();
-
- ($name) = $sth->fetchrow_array();
-
- if(!$sth->rows()) {
- $sth->finish();
- throw("Clone $name not found in database");
- }
-
- $sth->finish();
- }
-
- my $clone = $self->fetch_by_region($clone_cs->name(), $name);
- return undef if(!$clone);
-
- my @projection = @{$clone->project('toplevel')};
-
- if(@projection != 1) {
- warning("$name is mapped to multiple locations.");
- }
-
- return $projection[0]->[2]->expand($size, $size);
-}
-
-
-=head2 fetch_by_supercontig_name
-
- Description: DEPRECATED. Use fetch_by_region(), Slice::project() and
- Slice::expand() instead
-
-=cut
-
-sub fetch_by_supercontig_name {
- my ($self,$name, $size) = @_;
-
- deprecate('fetch_by_supercontig_name is deprecated and will be removed in e87. Please use fetch_by_region(), Slice::project() and Slice::expand().');
-
- my $csa = $self->db()->get_CoordSystemAdaptor();
- my $sc_level = $csa->fetch_by_name('supercontig');
-
- if(!$sc_level) {
- warning('No supercontig coordinate system exists for this species.');
- return undef;
- }
-
- my $sc_slice = $self->fetch_by_region($sc_level->name(),$name);
-
- return undef if(!$sc_slice);
-
- my @projection = @{$sc_slice->project('toplevel')};
-
- if(@projection > 1) {
- warning("$name is mapped to multiple locations in toplevel");
- }
-
- return $projection[0]->[2]->expand($size, $size);
-}
-
-
-
-
-=head2 list_overlapping_supercontigs
-
- Description: DEPRECATED use Slice::project instead
-
-=cut
-
-sub list_overlapping_supercontigs {
- my ($self,$slice) = @_;
-
- deprecate('list_overlapping_supercontigs is deprecated and will be removed in e87. Please use Slice::project() instead.');
-
- my $csa = $self->db()->get_CoordSystemAdaptor();
- my $sc_level = $csa->fetch_by_name('supercontig');
-
- if(!$sc_level) {
- warning('No supercontig coordinate system exists for this species.');
- return undef;
- }
-
- my @out;
- foreach my $seg (@{$slice->project($sc_level->name(), $sc_level->version)}){
- push @out, $seg->[2]->seq_region_name();
- }
-
- return \@out;
-}
-
-
-
-=head2 fetch_by_chr_name
-
- Description: DEPRECATED. Use fetch by region instead
-
-=cut
-
-sub fetch_by_chr_name{
- my ($self,$chr_name) = @_;
- deprecate('fetch_by_chr_name is deprecated and will be removed in e87. Please use fetch_by_region() instead.');
-
- my $csa = $self->db->get_CoordSystemAdaptor();
-
- my $top_cs = @{$csa->fetch_all()};
-
- return $self->fetch_by_region($top_cs->name(),$chr_name,
- undef,undef,undef,$top_cs->version);
-}
-
-
-
-
-
-
1;
diff --git a/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
index da322dfd65d72b64a3cf18face842545867268fd..e18727d1617fc5ee1389fb30f4253c3f554d9f94 100644
--- a/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
@@ -2152,107 +2152,4 @@ sub fetch_all_by_transcript_supporting_evidence {
}
-##########################
-# #
-# DEPRECATED METHODS #
-# #
-##########################
-
-
-=head2 get_display_xref
-
- Description: DEPRECATED. Use $transcript->display_xref() instead.
-
-=cut
-
-sub get_display_xref {
- my ($self, $transcript) = @_;
-
- deprecate("get_display_xref is deprecated and will be removed in e87. display_xref should be retrieved from Transcript object directly.");
-
- if ( !defined $transcript ) {
- throw("Must call with a Transcript object");
- }
-
- my $sth = $self->prepare(qq(
- SELECT e.db_name,
- x.display_label,
- e.db_external_name,
- x.xref_id
- FROM transcript t,
- xref x,
- external_db e
- WHERE t.transcript_id = ?
- AND t.display_xref_id = x.xref_id
- AND x.external_db_id = e.external_db_id
- ));
-
- $sth->bind_param(1, $transcript->dbID, SQL_INTEGER);
- $sth->execute();
-
- my ($db_name, $display_label, $xref_id, $display_db_name ) =
- $sth->fetchrow_array();
-
- if ( !defined $xref_id ) {
- return undef;
- }
-
- my $db_entry = Bio::EnsEMBL::DBEntry->new(
- -dbid => $xref_id,
- -adaptor => $self->db->get_DBEntryAdaptor(),
- -dbname => $db_name,
- -display_id => $display_label
- -db_display_name => $display_db_name
- );
-
- return $db_entry;
-}
-
-
-=head2 get_stable_entry_info
-
- Description: DEPRECATED. Use $transcript->stable_id() instead.
-
-=cut
-
-sub get_stable_entry_info {
- my ($self, $transcript) = @_;
-
- deprecate("get_stable_entry_info is deprecated and will be removed in e87. Stable ids should be loaded directly instead");
-
- unless ( defined $transcript && ref $transcript &&
- $transcript->isa('Bio::EnsEMBL::Transcript') ) {
- throw("Needs a Transcript object, not a $transcript");
- }
-
- my $sth = $self->prepare(qq(
- SELECT stable_id, version
- FROM transcript
- WHERE transcript_id = ?
- ));
-
- $sth->bind_param(1, $transcript->dbID, SQL_INTEGER);
- $sth->execute();
-
- my @array = $sth->fetchrow_array();
- $transcript->{'_stable_id'} = $array[0];
- $transcript->{'_version'} = $array[1];
-
- return 1;
-}
-
-
-=head2 fetch_all_by_DBEntry
-
- Description: DEPRECATED. Use fetch_all_by_external_name() instead.
-
-=cut
-
-sub fetch_all_by_DBEntry {
- my $self = shift;
- deprecate('fetch_all_by_DBEntry is deprecated and will be removed in e87. Please use fetch_all_by_external_name instead.');
- return $self->fetch_all_by_external_name(@_);
-}
-
-
1;
diff --git a/modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm
index 2c89bc8cef9dddec3ea11495ae14b22a78ef0ba1..3870054cf85a3ddd6d76fa7047cd08edbf61e44b 100644
--- a/modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm
@@ -937,49 +937,6 @@ sub fetch_all_by_Transcript_list {
}
-
-=head2 fetch_all_by_DBEntry
-
- Description: DEPRECATED, this has been renames fetch_all_by_external_name
-
-=cut
-
-sub fetch_all_by_DBEntry {
- my $self = shift;
- deprecate("fetch_all_by_DBEntry is deprecated and will be removed in e87. Use fetch_all_by_external_name instead.");
- return $self->fetch_all_by_external_name(@_);
-}
-
-=head2 get_stable_entry_info
-
- Description: DEPRECATED - This method should no longer be needed. Stable
- id info is fetched when the transcript is.
-
-=cut
-
-sub get_stable_entry_info {
- my ($self,$translation) = @_;
-
- deprecate( "get_stable_entry_info is deprecated and will be removed in e87. Use $translation->stable_id instead." );
-
- unless(defined $translation && ref $translation &&
- $translation->isa('Bio::EnsEMBL::Translation') ) {
- throw("Needs a Translation object, not a [$translation]");
- }
-
- my $sth = $self->prepare("SELECT stable_id, version
- FROM translation
- WHERE translation_id = ?");
- $sth->bind_param(1,$translation->dbID,SQL_INTEGER);
- $sth->execute();
-
- my @array = $sth->fetchrow_array();
- $translation->{'_stable_id'} = $array[0];
- $translation->{'_version'} = $array[1];
-
- return 1;
-}
-
=head2 fetch_all
Example : $translations = $translation_adaptor->fetch_all();
diff --git a/modules/Bio/EnsEMBL/DensityPlot/BinValue.pm b/modules/Bio/EnsEMBL/DensityPlot/BinValue.pm
index 8dd301aea7368b548735561264db64ba7add4db2..be0bdc39f14f23478c2f3d70c6a95c492bdfbd89 100644
--- a/modules/Bio/EnsEMBL/DensityPlot/BinValue.pm
+++ b/modules/Bio/EnsEMBL/DensityPlot/BinValue.pm
@@ -48,9 +48,7 @@ use strict;
# Object preamble - inheriets from Bio::Root::Object
-use Bio::EnsEMBL::Root;
-
-@ISA = qw(Bio::EnsEMBL::Root Exporter);
+@ISA = qw(Exporter);
#@EXPORT_OK = qw();
# new() is inherited from Bio::Root::Object
diff --git a/modules/Bio/EnsEMBL/DensityPlot/BinValueSet.pm b/modules/Bio/EnsEMBL/DensityPlot/BinValueSet.pm
index 447779a066f58b17422f2266d725bc259665a5ee..6acb0d675c93c52a491af3acb3cda3b6c34aad50 100644
--- a/modules/Bio/EnsEMBL/DensityPlot/BinValueSet.pm
+++ b/modules/Bio/EnsEMBL/DensityPlot/BinValueSet.pm
@@ -49,9 +49,7 @@ use Bio::EnsEMBL::DensityPlot::BinValue;
# Object preamble - inheriets from Bio::Root::Object
-use Bio::EnsEMBL::Root;
-
-@ISA = qw(Bio::EnsEMBL::Root Exporter);
+@ISA = qw(Exporter);
#@EXPORT_OK = qw();
# new() is inherited from Bio::Root::Object
diff --git a/modules/Bio/EnsEMBL/Exon.pm b/modules/Bio/EnsEMBL/Exon.pm
index f4ccf71831f5c01cce275b426acf37a992a7a8b0..acc8c43b423d8be07d052c8f031ddf815ed41622 100755
--- a/modules/Bio/EnsEMBL/Exon.pm
+++ b/modules/Bio/EnsEMBL/Exon.pm
@@ -1650,72 +1650,5 @@ sub summary_as_hash {
return $summary_ref;
}
-=head1 DEPRECATED METHODS
-
-=cut
-
-
-
-=head2 temporary_id
-
- Description: DEPRECATED. This should not be necessary.
-
-=cut
-
-sub temporary_id {
- my $self = shift;
- deprecate('temporary_id is deprecated and will be removed in e87.');
- $self->{'tempID'} = shift if(@_);
- return $self->{'tempID'};
-}
-
-
-=head2 created
-
- Description: DEPRECATED. Do not use.
-
-=cut
-
-sub created {
- my ($self,$value) = @_;
- deprecate( "created is deprecated and will be removed in e87." );
- if(defined $value ) {
- $self->{'_created'} = $value;
- }
- return $self->{'_created'};
-}
-
-=head2 modified
-
- Description: DEPRECATED. Do not use.
-
-=cut
-
-
-sub modified {
- my ($self,$value) = @_;
- deprecate( "Modified is deprecated and will be removed in e87." );
- if( defined $value ) {
- $self->{'_modified'} = $value;
- }
- return $self->{'_modified'};
-}
-
-
-=head2 type
-
- Description: DEPRECATED. Do not use.
-
-=cut
-
-sub type {
- my ($self,$value) = @_;
- deprecate("Type is deprecated and will be removed in e87.");
- if (defined($value)) {
- $self->{'type'} = $value;
- }
- return $self->{'type'};
-}
-
1;
diff --git a/modules/Bio/EnsEMBL/Feature.pm b/modules/Bio/EnsEMBL/Feature.pm
index c897e9623b76d98778c0dd7db4f69a73058b9219..c7900a1e04a0dfbc3c6c6c8c9f2544e279032bab 100644
--- a/modules/Bio/EnsEMBL/Feature.pm
+++ b/modules/Bio/EnsEMBL/Feature.pm
@@ -1497,17 +1497,6 @@ sub species {
}
-=head2 contig
-
- Deprecated - Included for backwards compatibility only.
- Use slice() instead
-=cut
-sub contig {
- deprecate('contig is deprecated and will be removed in e87. Please use slice() instead');
- slice(@_);
-}
-
-
=head2 sub_SeqFeature
@@ -1595,22 +1584,6 @@ sub _deprecated_transform {
}
-=head2 id
-
-Deprecated - only included for backwards compatibility.
-Use display_id, hseqname, dbID or stable_id instead
-
-=cut
-
-sub id {
- my $self = shift;
- deprecate("id method is deprecated and will be removed in e87. Please use display_id instead");
- return $self->{'stable_id'} if($self->{'stable_id'});
- return $self->{'hseqname'} if($self->{'hseqname'});
- return $self->{'seqname'} if($self->{'seqname'});
- return $self->{'dbID'};
-}
-
my $feature_tables =
{
'Bio::EnsEMBL::AssemblyExceptionFeature' => 'assembly_exception',
diff --git a/modules/Bio/EnsEMBL/FeaturePair.pm b/modules/Bio/EnsEMBL/FeaturePair.pm
index 01eb45582003b4dd19aad9700c3fb847d86d403d..49919314262b89d2f6f650ab6f0ab71e25038387 100755
--- a/modules/Bio/EnsEMBL/FeaturePair.pm
+++ b/modules/Bio/EnsEMBL/FeaturePair.pm
@@ -718,64 +718,6 @@ sub level_id {
=head1 DEPRECATED METHODS
-=cut
-
-=head2 feature1
-
- Description: DEPRECATED use start(), end(), strand(), slice(), etc.
- methods instead
-
-=cut
-
-sub feature1 {
- my ($self, $arg) = @_;
-
- deprecate('feature1 is deprecated and will be removed in e87. Please use start(), end(), strand(), slice(), etc. methods instead.');
-
- if ($arg) {
- $self->start($arg->start());
- $self->end($arg->end());
- $self->strand($arg->strand());
- $self->score($arg->score());
- $self->percent_id($arg->percent_id());
- $self->analysis($arg->analysis);
- if ($arg->contig) {
- $self->slice($arg->contig);
- }
- }
-
- return $self;
-}
-
-=head2 feature2
-
- Description: DEPRECATED use hstart(), hend(), hstrand() etc.
- methods instead
-
-=cut
-
-sub feature2 {
- my ($self, $arg) = @_;
-
- deprecate('feature2 is deprecated and will be removed in e87. Please use hstart(),hend(),hstrand(),hseqname() methods instead.');
-
- if (defined($arg)) {
- $self->hstart($arg->start());
- $self->hend($arg->end());
- $self->hstrand($arg->strand());
- $self->hseqname($arg->seqname());
- return $arg;
- }
-
- return
- new Bio::EnsEMBL::Feature(-START => $self->hstart(),
- -END => $self->hend(),
- -STRAND => $self->hstrand(),
- -SCORE => $self->score(),
- -PERCENT_ID => $self->percent_id(),
- -ANALYSIS => $self->analysis,
- -SEQNAME => $self->hseqname());
-}
=head2 invert
@@ -829,106 +771,6 @@ sub invert {
$self->{'slice'} = $slice;
} ## end sub invert
-=head2 set_featurepair_fields
-
- Description: DEPRECATED do not use
-
-=cut
-
-sub set_featurepair_fields {
- my ($self, $start, $end, $strand, $score, $seqname, $hstart, $hend, $hstrand, $hseqname, $analysis, $e_value, $perc_id, $phase, $end_phase) = @_;
-
- deprecate("set_featurepair_fields is deprecated and will be removed in e87. Please use individual Getter/Setters or Constructor arguments instead.");
-
- throw('interface fault') if (@_ < 12 or @_ > 15);
-
- $self->start($start);
- $self->end($end);
- $self->strand($strand);
- $self->score($score);
- $self->seqname($seqname);
- $self->hstart($hstart);
- $self->hend($hend);
- $self->hstrand($hstrand);
- $self->hseqname($hseqname);
- $self->analysis($analysis);
- $self->p_value($e_value) if (defined $e_value);
- $self->percent_id($perc_id) if (defined $perc_id);
- $self->phase($phase) if (defined $phase);
- $self->end_phase($end_phase) if (defined $end_phase);
-}
-
-=head2 gffstring
-
- Description: DEPRECATED do not use
-
-=cut
-
-sub gffstring {
- my ($self) = @_;
-
- deprecate('gffstring is deprecated and will be removed in e87.');
-
- my $str .= (defined $self->slice) ? $self->slice->name() . "\t" : "\t";
- $str .= "\t"; #source tag
- $str .= "\t"; #primary tag
- $str .= (defined $self->start) ? $self->start . "\t" : "\t";
- $str .= (defined $self->end) ? $self->end . "\t" : "\t";
- $str .= (defined $self->score) ? $self->score . "\t" : "\t";
- $str .= (defined $self->strand) ? $self->strand . "\t" : ".\t";
- $str .= ".\t"; #phase
- $str .= ".\t"; #end phase
-
- my $hstrand = "+";
-
- if (($self->hstrand) && ($self->hstrand == -1)) {
- $hstrand = "-";
- }
-
- #Append a few FeaturePair specific things
- $str .= (defined $self->hseqname) ? $self->hseqname . "\t" : "\t";
- $str .= (defined $self->hstart) ? $self->hstart . "\t" : "\t";
- $str .= (defined $self->hend) ? $self->hend . "\t" : "\t";
- $str .= (defined $self->hstrand) ? $hstrand . "\t" : "\t";
- $str .= (defined $self->hphase) ? $self->hphase . "\t" : ".\t";
-
- return $str;
-} ## end sub gffstring
-
-=head2 hphase
-
- Description: DEPRECATED do not use
-
-=cut
-
-sub hphase {
- my ($self, $value) = @_;
-
- deprecate('hphase is deprecated and will be removed in e87.');
-
- if (defined($value)) {
- $self->{_hphase} = $value;
- }
-
- return $self->{_hphase};
-}
-
-=head2 hend_phase
-
- Description: DEPRECATED do not use
-
-=cut
-
-sub hend_phase {
- my ($self, $value) = @_;
-
- deprecate('hend_phase is deprecated and will be removed in e87.');
-
- if (defined($value)) {
- $self->{_hend_phase} = $value;
- }
- return $self->{_hend_phase};
-}
sub extra_data {
my $self = shift;
diff --git a/modules/Bio/EnsEMBL/Gene.pm b/modules/Bio/EnsEMBL/Gene.pm
index d6a4b5a7e60cb6b94b5645f4268751f8614e4966..16840e0e35e166582af8d0d8ae98090feedb3fc8 100755
--- a/modules/Bio/EnsEMBL/Gene.pm
+++ b/modules/Bio/EnsEMBL/Gene.pm
@@ -1554,76 +1554,6 @@ sub havana_gene {
# DEPRECATED METHODS FOLLOW
###########################
-=head2 DEPRECATED add_DBLink
-
- Description: DEPRECATED This method has been deprecated in favour of the
- add_DBEntry method. Objects are responible for holding only
- xrefs directly associated with themselves now.
-
-=cut
-
-
-sub add_DBLink{
- my ($self,$value) = @_;
-
- throw("add_DBLink is deprecated and will be removed in e87. Please use add_DBEntry instead.");
-
- # unless(defined $value && ref $value
- # && $value->isa('Bio::Annotation::DBLink') ) {
- # throw("This [$value] is not a DBLink");
- # }
-
- # if( !defined $self->{'_db_link'} ) {
- # $self->{'_db_link'} = [];
- # }
-
- # push(@{$self->{'_db_link'}},$value);
-}
-
-
-=head2 temporary_id
-
- Function: DEPRECATED: Use dbID or stable_id or something else instead
-
-=cut
-
-sub temporary_id {
- my ($obj,$value) = @_;
- deprecate('temporary_id is deprecated and will be removed in e87.');
- if( defined $value) {
- $obj->{'temporary_id'} = $value;
- }
- return $obj->{'temporary_id'};
-}
-
-
-=head2 chr_name
-
- Description: DEPRECATED. Use project, tranform, or transfer to obtain this
- gene in another coord system. Use $gene->slice->seq_region_name
- to get the name of the underlying coord system. Or
- $gene->slice->name().
-
-=cut
-
-sub chr_name {
- my $self = shift;
-
- deprecate( "chr_name is deprecated and will be removed in e87. Please use project() to obtain other coordinate systems" );
-
- my $gene_slice = $self->slice();
- if( $gene_slice->coord_system()->name eq "chromosome" ) {
- return $gene_slice->seq_region_name();
- }
-
- my $coords = $self->project( "toplevel" );
-
- if( @$coords ) {
- return $coords->[0]->[2]->seq_region_name();
- }
-}
-
-
=head2 fetch_coded_for_regulatory_factors
Arg [1] : none
@@ -1649,29 +1579,5 @@ sub fetch_coded_for_regulatory_factors {
}
-=head2 type
-
- Description: DEPRECATED. Use biotype() instead.
-
-=cut
-
-sub type {
- deprecate("type is deprecated and will be removed in e87. Please use biotype() instead");
- biotype(@_);
-}
-
-
-=head2 confidence
-
- Description: DEPRECATED. Use status() instead.
-
-=cut
-
-sub confidence {
- deprecate("confidence is deprecated and will be removed in e87. Please use status() instead");
- status(@_);
-}
-
-
1;
diff --git a/modules/Bio/EnsEMBL/IdentityXref.pm b/modules/Bio/EnsEMBL/IdentityXref.pm
index d609561d7dcd9298f881d731c78584059d619b53..dfe630b76e834c7b87dcd6830ac483ed6fc5d340 100644
--- a/modules/Bio/EnsEMBL/IdentityXref.pm
+++ b/modules/Bio/EnsEMBL/IdentityXref.pm
@@ -441,92 +441,4 @@ sub map_feature {
}
-###########################
-# DEPRECATED METHODS FOLLOW
-###########################
-
-=head2 query_identity
-
- Description: DEPRECATED. Use xref_identity() instead.
- Status : At Risk
-
-=cut
-
-sub query_identity{
- deprecate("query_identity is deprecated and will be removed in e87. Please use xref_identity instead");
- xref_identity(@_);
-}
-
-
-=head2 target_identity
-
- Description: DEPRECATED. Use ensembl_identity() instead.
- Status : At Risk
-
-=cut
-
-sub target_identity{
- deprecate("target_identity is deprecated and will be removed in e87. Please use ensembl_identity instead");
- ensembl_identity(@_);
-}
-
-
-
-=head2 translation_start
-
- Description: DEPRECATED. Use ensembl_start() instead.
- Status : At Risk
-
-=cut
-
-sub translation_start {
- deprecate("translation_start is deprecated and will be removed in e87. Please use ensembl_start instead");
- ensembl_start(@_);
-
-}
-
-
-=head2 translation_end
-
- Description: DEPRECATED. Use ensembl_end() instead.
- Status : At Risk
-
-=cut
-
-sub translation_end {
- deprecate("translation_end is deprecated and will be removed in e87. Please use ensembl_end instead");
- ensembl_end(@_);
-}
-
-
-
-=head2 query_start
-
- Description: DEPRECATED. Use xref_start() instead.
- Status : At Risk
-
-=cut
-
-sub query_start {
- deprecate("query_start is deprecated and will be removed in e87. Please use xref_start instead");
- xref_start(@_);
-
-}
-
-
-
-=head2 query_end
-
- Description: DEPRECATED. Use xref_end() instead.
- Status : At Risk
-
-=cut
-
-sub query_end {
- deprecate("query_end is deprecated and will be removed in e87. Please use xref_end instead");
- xref_end(@_);
-
-}
-
-
1;
diff --git a/modules/Bio/EnsEMBL/KaryotypeBand.pm b/modules/Bio/EnsEMBL/KaryotypeBand.pm
index e3bfb6d953d701f9f138bb850e44c4f8ce594d59..9df1d642ee06822989ff92116a3ee9e4463baa49 100644
--- a/modules/Bio/EnsEMBL/KaryotypeBand.pm
+++ b/modules/Bio/EnsEMBL/KaryotypeBand.pm
@@ -222,23 +222,5 @@ sub display_id {
}
-=head2 chr_name
-
- Description: DEPRECATED - use $kary_band->slice()->seq_region_name() instead
-
-=cut
-
-sub chr_name {
- my $self = shift;
-
- deprecate('chr_name is deprecated and will be removed in e87. Please use $kary_band->slice()->seq_region_name() instead.');
- if(!$self->slice) {
- warning('KaryotypeBand does not have Slice - cannot get seq_region_name.');
- return '';
- }
-
- return $self->slice->seq_region_name();
-}
-
1;
diff --git a/modules/Bio/EnsEMBL/Map/DBSQL/MarkerFeatureAdaptor.pm b/modules/Bio/EnsEMBL/Map/DBSQL/MarkerFeatureAdaptor.pm
index be7e44522f1accd013217a6e403577b0ce0ca4a8..6f690a70ac80999fa4e57bda5f5455cc0b94ec3a 100644
--- a/modules/Bio/EnsEMBL/Map/DBSQL/MarkerFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/Map/DBSQL/MarkerFeatureAdaptor.pm
@@ -145,24 +145,6 @@ sub fetch_all_by_Slice_and_priority {
-=head2 fetch_all_by_RawContig_and_priority
-
- Description: DEPRECATED use fetch_all_by_Slice_and_priority instead
-
-=cut
-
-sub fetch_all_by_RawContig_and_priority {
- deprecate('fetch_all_by_RawContig_and_priority is deprecated and will be removed in e87. Please use fetch_all_by_Slice_and_priority() instead.');
- fetch_all_by_Slice_and_priority(@_);
-}
-
-
-sub fetch_all_by_Slice_and_score {
- my $self = shift;
- throw('fetch_all_by_Slice_and_score should not be' .
- 'used to fetch marker_features');
-}
-
sub _columns {
my $self = shift;
diff --git a/modules/Bio/EnsEMBL/Map/DitagFeature.pm b/modules/Bio/EnsEMBL/Map/DitagFeature.pm
index db94aa34e97fd6e4d3eaae885630fd7a99626b2d..7e2365d41547d9702fd3b2311b14a09120e86fb9 100644
--- a/modules/Bio/EnsEMBL/Map/DitagFeature.pm
+++ b/modules/Bio/EnsEMBL/Map/DitagFeature.pm
@@ -165,17 +165,6 @@ sub new {
}
-=head2 fetch_ditag
-
- Description: Deprecated, use ditag() instead
-
-=cut
-
-sub fetch_ditag {
- deprecate("fetch_ditag is deprecated and will be removed in e87. Please use ditag() instead.")
-}
-
-
=head2 ditag
Arg [1] : (optional) ditag object
diff --git a/modules/Bio/EnsEMBL/Map/MapLocation.pm b/modules/Bio/EnsEMBL/Map/MapLocation.pm
index aae4839282398d1c169ef37eaa9c230cf7d93775..e1caf7800e5e90127c953a4f778c4c91e3a2e931 100644
--- a/modules/Bio/EnsEMBL/Map/MapLocation.pm
+++ b/modules/Bio/EnsEMBL/Map/MapLocation.pm
@@ -187,32 +187,4 @@ sub lod_score {
}
-
-=head2 chromosome
-
- Description: DEPRECATED use chromosome_name() instead
-
-=cut
-
-sub chromosome {
- my $self = shift;
- deprecate('chromosome is deprecated and will be removed in e87. Please use chromosome_name instead');
-
- if(@_) {
- my $chr = shift;
- if(ref($chr)) {
- $self->chromosome_name($chr->seq_region_name());
- } else {
- $self->chromosome_name($chr);
- }
- }
-
- #this object has no way to talk to db and thus no way to
- #get a chromosome object
- return $self->chromosome_name();
-}
-
-
-
-
1;
diff --git a/modules/Bio/EnsEMBL/OperonTranscript.pm b/modules/Bio/EnsEMBL/OperonTranscript.pm
index f8d64c1cec063ec42f1bb5458be02d5d361ae243..150c9c7579066607edb3fcae4418e38053c1bc29 100755
--- a/modules/Bio/EnsEMBL/OperonTranscript.pm
+++ b/modules/Bio/EnsEMBL/OperonTranscript.pm
@@ -292,21 +292,6 @@ sub add_Gene {
return;
}
-=head2 add_gene
-
- Arg [1] : Bio::EnsEMBL::Gene - gene to attach to this polycistronic transcript
- Example : $operon->add_gene($gene);
- Description: Attach a gene to this polycistronic transcript
- Exceptions : if argument is not Bio::EnsEMBL::Gene
- Caller : general
- Status : DEPRECATED - use add_Gene
-
-=cut
-sub add_gene {
- my ($self,$gene) = @_;
- deprecate('add_gene is deprecated and will be removed in e87. Please use $self->add_Gene()');
- return $self->add_Gene($gene);
-}
=head2 add_DBEntry
Arg [1] : Bio::EnsEMBL::DBEntry $dbe
diff --git a/modules/Bio/EnsEMBL/PredictionTranscript.pm b/modules/Bio/EnsEMBL/PredictionTranscript.pm
index 43d044d95cb6afa4f7d4dad030a141acacb5c8fa..5cd3cec948dfcfb6b0bbf9bd6a94db5b6a2b7432 100644
--- a/modules/Bio/EnsEMBL/PredictionTranscript.pm
+++ b/modules/Bio/EnsEMBL/PredictionTranscript.pm
@@ -582,31 +582,4 @@ sub get_all_Attributes {
}
-
-=head2 get_exon_count
-
- Description: DEPRECATED - use get_all_Exons instead
-
-=cut
-
-sub get_exon_count {
- my $self = shift;
- deprecate('get_exon_count is deprecated and will be removed in e87. Please use scalar(@{$transcript->get_all_Exon()s}) instead');
- return scalar( @{$self->get_all_Exons} );
-}
-
-
-
-=head2 get_cdna
-
- Description : DEPRECATED - use spliced_seq() or translateable_seq instead
-
-=cut
-
-sub get_cdna {
- my $self = shift;
- deprecate('get_cdna is deprecated and will be removed in e87. Please use spliced_seq instead');
- return $self->spliced_seq();
-}
-
1;
diff --git a/modules/Bio/EnsEMBL/Registry.pm b/modules/Bio/EnsEMBL/Registry.pm
index 9f05be88beecd606636184f79e8f6a37f51e3e6e..1953cbb1eeb515bbac3b7810335af424e673306a 100644
--- a/modules/Bio/EnsEMBL/Registry.pm
+++ b/modules/Bio/EnsEMBL/Registry.pm
@@ -2709,32 +2709,6 @@ sub load_registry_from_multiple_dbs {
# Web specific routines
#
-=head2 DEPRECATED load_registry_with_web_adaptors
-
- DEPRECATED: Use load_registry_from_db instead.
-
-=cut
-
-sub load_registry_with_web_adaptors{
- my $class = shift;
-
- deprecate('load_registry_with_web_adaptors is deprecated and will be removed in e87. Please use the load_registry_from_db instead');
- my $site_eval = eval{ require SiteDefs };
- if ($@ or (!defined($site_eval))){ die "Can't use SiteDefs.pm - $@\n"; }
- SiteDefs->import(qw(:ALL));
-
- my $species_eval = eval{ require SpeciesDefs };
- if ($@ or (!defined($species_eval))){ die "Can't use SpeciesDefs.pm - $@\n"; }
- my $conf = new SpeciesDefs();
-
- my %species_alias = %{$SiteDefs::ENSEMBL_SPECIES_ALIASES};
-
- foreach my $spec (keys %species_alias){
- Bio::EnsEMBL::Registry->add_alias($species_alias{$spec},$spec);
- }
- return;
-}
-
=head2 set_default_track
Sets a flag to say that that this species/group are a default track and do not
diff --git a/modules/Bio/EnsEMBL/Root.pm b/modules/Bio/EnsEMBL/Root.pm
deleted file mode 100644
index 14df9238093323c2df667f92725fa0df38d5490e..0000000000000000000000000000000000000000
--- a/modules/Bio/EnsEMBL/Root.pm
+++ /dev/null
@@ -1,168 +0,0 @@
-=head1 LICENSE
-
-Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016] EMBL-European Bioinformatics Institute
-
-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and
-limitations under the License.
-
-=cut
-
-
-=head1 CONTACT
-
- Please email comments or questions to the public Ensembl
- developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.
-
- Questions may also be sent to the Ensembl help desk at
- <http://www.ensembl.org/Help/Contact>.
-
-=head1 AUTHOR
-
- Originally from Steve Chervitz. Refactored by Ewan Birney.
-
-=cut
-
-=head1 NAME
-
-Bio::EnsEMBL::Root
-
-=head1 DESCRIPTION
-
-Do not use Bio::EnsEMBL::Root anymore. It is included for backwards
-compatibility (every object in EnsEMBL used to inherit from this class)
-but will eventually be phased out. The replacement for the _rearrage
-method is the rearrange method which can be imported in the following
-way:
-
- use Bio::EnsEMBL::Utils::Argument qw(rearrange);
-
- # can now call rearrange as a class method (instead as object method)
- my ( $start, $end ) = rearrange( [ 'START', 'END' ], @args );
-
-If you want to use the throw or warn methods the replacement use the
-class methods throw and warning from the Bio::EnsEMBL::Utils::Exception
-class:
-
- use Bio::EnsEMBL::Utils::Exception qw(throw warning);
-
- # can now call throw or warning even without blessed reference
- warning('This is a warning');
- throw('This is an exception');
-
-This module was stolen from BioPerl to avoid problems with moving to
-BioPerl 1 from 0.7
-
-=head1 METHODS
-
-=cut
-
-package Bio::EnsEMBL::Root;
-
-use strict;
-use vars qw($VERBOSITY);
-use Bio::EnsEMBL::Utils::Exception qw( );
-use Bio::EnsEMBL::Utils::Argument qw( );
-
-
-$VERBOSITY = 0;
-
-sub new{
- my($caller,@args) = @_;
-
- my $class = ref($caller) || $caller;
- return bless({}, $class);
-}
-
-
-=head2 throw
-
- DEPRECATED
-
-=cut
-
-sub throw{
- my ($self,$string) = @_;
-
- deprecate('Root->throw is deprecated and will be removed in e87. Please use Exception->throw instead');
-
- Bio::EnsEMBL::Utils::Exception->throw($string);
-
-
-}
-
-=head2 warn
-
- DEPRECATED
-
-=cut
-
-sub warn{
- my ($self,$string) = @_;
-
- deprecate('Root->warn is deprecated and will be removed in e87. Please use Exception->warning instead');
-
- Bio::EnsEMBL::Utils::Exception->warning($string);
-
-}
-
-
-
-
-=head2 verbose
-
- DEPRECATED
-
-=cut
-
-sub verbose{
- my ($self,$value) = @_;
-
- deprecate('Root->verbose is deprecated and will be removed in e87. Please use Exception->verbose instead');
-
- Bio::EnsEMBL::Utils::Exception->verbose($value);
-
- }
-
-=head2 stack_trace_dump
-
- DEPRECATED
-
-=cut
-
-sub stack_trace_dump{
- my ($self) = @_;
-
- deprecate('Root->stack_trace_dump is deprecated and will be removed in e87. Please use Exception->stack_trace_dump instead');
-
- Bio::EnsEMBL::Utils::Exception->stack_trace_dump();
-
-}
-
-
-=head2 stack_trace
-
- DEPRECATED
-
-=cut
-
-sub stack_trace{
- my ($self) = @_;
-
- deprecate('Root->stack_trace is deprecated and will be removed in e87. Please use Exception->stack_trace instead');
-
- Bio::EnsEMBL::Utils::Exception->stack_trace();
-
-}
-
-
-1;
diff --git a/modules/Bio/EnsEMBL/SeqFeature.pm b/modules/Bio/EnsEMBL/SeqFeature.pm
index 578f79360b2fc072e6836e802273ac736510325e..8a063c63398abbcaaefb5a71438a6853000848db 100755
--- a/modules/Bio/EnsEMBL/SeqFeature.pm
+++ b/modules/Bio/EnsEMBL/SeqFeature.pm
@@ -71,9 +71,6 @@ use strict;
use Bio::EnsEMBL::Analysis;
-use Bio::EnsEMBL::Root;
-
-@ISA = qw(Bio::EnsEMBL::Root);
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
diff --git a/modules/Bio/EnsEMBL/Slice.pm b/modules/Bio/EnsEMBL/Slice.pm
index 95e4bfd8161417ab4a397cef3487a732c3229962..e8efd8a19cf2b875abb35eff540fc595a0845a2a 100644
--- a/modules/Bio/EnsEMBL/Slice.pm
+++ b/modules/Bio/EnsEMBL/Slice.pm
@@ -2704,47 +2704,6 @@ sub get_all_genotyped_VariationFeatures{
}
-=head2 get_all_SNPs
-
- Description: DEPRECATED. Use get_all_VariationFeatures insted
-
-=cut
-
-sub get_all_SNPs {
- my $self = shift;
- deprecate('get_all_SNPs is deprecated and will be removed in e87. Please use get_all_VariationFeatures() instead.');
- my $snps;
- my $vf = $self->get_all_genotyped_VariationFeatures();
- if( $vf->[0] ) {
- #necessary to convert the VariationFeatures into SNP objects
- foreach my $variation_feature (@{$vf}){
- push @{$snps},$variation_feature->convert_to_SNP();
- }
- return $snps;
- }
- return [];
-}
-
-=head2 get_all_genotyped_SNPs
-
- Description : DEPRECATED. Use get_all_genotyped_VariationFeatures insted
-
-=cut
-
-sub get_all_genotyped_SNPs {
- my $self = shift;
- deprecate("get_all_genotypes_SNPs is deprecated and will be removed in e87. Please use get_all_genotyped_VariationFeatures instead");
- my $vf = $self->get_all_genotyped_VariationFeatures;
- my $snps;
- if ($vf->[0]){
- foreach my $variation_feature (@{$vf}){
- push @{$snps},$variation_feature->convert_to_SNP();
- }
- return $snps;
- }
- return [];
-}
-
=head2 get_all_Genes
Arg [1] : (optional) string $logic_name
@@ -3926,165 +3885,4 @@ sub alphabet { return 'dna'; }
sub accession_number { name(@_); }
-
-# sub DEPRECATED METHODS #
-###############################################################################
-
-=head1 DEPRECATED METHODS
-
-
-=head2 get_all_supercontig_Slices
-
- Description: DEPRECATED use get_tiling_path("NTcontig") instead
-
-=cut
-
-sub get_all_supercontig_Slices {
- my $self = shift;
-
- deprecate("get_all_supercontig_Slices is deprecated and will be removed in e87. Please use get_tiling_path('NTcontig') instead");
-
- my $result = [];
-
- if( $self->adaptor() ) {
- my $superctg_names =
- $self->adaptor()->list_overlapping_supercontigs( $self );
-
- for my $name ( @$superctg_names ) {
- my $slice;
- $slice = $self->adaptor()->fetch_by_supercontig_name( $name );
- $slice->name( $name );
- push( @$result, $slice );
- }
- } else {
- warning( "Slice needs to be attached to a database to get supercontigs" );
- }
-
- return $result;
-}
-
-
-
-
-
-=head2 get_Chromosome
-
- Description: DEPRECATED use this instead:
- $slice_adp->fetch_by_region('chromosome',
- $slice->seq_region_name)
-
-=cut
-
-sub get_Chromosome {
- my $self = shift @_;
-
- deprecate("get_Chromosome is deprecated and will be removed in e87. Please use SliceAdaptor::fetch_by_region('chromosome',slice->seq_region_name) instead");
-
- my $csa = $self->adaptor->db->get_CoordSystemAdaptor();
- my ($top_cs) = @{$csa->fetch_all()};
-
- return $self->adaptor->fetch_by_region($top_cs->name(),
- $self->seq_region_name(),
- undef,undef,undef,
- $top_cs->version());
-}
-
-
-
-=head2 chr_name
-
- Description: DEPRECATED use seq_region_name() instead
-
-=cut
-
-sub chr_name{
- deprecate("chr_name is deprecated and will be removed in e87. Please use seq_region_name() instead");
- seq_region_name(@_);
-}
-
-
-
-=head2 chr_start
-
- Description: DEPRECATED use start() instead
-
-=cut
-
-sub chr_start{
- deprecate('chr_start is deprecated and will be removed in e87. Please use start() instead');
- start(@_);
-}
-
-
-
-=head2 chr_end
-
- Description: DEPRECATED use end() instead
- Returntype : int
- Exceptions : none
- Caller : SliceAdaptor, general
-
-=cut
-
-sub chr_end{
- deprecate('chr_end is deprecated and will be removed in e87. Please use end() instead');
- end(@_);
-}
-
-
-=head2 assembly_type
-
- Description: DEPRECATED use version instead
-
-=cut
-
-sub assembly_type{
- my $self = shift;
- deprecate('assembly_type is deprecated and will be removed in e87. Please use $slice->coord_system()->version() instead.');
- return $self->coord_system->version();
-}
-
-
-=head2 dbID
-
- Description: DEPRECATED use SliceAdaptor::get_seq_region_id instead
-
-=cut
-
-sub dbID {
- my $self = shift;
- deprecate('dbID is deprecated and will be removed in e87. Please use SliceAdaptor::get_seq_region_id instead.');
- if(!$self->adaptor) {
- warning('Cannot retrieve seq_region_id without attached adaptor.');
- return 0;
- }
- return $self->adaptor->get_seq_region_id($self);
-}
-
-
-=head2 get_all_MapFrags
-
- Description: DEPRECATED use get_all_MiscFeatures instead
-
-=cut
-
-sub get_all_MapFrags {
- my $self = shift;
- deprecate('get_all_MapFrags is deprecated and will be removed in e87. Please use get_all_MiscFeatures instead');
- return $self->get_all_MiscFeatures(@_);
-}
-
-=head2 has_MapSet
-
- Description: DEPRECATED use get_all_MiscFeatures instead
-
-=cut
-
-sub has_MapSet {
- my( $self, $mapset_name ) = @_;
- deprecate('has_MapSet is deprecated and will be removed in e87. Please use get_all_MiscFeatures instead');
- my $mfs = $self->get_all_MiscFeatures($mapset_name);
- return (@$mfs > 0);
-}
-
1;
diff --git a/modules/Bio/EnsEMBL/StrainSlice.pm b/modules/Bio/EnsEMBL/StrainSlice.pm
index 7d42836c0ee2ee3eb1d6051bc1a6c45bdd421240..b989a13314cfe8618e4218d464eecf01e47398b3 100644
--- a/modules/Bio/EnsEMBL/StrainSlice.pm
+++ b/modules/Bio/EnsEMBL/StrainSlice.pm
@@ -799,17 +799,6 @@ sub mapper{
return $self->{'mapper'};
}
-=head2 get_all_differences_Slice
-
- Description : DEPRECATED use get_all_AlleleFeatures instead
-
-=cut
-
-sub get_all_differences_Slice{
- my $self = shift;
- deprecate('get_all_differences_Slice is deprecated and will be removed in e87. Please use get_all_AlleleFeatures_Slice instead');
- return $self->get_all_AlleleFeatures_Slice(@_);
-}
=head2 get_all_VariationFeatures
diff --git a/modules/Bio/EnsEMBL/Transcript.pm b/modules/Bio/EnsEMBL/Transcript.pm
index b5ab18231fc6540815f29cd91bb8f84ed9ffa50d..cfdc9c4bc09a8837b8cfd6abfbc45b8055d5c383 100755
--- a/modules/Bio/EnsEMBL/Transcript.pm
+++ b/modules/Bio/EnsEMBL/Transcript.pm
@@ -3225,83 +3225,6 @@ sub get_Gene {
return $parent_gene;
}
-###########################
-# DEPRECATED METHODS FOLLOW
-###########################
-
-=head2 created
-
- Description: DEPRECATED - this attribute is not part of transcript anymore
-
-=cut
-
-sub created{
- my $obj = shift;
- deprecate( "created is deprecated and will be removed in e87." );
- if( @_ ) {
- my $value = shift;
- $obj->{'created'} = $value;
- }
- return $obj->{'created'};
-}
-
-
-=head2 modified
-
- Description: DEPRECATED - this attribute is not part of transcript anymore
-
-=cut
-
-sub modified{
- my $obj = shift;
- deprecate( "modified is deprecated and will be removed in e87." );
- if( @_ ) {
- my $value = shift;
- $obj->{'modified'} = $value;
- }
- return $obj->{'modified'};
-}
-
-
-=head2 temporary_id
-
- Function: DEPRECATED: Use dbID or stable_id or something else instead
-
-=cut
-
-sub temporary_id{
- my ($obj,$value) = @_;
- deprecate( "temporary_id is deprecated and will be removed in e87." );
- if( defined $value) {
- $obj->{'temporary_id'} = $value;
- }
- return $obj->{'temporary_id'};
-}
-
-
-=head2 type
-
- Description: DEPRECATED. Use biotype() instead.
-
-=cut
-
-sub type {
- deprecate("type is deprecated and will be removed in e87. Please use biotype() instead");
- biotype(@_);
-}
-
-
-=head2 confidence
-
- Description: DEPRECATED. Use status() instead.
-
-=cut
-
-sub confidence {
- deprecate("confidence is deprecated and will be removed in e87. Please use status() instead");
- status(@_);
-}
-
1;
diff --git a/modules/Bio/EnsEMBL/Translation.pm b/modules/Bio/EnsEMBL/Translation.pm
index 7a977a9ae0aca17046c5904c6c3adb0c0e9f5efa..f4ad27c4025f3eb0784d8aa281c52e2fcd9dec01 100755
--- a/modules/Bio/EnsEMBL/Translation.pm
+++ b/modules/Bio/EnsEMBL/Translation.pm
@@ -1192,20 +1192,6 @@ sub load {
}
}
-=head2 temporary_id
-
- Description: DEPRECATED This method should not be needed. Use dbID,
- stable_id or something else.
-
-=cut
-
-sub temporary_id {
- my $self = shift;
- deprecate( "temporary_id is deprecated and will be removed in e87.");
- $self->{'temporary_id'} = shift if( @_ );
- return $self->{'temporary_id'};
-}
-
=head2 get_all_DASFactories
diff --git a/modules/Bio/EnsEMBL/Utils/CigarString.pm b/modules/Bio/EnsEMBL/Utils/CigarString.pm
index c08ba9f0d58fde182c92e2f6b605a3a9ffb47f57..93f15537c1c61c9d72c54a6c9bc898674aa14837 100644
--- a/modules/Bio/EnsEMBL/Utils/CigarString.pm
+++ b/modules/Bio/EnsEMBL/Utils/CigarString.pm
@@ -76,9 +76,6 @@ package Bio::EnsEMBL::Utils::CigarString;
use strict;
use vars qw(@ISA);
-use Bio::EnsEMBL::Root;
-
-@ISA = qw(Bio::EnsEMBL::Root);
=head2 split_hsp
diff --git a/modules/Bio/EnsEMBL/Utils/ConversionSupport.pm b/modules/Bio/EnsEMBL/Utils/ConversionSupport.pm
index 98248e3de1a76c745e99464a5d46a39306405c63..7329627ddfc25769271df47aa49cb471c1f24422 100644
--- a/modules/Bio/EnsEMBL/Utils/ConversionSupport.pm
+++ b/modules/Bio/EnsEMBL/Utils/ConversionSupport.pm
@@ -563,17 +563,6 @@ sub user_proceed {
return(1);
}
-=head2 user_confirm
-
- Description : DEPRECATED - please use user_proceed() instead
-
-=cut
-
-sub user_confirm {
- my $self = shift;
- deprecate("user_confirm is deprecated and will be removed in e87.");
- exit unless $self->user_proceed("Continue?");
-}
=head2 read_user_input
diff --git a/modules/Bio/EnsEMBL/Utils/Converter.pm b/modules/Bio/EnsEMBL/Utils/Converter.pm
index 5b99f754f24a10b18a2e72b260e9210175eae3da..0985c7d2ad4ac63d856831c28ca90c7768e1eeda 100644
--- a/modules/Bio/EnsEMBL/Utils/Converter.pm
+++ b/modules/Bio/EnsEMBL/Utils/Converter.pm
@@ -70,8 +70,6 @@ What the ready conversions are,
package Bio::EnsEMBL::Utils::Converter;
use strict;
-use Bio::EnsEMBL::Root;
-our @ISA =qw(Bio::EnsEMBL::Root);
=head2 new
diff --git a/modules/Bio/EnsEMBL/Utils/Exception.pm b/modules/Bio/EnsEMBL/Utils/Exception.pm
index f3cdcb9069622654ec11383d3f5e90b017c3555b..ee2b4892496f58599f1672050be0dcf003cf5fc5 100644
--- a/modules/Bio/EnsEMBL/Utils/Exception.pm
+++ b/modules/Bio/EnsEMBL/Utils/Exception.pm
@@ -80,7 +80,7 @@ Bio::EnsEMBL::Utils::Exception - Utility functions for error handling
This is derived from the Bio::Root module in BioPerl. Some formatting
has been changed and the deprecate function has been added. Most
notably the object methods are now static class methods that can be
-called without inheriting from Bio::Root or Bio::EnsEMBL::Root. This is
+called without inheriting from Bio::Root. This is
especially useful for throwing exceptions with stack traces outside of a
blessed context.
@@ -88,7 +88,7 @@ The originaly implementations of these methods were by Steve Chervitz
and refactored by Ewan Birney.
It is recommended that these functions be used instead of inheriting
-unnecessarily from the Bio::EnsEMBL::Root or Bio::Root object. The
+unnecessarily from the Bio::Root object. The
functions exported by this package provide a set of useful error
handling methods.
diff --git a/modules/Bio/EnsEMBL/Utils/IO/BEDSerializer.pm b/modules/Bio/EnsEMBL/Utils/IO/BEDSerializer.pm
index 116ca6aeb4049f81f2edabe7a463c7f42fe4ac10..b0da132f952e91fb1fa75eb4323003b36952d16c 100644
--- a/modules/Bio/EnsEMBL/Utils/IO/BEDSerializer.pm
+++ b/modules/Bio/EnsEMBL/Utils/IO/BEDSerializer.pm
@@ -49,7 +49,7 @@ use base qw(Bio::EnsEMBL::Utils::IO::FeatureSerializer);
Arg [2] : Default source of the features. Defaults to .
Arg [3] : RGB colour to emit. Defaults to black (0,0,0)
- Returntype : Bio::EnsEMBL::Utils::IO::GFFSerializer
+ Returntype : Bio::EnsEMBL::Utils::IO::BEDSerializer
=cut
diff --git a/modules/Bio/EnsEMBL/Utils/PolyA.pm b/modules/Bio/EnsEMBL/Utils/PolyA.pm
index a339c9f09df270a5062dcad34f776302fb22805b..de1b09965aed73dcf4d82b99f265c098232947df 100644
--- a/modules/Bio/EnsEMBL/Utils/PolyA.pm
+++ b/modules/Bio/EnsEMBL/Utils/PolyA.pm
@@ -59,14 +59,11 @@ Bio::EnsEMBL::Utils::PolyA
package Bio::EnsEMBL::Utils::PolyA;
-use Bio::EnsEMBL::Root;
use Bio::Seq;
use vars qw(@ISA);
use strict;
-@ISA = qw(Bio::EnsEMBL::Root);
-
=head2 new
@@ -172,10 +169,10 @@ sub _find_polyA{
$count = $chunk =~ tr/Aa//;
$n_count = $chunk =~ tr/Nn//;
if ( ($count + $n_count) >= 2*( $piece )/3 ){
- $length_to_mask += 3;
+ $length_to_mask += 3;
}
else{
- last;
+ last;
}
}
@@ -184,27 +181,27 @@ sub _find_polyA{
my $last_base = substr( $seq, ( $length - $length_to_mask ), 1);
my $previous_to_last = substr( $seq, ( $length - $length_to_mask - 1), 1);
if ( !( $last_base eq 'A' || $last_base eq 'a') ){
- $length_to_mask--;
+ $length_to_mask--;
}
elsif( $previous_to_last eq 'A' || $previous_to_last eq 'a' ){
- $length_to_mask++;
+ $length_to_mask++;
}
my $clipped_seq = substr( $seq, 0, $length - $length_to_mask );
my $mask;
if ( $self->_clip ){
- $mask = "";
+ $mask = "";
}
elsif( $self->_mask ){
- $mask = "N" x ($length_to_mask);
+ $mask = "N" x ($length_to_mask);
}
elsif ( $self->_softmask ){
- $mask = lc substr( $seq, ( $length - $length_to_mask ) );
+ $mask = lc substr( $seq, ( $length - $length_to_mask ) );
}
$new_seq = $clipped_seq . $mask;
}
else{
$new_seq = $seq;
- }
+ }
}
#### polyT ####
elsif( $t_count >=5 && $t_count > $a_count ){
@@ -226,11 +223,11 @@ sub _find_polyA{
$count = $chunk =~ tr/Tt//;
$n_count = $chunk =~ tr/Nn//;
if ( ($count+$n_count) >= 2*( $piece )/3 ){
- $length_to_mask +=3;
+ $length_to_mask +=3;
}
else{
- last;
-
+ last;
+
}
}
if ( $length_to_mask >= 0 ){
@@ -239,21 +236,21 @@ sub _find_polyA{
my $last_base = substr( $seq, ( $length_to_mask + 3 - 1 ), 1 );
my $previous_to_last = substr( $seq, ( $length_to_mask + 3 ), 1 );
if ( !( $last_base eq 'T' || $last_base eq 't' ) ){
- $length_to_mask--;
+ $length_to_mask--;
}
elsif( $previous_to_last eq 'T' || $previous_to_last eq 't' ){
- $length_to_mask++;
+ $length_to_mask++;
}
my $clipped_seq = substr( $seq, $length_to_mask + 3);
my $mask;
if ( $self->_clip ){
- $mask = "";
+ $mask = "";
}
elsif( $self->_mask ){
- $mask = "N" x ($length_to_mask+3);
+ $mask = "N" x ($length_to_mask+3);
}
elsif ($self->_softmask){
- $mask = lc substr( $seq, 0, ($length_to_mask + 3) );
+ $mask = lc substr( $seq, 0, ($length_to_mask + 3) );
}
$new_seq = $mask.$clipped_seq;
}
@@ -330,3 +327,4 @@ sub has_polyA_track{
################
1;
+
diff --git a/modules/t/gene.t b/modules/t/gene.t
index 5a47bf2562be6a1b49e68ab01c5fa3870608a9bc..23788f72c2eb9b1a6304018ce4f9c8b0689540eb 100644
--- a/modules/t/gene.t
+++ b/modules/t/gene.t
@@ -398,17 +398,7 @@ $multi->restore();
$slice = $db->get_SliceAdaptor()->fetch_by_region("chromosome", "20", 30_252_000, 31_252_001);
-my $known = 0;
-my $unknown = 0;
-
$genes = $slice->get_all_Genes();
-for my $gene (@$genes) {
- if ($gene->is_known()) {
- $known++;
- } else {
- $unknown++;
- }
-}
# try and count the genes on the slice
note 'Processing counts';
@@ -433,9 +423,6 @@ is($geneCount, scalar(@$genes) - $vega_geneCount, "Almost all genes are of sourc
is($gene_count, 14, 'Counts should span slices when given patches/haps/pars');
}
-debug("known: $known Unknown: $unknown\n");
-
-ok($known == 17);
#save contents of gene table
$multi->save('core', 'gene');
diff --git a/modules/t/metaContainer.t b/modules/t/metaContainer.t
index 69c409d6e981c43c21ead48734823459791da70e..0826f9c9cd935530d91d38127ab9d61e8f7b7462 100644
--- a/modules/t/metaContainer.t
+++ b/modules/t/metaContainer.t
@@ -85,17 +85,6 @@ ok($div eq $divname);
my $classification = [ qw/Hominidae Catarrhini Primates Eutheria Mammalia Vertebrata Chordata Metazoa Eukaryota/ ];
is_deeply($mc->get_classification(), $classification, 'Checking classification as expected');
-#
-# Testing get_Species()
-#
-
-capture_std_streams(sub {
- my ($stdout_ref, $stderr_ref) = @_;
- my $s = $mc->get_Species();
- is($s->binomial(), 'Homo sapiens', 'Checking binomial from Bio::Species continues to work');
- like(${$stderr_ref}, qr/.+ deprecated .+ get_scientific_name\(\)/xms, 'Make sure we warn about deprecation');
-});
-
$mdb->restore('core', 'meta');
done_testing();
diff --git a/modules/t/proteinFeature.t b/modules/t/proteinFeature.t
index 251c679d60fe1787661cf69d379de3684416c5ea..96500d203881419124d9bf774845a8c66e3c9e9f 100644
--- a/modules/t/proteinFeature.t
+++ b/modules/t/proteinFeature.t
@@ -45,6 +45,7 @@ my $hdes = "Hit description";
my $idesc = 'interpro description';
my $ilabel = 'interpro label';
my $interpro_ac = 'interpro accession';
+my $translation_id = 1234;
my $analysis = Bio::EnsEMBL::Analysis->new(-LOGIC_NAME => 'test');
@@ -64,7 +65,8 @@ my $f = Bio::EnsEMBL::ProteinFeature->new
-HDESCRIPTION=> $hdes,
-IDESC => $idesc,
-ILABEL => $ilabel,
- -INTERPRO_AC => $interpro_ac);
+ -INTERPRO_AC => $interpro_ac,
+ -TRANSLATION_ID => $translation_id);
@@ -73,6 +75,7 @@ ok($f && $f->isa('Bio::EnsEMBL::ProteinFeature'));
ok($f->start == $start);
ok($f->end == $end);
ok($f->analysis == $analysis);
+ok($f->translation_id == $translation_id);
ok($f->hstart == $hstart);
ok($f->hend == $hend);
diff --git a/modules/t/proteinFeatureAdaptor.t b/modules/t/proteinFeatureAdaptor.t
index c0f57e8763fba34b93fc01b5b9c6273f4f7bae66..a32b7649b7780b49225849c4294bfa0396e9d80b 100644
--- a/modules/t/proteinFeatureAdaptor.t
+++ b/modules/t/proteinFeatureAdaptor.t
@@ -88,9 +88,29 @@ my $f = Bio::EnsEMBL::ProteinFeature->new
-IDESC => $idesc,
-INTERPRO_AC => $interpro_ac);
-$pfa->store($f,21724);
+my $dbID = $pfa->store($f,21724);
-my $pfs = $pfa->fetch_all_by_translation_id(21724);
+ok($dbID, "New object created has dbID");
+
+#fetch protein feature object by dbID and compare the core attributes
+#deep comparison is not possible because all the attributes are not stored in the protein_feature table
+my $f_by_dbID = $pfa->fetch_by_dbID($dbID);
+
+is($f_by_dbID->translation_id, 21724);
+is($f_by_dbID->start, $start);
+is($f_by_dbID->end, $end);
+is($f_by_dbID->dbID, $dbID);
+is($f_by_dbID->analysis->logic_name, 'test');
+is($f_by_dbID->hstart, $hstart);
+is($f_by_dbID->hend, $hend);
+is($f_by_dbID->hseqname, $hseqname);
+is($f_by_dbID->hdescription, $hdes);
+is($f_by_dbID->score, $score);
+is($f_by_dbID->percent_id, $percent_id);
+is($f_by_dbID->p_value, $p_value);
+
+
+$pfs = $pfa->fetch_all_by_translation_id(21724);
ok(@$pfs == 16);