From d1b8f7f58111a8389d6692cecc6c7e09379c70a5 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Fri, 12 Aug 2005 13:45:13 +0000
Subject: [PATCH] status reports added plus some tiding up of docs
---
modules/Bio/EnsEMBL/AffyArray.pm | 15 +-
modules/Bio/EnsEMBL/AffyFeature.pm | 43 +++--
modules/Bio/EnsEMBL/AffyProbe.pm | 32 ++--
modules/Bio/EnsEMBL/Analysis.pm | 18 ++
modules/Bio/EnsEMBL/ArchiveStableId.pm | 16 ++
.../Bio/EnsEMBL/AssemblyExceptionFeature.pm | 14 ++
modules/Bio/EnsEMBL/AssemblyMapper.pm | 50 ++++++
modules/Bio/EnsEMBL/Attribute.pm | 5 +
modules/Bio/EnsEMBL/BaseAlignFeature.pm | 11 ++
modules/Bio/EnsEMBL/ChainedAssemblyMapper.pm | 156 ++++++++++++++++++
modules/Bio/EnsEMBL/CoordSystem.pm | 8 +
modules/Bio/EnsEMBL/DBEntry.pm | 27 ++-
modules/Bio/EnsEMBL/DBLoader.pm | 1 +
modules/Bio/EnsEMBL/DBSQL/AffyArrayAdaptor.pm | 14 ++
.../Bio/EnsEMBL/DBSQL/AffyFeatureAdaptor.pm | 17 +-
modules/Bio/EnsEMBL/DBSQL/AffyProbeAdaptor.pm | 22 ++-
modules/Bio/EnsEMBL/DBSQL/AnalysisAdaptor.pm | 11 ++
.../EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm | 27 ++-
.../DBSQL/AssemblyExceptionFeatureAdaptor.pm | 3 +
.../EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm | 9 +-
modules/Bio/EnsEMBL/DBSQL/AttributeAdaptor.pm | 11 ++
modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm | 9 +-
.../EnsEMBL/DBSQL/BaseAlignFeatureAdaptor.pm | 2 +
.../Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm | 14 +-
.../Bio/EnsEMBL/DBSQL/BaseMetaContainer.pm | 4 +
.../DBSQL/CompressedSequenceAdaptor.pm | 1 +
.../Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm | 10 ++
modules/Bio/EnsEMBL/DBSQL/DBConnection.pm | 17 ++
modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm | 19 ++-
.../EnsEMBL/DBSQL/DensityFeatureAdaptor.pm | 5 +
.../Bio/EnsEMBL/DBSQL/DensityTypeAdaptor.pm | 7 +-
.../EnsEMBL/DBSQL/DnaAlignFeatureAdaptor.pm | 5 +
modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm | 8 +-
modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm | 20 +++
.../Bio/EnsEMBL/DBSQL/KaryotypeBandAdaptor.pm | 5 +-
modules/Bio/EnsEMBL/DBSQL/MetaContainer.pm | 3 +
.../Bio/EnsEMBL/DBSQL/MetaCoordContainer.pm | 3 +
.../Bio/EnsEMBL/DBSQL/MiscFeatureAdaptor.pm | 4 +
modules/Bio/EnsEMBL/DBSQL/MiscSetAdaptor.pm | 5 +
.../EnsEMBL/DBSQL/PredictionExonAdaptor.pm | 6 +-
.../DBSQL/PredictionTranscriptAdaptor.pm | 30 ++--
.../DBSQL/ProteinAlignFeatureAdaptor.pm | 3 +
.../EnsEMBL/DBSQL/ProteinFeatureAdaptor.pm | 3 +
.../EnsEMBL/DBSQL/RegulatoryFactorAdaptor.pm | 10 ++
.../EnsEMBL/DBSQL/RegulatoryFeatureAdaptor.pm | 16 ++
.../EnsEMBL/DBSQL/RepeatConsensusAdaptor.pm | 6 +
.../Bio/EnsEMBL/DBSQL/RepeatFeatureAdaptor.pm | 7 +-
modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm | 3 +
.../Bio/EnsEMBL/DBSQL/SimpleFeatureAdaptor.pm | 9 +-
modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm | 20 ++-
.../EnsEMBL/DBSQL/SupportingFeatureAdaptor.pm | 1 +
.../Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm | 18 +-
.../TranscriptSupportingFeatureAdaptor.pm | 1 +
.../Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm | 21 ++-
modules/Bio/EnsEMBL/DensityFeature.pm | 20 +++
modules/Bio/EnsEMBL/DensityFeatureSet.pm | 12 +-
modules/Bio/EnsEMBL/DensityType.pm | 10 +-
modules/Bio/EnsEMBL/DnaDnaAlignFeature.pm | 5 +
modules/Bio/EnsEMBL/DnaPepAlignFeature.pm | 5 +
modules/Bio/EnsEMBL/Exon.pm | 93 ++++++++++-
modules/Bio/EnsEMBL/Feature.pm | 39 ++++-
modules/Bio/EnsEMBL/FeaturePair.pm | 24 ++-
modules/Bio/EnsEMBL/Gene.pm | 90 +++++++++-
modules/Bio/EnsEMBL/GoXref.pm | 3 +
modules/Bio/EnsEMBL/IdentityXref.pm | 32 +++-
modules/Bio/EnsEMBL/Intron.pm | 5 +-
modules/Bio/EnsEMBL/KaryotypeBand.pm | 6 +
modules/Bio/EnsEMBL/Mapper.pm | 78 +++++----
modules/Bio/EnsEMBL/MiscFeature.pm | 81 ++++++++-
modules/Bio/EnsEMBL/MiscSet.pm | 5 +
modules/Bio/EnsEMBL/PepDnaAlignFeature.pm | 38 +++++
modules/Bio/EnsEMBL/PredictionExon.pm | 13 +-
modules/Bio/EnsEMBL/PredictionTranscript.pm | 15 +-
modules/Bio/EnsEMBL/ProjectionSegment.pm | 3 +
modules/Bio/EnsEMBL/ProteinFeature.pm | 12 ++
modules/Bio/EnsEMBL/Registry.pm | 63 +++++--
modules/Bio/EnsEMBL/RegulatoryFactor.pm | 6 +
modules/Bio/EnsEMBL/RegulatoryFeature.pm | 10 ++
modules/Bio/EnsEMBL/RepeatConsensus.pm | 22 ++-
modules/Bio/EnsEMBL/RepeatFeature.pm | 9 +-
modules/Bio/EnsEMBL/RepeatMaskedSlice.pm | 6 +
modules/Bio/EnsEMBL/SeqEdit.pm | 15 +-
modules/Bio/EnsEMBL/SimpleFeature.pm | 16 ++
modules/Bio/EnsEMBL/Slice.pm | 87 ++++++++--
modules/Bio/EnsEMBL/Storable.pm | 29 ++--
modules/Bio/EnsEMBL/TopLevelAssemblyMapper.pm | 104 ++++++++++++
modules/Bio/EnsEMBL/Transcript.pm | 135 +++++++++++++--
modules/Bio/EnsEMBL/TranscriptMapper.pm | 32 +++-
modules/Bio/EnsEMBL/Translation.pm | 57 ++++++-
modules/Bio/EnsEMBL/Upstream.pm | 14 ++
90 files changed, 1784 insertions(+), 215 deletions(-)
diff --git a/modules/Bio/EnsEMBL/AffyArray.pm b/modules/Bio/EnsEMBL/AffyArray.pm
index 425d33898b..b3a1056442 100644
--- a/modules/Bio/EnsEMBL/AffyArray.pm
+++ b/modules/Bio/EnsEMBL/AffyArray.pm
@@ -66,7 +66,8 @@ use Bio::EnsEMBL::Storable;
Returntype :
Exceptions : none
Caller :
-
+ Status : Medium Risk
+ : may be replaced with none affy specific methods
=cut
@@ -101,7 +102,8 @@ sub new {
Returntype : listref of Bio::EnsEMBL::AffyProbe
Exceptions : none
Caller : general
-
+ Status : Medium Risk
+ : may be replaced with none affy specific methods
=cut
@@ -129,7 +131,8 @@ sub get_all_AffyProbes {
Returntype : string
Exceptions : none
Caller : general
-
+ Status : Medium Risk
+ : may be replaced with none affy specific methods
=cut
@@ -153,7 +156,8 @@ sub name {
Returntype : listref of Bio::EnsEMBL::AffyFeature
Exceptions : none
Caller : general
-
+ Status : Medium Risk
+ : may be replaced with none affy specific methods
=cut
@@ -179,7 +183,8 @@ sub setsize {
Returntype : Bio::EnsEMBL::AffyArray
Exceptions : none
Caller : general
-
+ Status : Medium Risk
+ : may be replaced with none affy specific methods
=cut
diff --git a/modules/Bio/EnsEMBL/AffyFeature.pm b/modules/Bio/EnsEMBL/AffyFeature.pm
index ec25ce71f8..c416a2f966 100644
--- a/modules/Bio/EnsEMBL/AffyFeature.pm
+++ b/modules/Bio/EnsEMBL/AffyFeature.pm
@@ -58,11 +58,24 @@ use vars qw(@ISA);
=head2 new
- Arg [PROBE] :
- Every AffyFeature needs an AffyProbe on construction. This should be already
- stored if you plan to store this feature.
- Arg [MISMATCHCOUNT] :
- How many mismatches over the length of the probe? (0,1)
+ Arg [PROBE] : Every AffyFeature needs an AffyProbe on construction. This should be already
+ stored if you plan to store this feature.
+ Arg [MISMATCHCOUNT] : How many mismatches over the length of the probe? (0,1)
+ Arg [-SLICE]: Bio::EnsEMBL::SLice - Represents the sequence that this
+ feature is on. The coordinates of the created feature are
+ relative to the start of the slice.
+ Arg [-START]: The start coordinate of this feature relative to the start
+ of the slice it is sitting on. Coordinates start at 1 and
+ are inclusive.
+ Arg [-END] : The end coordinate of this feature relative to the start of
+ the slice it is sitting on. Coordinates start at 1 and are
+ inclusive.
+ Arg [-STRAND]: The orientation of this feature. Valid values are 1,-1,0.
+ Arg [-SEQNAME] : A seqname to be used instead of the default name of the
+ of the slice. Useful for features that do not have an
+ attached slice such as protein features.
+ Arg [-dbID] : (optional) internal database id
+ Arg [-ADAPTOR]: (optional) Bio::EnsEMBL::DBSQL::BaseAdaptor
Example : my $feature = Bio::EnsEMBL::AffyFeature->new(
-PROBE => $affyProbe,
-MISMATCHCOUNT => 0,
@@ -75,7 +88,8 @@ use vars qw(@ISA);
Returntype : Bio::EnsEMBL::AffyFeature
Exceptions : none
Caller : general
-
+ Status : Medium Risk
+ : may be replaced with none affy specific methods
=cut
@@ -108,7 +122,8 @@ sub new {
Returntype : Bio::EnsEMBL::AffyFeature
Exceptions : none
Caller : general
-
+ Status : Medium Risk
+ : may be replaced with none affy specific methods
=cut
@@ -130,7 +145,8 @@ sub new_fast {
Returntype : string
Exceptions : none
Caller : general
-
+ Status : At Risk
+ : This maybe removed. Use $feature->probe->probeset() to be safe
=cut
@@ -153,7 +169,8 @@ sub probeset {
Returntype : int
Exceptions : none
Caller : general
-
+ Status : Medium Risk
+ : may be replaced with none affy specific methods
=cut
@@ -174,7 +191,8 @@ sub mismatchcount {
Returntype : int
Exceptions : none
Caller : general
-
+ Status : Medium Risk
+ : may be replaced with none affy specific methods
=cut
@@ -196,7 +214,8 @@ sub probelength {
Returntype : Bio::EnsEMBL::AffyProbe
Exceptions : none
Caller : general
-
+ Status : Medium Risk
+ : may be replaced with none affy specific methods
=cut
@@ -220,7 +239,7 @@ sub probe {
return $self->{'probe'};
}
-
+1;
diff --git a/modules/Bio/EnsEMBL/AffyProbe.pm b/modules/Bio/EnsEMBL/AffyProbe.pm
index b193d001a5..c959a6ccde 100644
--- a/modules/Bio/EnsEMBL/AffyProbe.pm
+++ b/modules/Bio/EnsEMBL/AffyProbe.pm
@@ -69,9 +69,10 @@ use vars qw(@ISA);
Example : none
Description: Constructor for an array probe
Returntype : Bio::EnsEMBL::AffyProbe
- Exceptions : none
+ Exceptions : throws if each probe does not have a name
Caller : general
-
+ Status : Medium Risk
+ : may be replaced with none affy specific methods
=cut
@@ -104,7 +105,7 @@ sub new {
throw( "Provide array or arrayname with probename" );
}
} else {
- throw( "You need to provide probenames to generat a probe" );
+ throw( "You need to provide probenames to generate a probe" );
}
# check the parameters and fill internal data structures
@@ -145,7 +146,8 @@ sub new {
Returntype : none
Exceptions : none
Caller : general, constructor, AffyProbeAdaptor->_obj_from_sth()
-
+ Status : Medium Risk
+ : may be replaced with none affy specific methods
=cut
@@ -168,7 +170,8 @@ sub add_Array_probename {
Returntype : listref Bio::EnsEMBL:AffyFeature
Exceptions : none
Caller : general
-
+ Status : Medium Risk
+ : may be replaced with none affy specific methods
=cut
@@ -194,7 +197,8 @@ sub get_all_AffyFeatures {
Returntype : listref Bio::EnsEMBL::AffyArray
Exceptions : none
Caller : general
-
+ Status : Medium Risk
+ : may be replaced with none affy specific methods
=cut
@@ -224,6 +228,8 @@ sub get_all_AffyArrays {
Returntype : listref of strings
Exceptions : none
Caller : general
+ Status : Medium Risk
+ : may be replaced with none affy specific methods
=cut
@@ -248,6 +254,8 @@ sub get_all_complete_names {
Returntype : string
Exceptions : throws if the arrayname is not known in this probe
Caller : general
+ Status : Medium Risk
+ : may be replaced with none affy specific methods
=cut
@@ -274,7 +282,8 @@ sub get_complete_name {
Returntype : listref of strings
Exceptions : none
Caller : general
-
+ Status : Medium Risk
+ : may be replaced with none affy specific methods
=cut
@@ -292,7 +301,8 @@ sub get_all_probenames {
Returntype : string
Exceptions : throw if arrayname is not known for this probe
Caller : general
-
+ Status : Medium Risk
+ : may be replaced with none affy specific methods
=cut
@@ -318,7 +328,8 @@ sub get_probename {
Returntype : none
Exceptions : none
Caller : general
-
+ Status : Medium Risk
+ : may be replaced with none affy specific methods
=cut
@@ -337,7 +348,8 @@ sub add_arrayname_probename {
Returntype : string
Exceptions : none
Caller : general
-
+ Status : Medium Risk
+ : may be replaced with none affy specific methods
=cut
diff --git a/modules/Bio/EnsEMBL/Analysis.pm b/modules/Bio/EnsEMBL/Analysis.pm
index 16ebe373e1..1dc0aaa7bc 100755
--- a/modules/Bio/EnsEMBL/Analysis.pm
+++ b/modules/Bio/EnsEMBL/Analysis.pm
@@ -83,6 +83,7 @@ use Bio::EnsEMBL::Utils::Argument qw(rearrange);
Returntype : Bio::EnsEMBL::Analysis
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -143,6 +144,7 @@ sub new {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -165,6 +167,7 @@ sub db {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -187,6 +190,7 @@ sub db_version {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -210,6 +214,7 @@ sub db_file {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -232,6 +237,7 @@ sub program {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -254,6 +260,7 @@ sub program_version {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -277,6 +284,7 @@ sub program_file {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -299,6 +307,7 @@ sub module {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -321,6 +330,7 @@ sub module_version {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -343,6 +353,7 @@ sub gff_source {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -366,6 +377,7 @@ sub gff_feature {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -388,6 +400,7 @@ sub parameters {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -411,6 +424,7 @@ sub created {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -431,6 +445,7 @@ sub logic_name {
Returntype : int 0,1
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -450,6 +465,7 @@ sub has_database{
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -472,6 +488,7 @@ sub description {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -496,6 +513,7 @@ sub display_label {
Returntype : int -1,0,1
Exceptions : none
Caller : unknown
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/ArchiveStableId.pm b/modules/Bio/EnsEMBL/ArchiveStableId.pm
index 14c7430a30..00fa469865 100644
--- a/modules/Bio/EnsEMBL/ArchiveStableId.pm
+++ b/modules/Bio/EnsEMBL/ArchiveStableId.pm
@@ -33,6 +33,8 @@ ArchiveStableId objects are the main workunit for retrieving stable id archived
get_components:
+ Status: At Risk. This module is in development.
+
=cut
@@ -64,6 +66,8 @@ use vars qw(@ISA);
Returntype : Bio::EnsEMBL::ArchiveStableId
Exceptions : none
Caller : Adaptor
+ Status : At Risk
+ : under development
=cut
@@ -100,6 +104,8 @@ sub new {
Returntype : Bio::EnsEMBL::ArchiveStableId
Exceptions : none
Caller : general, Adaptor
+ Status : At Risk
+ : under development
=cut
@@ -128,6 +134,8 @@ sub new_fast {
Returntype : listref Bio::EnsEMBL::ArchiveStableId
Exceptions : none
Caller : general
+ Status : At Risk
+ : under development
=cut
@@ -146,6 +154,8 @@ sub get_all_predecessors {
Returntype : listref Bio::EnsEMBL::ArchiveStableId
Exceptions : none
Caller : general
+ Status : At Risk
+ : under development
=cut
@@ -166,6 +176,8 @@ sub get_all_successors {
Returntype : string
Exceptions : none
Caller : general
+ Status : At Risk
+ : under development
=cut
@@ -189,6 +201,8 @@ sub get_peptide {
Returntype : listref Bio::EnsEMBL::ArchiveStableId
Exceptions : empty if not a gene stable id or not in database
Caller : general
+ Status : At Risk
+ : under development
=cut
@@ -214,6 +228,8 @@ sub get_all_transcript_archive_ids {
Returntype : Bio::EnsEMBL::ArchiveStableId
Exceptions : undef if not in db or not a Transcript
Caller : general
+ Status : At Risk
+ : under development
=cut
diff --git a/modules/Bio/EnsEMBL/AssemblyExceptionFeature.pm b/modules/Bio/EnsEMBL/AssemblyExceptionFeature.pm
index f8cc0125d1..b8347ee913 100644
--- a/modules/Bio/EnsEMBL/AssemblyExceptionFeature.pm
+++ b/modules/Bio/EnsEMBL/AssemblyExceptionFeature.pm
@@ -71,6 +71,7 @@ use Bio::EnsEMBL::Utils::Argument qw(rearrange);
Returntype : Bio::EnsEMBL::Feature
Exceptions : Thrown on invalid -SLICE arguments
Caller : general, subclass constructors
+ Status : Stable
=cut
@@ -89,6 +90,16 @@ sub new {
return $self;
}
+=head2 new_fast
+
+ Arg [1] : hashref to be blessed
+ Description: Construct a new Bio::EnsEMBL::Feature using the hashref.
+ Exceptions : none
+ Returntype : Bio::EnsEMBL::Feature
+ Caller : general, subclass constructors
+ Status : Stable
+
+=cut
sub new_fast {
my $class = shift;
@@ -106,6 +117,7 @@ sub new_fast {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -128,6 +140,7 @@ sub type {
Returntype : Bio::EnsEMBL::Slice
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -153,6 +166,7 @@ sub alternate_slice {
Returntype : string
Exceptions : none
Caller : web drawing code
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/AssemblyMapper.pm b/modules/Bio/EnsEMBL/AssemblyMapper.pm
index 8f3ec9f763..15be05cf37 100644
--- a/modules/Bio/EnsEMBL/AssemblyMapper.pm
+++ b/modules/Bio/EnsEMBL/AssemblyMapper.pm
@@ -82,6 +82,7 @@ my $DEFAULT_MAX_PAIR_COUNT = 1000;
Returntype : Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor
Exceptions : thrown if multiple coord_systems are provided
Caller : AssemblyMapperAdaptor
+ Status : Stable
=cut
@@ -131,6 +132,7 @@ sub new {
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -157,6 +159,7 @@ sub max_pair_count {
Returntype : none
Exceptions : none
Caller : specialised programs doing a lot of mapping
+ Status : Stable
=cut
@@ -190,6 +193,7 @@ sub register_all {
Exceptions : thrown if if the specified TO coordinat system is not one
of the coordinate systems associated with this assembly mapper
Caller : general
+ Status : Stable
=cut
@@ -244,6 +248,7 @@ sub map {
Returntype : none
Exceptions : none
Caller : AssemblyMapperAdaptor
+ Status : Stable
=cut
@@ -255,12 +260,47 @@ sub flush {
$self->{'asm_register'} = {};
}
+=head2 size
+
+ Args : none
+ Example : $num_of_pairs = $mapper->size();
+ Description: return the number of pairs currently stored.
+ Returntype : int
+ Exceptions : none
+ Caller : general
+ Status : Stable
+
+=cut
sub size {
my $self = shift;
return $self->{'mapper'}->{'pair_count'};
}
+=head2 fastmap
+
+ Arg [1] : string $frm_seq_region
+ The name of the sequence region to transform FROM
+ Arg [2] : int $frm_start
+ The start of the region to transform FROM
+ Arg [3] : int $frm_end
+ The end of the region to transform FROM
+ Arg [4] : int $strand
+ The strand of the region to transform FROM
+ Arg [5] : Bio::EnsEMBL::CoordSystem
+ The coordinate system to transform FROM
+ Example : @coords = $asm_mapper->map('X', 1_000_000, 2_000_000,
+ 1, $chr_cs);
+ Description: Transforms coordinates from one coordinate system
+ to another.
+ Returntype : List of Bio::EnsEMBL::Mapper::Coordinate and/or
+ Bio::EnsEMBL::Mapper:Gap objects
+ Exceptions : thrown if if the specified TO coordinat system is not one
+ of the coordinate systems associated with this assembly mapper
+ Caller : general
+ Status : Stable
+
+=cut
sub fastmap {
@@ -323,6 +363,7 @@ sub fastmap {
Returntype : List of strings
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -381,6 +422,7 @@ sub list_seq_regions {
Returntype : List of ints
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -420,6 +462,7 @@ sub list_ids {
Returntype : 0 or 1
Exceptions : throw on incorrect arguments
Caller : internal, AssemblyMapperAdaptor
+ Status : Stable
=cut
@@ -454,6 +497,7 @@ sub have_registered_component {
Returntype : 0 or 1
Exceptions : throw on incorrect arguments
Caller : internal, AssemblyMapperAdaptor
+ Status : Stable
=cut
@@ -484,6 +528,7 @@ sub have_registered_assembled {
Returntype : none
Exceptions : throw on incorrect arguments
Caller : internal, AssemblyMapperAdaptor
+ Status : Stable
=cut
@@ -511,6 +556,7 @@ sub register_component {
Returntype : none
Exceptions : throw on incorrect arguments
Caller : internal, AssemblyMapperAdaptor
+ Status : Stable
=cut
@@ -537,6 +583,7 @@ sub register_assembled {
Returntype : Bio::EnsEMBL::Mapper
Exceptions : none
Caller : internal, AssemblyMapperAdaptor
+ Status : Stable
=cut
@@ -554,6 +601,7 @@ sub mapper {
Returntype : Bio::EnsEMBL::CoordSystem
Exceptions : none
Caller : internal, AssemblyMapperAdaptor
+ Status : Stable
=cut
@@ -571,6 +619,7 @@ sub assembled_CoordSystem {
Returntype : Bio::EnsEMBL::CoordSystem
Exceptions : none
Caller : internal, AssemblyMapperAdaptor
+ Status : Stable
=cut
@@ -588,6 +637,7 @@ sub component_CoordSystem {
Returntype : Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor
Exceptions : none
Caller : general
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/Attribute.pm b/modules/Bio/EnsEMBL/Attribute.pm
index 5c927f449b..8a92cb720b 100644
--- a/modules/Bio/EnsEMBL/Attribute.pm
+++ b/modules/Bio/EnsEMBL/Attribute.pm
@@ -67,6 +67,7 @@ use Bio::EnsEMBL::Utils::Argument qw(rearrange);
Returntype : Bio::EnsEMBL::Attribute
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -95,6 +96,7 @@ sub new {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -113,6 +115,7 @@ sub code {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -130,6 +133,7 @@ sub name {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -148,6 +152,7 @@ sub description {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/BaseAlignFeature.pm b/modules/Bio/EnsEMBL/BaseAlignFeature.pm
index e4759db1e0..d97dfc1677 100644
--- a/modules/Bio/EnsEMBL/BaseAlignFeature.pm
+++ b/modules/Bio/EnsEMBL/BaseAlignFeature.pm
@@ -109,6 +109,7 @@ use strict;
Exceptions : thrown if both feature and cigar string args are provided
thrown if neither feature nor cigar string args are provided
Caller : general
+ Status : Stable
=cut
@@ -151,6 +152,7 @@ sub new {
Returntype : Bio::EnsEMBL::BaseAlignFeature
Exceptions : none
Caller : none currently
+ Status : Stable
=cut
@@ -173,6 +175,7 @@ sub new_fast {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -191,6 +194,7 @@ sub cigar_string {
Returntype : int
Exceptions :
Caller :
+ Status : Stable
=cut
@@ -225,6 +229,7 @@ sub alignment_length {
Returntype : list of Bio::EnsEMBL::FeaturePair
Exceptions : cigar_string not set internally
Caller : general
+ Status : Stable
=cut
@@ -252,6 +257,7 @@ sub ungapped_features {
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -276,6 +282,7 @@ sub strands_reversed {
Returntype : none
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -317,6 +324,7 @@ sub reverse_complement {
Returntype : list of Bio::EnsEMBL::FeaturePair
Exceptions : none
Caller : ungapped_features
+ Status : Stable
=cut
@@ -463,6 +471,7 @@ sub _parse_cigar {
Exceptions : argument list undergoes many sanity checks - throws under many
invalid conditions
Caller : new
+ Status : Stable
=cut
@@ -764,6 +773,7 @@ sub _parse_features {
Returntype : int 1,3
Exceptions : none
Caller : internal
+ Status : Stable
=cut
@@ -783,6 +793,7 @@ sub _hit_unit {
Returntype : int 1,3
Exceptions : none
Caller : internal
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/ChainedAssemblyMapper.pm b/modules/Bio/EnsEMBL/ChainedAssemblyMapper.pm
index 3fbf3fd863..58a6ef0ba5 100644
--- a/modules/Bio/EnsEMBL/ChainedAssemblyMapper.pm
+++ b/modules/Bio/EnsEMBL/ChainedAssemblyMapper.pm
@@ -92,6 +92,7 @@ my $DEFAULT_MAX_PAIR_COUNT = 6000;
Returntype : Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor
Exceptions : thrown if wrong number of coord_systems are provided
Caller : AssemblyMapperAdaptor
+ Status : Stable
=cut
@@ -150,6 +151,7 @@ sub new {
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -177,6 +179,7 @@ sub max_pair_count {
Returntype : none
Exceptions : none
Caller : specialised programs doing a lot of mapping
+ Status : Stable
=cut
@@ -199,6 +202,18 @@ sub flush {
$self->{'first_last_mapper'}->flush();
}
+=head2 size
+
+ Args : none
+ Example : $num_of_pairs = $mapper->size();
+ Description: return the number of pairs currently stored.
+ Returntype : int
+ Exceptions : none
+ Caller : general
+ Status : Stable
+
+=cut
+
sub size {
my $self = shift;
return ( $self->{'first_last_mapper'}->{'pair_count'} +
@@ -229,6 +244,7 @@ sub size {
Exceptions : thrown if the specified TO coordinat system is not one
of the coordinate systems associated with this assembly mapper
Caller : general
+ Status : Stable
=cut
@@ -345,6 +361,7 @@ sub fastmap {
Returntype : List of strings
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -436,6 +453,7 @@ sub list_seq_regions {
Returntype : List of ints
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -465,43 +483,140 @@ sub list_ids {
+=head2 first_last_mapper
+
+ Args : none
+ Example : $mapper = $cam->first_last_mapper();
+ Description: return the mapper.
+ Returntype : Bio::EnsEMBL::Mapper
+ Exceptions : none
+ Caller : internal
+ Status : Stable
+
+=cut
+
sub first_last_mapper {
my $self = shift;
return $self->{'first_last_mapper'};
}
+=head2 first_middle_mapper
+
+ Args : none
+ Example : $mapper = $cam->first_middle_mapper();
+ Description: return the mapper.
+ Returntype : Bio::EnsEMBL::Mapper
+ Exceptions : none
+ Caller : internal
+ Status : Stable
+
+=cut
+
+
sub first_middle_mapper {
my $self = shift;
return $self->{'first_mid_mapper'};
}
+=head2 last_middle_mapper
+
+ Args : none
+ Example : $mapper = $cam->last_middle_mapper();
+ Description: return the mapper.
+ Returntype : Bio::EnsEMBL::Mapper
+ Exceptions : none
+ Caller : internal
+ Status : Stable
+
+=cut
+
sub last_middle_mapper {
my $self = shift;
return $self->{'last_mid_mapper'};
}
+=head2 first_CoordSystem
+
+ Args : none
+ Example : $coordsys = $cam->first_CoordSystem();
+ Description: return the CoordSystem.
+ Returntype : Bio::EnsEMBL::CoordSystem
+ Exceptions : none
+ Caller : internal
+ Status : Stable
+
+=cut
+
sub first_CoordSystem {
my $self = shift;
return $self->{'first_cs'};
}
+=head2 middle_CoordSystem
+
+ Args : none
+ Example : $coordsys = $cam->middle_CoordSystem();
+ Description: return the CoordSystem.
+ Returntype : Bio::EnsEMBL::CoordSystem
+ Exceptions : none
+ Caller : internal
+ Status : Stable
+
+=cut
+
sub middle_CoordSystem {
my $self = shift;
return $self->{'mid_cs'};
}
+=head2 last_CoordSystem
+
+ Args : none
+ Example : $coordsys = $cam->last_CoordSystem();
+ Description: return the CoordSystem.
+ Returntype : Bio::EnsEMBL::CoordSystem
+ Exceptions : none
+ Caller : internal
+ Status : Stable
+
+=cut
+
sub last_CoordSystem {
my $self = shift;
return $self->{'last_cs'};
}
+=head2 first_registry
+
+ Args : none
+ Example : $coordsys = $cam->first_registry();
+ Description: return the Registry.
+ Returntype : Bio::EnsEMBL::Mapper::RangeRegistry
+ Exceptions : none
+ Caller : internal
+ Status : Stable
+
+=cut
+
sub first_registry {
my $self = shift;
return $self->{'first_registry'};
}
+=head2 lsst_registry
+
+ Args : none
+ Example : $coordsys = $cam->lsst_registry();
+ Description: return the Registry.
+ Returntype : Bio::EnsEMBL::Mapper::RangeRegistry
+ Exceptions : none
+ Caller : internal
+ Status : Stable
+
+=cut
+
sub last_registry {
my $self = shift;
return $self->{'last_registry'};
@@ -517,14 +632,54 @@ sub last_registry {
# ordering is arbitrary and both ends might actually be assembled, but these
# methods provide convenient synonyms
#
+
+=head2 mapper
+
+ Args : none
+ Example : $mapper = $cam->mapper();
+ Description: return the first_last_mapper.
+ Returntype : Bio::EnsEMBL::Mapper
+ Exceptions : none
+ Caller : internal
+ Status : Stable
+
+=cut
+
sub mapper {
my $self = shift;
return $self->first_last_mapper();
}
+
+=head2 assembled_CoordSystem
+
+ Args : none
+ Example : $coordsys = $cam->assembled_CoordSystem();
+ Description: return the first CoordSystem.
+ Returntype : Bio::EnsEMBL::CoordSystem
+ Exceptions : none
+ Caller : internal
+ Status : Stable
+
+=cut
+
+
sub assembled_CoordSystem {
my $self = shift;
return $self->{'first_cs'};
}
+
+=head2 component_CoordSystem
+
+ Args : none
+ Example : $coordsys = $cam->component_CoordSystem();
+ Description: return the last CoordSystem.
+ Returntype : Bio::EnsEMBL::CoordSystem
+ Exceptions : none
+ Caller : internal
+ Status : Stable
+
+=cut
+
sub component_CoordSystem {
my $self = shift;
return $self->{'last_cs'};
@@ -539,6 +694,7 @@ sub component_CoordSystem {
Returntype : Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor
Exceptions : none
Caller : general
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/CoordSystem.pm b/modules/Bio/EnsEMBL/CoordSystem.pm
index 03d8146d6e..53d7c2e394 100644
--- a/modules/Bio/EnsEMBL/CoordSystem.pm
+++ b/modules/Bio/EnsEMBL/CoordSystem.pm
@@ -99,6 +99,7 @@ use vars qw(@ISA);
Returntype : Bio::EnsEMBL::CoordSystem
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -172,6 +173,7 @@ sub new {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -192,6 +194,7 @@ sub name {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -214,6 +217,7 @@ sub version {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -247,6 +251,7 @@ sub equals {
Returntype : 0 or 1
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -264,6 +269,7 @@ sub is_top_level {
Returntype : 0 or 1
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -282,6 +288,7 @@ sub is_sequence_level {
Returntype : 0 or 1
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -307,6 +314,7 @@ sub is_default {
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/DBEntry.pm b/modules/Bio/EnsEMBL/DBEntry.pm
index abc1c6c630..971cae42c7 100644
--- a/modules/Bio/EnsEMBL/DBEntry.pm
+++ b/modules/Bio/EnsEMBL/DBEntry.pm
@@ -46,6 +46,7 @@ use strict;
@ISA = qw( Bio::EnsEMBL::Storable Bio::Annotation::DBLink );
+
=head2 new_fast
Arg [1] : hash reference $hashref
@@ -56,6 +57,7 @@ use strict;
Returntype : Bio::EnsEMBL::DBEntry
Exceptions : none
Caller : ?
+ Status : Stable
=cut
@@ -88,6 +90,10 @@ sub new_fast {
Returntype : Bio::EnsEMBL::DBEntry
Exceptions : none
Caller : Bio::EnsEMBL::DBEntryAdaptor
+ Status : At Risk
+ : due to 'PRIMARY_ID_LINKABLE','DISPLAY_ID_LINKABLE','PRIORITY'
+ : being under development
+ : If you don't use any of these the sub can be considered Stable
=cut
@@ -134,6 +140,7 @@ sub new {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -157,6 +164,7 @@ sub primary_id {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -179,6 +187,7 @@ sub display_id{
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -201,6 +210,7 @@ sub dbname {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -220,6 +230,7 @@ sub database {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -238,6 +249,7 @@ sub optional_id {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -258,6 +270,7 @@ sub release {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -280,6 +293,7 @@ sub version {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -300,6 +314,8 @@ sub description {
Returntype : string
Exceptions : none
Caller : general
+ Status : At Risk
+ : due to it being under development
=cut
@@ -319,6 +335,8 @@ sub primary_id_linkable {
Returntype : string
Exceptions : none
Caller : general
+ Status : At Risk
+ : due to it being under development
=cut
@@ -335,10 +353,12 @@ sub display_id_linkable {
Arg [1] : int $priority
Example : none
- Priority: get/set for attribute priority
+ Priority : get/set for attribute priority
Returntype : string
Exceptions : none
Caller : general
+ Status : At Risk
+ : due to it being under development
=cut
@@ -379,6 +399,7 @@ sub db_display_name {
Returntype : none
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -399,6 +420,7 @@ sub add_synonym {
Returntype : list reference of strings
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -416,6 +438,7 @@ sub get_all_synonyms {
Returntype : none
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -433,6 +456,7 @@ sub flush_synonyms {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -455,6 +479,7 @@ sub status{
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/DBLoader.pm b/modules/Bio/EnsEMBL/DBLoader.pm
index 85ddfdc78a..66f78ce3fc 100755
--- a/modules/Bio/EnsEMBL/DBLoader.pm
+++ b/modules/Bio/EnsEMBL/DBLoader.pm
@@ -64,6 +64,7 @@ use strict;
Exceptions : thrown if the specified module cannot be instantiated or the
locator string cannot be parsed
Caller : ?
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/DBSQL/AffyArrayAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/AffyArrayAdaptor.pm
index 8fcc82d552..8a0043433d 100644
--- a/modules/Bio/EnsEMBL/DBSQL/AffyArrayAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/AffyArrayAdaptor.pm
@@ -48,6 +48,8 @@ use Bio::EnsEMBL::Utils::Exception qw(throw warning);
Returntype : string
Exceptions : none
Caller : general
+ Status : Medium Risk
+ : may be replaced with none affy specific methods
=cut
@@ -73,6 +75,8 @@ sub fetch_by_name {
Returntype : none
Exceptions : none
Caller : lazy load Array attributes into empty array from AffyArray object
+ Status : Medium Risk
+ : may be replaced with none affy specific methods
=cut
@@ -94,6 +98,8 @@ sub fetch_attributes {
Returntype : list of listrefs of strings
Exceptions : none
Caller : internal
+ Status : Medium Risk
+ : may be replaced with none affy specific methods
=cut
@@ -113,6 +119,8 @@ sub _tables {
Returntype : list of strings
Exceptions : none
Caller : internal
+ Status : Medium Risk
+ : may be replaced with none affy specific methods
=cut
@@ -133,6 +141,8 @@ sub _columns {
Returntype : list reference to Bio::EnsEMBL::AffyFeature objects
Exceptions : none
Caller : internal
+ Status : Medium Risk
+ : may be replaced with none affy specific methods
=cut
@@ -173,6 +183,8 @@ sub _objs_from_sth {
Returntype : none
Exceptions : none
Caller : affy feature calculating scripts
+ Status : Medium Risk
+ : may be replaced with none affy specific methods
=cut
@@ -222,6 +234,8 @@ sub store {
Returntype : list of ints
Exceptions : none
Caller : ?
+ Status : Medium Risk
+ : may be replaced with none affy specific methods
=cut
diff --git a/modules/Bio/EnsEMBL/DBSQL/AffyFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/AffyFeatureAdaptor.pm
index 4e55b371ef..53fa5caf02 100644
--- a/modules/Bio/EnsEMBL/DBSQL/AffyFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/AffyFeatureAdaptor.pm
@@ -50,7 +50,8 @@ use Bio::EnsEMBL::Utils::Exception qw(throw warning);
Returntype : listref of Bio::EnsEMBL::AffyFeature
Exceptions : none
Caller : AffyProbe->get_all_AffyFeatures()
-
+ Status : Medium Risk
+ : may be replaced with none affy specific methods
=cut
@@ -78,8 +79,10 @@ sub fetch_all_by_AffyProbe {
Arrays that are given by their names. If none is given, all features on that Slice
are returned.
Returntype : listref of Bio::EnsEMBL::AffyFeature
- Exceptions : none
+ Exceptions : throws if arraynames passed
Caller : slice->get_all_AffyFeatures()
+ Status : Medium Risk
+ : may be replaced with none affy specific methods
=cut
@@ -111,6 +114,8 @@ sub fetch_all_by_Slice_arrayname {
have an attached slice or atached probe.
or if any elements of @afs are not Bio::EnsEMBL::AffyFeatures
Caller : general
+ Status : Medium Risk
+ : may be replaced with none affy specific methods
=cut
@@ -174,6 +179,8 @@ sub store{
Returntype : list of listrefs of strings
Exceptions : none
Caller : internal
+ Status : Medium Risk
+ : may be replaced with none affy specific methods
=cut
@@ -201,6 +208,8 @@ sub _default_where_clause {
Returntype : list of strings
Exceptions : none
Caller : internal
+ Status : Medium Risk
+ : may be replaced with none affy specific methods
=cut
@@ -224,6 +233,8 @@ sub _columns {
Returntype : list reference to Bio::EnsEMBL::AffyFeature objects
Exceptions : none
Caller : internal
+ Status : Medium Risk
+ : may be replaced with none affy specific methods
=cut
@@ -375,6 +386,8 @@ sub _objs_from_sth {
Returntype : list of ints
Exceptions : none
Caller : ?
+ Status : Medium Risk
+ : may be replaced with none affy specific methods
=cut
diff --git a/modules/Bio/EnsEMBL/DBSQL/AffyProbeAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/AffyProbeAdaptor.pm
index d6efea45e1..b3d3a9e26c 100644
--- a/modules/Bio/EnsEMBL/DBSQL/AffyProbeAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/AffyProbeAdaptor.pm
@@ -41,6 +41,8 @@ use Bio::EnsEMBL::Utils::Exception qw(throw warning);
Returntype : none
Exceptions : throw on arong argument type
Caller : general
+ Status : Medium Risk
+ : may be replaced with none affy specific methods
=cut
@@ -111,7 +113,8 @@ PROBE:
Returntype : a single Bio::EnsEMBL::AffyProbe
Exceptions : none
Caller : general
-
+ Status : Medium Risk
+ : may be replaced with none affy specific methods
=cut
@@ -147,7 +150,8 @@ sub fetch_by_array_probeset_probe {
Returntype : listref of Bio::EnsEMBL::AffyProbe
Exceptions : none
Caller : general
-
+ Status : Medium Risk
+ : may be replaced with none affy specific methods
=cut
@@ -166,7 +170,8 @@ sub fetch_all_by_probeset {
Returntype : listref of Bio::EnsEMBL::AffyFeature
Exceptions : none
Caller : AffyProbe->get_all_AffyFeatures()
-
+ Status : Medium Risk
+ : may be replaced with none affy specific methods
=cut
@@ -195,7 +200,8 @@ sub fetch_by_AffyArray {
Returntype : listref of Bio::EnsEMBL::AffyFeature
Exceptions : none
Caller : AffyProbe->get_all_AffyFeatures()
-
+ Status : Medium Risk
+ : may be replaced with none affy specific methods
=cut
@@ -222,6 +228,8 @@ sub fetch_by_AffyFeature {
Returntype : list of listrefs of strings
Exceptions : none
Caller : internal
+ Status : Medium Risk
+ : may be replaced with none affy specific methods
=cut
@@ -240,6 +248,8 @@ sub _tables {
Returntype : list of strings
Exceptions : none
Caller : internal
+ Status : Medium Risk
+ : may be replaced with none affy specific methods
=cut
@@ -259,6 +269,8 @@ sub _columns {
Returntype : list reference to Bio::EnsEMBL::AffyFeature objects
Exceptions : none
Caller : internal
+ Status : Medium Risk
+ : may be replaced with none affy specific methods
=cut
@@ -294,6 +306,8 @@ sub _objs_from_sth {
Returntype : list of ints
Exceptions : none
Caller : ?
+ Status : Medium Risk
+ : may be replaced with none affy specific methods
=cut
diff --git a/modules/Bio/EnsEMBL/DBSQL/AnalysisAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/AnalysisAdaptor.pm
index e8d343fdf2..50628c0697 100755
--- a/modules/Bio/EnsEMBL/DBSQL/AnalysisAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/AnalysisAdaptor.pm
@@ -61,6 +61,7 @@ use strict;
Returntype : Bio::EnsEMBL::DBSQL::AnalysisAdaptor
Exceptions : none
Caller : Bio::EnsEMBL::DBSQL::DBAdaptor
+ Status : Stable
=cut
@@ -85,6 +86,7 @@ sub new {
Returntype : listref of Bio::EnsEMBL::Analysis retrieved from the database
Exceptions : none
Caller : AnalysisAdaptor::new
+ Status : Stable
=cut
@@ -130,6 +132,7 @@ sub fetch_all {
Returntype : Listref of Bio::EnsEMBL::Analysis
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -171,6 +174,7 @@ WHERE a.analysis_id=f.analysis_id |;
Returntype : List of feature classes
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -201,6 +205,7 @@ sub feature_classes{
Returntype : Bio::EnsEMBL::Analysis
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -247,6 +252,7 @@ sub fetch_by_dbID {
Returntype : Bio::EnsEMBL::Analysis
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -304,6 +310,7 @@ sub fetch_by_logic_name {
Exceptions : throw on incorrect argument
throw if analysis argument does not have a logic name
Caller : general
+ Status : Stable
=cut
@@ -452,6 +459,7 @@ sub store {
Returntype : int 1 if update is performed, undef if it is not
Exceptions : throw if arg is not an analysis object
Caller : ?
+ Status : Stable
=cut
@@ -503,6 +511,7 @@ sub update {
Returntype : none
Exceptions : thrown if $anal arg is not an analysis object
Caller : ?
+ Status : Stable
=cut
@@ -549,6 +558,7 @@ sub remove {
Returntype : int dbID if analysis is found, otherwise returns undef
Exceptions : thrown if $anal arg is not an analysis object
Caller : store
+ Status : Stable
=cut
@@ -586,6 +596,7 @@ sub exists {
Returntype : Bio::EnsEMBL::Analysis
Exceptions : none
Caller : Bio::EnsEMBL::DBSQL::AnalsisAdaptor::fetch_* methods
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm
index a78b25d7c4..7eeb3d5ddb 100644
--- a/modules/Bio/EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm
@@ -31,6 +31,8 @@ tables inside EnsEMBL core.
_resolve_type
+This whole module has a status of At Risk as it is under development.
+
=head1 DESCRIPTION
@@ -61,14 +63,11 @@ use vars qw(@ISA);
Returntype : Bio::EnsEMBL::ArchiveStableId
Exceptions : none
Caller : general
+ Status : At Risk
+ : under development
=cut
-# sub prepare {
-# my $self = shift;
-# warn @_;
-# $self->SUPER::prepare( @_ );
-# }
sub fetch_by_stable_id {
my $self = shift;
@@ -100,6 +99,8 @@ sub fetch_by_stable_id {
Returntype : Bio::EnsEMBL::ArchiveStableId
Exceptions : none
Caller : general
+ Status : At Risk
+ : under development
=cut
@@ -134,6 +135,8 @@ sub fetch_by_stable_id_version {
Returntype : Bio::EnsEMBL::ArchiveStableId
Exceptions : none
Caller : general
+ Status : At Risk
+ : under development
=cut
@@ -170,6 +173,8 @@ sub fetch_by_stable_id_dbname {
Returntype : listref Bio::EnsEMBL::ArchiveStableId
Exceptions : empty if not a gene stable id or not in database
Caller : ArchiveStableId->get_all_transcripts()
+ Status : At Risk
+ : under development
=cut
@@ -224,6 +229,8 @@ sub fetch_all_by_gene_archive_id {
Returntype : Bio::EnsEMBL::ArchiveStableId
Exceptions : undef if not in db or not a Transcript
Caller : Bio::EnsEMBL::ArchiveStableId->get_translation_archive_id
+ Status : At Risk
+ : under development
=cut
@@ -279,6 +286,8 @@ sub fetch_by_transcript_archive_id {
Returntype : listref Bio::EnsEMBL::ArchiveStableId
Exceptions : none
Caller : Bio::EnsEMBL::ArchiveStableId->get_all_predecessors
+ Status : At Risk
+ : under development
=cut
@@ -336,6 +345,8 @@ sub fetch_pre_by_arch_id {
Returntype : listref Bio::EnsEMBL::ArchiveStableId
Exceptions : none
Caller : webcode for archive
+ Status : At Risk
+ : under development
=cut
@@ -393,6 +404,8 @@ sub fetch_all_currently_related {
Returntype : listref Bio::EnsEMBL::ArchiveStableId
Exceptions : none
Caller : Bio::EnsEMBL::ArchiveStableId->get_all_successors
+ Status : At Risk
+ : under development
=cut
@@ -448,6 +461,8 @@ sub fetch_succ_by_arch_id {
Returntype : listref string
Exceptions : none
Caller : general
+ Status : At Risk
+ : under development
=cut
@@ -499,6 +514,8 @@ sub list_dbnames {
Returntype : string
Exceptions : none
Caller : ArchiveStableId->get_peptide or general
+ Status : At Risk
+ : under development
=cut
diff --git a/modules/Bio/EnsEMBL/DBSQL/AssemblyExceptionFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/AssemblyExceptionFeatureAdaptor.pm
index 7efb14d22c..7a1c06a6f4 100644
--- a/modules/Bio/EnsEMBL/DBSQL/AssemblyExceptionFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/AssemblyExceptionFeatureAdaptor.pm
@@ -50,6 +50,7 @@ use Bio::EnsEMBL::Utils::Exception qw(throw warning);
Returntype : reference to list of Bio::EnsEMBL::AssemblyExceptionFeatures
Exceptions : none
Caller : fetch_by_dbID, fetch_by_Slice
+ Status : Stable
=cut
@@ -129,6 +130,7 @@ sub fetch_all {
Returntype : Bio::EnsEMBL::AssemblyExceptionFeature
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -155,6 +157,7 @@ sub fetch_by_dbID {
Returntype : reference to list of Bio::EnsEMBL::AssemblyException features
Exceptions : none
Caller : Feature::get_all_alt_locations, general
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm
index 03e9be092d..0e54bf9f50 100644
--- a/modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm
@@ -88,6 +88,7 @@ my $CHUNKFACTOR = 20; # 2^20 = approx. 10^6
Returntype : Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor
Exceptions : none
Caller : Bio::EnsEMBL::DBSQL::DBAdaptor
+ Status : Stable
=cut
@@ -129,6 +130,7 @@ sub new {
Returntype : Bio::EnsEMBL::AssemblyMapper
Exceptions : wrong argument types
Caller : general
+ Status : Stable
=cut
@@ -238,6 +240,7 @@ sub fetch_by_CoordSystems {
or if it associated with multiple assembled pieces (bad data
in assembly table)
Caller : Bio::EnsEMBL::AssemblyMapper
+ Status : Stable
=cut
@@ -445,6 +448,7 @@ sub _seq_region_name_to_id {
or if it associated with multiple assembled pieces (bad data
in assembly table)
Caller : Bio::EnsEMBL::AssemblyMapper
+ Status : Stable
=cut
@@ -559,7 +563,7 @@ sub register_component {
error in the data in the meta table or in the code that creates
the mapping paths.
Caller : Bio::EnsEMBL::AssemblyMapper
-
+ Status : Stable
=cut
@@ -863,6 +867,7 @@ sub register_chained {
Returntype : none
Exceptions : none
Caller : specialised prograhsm
+ Status : Stable
=cut
@@ -972,6 +977,7 @@ sub register_all {
Exceptions : throw if mapper is between coord systems with unexpected
mapping paths
Caller : specialised programs doing a lot of genome-wide mapping
+ Status : Stable
=cut
@@ -1242,6 +1248,7 @@ sub _build_combined_mapper {
Returntype : listref of ints
Exceptions : throw if a non-existant seqregion is provided
Caller : general
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/DBSQL/AttributeAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/AttributeAdaptor.pm
index 5b49533f97..9322e37531 100644
--- a/modules/Bio/EnsEMBL/DBSQL/AttributeAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/AttributeAdaptor.pm
@@ -61,6 +61,7 @@ use vars qw(@ISA);
Returntype : Bio::EnsEMBL::AttributeAdaptor
Exceptions : none
Caller : DBAdaptor
+ Status : Stable
=cut
@@ -86,6 +87,7 @@ sub new {
Exceptions : throw if incorrect arguments
throw if provided MiscFeature does not have a dbID
Caller : MiscFeature
+ Status : Stable
=cut
@@ -128,6 +130,7 @@ sub fetch_all_by_MiscFeature {
Exceptions : throw if incorrect arguments
throw if provided MiscFeature does not have a dbID
Caller : Transcript
+ Status : Stable
=cut
@@ -170,6 +173,7 @@ sub fetch_all_by_Transcript {
Exceptions : throw if incorrect arguments
throw if provided Translation does not have a dbID
Caller : Transcript
+ Status : Stable
=cut
@@ -215,6 +219,7 @@ sub fetch_all_by_Translation {
Exceptions : throw if incorrect arguments
throw if cannot get seq_region_id from provided Slice
Caller : Slice
+ Status : Stable
=cut
@@ -261,6 +266,7 @@ sub fetch_all_by_Slice {
Returntype : none
Exceptions : throw if $slice argument not provided
Caller : general
+ Status : Stable
=cut
@@ -314,6 +320,7 @@ sub store_on_Slice {
Exceptions : throw on incorrect arguments
throw if provided feature is not stored in this database
Caller : general, MiscFeatureAdaptor
+ Status : Stable
=cut
@@ -367,6 +374,7 @@ sub store_on_MiscFeature {
Exceptions : throw on incorrect arguments
throw if provided Transcript is not stored in this database
Caller : general, TranscriptAdaptor
+ Status : Stable
=cut
@@ -421,6 +429,7 @@ sub store_on_Transcript {
Exceptions : throw on incorrect arguments
throw if provided Translation is not stored in this database
Caller : general, TranslationAdaptor
+ Status : Stable
=cut
@@ -473,6 +482,7 @@ sub store_on_Translation {
Exceptions : throw on incorrect arguments
throw if cannot obtain seq_region_id from provided Slice
Caller : general
+ Status : Stable
=cut
@@ -518,6 +528,7 @@ sub remove_from_Slice {
Exceptions : throw on incorrect arguments
throw if MiscFeature is not stored in this database
Caller : general
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm
index 30ad3ed31f..c87ac7b503 100755
--- a/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm
@@ -90,10 +90,8 @@ Internal methods are usually preceded with a _
package Bio::EnsEMBL::DBSQL::BaseAdaptor;
use vars qw(@ISA);
use strict;
-use Bio::EnsEMBL::Root;
use Bio::EnsEMBL::Utils::Exception qw(throw);
-@ISA = qw(Bio::EnsEMBL::Root);
=head2 new
@@ -107,6 +105,7 @@ use Bio::EnsEMBL::Utils::Exception qw(throw);
Returntype : Bio::EnsEMBL::DBSQL::BaseAdaptor
Exceptions : none
Caller : Bio::EnsEMBL::DBSQL::DBConnection
+ Status : Stable
=cut
@@ -149,6 +148,7 @@ sub new {
Returntype : DBI::StatementHandle
Exceptions : none
Caller : Adaptors inherited from BaseAdaptor
+ Status : Stable
=cut
@@ -169,6 +169,7 @@ sub prepare{
Returntype : Bio::EnsEMBL::DBSQL::DBAdaptor
Exceptions : none
Caller : Adaptors inherited fro BaseAdaptor
+ Status : Stable
=cut
@@ -190,6 +191,7 @@ sub db{
Returntype : Bio::EnsEMBL::DBSQL::DBConnection
Exceptions : none
Caller : Adaptors inherited fro BaseAdaptor
+ Status : Stable
=cut
@@ -263,6 +265,7 @@ sub _straight_join {
Returntype : listref of Bio::EnsEMBL::SeqFeature in contig coordinates
Exceptions : none
Caller : BaseFeatureAdaptor, ProxyDnaAlignFeatureAdaptor::generic_fetch
+ Status : Stable
=cut
@@ -348,6 +351,7 @@ sub generic_fetch {
Exceptions : thrown if $id arg is not provided
does not exist
Caller : general
+ Status : Stable
=cut
@@ -387,6 +391,7 @@ sub fetch_by_dbID{
Exceptions : thrown if $id arg is not provided
does not exist
Caller : general
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/DBSQL/BaseAlignFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/BaseAlignFeatureAdaptor.pm
index 87b8dcfbd7..4ada51f69f 100644
--- a/modules/Bio/EnsEMBL/DBSQL/BaseAlignFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/BaseAlignFeatureAdaptor.pm
@@ -56,6 +56,7 @@ use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
Returntype : listref of Bio::EnsEMBL::BaseAlignFeatures in Slice coordinates
Exceptions : thrown if pid is not defined
Caller : general
+ Status : Stable
=cut
@@ -95,6 +96,7 @@ sub fetch_all_by_Slice_and_pid {
Returntype : listref of Bio::EnsEMBL::BaseAlignFeatures
Exceptions : thrown if hit_name is not defined
Caller : general
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
index a4743b35de..d40b22b811 100644
--- a/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
@@ -52,6 +52,7 @@ our $MAX_SPLIT_QUERY_SEQ_REGIONS = 3;
Returntype : Bio::EnsEMBL::BaseFeatureAdaptor
Exceptions : none
Caller : implementing subclass constructors
+ Status : Stable
=cut
@@ -85,6 +86,7 @@ sub new {
Returntype : listref of Bio::EnsEMBL::SeqFeatures in Slice coordinates
Exceptions : none
Caller : Bio::EnsEMBL::Slice
+ Status : Stable
=cut
@@ -103,15 +105,16 @@ sub fetch_all_by_Slice {
lower bound of the the score of the features retrieved
Arg [3] : (optional) string $logic_name
the logic name of the type of features to obtain
- Example : $fts = $a->fetch_all_by_Slice($slice, 'Swall');
+ Example : $fts = $a->fetch_all_by_Slice_and_score($slice,90,'Swall');
Description: Returns a list of features created from the database which are
are on the Slice defined by $slice and which have a score
- greated than $score. If $logic_name is defined,
+ greater than $score. If $logic_name is defined,
only features with an analysis of type $logic_name will be
returned.
Returntype : listref of Bio::EnsEMBL::SeqFeatures in Slice coordinates
Exceptions : none
Caller : Bio::EnsEMBL::Slice
+ Status : Stable
=cut
@@ -147,6 +150,7 @@ sub fetch_all_by_Slice_and_score {
Returntype : listref of Bio::EnsEMBL::SeqFeatures in Slice coordinates
Exceptions : thrown if $slice is not defined
Caller : Bio::EnsEMBL::Slice
+ Status : Stable
=cut
@@ -615,6 +619,8 @@ sub _logic_name_to_constraint {
Returntype : none
Exceptions : thrown method is not implemented by subclass
Caller : general
+ Status : At Risk
+ : throws if called.
=cut
@@ -640,6 +646,7 @@ sub store{
Exceptions : thrown if $feature arg does not implement dbID(), or if
$feature->dbID is not a true value
Caller : general
+ Status : Stable
=cut
@@ -672,7 +679,7 @@ sub remove {
=head2 remove_by_Slice
Arg [1] : Bio::Ensembl::Slice $slice
- Example : $feature_adaptor->remove_by_RawContig($slice);
+ Example : $feature_adaptor->remove_by_Slice($slice);
Description: This removes features from the database which lie on a region
represented by the passed in slice. Only features which are
fully contained by the slice are deleted; features which overlap
@@ -682,6 +689,7 @@ sub remove {
Returntype : none
Exceptions : thrown if no slice is supplied
Caller : general
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/DBSQL/BaseMetaContainer.pm b/modules/Bio/EnsEMBL/DBSQL/BaseMetaContainer.pm
index bc655cc53e..c7d91f3784 100644
--- a/modules/Bio/EnsEMBL/DBSQL/BaseMetaContainer.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/BaseMetaContainer.pm
@@ -53,6 +53,7 @@ use Bio::EnsEMBL::Utils::Exception qw(deprecate);
Returntype : listref of strings
Exceptions : none
Caller : ?
+ Status : Stable
=cut
@@ -89,6 +90,7 @@ sub list_value_by_key {
Returntype : none
Exceptions : none
Caller : ?
+ Status : Stable
=cut
@@ -118,6 +120,7 @@ sub store_key_value {
Returntype : none
Exceptions : none
Caller : ?
+ Status : Stable
=cut
@@ -141,6 +144,7 @@ sub update_key_value {
Returntype : none
Exceptions : none
Caller : dna_compress script, general
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/DBSQL/CompressedSequenceAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/CompressedSequenceAdaptor.pm
index 4f75755998..3a39e484d7 100644
--- a/modules/Bio/EnsEMBL/DBSQL/CompressedSequenceAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/CompressedSequenceAdaptor.pm
@@ -111,6 +111,7 @@ sub _fetch_seq {
Returntype : int
Exceptions : none
Caller : Bio::EnsEMBL::DBSQL::RawContigAdaptor::store
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm
index dd72103b0a..5640cb9819 100644
--- a/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm
@@ -115,6 +115,7 @@ use vars qw(@ISA);
Returntype : Bio::EnsEMBL::DBSQL::CoordSystemAdaptor
Exceptions : none
Caller :
+ Status : Stable
=cut
@@ -269,6 +270,7 @@ sub new {
Returntype : listref of Bio::EnsEMBL::CoordSystems
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -298,6 +300,7 @@ sub fetch_all {
Returntype : Bio::EnsEMBL::CoordSystem
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -339,6 +342,7 @@ sub fetch_by_rank {
Exceptions : throw if no name argument provided
warning if no version provided and default does not exist
Caller : general
+ Status : Stable
=cut
@@ -405,6 +409,7 @@ sub fetch_by_name {
Returntype : listref of Bio::EnsEMBL::CoordSystem objects
Exceptions : throw if no name argument provided
Caller : general
+ Status : Stable
=cut
@@ -437,6 +442,7 @@ sub fetch_all_by_name {
Returntype : Bio::EnsEMBL::CoordSystem or undef
Exceptions : thrown if no coord_system exists for specified dbID
Caller : general
+ Status : Stable
=cut
@@ -463,6 +469,7 @@ sub fetch_by_dbID {
Returntype : a Bio::EnsEMBL::CoordSystem object
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -483,6 +490,7 @@ sub fetch_top_level {
Exceptions : throw if no sequence_level coord system exists at all
throw if multiple sequence_level coord systems exists
Caller : general
+ Status : Stable
=cut
@@ -556,6 +564,7 @@ sub fetch_sequence_level {
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -715,6 +724,7 @@ sub _fetch_all_by_attrib {
Returntype : none
Exceptions : Warning if CoordSystem is already stored in this database.
Caller : none
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm b/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm
index 935db287f2..3618e7e203 100644
--- a/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm
@@ -102,6 +102,7 @@ use Bio::EnsEMBL::Utils::Argument qw(rearrange);
cannot be connected to.
Caller : Bio::EnsEMBL::::Utils::ConfigRegistry ( for newer code using the registry)
Bio::EnsEMBL::DBSQL::DBAdaptor ( for old style code)
+ Status : Stable
=cut
@@ -170,6 +171,7 @@ sub new {
Returntype : none
Exceptions : none
Caller : new, db_handle
+ Status : Stable
=cut
@@ -207,12 +209,15 @@ sub connect {
=head2 connected
+
Example : $dbcon->connected()
Description: Boolean which tells if DBConnection is connected or not.
State is set internally, and external processes should not alter state.
Returntype : undef or 1
Exceptions : none
Caller : db_handle, connect, disconnect_if_idle, user processes
+ Status : Stable
+
=cut
sub connected {
@@ -268,6 +273,7 @@ sub equals{
Returntype : string
Exceptions : none
Caller : new
+ Status : Stable
=cut
@@ -292,6 +298,7 @@ sub driver {
Returntype : string
Exceptions : none
Caller : new
+ Status : Stable
=cut
@@ -316,6 +323,7 @@ sub port {
Returntype : string
Exceptions : none
Caller : new
+ Status : Stable
=cut
@@ -339,6 +347,7 @@ sub dbname {
Returntype : string
Exceptions : none
Caller : new
+ Status : Stable
=cut
@@ -362,6 +371,7 @@ sub username {
Returntype : string
Exceptions : none
Caller : new
+ Status : Stable
=cut
@@ -385,6 +395,7 @@ sub host {
Returntype : string
Exceptions : none
Caller : new
+ Status : Stable
=cut
@@ -409,6 +420,7 @@ sub password {
Returntype : boolean
Exceptions : none
Caller : Pipeline
+ Status : Stable
=cut
@@ -437,6 +449,7 @@ sub disconnect_when_inactive {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -460,6 +473,7 @@ sub locator {
Returntype : DBI Database Handle
Exceptions : none
Caller : new, DESTROY
+ Status : Stable
=cut
@@ -489,6 +503,7 @@ sub db_handle {
Exceptions : thrown if the SQL statement is empty, or if the internal
database handle is not present
Caller : Adaptor modules
+ Status : Stable
=cut
@@ -524,6 +539,7 @@ sub prepare {
Exceptions : thrown if the SQL statement is empty, or if the internal
database handle is not present.
Caller : Adaptor modules
+ Status : Stable
=cut
@@ -568,6 +584,7 @@ sub do {
Exceptions : none
Caller : Bio::EnsEMBL::DBSQL::SQL::StatementHandle::DESTROY
Bio::EnsEMBL::DBSQL::DBConnection::do
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
index f43c9b5094..611e592539 100644
--- a/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
@@ -55,6 +55,7 @@ use strict;
Returntype : Bio::EnsEMBL::DBEntry
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -122,6 +123,7 @@ sub fetch_by_dbID {
Returntype : Bio::EnsEMBL::DBSQL::DBEntry
Exceptions : thrown if arguments are incorrect
Caller : general, domainview
+ Status : Stable
=cut
@@ -208,6 +210,7 @@ sub fetch_by_db_accession {
Returntype : int - the identifier of the newly created external refernce
Exceptions : none
Caller : scripts which load Xrefs and ObjectXrefs, etc. into EnsEMBL.
+ Status : Stable
=cut
@@ -375,6 +378,7 @@ sub store {
Returntype : int
Exceptions : thrown on incorrect args
Caller : GeneAdaptor::store, TranscriptAdaptor::store
+ Status : Stable
=cut
@@ -413,8 +417,9 @@ sub exists {
all of the gene, transcript, and translation xrefs associated
with this gene.
Returntype : listref of Bio::EnsEMBL::DBEntries
- Exceptions : none
+ Exceptions : thows if gene object not passed
Caller : Bio::EnsEMBL::Gene
+ Status : Stable
=cut
@@ -439,8 +444,9 @@ sub fetch_all_by_Gene {
to contain all of the gene, transcript, and translation xrefs
associated with this gene.
Returntype : listref of Bio::EnsEMBL::DBEntries
- Exceptions : none
+ Exceptions : throes if transcript argument not passed
Caller : Bio::EnsEMBL::Gene
+ Status : Stable
=cut
@@ -462,8 +468,9 @@ sub fetch_all_by_Transcript {
Example : @db_entries = @{$db_entry_adptr->fetch_by_Translation($trans)};
Description: Retrieves external database entries for an EnsEMBL translation
Returntype : listref of Bio::EnsEMBL::DBEntries
- Exceptions : none
+ Exceptions : throws if translation object not passed
Caller : general
+ Status : Stable
=cut
@@ -503,6 +510,7 @@ sub fetch_all_by_Translation {
Warning if object or dbentry is not stored in this database.
Caller : TranscriptAdaptor::remove, GeneAdaptor::remove,
TranslationAdaptor::remove
+ Status : Stable
=cut
@@ -587,6 +595,7 @@ sub remove_from_object {
Caller : fetch_all_by_Gene
fetch_all_by_Translation
fetch_all_by_Transcript
+ Status : Stable
=cut
@@ -713,6 +722,7 @@ sub _fetch_by_object_type {
Returntype : list of ints
Exceptions : none
Caller : unknown
+ Status : Stable
=cut
@@ -738,6 +748,7 @@ sub list_gene_ids_by_extids{
Returntype : list of ints
Exceptions : none
Caller : unknown
+ Status : Stable
=cut
@@ -760,6 +771,7 @@ sub list_transcript_ids_by_extids{
Returntype : list of Ints
Exceptions : none
Caller : unknown
+ Status : Stable
=cut
@@ -783,6 +795,7 @@ sub list_translation_ids_by_extids{
Caller : list_translation_ids_by_extids
translationids_by_extids
geneids_by_extids
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/DBSQL/DensityFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/DensityFeatureAdaptor.pm
index 02521140f4..2f92d8d5ca 100644
--- a/modules/Bio/EnsEMBL/DBSQL/DensityFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/DensityFeatureAdaptor.pm
@@ -60,6 +60,7 @@ our $DENSITY_FEATURE_CACHE_SIZE = 20;
Returntype : Bio::EnsEMBL::DBSQL::DensityFeatureAdaptor
Exceptions : none
Caller : implementing subclass constructors
+ Status : Stable
=cut
@@ -122,6 +123,7 @@ sub new {
warning if no features with logic_name $logic_name exist
warning if density_type table has invalid block_size value
Caller : general
+ Status : Stable
=cut
@@ -454,6 +456,7 @@ sub _objs_from_sth {
Returntype : list of ints
Exceptions : none
Caller : ?
+ Status : Stable
=cut
@@ -475,6 +478,7 @@ sub list_dbIDs {
have an attached slice.
or if any elements of @df are not Bio::EnsEMBL::SeqFeatures
Caller : general
+ Status : Stable
=cut
@@ -554,6 +558,7 @@ sub store{
Returntype : Bio::EnsEMBL::DensityFeatureSet
Exceptions : none
Caller : general
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/DBSQL/DensityTypeAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/DensityTypeAdaptor.pm
index ad76b5771f..20266cdb6a 100644
--- a/modules/Bio/EnsEMBL/DBSQL/DensityTypeAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/DensityTypeAdaptor.pm
@@ -48,6 +48,7 @@ use Bio::EnsEMBL::Utils::Exception qw(throw warning);
Returntype : Bio::EnsEMBL::DBSQL::DensityTypeAdaptor
Exceptions : none
Caller : DBAdaptor
+ Status : Stable
=cut
@@ -71,6 +72,7 @@ sub new {
Returntype : reference to list of Bio::EnsEMBL::DensityType objects
Exceptions : none
Caller : general, new
+ Status : Stable
=cut
@@ -122,6 +124,7 @@ sub fetch_all {
Returntype : Bio::EnsEMBL::DensityType
Exceptions : throw if dbID argument not defined
Caller : general
+ Status : Stable
=cut
@@ -152,6 +155,7 @@ sub fetch_by_dbID {
Returntype : reference to list of Bio::EnsEMBL::DensityTypes
Exceptions : thrown if logic_name argument is not provided
Caller : general
+ Status : Stable
=cut
@@ -205,12 +209,13 @@ sub fetch_all_by_logic_name {
Arg [1] : list of Bio::EnsEMBL::DensityType @dt
the density types to store in the database
- Example : $density_type->store(1234, @density_types);
+ Example : $density_type->store(@density_types);
Description: Stores a list of density type objects in the database
Returntype : none
Exceptions : thrown if @dt is not defined
or if any elements of @dt are not Bio::EnsEMBL::DensityType
Caller : general
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/DBSQL/DnaAlignFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/DnaAlignFeatureAdaptor.pm
index 8d9742590d..68b4e7ca51 100644
--- a/modules/Bio/EnsEMBL/DBSQL/DnaAlignFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/DnaAlignFeatureAdaptor.pm
@@ -51,6 +51,7 @@ use Bio::EnsEMBL::Utils::Exception qw(throw warning);
Returntype : list of listrefs of strings
Exceptions : none
Caller : Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::generic_fetch
+ Status : Stable
=cut
@@ -70,6 +71,7 @@ sub _tables {
Returntype : list of strings
Exceptions : none
Caller : Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::generic_fetch
+ Status : Stable
=cut
@@ -110,6 +112,7 @@ sub _columns {
A warning is given if:
* The feature has already been stored in this db
Caller : Pipeline
+ Status : Stable
=cut
@@ -198,6 +201,7 @@ sub store {
Returntype : listref of Bio::EnsEMBL::DnaDnaAlignFeatures
Exceptions : none
Caller : Bio::EnsEMBL::BaseFeatureAdaptor::generic_fetch
+ Status : Stable
=cut
@@ -355,6 +359,7 @@ sub _objs_from_sth {
Returntype : list of ints
Exceptions : none
Caller : ?
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm
index 25eb57e830..3e63406f00 100644
--- a/modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm
@@ -119,6 +119,7 @@ sub _final_clause {
Returntype : Bio::EnsEMBL::Exon in contig coordinates
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -142,8 +143,9 @@ sub fetch_by_stable_id {
Example : none
Description: Retrieves all Exons for the Transcript in 5-3 order
Returntype : listref Bio::EnsEMBL::Exon on Transcript slice
- Exceptions : none
+ Exceptions : throws if transcript has no slice
Caller : Transcript->get_all_Exons()
+ Status : Stable
=cut
@@ -204,6 +206,7 @@ sub fetch_all_by_Transcript {
or if $exon->start, $exon->end, $exon->strand, or $exon->phase
are not defined or if $exon is not a Bio::EnsEMBL::Exon
Caller : general
+ Status : Stable
=cut
@@ -331,6 +334,7 @@ sub store {
Returntype : none
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -412,6 +416,7 @@ sub remove {
Returntype : list of ints
Exceptions : none
Caller : ?
+ Status : Stable
=cut
@@ -429,6 +434,7 @@ sub list_dbIDs {
Returntype : list of ints
Exceptions : none
Caller : ?
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
index 07eb77901f..308d35ccbd 100644
--- a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
@@ -66,6 +66,7 @@ use vars '@ISA';
# Returntype : list of listrefs of strings
# Exceptions : none
# Caller : internal
+# Status : Stable
sub _tables {
my $self = shift;
@@ -85,6 +86,7 @@ sub _tables {
# Returntype : list of strings
# Exceptions : none
# Caller : internal
+# Status : Stable
sub _columns {
my $self = shift;
@@ -115,6 +117,7 @@ sub _left_join {
Returntype : list of ints
Exceptions : none
Caller : ?
+ Status : Stable
=cut
@@ -132,6 +135,7 @@ sub list_dbIDs {
Returntype : reference to a list of strings
Exceptions : none
Caller : ?
+ Status : Stable
=cut
@@ -151,6 +155,7 @@ sub list_stable_ids {
Returntype : Bio::EnsEMBL::Gene
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -178,6 +183,7 @@ sub fetch_by_display_label {
Returntype : Bio::EnsEMBL::Gene in given coordinate system
Exceptions : if we cant get the gene in given coord system
Caller : general
+ Status : Stable
=cut
@@ -215,6 +221,7 @@ sub fetch_by_stable_id {
Returntype : Bio::EnsEMBL::Gene (or undef)
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -256,6 +263,7 @@ sub fetch_by_exon_stable_id{
Returntype : list of Bio::EnsEMBL::Genes
Exceptions : none
Caller : domainview
+ Status : Stable
=cut
@@ -304,6 +312,7 @@ sub fetch_all_by_domain {
Returntype : reference to list of transcripts
Exceptions : thrown if exon cannot be placed on transcript slice
Caller : Slice::get_all_Transcripts
+ Status : Stable
=cut
@@ -418,6 +427,7 @@ sub fetch_all_by_Slice {
Returntype : Bio::EnsEMBL::Gene
Exceptions : none
Caller : ?
+ Status : Stable
=cut
@@ -452,6 +462,7 @@ sub fetch_by_transcript_id {
Returntype : Bio::EnsEMBL::Gene
Exceptions : none
Caller : ?
+ Status : Stable
=cut
@@ -490,6 +501,7 @@ sub fetch_by_transcript_stable_id {
Returntype : Bio::EnsEMBL::Gene
Exceptions : none
Caller : geneview
+ Status : Stable
=cut
@@ -532,6 +544,7 @@ sub fetch_by_translation_stable_id {
Returntype : listref of Bio::EnsEMBL::Genes
Exceptions : none
Caller : goview
+ Status : Stable
=cut
@@ -569,6 +582,7 @@ sub fetch_all_by_external_name {
Exceptions : throw if incorrect arg provided
warning if gene arg does not have dbID
Caller : Gene::get_all_alt_alleles
+ Status : Stable
=cut
@@ -627,6 +641,7 @@ sub fetch_all_alt_alleles {
Exceptions : throw on incorrect arguments
throw on sql error (e.g. duplicate unique id)
Caller : ?
+ Status : Stable
=cut
@@ -724,6 +739,7 @@ sub store_alt_alleles {
Exceptions : thrown if the $gene is not a Bio::EnsEMBL::Gene or if
$gene does not have an analysis object
Caller : general
+ Status : Stable
=cut
@@ -910,6 +926,7 @@ sub store {
Exceptions : throw on incorrect arguments
warning if gene is not stored in this database
Caller : general
+ Status : Stable
=cut
@@ -979,6 +996,7 @@ sub remove {
Returntype : listref of strings
Exceptions : none
Caller : domainview?
+ Status : Stable
=cut
@@ -1029,6 +1047,7 @@ sub get_Interpro_by_geneid {
Returntype : None
Exceptions : thrown if the $gene is not a Bio::EnsEMBL::Gene
Caller : general
+ Status : Stable
=cut
@@ -1078,6 +1097,7 @@ sub update {
# Returntype : listref of Bio::EnsEMBL::Genes in target coordinate system
# Exceptions : none
# Caller : internal
+# Status : Stable
sub _objs_from_sth {
my ($self, $sth, $mapper, $dest_slice) = @_;
diff --git a/modules/Bio/EnsEMBL/DBSQL/KaryotypeBandAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/KaryotypeBandAdaptor.pm
index 7d326404c2..c721af4953 100644
--- a/modules/Bio/EnsEMBL/DBSQL/KaryotypeBandAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/KaryotypeBandAdaptor.pm
@@ -146,6 +146,7 @@ sub _objs_from_sth {
(assembly) coordinates
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -177,8 +178,9 @@ sub fetch_all_by_chr_name {
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 : none
+ Exceptions : throws if chr or band is missing in arguments
Caller : general
+ Status : Stable
=cut
@@ -215,6 +217,7 @@ sub fetch_by_chr_band {
Returntype : reference to a list of ints
Exceptions : none
Caller : ?
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/DBSQL/MetaContainer.pm b/modules/Bio/EnsEMBL/DBSQL/MetaContainer.pm
index 1bd7728e73..c281b9ba70 100644
--- a/modules/Bio/EnsEMBL/DBSQL/MetaContainer.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/MetaContainer.pm
@@ -55,6 +55,7 @@ use Bio::Species;
Returntype : Bio::Species
Exceptions : none
Caller : ?
+ Status : Stable
=cut
@@ -90,6 +91,7 @@ sub get_Species {
Returntype : string
Exceptions : none
Caller : ?
+ Status : Stable
=cut
@@ -157,6 +159,7 @@ sub get_max_assembly_contig {
Returntype : string
Exceptions : none
Caller : ?
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/DBSQL/MetaCoordContainer.pm b/modules/Bio/EnsEMBL/DBSQL/MetaCoordContainer.pm
index b5d8dc7c5a..d121a19f3e 100644
--- a/modules/Bio/EnsEMBL/DBSQL/MetaCoordContainer.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/MetaCoordContainer.pm
@@ -52,6 +52,7 @@ sub new {
Returntype : listref of Bio::EnsEMBL::CoordSystem objects
Exceptions : throw if name argument not provided
Caller : BaseFeatureAdaptor
+ Status : Stable
=cut
@@ -96,6 +97,7 @@ sub fetch_all_CoordSystems_by_feature_type {
Returntype : int or undef
Exceptions : throw on incorrect argument
Caller : BaseFeatureAdaptor
+ Status : Stable
=cut
@@ -133,6 +135,7 @@ sub fetch_max_length_by_CoordSystem_feature_type {
Returntype : none
Exceptions : none
Caller : BaseFeatureAdaptor
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/DBSQL/MiscFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/MiscFeatureAdaptor.pm
index f6d7634605..0e59091921 100644
--- a/modules/Bio/EnsEMBL/DBSQL/MiscFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/MiscFeatureAdaptor.pm
@@ -76,6 +76,7 @@ use vars qw(@ISA);
Exceptions : throw if set_code is not provided
warning if no set for provided set code exists
Caller : general
+ Status : Stable
=cut
@@ -136,6 +137,7 @@ sub fetch_all_by_Slice_and_set_code {
Returntype : listref of Bio::EnsEMBL::MiscFeatures
Exceptions : throw if attrib_type code arg is not provided
Caller : general
+ Status : Stable
=cut
@@ -507,6 +509,7 @@ sub _objs_from_sth {
Returntype : list of ints
Exceptions : none
Caller : ?
+ Status : Stable
=cut
@@ -528,6 +531,7 @@ sub list_dbIDs {
warning if misc feature is already stored in this database
throw if start/end/strand attribs are not valid
Caller : general
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/DBSQL/MiscSetAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/MiscSetAdaptor.pm
index 0a1fa1488a..18dd35016a 100644
--- a/modules/Bio/EnsEMBL/DBSQL/MiscSetAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/MiscSetAdaptor.pm
@@ -60,6 +60,7 @@ use vars qw(@ISA);
Returntype : Bio::EnsEMBL::MiscSet
Exceptions : none
Caller : MiscFeatureAdaptor
+ Status : Stable
=cut
@@ -94,6 +95,7 @@ sub new {
Returntype : listref of Bio::EnsEMBL::MiscSets
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -140,6 +142,7 @@ sub fetch_all {
Returntype : Bio::EnsEMBL::MiscSet
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -166,6 +169,7 @@ sub fetch_by_dbID {
Returntype : Bio::EnsEMBL::MiscSet
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -193,6 +197,7 @@ sub fetch_by_code {
Exceptions : throw on incorrect arguments
warning if a feature is already stored in this database
Caller : MiscFeatureAdaptor::store
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/DBSQL/PredictionExonAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/PredictionExonAdaptor.pm
index 934d98f86f..95e0a08aa8 100644
--- a/modules/Bio/EnsEMBL/DBSQL/PredictionExonAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/PredictionExonAdaptor.pm
@@ -107,8 +107,9 @@ sub _final_clause {
Example : none
Description: Retrieves all Exons for the Transcript in 5-3 order
Returntype : listref Bio::EnsEMBL::Exon on Transcript slice
- Exceptions : none
+ Exceptions : throws if transcript does not have a slice
Caller : Transcript->get_all_Exons()
+ Status : Stable
=cut
@@ -160,6 +161,7 @@ sub fetch_all_by_PredictionTranscript {
or if $exon->start, $exon->end, $exon->strand, or $exon->phase
are not defined or if $exon is not a Bio::EnsEMBL::PredictionExon
Caller : general
+ Status : Stable
=cut
@@ -227,6 +229,7 @@ sub store {
Returntype : none
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -258,6 +261,7 @@ sub remove {
Returntype : list of ints
Exceptions : none
Caller : ?
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/DBSQL/PredictionTranscriptAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/PredictionTranscriptAdaptor.pm
index b9843c4ff6..193e456d16 100644
--- a/modules/Bio/EnsEMBL/DBSQL/PredictionTranscriptAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/PredictionTranscriptAdaptor.pm
@@ -86,17 +86,18 @@ sub _columns {
=head2 fetch_by_stable_id
-Arg [1] : string $stable_id
- The stable id of the transcript to retrieve
-Example : $trans = $trans_adptr->fetch_by_stable_id('GENSCAN00000001234');
-Description: Retrieves a prediction transcript via its display_label.
- This method is called fetch_by_stable_id for polymorphism with
- the TranscriptAdaptor. Prediction transcript display_labels are
- not necessarily stable in that the same identifier may be reused
- for a completely different prediction transcript in a subsequent
- database release.
-Returntype : Bio::EnsEMBL::PredictionTranscript
-Caller : general
+ Arg [1] : string $stable_id
+ The stable id of the transcript to retrieve
+ Example : $trans = $trans_adptr->fetch_by_stable_id('GENSCAN00000001234');
+ Description: Retrieves a prediction transcript via its display_label.
+ This method is called fetch_by_stable_id for polymorphism with
+ the TranscriptAdaptor. Prediction transcript display_labels are
+ not necessarily stable in that the same identifier may be reused
+ for a completely different prediction transcript in a subsequent
+ database release.
+ Returntype : Bio::EnsEMBL::PredictionTranscript
+ Caller : general
+ Status : Stable
=cut
@@ -130,6 +131,7 @@ sub fetch_by_stable_id {
Returntype : reference to list of transcripts
Exceptions : thrown if exon cannot be placed on transcript slice
Caller : Slice::get_all_Transcripts
+ Status : Stable
=cut
@@ -244,6 +246,7 @@ sub fetch_all_by_Slice {
Returntype : reference to a list of Bio::EnsEMBL::PredictionTranscripts
Exceptions : none
Caller : superclass generic_fetch
+ Status : Stable
=cut
@@ -404,6 +407,7 @@ sub _objs_from_sth {
Returntype : none
Exceptions : on wrong argument type
Caller : general
+ Status : Stable
=cut
@@ -489,8 +493,9 @@ sub store {
Example : $prediction_transcript_adaptor->remove($pt);
Description: removes given prediction transcript $pt from database.
Returntype : none
- Exceptions : none
+ Exceptions : throws if argument not a Bio::EnsEMBL::PredictionTranscript
Caller : general
+ Status : Stable
=cut
@@ -533,6 +538,7 @@ sub remove {
Returntype : list of ints
Exceptions : none
Caller : ?
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/DBSQL/ProteinAlignFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/ProteinAlignFeatureAdaptor.pm
index faba67da36..85b756a52d 100644
--- a/modules/Bio/EnsEMBL/DBSQL/ProteinAlignFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/ProteinAlignFeatureAdaptor.pm
@@ -58,6 +58,7 @@ use Bio::EnsEMBL::Utils::Exception qw(throw warning);
A warning is given if:
* The feature has already been stored in this db
Caller : Pipeline
+ Status : Stable
=cut
@@ -152,6 +153,7 @@ sub store{
Returntype : listref of Bio::EnsEMBL::ProteinAlignFeatures
Exceptions : none
Caller : Bio::EnsEMBL::BaseFeatureAdaptor::generic_fetch
+ Status : Stable
=cut
@@ -336,6 +338,7 @@ sub _columns {
Returntype : listref of ints
Exceptions : none
Caller : ?
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/DBSQL/ProteinFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/ProteinFeatureAdaptor.pm
index 5efb65ecca..dbf7c4ec11 100755
--- a/modules/Bio/EnsEMBL/DBSQL/ProteinFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/ProteinFeatureAdaptor.pm
@@ -69,6 +69,7 @@ use vars qw(@ISA);
Returntype : listref of Bio::EnsEMBL::ProteinFeatures
Exceptions : none
Caller : ?
+ Status : Stable
=cut
@@ -138,6 +139,7 @@ sub fetch_all_by_translation_id {
Returntype : Bio::EnsEMBL::ProteinFeauture
Exceptions : none
Caller : ?
+ Status : Stable
=cut
@@ -198,6 +200,7 @@ sub fetch_by_dbID{
Returntype : int - the new internal identifier of the stored protein feature
Exceptions : thrown if arg is not a Bio::EnsEMBL:
Caller : none
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/DBSQL/RegulatoryFactorAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/RegulatoryFactorAdaptor.pm
index 7608718d7f..1122f7c7a7 100644
--- a/modules/Bio/EnsEMBL/DBSQL/RegulatoryFactorAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/RegulatoryFactorAdaptor.pm
@@ -58,6 +58,8 @@ use vars qw(@ISA);
Returntype : Bio::EnsEMBL::RegulatoryFactor
Exceptions : none
Caller : general, Bio::EnsEMBL::RegulatoryFactorAdaptor
+ Status : At Risk
+ : under development
=cut
@@ -80,6 +82,8 @@ sub fetch_by_dbID {
Returntype : Bio::EnsEMBL::RegulatoryFactor
Exceptions : none
Caller : general
+ Status : At Risk
+ : under development
=cut
@@ -101,6 +105,8 @@ sub fetch_by_name {
Returntype : listREF of Bio::EnsEMBL::RegulatoryFactors
Exceptions : none
Caller : general
+ Status : At Risk
+ : under development
=cut
@@ -121,6 +127,8 @@ sub fetch_all_by_type {
Returntype : listref of Bio::EnsEMBL::RegulatoryFactor objects
Exceptions : none
Caller : internal
+ Status : At Risk
+ : under development
=cut
@@ -156,6 +164,8 @@ sub _generic_fetch {
Returntype : none
Exceptions : none
Caller : ?
+ Status : At Risk
+ : under development
=cut
diff --git a/modules/Bio/EnsEMBL/DBSQL/RegulatoryFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/RegulatoryFeatureAdaptor.pm
index 359971ffc4..c1b76cea9a 100644
--- a/modules/Bio/EnsEMBL/DBSQL/RegulatoryFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/RegulatoryFeatureAdaptor.pm
@@ -61,6 +61,8 @@ use vars qw(@ISA);
Returntype : reference to a list of Bio::EnsEMBL::RegulatoryFeatures.
Exceptions : throw on bad argument
Caller : Slice::get_all_RegulatoryFeatures
+ Status : At Risk
+ : under development
=cut
@@ -299,6 +301,8 @@ sub _objs_from_sth {
Returntype : listREF of Bio::EnsEMBL::RegulatoryFeatures
Exceptions : none
Caller : general
+ Status : At Risk
+ : under development
=cut
@@ -328,6 +332,8 @@ sub fetch_all_by_factor {
Returntype : none
Exceptions :
Caller : general
+ Status : At Risk
+ : under development
=cut
@@ -412,6 +418,8 @@ sub store {
Returntype : list of ints
Exceptions : none
Caller : ?
+ Status : At Risk
+ : under development
=cut
@@ -432,6 +440,8 @@ sub list_dbIDs {
Returntype : Listref of Bio::EnsEMBL::RegulatoryFeature
Exceptions : none
Caller : ?
+ Status : At Risk
+ : under development
=cut
@@ -472,6 +482,8 @@ sub fetch_all_by_ensembl_object_type {
Returntype : Listref of Bio::EnsEMBL::RegulatoryFeature
Exceptions : If arg is not of correct type.
Caller : ?
+ Status : At Risk
+ : under development
=cut
@@ -499,6 +511,8 @@ sub fetch_all_by_transcript {
Returntype : Listref of Bio::EnsEMBL::RegulatoryFeature
Exceptions : If arg is not of correct type.
Caller : ?
+ Status : At Risk
+ : under development
=cut
@@ -529,6 +543,8 @@ sub fetch_all_by_translation {
Returntype : Listref of Bio::EnsEMBL::RegulatoryFeature
Exceptions : If arg is not of correct type.
Caller : ?
+ Status : At Risk
+ : under development
=cut
diff --git a/modules/Bio/EnsEMBL/DBSQL/RepeatConsensusAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/RepeatConsensusAdaptor.pm
index df4b933308..332f5e2530 100644
--- a/modules/Bio/EnsEMBL/DBSQL/RepeatConsensusAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/RepeatConsensusAdaptor.pm
@@ -57,6 +57,7 @@ use vars qw(@ISA);
Returntype : Bio::EnsEMBL::RepeatConsensus
Exceptions : none
Caller : general, Bio::EnsEMBL::RepeatFeatureAdaptor
+ Status : Stable
=cut
@@ -79,6 +80,7 @@ sub fetch_by_dbID {
Returntype : Bio::EnsEMBL::RepeatConsensus
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -104,6 +106,7 @@ sub fetch_by_name {
Returntype : Bio::EnsEMBL::RepeatConsensus
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -133,6 +136,7 @@ sub fetch_by_name_class {
Returntype : listREF of Bio::EnsEMBL::RepeatConsensus
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -161,6 +165,7 @@ sub fetch_by_class_seq {
Returntype : listref of Bio::EnsEMBL::RepeatConsensus objects
Exceptions : none
Caller : internal
+ Status : Stable
=cut
@@ -218,6 +223,7 @@ sub _generic_fetch {
Returntype : none
Exceptions : none
Caller : ?
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/DBSQL/RepeatFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/RepeatFeatureAdaptor.pm
index b89c18d762..eb59521f06 100644
--- a/modules/Bio/EnsEMBL/DBSQL/RepeatFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/RepeatFeatureAdaptor.pm
@@ -21,7 +21,7 @@ my @repeats = @{$rfa->fetch_all_by_Slice($slice)};
=head1 DESCRIPTION
This is an adaptor for the retrieval and storage of RepeatFeature objects
-from the RepeatFeature database. Most of the implementation is in the
+from the database. Most of the implementation is in the
superclass BaseFeatureAdaptor.
=head1 AUTHOR - James Gilbert
@@ -65,6 +65,7 @@ use vars qw(@ISA);
Returntype : reference to a list of Bio::EnsEMBL::RepeatFeatures.
Exceptions : throw on bad argument
Caller : Slice::get_all_RepeatFeatures
+ Status : Stable
=cut
@@ -325,12 +326,13 @@ sub _objs_from_sth {
Arg [1] : list of Bio::EnsEMBL::RepeatFeatures $repeat_feature_id
the list of repeat features to store in the database
- Example : $repeat_feature_adaptor->store(1234, @repeat_features);
+ Example : $repeat_feature_adaptor->store(@repeat_features);
Description: stores a repeat feature in the database
Returntype : none
Exceptions : if the repeat features do not have attached sequences
or if repeat_consensus are not present
Caller : general
+ Status : Stable
=cut
@@ -460,6 +462,7 @@ sub store {
Returntype : list of ints
Exceptions : none
Caller : ?
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm
index 486ec2955c..f51f3af04e 100644
--- a/modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm
@@ -56,6 +56,7 @@ our $SEQ_CACHE_MAX = (2 ** $SEQ_CHUNK_PWR) * $SEQ_CACHE_SZ;
Returntype : Bio::EnsEMBL:DBSQL::SequenceAdaptor
Exceptions : none
Caller : DBAdaptor::get_SequenceAdaptor
+ Status : Stable
=cut
@@ -100,6 +101,7 @@ sub new {
Returntype : string
Exceptions : endBasePair should be less or equal to length of slice
Caller : Bio::EnsEMBL::Slice::seq(), Slice::subseq()
+ Status : Stable
=cut
@@ -292,6 +294,7 @@ sub _fetch_seq {
Returntype : none
Exceptions : throw if the database insert fails
Caller : sequence loading scripts
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/DBSQL/SimpleFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/SimpleFeatureAdaptor.pm
index 93f69dfc9f..de698999b8 100644
--- a/modules/Bio/EnsEMBL/DBSQL/SimpleFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/SimpleFeatureAdaptor.pm
@@ -42,13 +42,14 @@ use Bio::EnsEMBL::Utils::Exception qw(throw warning);
Arg [1] : list of Bio::EnsEMBL::SimpleFeatures @sf
the simple features to store in the database
- Example : $simple_feature_adaptor->store(1234, @simple_feats);
+ Example : $simple_feature_adaptor->store(@simple_feats);
Description: Stores a list of simple feature objects in the database
Returntype : none
Exceptions : thrown if @sf is not defined, if any of the features do not
have an attached slice.
- or if any elements of @sf are not Bio::EnsEMBL::SeqFeatures
+ or if any elements of @sf are not Bio::EnsEMBL::SimpleFeatures
Caller : general
+ Status : Stable
=cut
@@ -112,6 +113,7 @@ sub store{
Returntype : list of listrefs of strings
Exceptions : none
Caller : internal
+ Status : Stable
=cut
@@ -131,6 +133,7 @@ sub _tables {
Returntype : list of strings
Exceptions : none
Caller : internal
+ Status : Stable
=cut
@@ -152,6 +155,7 @@ sub _columns {
Returntype : list reference to Bio::EnsEMBL::SimpleFeature objects
Exceptions : none
Caller : internal
+ Status : Stable
=cut
@@ -300,6 +304,7 @@ sub _objs_from_sth {
Returntype : list of ints
Exceptions : none
Caller : ?
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
index 84df4a3d80..4a8cf533a3 100644
--- a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
@@ -163,6 +163,7 @@ sub new {
throw if invalid coord_system_name is provided
throw if start > end is provided
Caller : general
+ Status : Stable
=cut
@@ -341,6 +342,7 @@ sub fetch_by_region {
Returntype : Bio::EnsEMBL::Slice or undef
Exceptions : throw if incorrent arg provided
Caller : Pipeline
+ Status : Stable
=cut
@@ -386,6 +388,7 @@ sub fetch_by_name {
Returntype : Bio::EnsEMBL::Slice or undef
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -445,6 +448,7 @@ sub fetch_by_seq_region_id {
Exceptions : throw if the seq_region of the slice is not in the db
throw if incorrect arg provided
Caller : BaseFeatureAdaptor
+ Status : Stable
=cut
@@ -535,6 +539,7 @@ sub get_seq_region_id {
Returntype : listref of Bio::EnsEMBL::Slices
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -666,8 +671,9 @@ sub fetch_all {
Usage :
Function: create a Slice representing a series of bands
Example :
- Returns :
+ Returns : Bio::EnsEMBL::Slice
Args : the band name
+ Status : Stable
=cut
@@ -696,8 +702,9 @@ sub fetch_by_band {
Usage :
Function: create a Slice representing a series of bands
Example :
- Returns :
+ Returns : Bio::EnsEMBL::Slice
Args : the band name
+ Status : Stable
=cut
@@ -740,6 +747,7 @@ sub fetch_by_chr_band {
Returntype : Bio::EnsEMBL::Slice
Exceptions : Thrown if the exon is not in the database.
Caller : general
+ Status : Stable
=cut
@@ -772,6 +780,7 @@ sub fetch_by_exon_stable_id{
Returntype : Bio::EnsEMBL::Slice
Exceptions : Thrown if the transcript is not in the database.
Caller : general
+ Status : Stable
=cut
@@ -807,6 +816,7 @@ sub fetch_by_transcript_stable_id{
Exceptions : throw on incorrect args
throw if transcript is not in database
Caller : general
+ Status : Stable
=cut
@@ -842,6 +852,7 @@ sub fetch_by_transcript_id {
Exceptions : throw on incorrect args
throw if transcript does not exist
Caller : general
+ Status : Stable
=cut
@@ -879,6 +890,7 @@ sub fetch_by_gene_stable_id {
throw if feature argument is not provided
Caller : fetch_by_gene_stable_id, fetch_by_transcript_stable_id,
fetch_by_gene_id, fetch_by_transcript_id
+ Status : Stable
=cut
@@ -962,6 +974,7 @@ sub fetch_by_Feature{
Warning if multiple features with the specified attribute type
and value exist in the database.
Caller : webcode
+ Status : Stable
=cut
@@ -999,6 +1012,7 @@ sub fetch_by_misc_feature_attribute {
Returntype : [[start,end,$slice][]]
Exceptions : none
Caller : BaseFeatureAdaptor
+ Status : Stable
=cut
@@ -1163,6 +1177,7 @@ sub fetch_normalized_slice_projection {
throw if slice argument is not passed
throw if the slice end is not equal to seq_region_length
Caller : database loading scripts
+ Status : Stable
=cut
@@ -1258,6 +1273,7 @@ sub store {
Returntype : DBD::sth
Exceptions : none
Caller : internal, convenience method
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/DBSQL/SupportingFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/SupportingFeatureAdaptor.pm
index c2b6b57f1a..661e45e34a 100644
--- a/modules/Bio/EnsEMBL/DBSQL/SupportingFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/SupportingFeatureAdaptor.pm
@@ -48,6 +48,7 @@ use vars qw(@ISA);
Exceptions : warning if $exon is not in the database (i.e. dbID not defined)
throw if a retrieved supporting feature is of unknown type
Caller : Bio::EnsEMBL::Exon
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
index e984a9549e..29dc358d70 100644
--- a/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
@@ -74,7 +74,7 @@ use Bio::EnsEMBL::Utils::Exception qw( deprecate throw warning );
# Returntype : list of listrefs of strings
# Exceptions : none
# Caller : internal
-
+# Status : Stable
sub _tables {
my $self = shift;
@@ -93,6 +93,7 @@ sub _tables {
# Returntype : list of strings
# Exceptions : none
# Caller : internal
+# Status : Stable
sub _columns {
my $self = shift;
@@ -122,6 +123,7 @@ sub _left_join {
Returntype : Bio::EnsEMBL::Transcript
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -156,6 +158,7 @@ sub fetch_by_stable_id{
Returntype : Bio::EnsEMBL::Transcript
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -191,6 +194,7 @@ sub fetch_by_translation_stable_id {
Returntype : Bio::EnsEMBL::Transcript or undef
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -226,6 +230,7 @@ sub fetch_by_translation_id {
Returntype : listref Bio::EnsEMBL::Transcript
Exceptions : none
Caller : Gene->get_all_Transcripts()
+ Status : Stable
=cut
@@ -288,6 +293,7 @@ sub fetch_all_by_Gene {
Returntype : reference to list of transcripts
Exceptions : thrown if exon cannot be placed on transcript slice
Caller : Slice::get_all_Transcripts
+ Status : Stable
=cut
@@ -406,6 +412,7 @@ sub fetch_all_by_Slice {
Returntype : reference to a list of transcripts
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -431,6 +438,7 @@ sub fetch_all_by_external_name {
Returntype : Bio::EnsEMBL::Transcript
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -452,6 +460,7 @@ sub fetch_by_display_label {
Returntype : Bio::EnsEMBL::Transcript
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -491,6 +500,7 @@ sub fetch_all_by_exon_stable_id {
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -751,6 +761,7 @@ sub store {
Returntype : listref of strings
Exceptions : none
Caller : domainview? , GeneView
+ Status : Stable
=cut
@@ -802,6 +813,7 @@ sub get_Interpro_by_transid {
Exceptions : throw on incorrect arguments
warning if transcript is not in this database
Caller : GeneAdaptor::remove
+ Status : Stable
=cut
@@ -895,6 +907,7 @@ sub remove {
warn if the method is called on a transcript that does not exist
in the database.
Caller : general
+ Status : Stable
=cut
@@ -938,6 +951,7 @@ sub update {
Returntype : list of ints
Exceptions : none
Caller : ?
+ Status : Stable
=cut
@@ -956,6 +970,7 @@ sub list_dbIDs {
Returntype : listref of ints
Exceptions : none
Caller : ?
+ Status : Stable
=cut
@@ -975,6 +990,7 @@ sub list_stable_ids {
# Returntype : listref of Bio::EnsEMBL::Transcripts in target coord system
# Exceptions : none
# Caller : internal
+# Status : Stable
sub _objs_from_sth {
my ($self, $sth, $mapper, $dest_slice) = @_;
diff --git a/modules/Bio/EnsEMBL/DBSQL/TranscriptSupportingFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/TranscriptSupportingFeatureAdaptor.pm
index 2f6cd1c4b8..337f41c2e0 100644
--- a/modules/Bio/EnsEMBL/DBSQL/TranscriptSupportingFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/TranscriptSupportingFeatureAdaptor.pm
@@ -48,6 +48,7 @@ use vars qw(@ISA);
Exceptions : warning if $transcript is not in the database (i.e. dbID not defined)
throw if a retrieved supporting feature is of unknown type
Caller : Bio::EnsEMBL::Transcript
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm
index 84dec0d084..26435c945c 100644
--- a/modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm
@@ -65,6 +65,7 @@ use Bio::EnsEMBL::Utils::Exception qw( throw warning deprecate );
Returntype : Bio::EnsEMBL::Translation
Exceptions : throw on incorrect argument
Caller : Transcript
+ Status : Stable
=cut
@@ -149,6 +150,9 @@ sub fetch_by_Transcript {
Returntype : reference to a list of Translations
Exceptions : none
Caller : general
+ Status : Medium Risk
+ : At some time may be deprecated to instead use
+ : TranscriptAdaptor::fetch_all_by_external_name
=cut
@@ -187,6 +191,7 @@ sub fetch_all_by_external_name {
thrown if only partial stable id information is present (e.g.
identifier but not version number)
Caller : Transcript::store
+ Status : Stable
=cut
@@ -291,6 +296,7 @@ sub store {
Exceptions : throw on incorrect arguments
warning if translation is not in this database
Caller : TranscriptAdaptor::remove
+ Status : Stable
=cut
@@ -348,6 +354,7 @@ sub remove {
Returntype : list of ints
Exceptions : none
Caller : ?
+ Status : Stable
=cut
@@ -367,6 +374,7 @@ sub list_dbIDs {
Returntype : reference to a list of strings
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -392,6 +400,7 @@ sub list_stable_ids {
Exceptions : warning if an additional (old style) Transcript argument is
provided
Caller : ?
+ Status : Stable
=cut
@@ -416,12 +425,12 @@ sub fetch_by_dbID {
}
-=head2 fetch_by_dbID
+=head2 fetch_by_stable_id
- Arg [1] : int $dbID
- The internal identifier of the Translation to obtain
- Example : $translation = $translation_adaptor->fetch_by_dbID(1234);
- Description: This fetches a Translation object via its internal id. This
+ Arg [1] : string $stable_id
+ The stable identifier of the Translation to obtain
+ Example : $translation = $translation_adaptor->fetch_by_stable_id("ENSP00001");
+ Description: This fetches a Translation object via its stable id. This
is only debatably useful since translations do not make much
sense outside of the context of their Translation. Consider
using fetch_by_Transcript instead.
@@ -430,6 +439,7 @@ sub fetch_by_dbID {
Exceptions : warning if an additional (old style) Transcript argument is
provided
Caller : ?
+ Status : Stable
=cut
@@ -461,6 +471,7 @@ sub fetch_by_stable_id {
Returntype : Reference to list of Bio::EnsEMBL::Translations
Exceptions : None
Caller : general
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/DensityFeature.pm b/modules/Bio/EnsEMBL/DensityFeature.pm
index bb44014c55..962e89bbf4 100644
--- a/modules/Bio/EnsEMBL/DensityFeature.pm
+++ b/modules/Bio/EnsEMBL/DensityFeature.pm
@@ -75,6 +75,7 @@ use vars qw(@ISA);
Returntype : Bio::EnsEMBL::DensityFeature
Exceptions : throw if invalid density value type is provided
Caller : general
+ Status : Stable
=cut
@@ -107,6 +108,19 @@ sub new {
return $self;
}
+
+=head2 new_fast
+
+ Arg [...] : none
+ Example : $feature = Bio::EnsEMBL::DensityFeature->new_fast();
+ Description: Creates a new density feature.
+ Returntype : Bio::EnsEMBL::DensityFeature
+ Exceptions : none
+ Caller : general
+ Status : Stable
+
+=cut
+
sub new_fast{
my $caller = shift;
@@ -128,6 +142,7 @@ sub new_fast{
Returntype : int (always 0)
Exceptions : warning if an attempt is made to set the strand
Caller : general
+ Status : Stable
=cut
@@ -149,6 +164,7 @@ sub strand {
Returntype : float
Exceptions : throw if a negative density value is provided
Caller : general
+ Status : Stable
=cut
@@ -176,6 +192,7 @@ sub density_value {
Returntype : Bio::EnsEMBL::Analysis
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -200,6 +217,7 @@ sub analysis {
Returntype : Bio::EnsEMBL::DensityType
Exceptions : if object passed is not of type DensityType
Caller : general
+ Status : Stable
=cut
@@ -228,6 +246,7 @@ sub density_type{
Function:
Returns : this objects scaled value
Args : newvalue (optional)
+ Status : Stable
=cut
@@ -249,6 +268,7 @@ sub scaledvalue{
Function:
Returns : this object's url
Args : newvalue (optional)
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/DensityFeatureSet.pm b/modules/Bio/EnsEMBL/DensityFeatureSet.pm
index bf89efc5d1..cb8b07e449 100644
--- a/modules/Bio/EnsEMBL/DensityFeatureSet.pm
+++ b/modules/Bio/EnsEMBL/DensityFeatureSet.pm
@@ -52,6 +52,8 @@ use Data::Dumper;
Returntype : Bio::EnsEMBL::DensityFeatureSet
Exceptions : throw if invalid density value type is provided
Caller : general
+ Status : Stable
+
=cut
sub new {
@@ -84,7 +86,7 @@ sub new {
range (i.e. from min to max rather than absolute numbers).
Returns : value of _stretch
Args : newvalue (optional)
-
+ Status : Stable
=cut
@@ -104,6 +106,7 @@ sub stretch{
scaled in proportion.
Returns : scale_to_fit value
Args : newvalue (optional)
+ Status : Stable
=cut
@@ -122,6 +125,7 @@ sub scale_to_fit{
Function:
Returns : value of colour
Args : newvalue (optional)
+ Status : Stable
=cut
@@ -141,6 +145,7 @@ sub colour{
Function:
Returns : value of label
Args : newvalue (optional)
+ Status : Stable
=cut
@@ -160,6 +165,7 @@ sub label{
Function:
Returns : value of label2
Args : newvalue (optional)
+ Status : Stable
=cut
@@ -181,6 +187,7 @@ sub label2{
Returntype : reference to a list of DensityFeatures
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -225,6 +232,7 @@ sub get_all_binvalues{
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -240,6 +248,7 @@ sub max_value{ $_[0]->{'max_value'};}
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -256,6 +265,7 @@ sub min_value{ $_[0]->{'min_value'};}
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/DensityType.pm b/modules/Bio/EnsEMBL/DensityType.pm
index 68edb7d89c..e9ca13a4a0 100644
--- a/modules/Bio/EnsEMBL/DensityType.pm
+++ b/modules/Bio/EnsEMBL/DensityType.pm
@@ -7,7 +7,7 @@
=head1 NAME
-Bio::EnsEMBL::DensityType - A type representing a density, or precentage
+Bio::EnsEMBL::DensityType - A type representing a density, or percentage
coverage etc. in a given region.
=head1 SYNOPSIS
@@ -16,11 +16,11 @@ use Bio::EnsEMBL::DensityType;
$type = Bio::EnsEMBL::DensityType->new(-analysis => $analysis,
-blocksize => 1000000,
- -vlaue_type => $type);
+ -value_type => $type);
=head1 DESCRIPTION
-A density type represents a density, or precentage
+A density type represents a density, or percentage
coverage etc. in a given region.
@@ -61,6 +61,7 @@ use vars qw(@ISA);
valuetype must be 'sum' or 'ratio',
valid analysis object must be passed
Caller : general
+ Status : Stable
=cut
@@ -104,6 +105,7 @@ sub new {
Returntype : Bio::EnsEMBL::Analysis
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -128,6 +130,7 @@ sub analysis{
Returntype : float
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -146,6 +149,7 @@ sub value_type{
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/DnaDnaAlignFeature.pm b/modules/Bio/EnsEMBL/DnaDnaAlignFeature.pm
index 7948e4d8d8..a458ed4e0c 100644
--- a/modules/Bio/EnsEMBL/DnaDnaAlignFeature.pm
+++ b/modules/Bio/EnsEMBL/DnaDnaAlignFeature.pm
@@ -38,6 +38,7 @@ use Bio::LocatableSeq;
Returntype : int
Exceptions : none
Caller : Bio::EnsEMBL::BaseAlignFeature
+ Status : Stable
=cut
@@ -56,6 +57,7 @@ sub _hit_unit {
Returntype : int
Exceptions : none
Caller : Bio::EnsEMBL::BaseAlignFeature
+ Status : Stable
=cut
@@ -79,6 +81,7 @@ sub _query_unit {
Returntype : Bio::EnsEMBL::DnaDnaAlignFeature object
Exceptions :
Caller :
+ Status : Stable
=cut
@@ -196,6 +199,7 @@ sub restrict_between_positions {
the second corresponds to hseq
Exceptions :
Caller :
+ Status : Stable
=cut
@@ -272,6 +276,7 @@ sub alignment_strings {
Returntype : a Bio::SimpleAlign object
Exceptions :
Caller :
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/DnaPepAlignFeature.pm b/modules/Bio/EnsEMBL/DnaPepAlignFeature.pm
index 63a124ef0c..3952b5ae35 100644
--- a/modules/Bio/EnsEMBL/DnaPepAlignFeature.pm
+++ b/modules/Bio/EnsEMBL/DnaPepAlignFeature.pm
@@ -41,6 +41,7 @@ use strict;
Returntype : Bio::EnsEMBL::DnaPepAlignFeature
Exceptions : none
Caller : Bio::EnsEMBL::DBSQL::ProteinAlignFeatureAdaptor
+ Status : Stable
=cut
@@ -60,6 +61,8 @@ sub new_fast {
Returntype : int
Exceptions : none
Caller : Bio::EnsEMBL::BaseAlignFeature
+ Status : Stable
+
=cut
@@ -77,6 +80,8 @@ sub _hit_unit {
Returntype : int
Exceptions : none
Caller : Bio::EnsEMBL::BaseAlignFeature
+ Status : Stable
+
=cut
diff --git a/modules/Bio/EnsEMBL/Exon.pm b/modules/Bio/EnsEMBL/Exon.pm
index 112e97336d..4b1a88e4b1 100755
--- a/modules/Bio/EnsEMBL/Exon.pm
+++ b/modules/Bio/EnsEMBL/Exon.pm
@@ -65,12 +65,34 @@ use Bio::EnsEMBL::Utils::Argument qw( rearrange );
=head2 new
- Args : see SUPERCLASS B<Bio::EnsEMBL::Feature>
+ Arg [-SLICE]: Bio::EnsEMBL::SLice - Represents the sequence that this
+ feature is on. The coordinates of the created feature are
+ relative to the start of the slice.
+ Arg [-START]: The start coordinate of this feature relative to the start
+ of the slice it is sitting on. Coordinates start at 1 and
+ are inclusive.
+ Arg [-END] : The end coordinate of this feature relative to the start of
+ the slice it is sitting on. Coordinates start at 1 and are
+ inclusive.
+ Arg [-STRAND]: The orientation of this feature. Valid values are 1,-1,0.
+ Arg [-SEQNAME] : A seqname to be used instead of the default name of the
+ of the slice. Useful for features that do not have an
+ attached slice such as protein features.
+ Arg [-dbID] : (optional) internal database id
+ Arg [-ADAPTOR]: (optional) Bio::EnsEMBL::DBSQL::BaseAdaptor
+ Arg [-PHASE] :(optional) the phase.
+ Arg [-END_PHASE]:(optional) the end phase
+ Arg [-STABLE_ID]:(optional) the stable id of the exon
+ Arg [-VERSION] :(optional) the version
+ Arg [-CREATED_DATE] :(optional) the created date
+ Arg [-MODIFIED_DATE]:(optional) the last midifeid date
+
Example : none
Description: create an Exon object
Returntype : Bio::EnsEMBL::Exon
- Exceptions : none
+ Exceptions : if phase is not valid (i.e. 0,1, 2 -1)
Caller : general
+ Status : Stable
=cut
@@ -85,7 +107,7 @@ sub new {
rearrange( [ "PHASE", "END_PHASE", "STABLE_ID", "VERSION",
"CREATED_DATE", "MODIFIED_DATE" ], @_ );
- $self->{'phase'} = $phase;
+ $self->phase($phase) if (defined $phase); # make sure phase is valid.
$self->{'end_phase'} = $end_phase;
$self->{'stable_id'} = $stable_id;
$self->{'version'} = $version;
@@ -106,8 +128,9 @@ sub new {
Example : none
Description: create an Exon object
Returntype : Bio::EnsEMBL::Exon
- Exceptions : none
+ Exceptions : throws if end < start
Caller : general, creation in Bio::EnsEMBL::Lite::GeneAdaptor
+ Status : Stable
=cut
@@ -148,6 +171,7 @@ sub new_fast {
Exceptions : warning if end_phase is called without an argument and the
value is not set.
Caller : general
+ Status : Stable
=cut
@@ -170,8 +194,15 @@ sub end_phase {
=head2 phase
- my $phase = $exon->phase;
- $exon->phase(2);
+ Arg [1] : (optional) int $phase
+ Example : my $phase = $exon->phase;
+ $exon->phase(2);
+ Description: Gets/Sets the phase of the exon.
+ Returntype : int
+ Exceptions : throws if phase is not (0, 1 2 or -1).
+ Caller : general
+ Status : Stable
+
Get or set the phase of the Exon, which tells the
translation machinery, which makes a peptide from
@@ -229,6 +260,7 @@ sub phase {
Exceptions : thrown if an arg is passed
thrown if frame cannot be calculated due to a bad phase value
Caller : general
+ Status : Stable
=cut
@@ -273,6 +305,7 @@ sub frame {
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -294,6 +327,7 @@ sub start {
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -315,6 +349,7 @@ sub end {
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -336,6 +371,7 @@ sub strand {
Returntype : Bio::EnsEMBL::Slice
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -363,6 +399,7 @@ sub slice {
Returntype : none
Exceptions : Thrown is invalid arguments are provided
Caller : general
+ Status : Stable
=cut
@@ -384,6 +421,7 @@ sub move {
Returntype : Bio::EnsEMBL::Exon
Exceptions : wrong parameters
Caller : general
+ Status : Stable
=cut
@@ -426,6 +464,7 @@ sub transform {
Returntype : Bio::EnsEMBL::Gene
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -454,7 +493,7 @@ sub transfer {
=head2 add_supporting_features
- Arg [1] : Bio::EnsEMBL::SeqFeatureI $feature
+ Arg [1] : Bio::EnsEMBL::Feature $feature
Example : $exon->add_supporting_features(@features);
Description: Adds a list of supporting features to this exon.
Duplicate features are not added.
@@ -463,10 +502,11 @@ sub transfer {
get_all_supporting_features call will not retrieve supporting
features from the database.
Returntype : none
- Exceptions : throw if any of the features are not SeqFeatureIs
+ Exceptions : throw if any of the features are not Feature
throw if any of the features are not in the same coordinate
system as the exon
Caller : general
+ Status : Stable
=cut
@@ -516,6 +556,7 @@ sub add_supporting_features {
Returntype : listreference of Bio::EnsEMBL::BaseAlignFeature objects
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -535,7 +576,10 @@ sub get_all_supporting_features {
=head2 find_supporting_evidence
- Arg [1] : Bio::EnsEMBL::SeqFeatureI $features
+# This method is only for genebuild backwards compatibility.
+# Avoid using it if possible
+
+ Arg [1] : Bio::EnsEMBL::Feature $features
The list of features to search for supporting (i.e. overlapping)
evidence.
Arg [2] : (optional) boolean $sorted
@@ -549,6 +593,7 @@ sub get_all_supporting_features {
Returntype : none
Exceptions : none
Caller : general
+ Status : Medium Risk
=cut
@@ -583,6 +628,7 @@ sub find_supporting_evidence {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -593,12 +639,35 @@ sub stable_id {
}
+=head2 created_date
+
+ Arg [1] : string $created_date
+ Example : none
+ Description: get/set for attribute created_date
+ Returntype : string
+ Exceptions : none
+ Caller : general
+ Status : Stable
+
+=cut
+
sub created_date {
my $self = shift;
$self->{'created_date'} = shift if ( @_ );
return $self->{'created_date'};
}
+=head2 modified_date
+
+ Arg [1] : string $modified_date
+ Example : none
+ Description: get/set for attribute modified_date
+ Returntype : string
+ Exceptions : none
+ Caller : general
+ Status : Stable
+
+=cut
sub modified_date {
my $self = shift;
@@ -616,6 +685,7 @@ sub modified_date {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -635,6 +705,7 @@ sub version {
Returntype : Bio::EnsEMBL::Exon
Exceptions : none
Caller : Transcript->get_all_translateable_Exons()
+ Status : Stable
=cut
@@ -677,6 +748,7 @@ sub adjust_start_end {
Returntype : Bio::Seq
Exceptions : thrown if transcript argument is not provided
Caller : general
+ Status : Stable
=cut
@@ -738,6 +810,7 @@ sub peptide {
warning if exon does not have attatched slice
warning if exon strand is not defined (or 0)
Caller : general
+ Status : Stable
=cut
@@ -789,6 +862,7 @@ sub seq {
a unique hash value are set
set
Caller : general
+ Status : Stable
=cut
@@ -841,6 +915,7 @@ sub hashkey {
Returntype : string
Exceptions : none
Caller : web drawing code
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/Feature.pm b/modules/Bio/EnsEMBL/Feature.pm
index a797a34b5e..df971dab04 100644
--- a/modules/Bio/EnsEMBL/Feature.pm
+++ b/modules/Bio/EnsEMBL/Feature.pm
@@ -78,6 +78,8 @@ use vars qw(@ISA);
Arg [-SEQNAME] : A seqname to be used instead of the default name of the
of the slice. Useful for features that do not have an
attached slice such as protein features.
+ Arg [-dbID] : (optional) internal database id
+ Arg [-ADAPTOR]: (optional) Bio::EnsEMBL::DBSQL::BaseAdaptor
Example : $feature = Bio::EnsEMBL::Feature->new(-start => 1,
-end => 100,
-strand => 1,
@@ -86,8 +88,9 @@ use vars qw(@ISA);
Description: Constructs a new Bio::EnsEMBL::Feature. Generally subclasses
of this method are instantiated, rather than this class itself.
Returntype : Bio::EnsEMBL::Feature
- Exceptions : Thrown on invalid -SLICE, -ANALYSIS, -STRAND arguments
+ Exceptions : Thrown on invalid -SLICE, -ANALYSIS, -STRAND ,-ADAPTOR arguments
Caller : general, subclass constructors
+ Status : Stable
=cut
@@ -152,6 +155,7 @@ sub new {
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -176,6 +180,7 @@ sub start {
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -199,6 +204,7 @@ sub end {
Returntype : int
Exceptions : thrown if an invalid strand argument is passed
Caller : general
+ Status : Stable
=cut
@@ -232,6 +238,7 @@ sub strand {
Returntype : none
Exceptions : Thrown is invalid arguments are provided
Caller : general
+ Status : Stable
=cut
@@ -266,6 +273,7 @@ sub move {
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -287,6 +295,7 @@ sub length {
Returntype : Bio::EnsEMBL::Analysis
Exceptions : thrown if an invalid argument is passed
Caller : general
+ Status : Stable
=cut
@@ -318,6 +327,7 @@ sub analysis {
Returntype : Bio::EnsEMBL::Slice
Exceptions : thrown if an invalid argument is passed
Caller : general
+ Status : Stable
=cut
@@ -363,6 +373,7 @@ sub slice {
Exceptions : thrown if an invalid coordinate system is provided
warning if Feature is not attached to a slice
Caller : general, transfer()
+ Status : Stable
=cut
@@ -466,6 +477,7 @@ sub transform {
Exceptions : throw on incorrect argument
throw if feature does not have attached slice
Caller : general, transform()
+ Status : Stable
=cut
@@ -563,7 +575,7 @@ sub transfer {
}
Description: Returns the results of 'projecting' this feature onto another
coordinate system. This is useful to see where a feature
- where a feature would lie in a coordinate system in which it
+ would lie in a coordinate system in which it
crosses a boundary.
This method returns a reference to a list of
@@ -584,8 +596,9 @@ sub transfer {
Returntype : list reference of Bio::EnsEMBL::ProjectionSegments
which can also be used as [$start,$end,$slice] triplets
- Exceptions : none
+ Exceptions : slice does not have an adaptor
Caller : general
+ Status : Stable
=cut
@@ -633,6 +646,7 @@ sub project {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -665,6 +679,7 @@ sub seqname {
Returntype : string
Exceptions : none
Caller : web drawing code
+ Status : Stable
=cut
@@ -685,6 +700,7 @@ sub display_id {
Slice.
Exceptions : warning if Feature does not have attached slice.
Caller : web drawing code
+ Status : Stable
=cut
@@ -720,6 +736,7 @@ sub feature_Slice {
Returntype : string or undef
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -740,6 +757,7 @@ sub seq_region_name {
Returntype : unsigned int or undef
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -762,6 +780,7 @@ sub seq_region_length {
Returntype : 1,0,-1 or undef
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -786,6 +805,7 @@ sub seq_region_strand {
Returntype : int or undef
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -817,6 +837,7 @@ sub seq_region_start {
Returntype : int or undef
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -842,10 +863,10 @@ sub seq_region_end {
Example : print $feature->coord_system_name()
Description: Gets the name of the coord_system which this feature is on.
Returns undef if this Feature is not on a slice.
- Function :
- Returntype:
- Exceptions:
- Caller :
+ Returntype : string or undef
+ Exceptions : none
+ Caller : general
+ Status : Stable
=cut
@@ -867,6 +888,7 @@ sub coord_system_name {
Returntype : undef or string
Exceptions : warning if this feature is not stranded
Caller : general
+ Status : Stable
=cut
@@ -917,6 +939,7 @@ sub seq {
Returntype : reference to list of features of the same type of this feature.
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -1144,7 +1167,7 @@ sub id {
favour and use a simple one line comparison instead:
$overlaps = ($f1->end() >= $f2->start() &&
$f1->start() <= $f2->end());
-
+ Status : At Risk
=cut
sub overlaps {
diff --git a/modules/Bio/EnsEMBL/FeaturePair.pm b/modules/Bio/EnsEMBL/FeaturePair.pm
index 25806ddc6f..36bb07afbc 100755
--- a/modules/Bio/EnsEMBL/FeaturePair.pm
+++ b/modules/Bio/EnsEMBL/FeaturePair.pm
@@ -102,11 +102,12 @@ use Bio::EnsEMBL::Utils::Exception qw(throw deprecate warning);
-percent_id => 92.0,
-hseqname => 'ALUSX10.1',
-analysis => $analysis);
-Description: Creates a new Bio::EnsEMBL::FeaturePair object
+ Description: Creates a new Bio::EnsEMBL::FeaturePair object
Returntype : Bio::EnsEMBL::FeaturePair
Exceptions : throw if start > end
throw if invalid strand is provided
Caller : general
+ Status : Stable
=cut
@@ -188,6 +189,7 @@ sub new {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -207,6 +209,7 @@ sub hseqname {
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -225,6 +228,7 @@ sub hstart{
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -244,6 +248,7 @@ sub hend{
Returntype : 0,1,-1
Exceptions : thrown
Caller : general
+ Status : Stable
=cut
@@ -273,6 +278,7 @@ sub hstrand{
Returntype : Bio::EnsEMBL::Slice
Exceptions : thrown if an invalid argument is passed
Caller : general
+ Status : Stable
=cut
@@ -300,6 +306,7 @@ sub hslice {
Returntype : string or undef
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -321,6 +328,7 @@ sub hseq_region_name {
Returntype : 1,0,-1 or undef
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -344,6 +352,7 @@ sub hseq_region_strand {
Returntype : int or undef
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -375,6 +384,7 @@ sub hseq_region_start {
Returntype : int or undef
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -401,6 +411,7 @@ sub hseq_region_end {
Returntype : float
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -420,6 +431,7 @@ sub score{
Returntype : float
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -440,6 +452,7 @@ sub percent_id {
Returntype : string
Execeptions: none
Caller : general
+ Status : Stable
=cut
@@ -459,6 +472,7 @@ sub species{
Returntype : string
Execeptions: none
Caller : general
+ Status : Stable
=cut
@@ -477,6 +491,7 @@ sub hspecies{
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -495,6 +510,7 @@ sub coverage {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -513,6 +529,7 @@ sub hcoverage {
Returntype : float
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -534,6 +551,7 @@ sub p_value{
Returntype : string
Exceptions : none
Caller : web drawing code
+ Status : Stable
=cut
@@ -551,6 +569,7 @@ sub display_id {
Returntype : int
Execeptions: none
Caller : general
+ Status : Stable
=cut
@@ -571,6 +590,7 @@ sub identical_matches{
Returntype : int
Execeptions: none
Caller : general
+ Status : Stable
=cut
@@ -591,6 +611,7 @@ sub positive_matches{
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -611,6 +632,7 @@ sub group_id {
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/Gene.pm b/modules/Bio/EnsEMBL/Gene.pm
index 05d0590105..0d15e5bc19 100755
--- a/modules/Bio/EnsEMBL/Gene.pm
+++ b/modules/Bio/EnsEMBL/Gene.pm
@@ -40,15 +40,43 @@ use Bio::EnsEMBL::Utils::Exception qw(throw warning deprecate);
=head2 new
- Arg [start] : int $start
- Arg [end] : int $end
- Arg [strand] : 1,-1 $strand
- Arg [slice] : Bio::EnsEMBL::Slice $slice
+ Arg [-START] :
+ int - start postion of the gene
+ Arg [-END] :
+ int - end position of the gene
+ Arg [-STRAND] :
+ int - 1,-1 tehe strand the gene is on
+ Arg [-SLICE] :
+ Bio::EnsEMBL::Slice - the slice the gene is on
+ Arg [-STABLE_ID] :
+ string - the stable identifier of this gene
+ Arg [-VERSION] :
+ int - the version of the stable identifier of this gene
+ Arg [-EXTERNAL_NAME] :
+ string - the external database name associated with this gene
+ Arg [-EXTERNAL_DB] :
+ string - the name of the database the external name is from
+ Arg [-EXTERNAL_STATUS]:
+ string - the status of the external identifier
+ Arg [-DISPLAY_XREF]:
+ Bio::EnsEMBL::DBEntry - The external database entry that is used
+ to label this gene when it is displayed.
+ Arg [-CREATED_DATE]:
+ string - the date the gene was created
+ Arg [-MODIFIED_DATE]:
+ string - the date the gene was last modified
+ Arg [-DESCRIPTION]:
+ string - the genes description
+ Arg [-BIOTYPE]:
+ string - the biotype e.g. "protein_coding"
+ Arg [-CONFIDENCE]:
+ string - the gene confidence i.e. "KNOWN","NOVEL"
Example : $gene = Bio::EnsEMBL::Gene->new();
Description: Creates a new gene object
Returntype : Bio::EnsEMBL::Gene
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -98,6 +126,7 @@ sub new {
Returntype : 0,1
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -116,6 +145,7 @@ sub is_known{
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -146,6 +176,7 @@ sub external_name {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -165,6 +196,7 @@ sub confidence {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -185,6 +217,7 @@ sub source {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -215,6 +248,7 @@ sub external_db {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -243,6 +277,7 @@ sub external_status {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -265,6 +300,7 @@ sub description {
Returntype : none
Exceptions : thrown on incorrect argument type
Caller : general
+ Status : Stable
=cut
@@ -295,6 +331,7 @@ sub add_DBEntry {
Returntype : list reference to Bio::EnsEMBL::DBEntry objects
Exceptions : none
Caller : get_all_DBLinks, GeneAdaptor::store
+ Status : Stable
=cut
@@ -327,6 +364,7 @@ sub get_all_DBEntries {
Returntype : list reference to Bio::EnsEMBL::DBEntry objects
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -355,6 +393,7 @@ sub get_all_DBLinks {
Returntype : listref Bio::EnsEMBL::Exon
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -390,6 +429,7 @@ sub get_all_Exons {
]
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -456,6 +496,7 @@ sub get_all_homologous_Genes{
Returntype : string
Exceptions : none
Caller : general
+ Status : At Risk
=cut
@@ -507,6 +548,7 @@ sub type {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -529,6 +571,7 @@ sub biotype {
Returntype : none
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -556,6 +599,7 @@ sub add_Transcript {
Returntype : listref Bio::EnsEMBL::Transcript
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -585,6 +629,7 @@ sub get_all_Transcripts {
Returntype : listref of Bio::EnsEMBL::Gene
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -605,6 +650,7 @@ sub get_all_alt_alleles {
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -623,6 +669,7 @@ sub version{
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -633,12 +680,36 @@ sub stable_id{
}
+=head2 created_date
+
+ Arg [1] : (optional) string to be used for the created date
+ Example : none
+ Description: get/set for attribute created date
+ Returntype : string
+ Exceptions : none
+ Caller : general
+ Status : Stable
+
+=cut
+
sub created_date {
my $self = shift;
$self->{'created_date'} = shift if ( @_ );
return $self->{'created_date'};
}
+=head2 modified_date
+
+ Arg [1] : (optional) string to be used for the modified date
+ Example : none
+ Description: get/set for attribute modified date
+ Returntype : string
+ Exceptions : none
+ Caller : general
+ Status : Stable
+
+=cut
+
sub modified_date {
my $self = shift;
@@ -656,6 +727,7 @@ sub modified_date {
Returntype : Bio::EnsEMBL::Gene
Exceptions : wrong parameters
Caller : general
+ Status : Stable
=cut
@@ -695,6 +767,7 @@ sub transform {
Returntype : Bio::EnsEMBL::Gene
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -724,6 +797,7 @@ sub transfer {
Returntype : Bio::EnsEMBL::DBEntry
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -743,6 +817,7 @@ sub display_xref {
Returntype : none
Exceptions : none
Caller : internal
+ Status : Stable
=cut
@@ -800,6 +875,7 @@ sub recalculate_coordinates {
Returntype : string
Exceptions : none
Caller : web drawing code
+ Status : Stable
=cut
@@ -820,6 +896,7 @@ sub display_id {
Exceptions:
Caller :
Example : $dasref = $prot->get_all_DASFactories
+ Status : Stable
=cut
@@ -841,6 +918,7 @@ sub get_all_DASFactories {
Returntype : hashref of Bio::SeqFeatures
Exceptions : ?
Caller : webcode
+ Status : Stable
=cut
@@ -906,7 +984,7 @@ sub get_all_DASFeatures_by_slice{
Returntype : hashref of Bio::SeqFeatures
Exceptions : ?
Caller : webcode
-
+ Status : Stable
=cut
@@ -949,6 +1027,8 @@ sub get_all_DAS_Features{
Returntype : Listref of Bio::EnsEMBL::RegulatoryFeature
Exceptions : If arg is not of correct type.
Caller : ?
+ Status : At Risk
+ : regulatory features are under development
=cut
diff --git a/modules/Bio/EnsEMBL/GoXref.pm b/modules/Bio/EnsEMBL/GoXref.pm
index 404a057000..c5eb19e684 100644
--- a/modules/Bio/EnsEMBL/GoXref.pm
+++ b/modules/Bio/EnsEMBL/GoXref.pm
@@ -75,6 +75,7 @@ use strict;
Returntype : string
Exceptions : thrown if $linkage_type argument not supplied
Caller : DBEntryAdaptor
+ Status : Stable
=cut
@@ -97,6 +98,7 @@ sub add_linkage_type {
Returntype : none
Exceptions : none
Caller : geneview? general
+ Status : Stable
=cut
@@ -115,6 +117,7 @@ sub get_all_linkage_types {
Returntype : none
Exceptions : none
Caller : general
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/IdentityXref.pm b/modules/Bio/EnsEMBL/IdentityXref.pm
index 01b908235e..98cfd3f078 100644
--- a/modules/Bio/EnsEMBL/IdentityXref.pm
+++ b/modules/Bio/EnsEMBL/IdentityXref.pm
@@ -42,19 +42,22 @@ Post questions to the ensembl development list: <ensembl-dev@ebi.ac.uk>
package Bio::EnsEMBL::IdentityXref;
use vars qw(@ISA $AUTOLOAD);
use strict;
-
+use Bio::EnsEMBL::Utils::Argument qw( rearrange );
@ISA = qw( Bio::EnsEMBL::DBEntry );
=head2 new
- Arg [1] :
- Example :
- Description:
- Returntype :
- Exceptions :
- Caller :
+ Arg [...] : QUERY_IDENTITY TARGET_IDENTITY SCORE EVALUE CIGAR_LINE
+ : QUERY_START QUERY_END TRANSLATION_START TRANSLATION_END
+ : ANALYSIS pairs
+ Example : see synopsis
+ Description: Create a new Bio::EnsEMBL::IdentityXref object
+ Returntype : Bio::EnsEMBL::IdentityXref
+ Exceptions : none
+ Caller : general
+ Status : Stable
=cut
@@ -63,7 +66,7 @@ sub new {
my $self = $class->SUPER::new(@args);
my ($query_identity, $target_identity, $score, $evalue,
$cigar_line, $query_start, $query_end, $translation_start,
- $translation_end, $analysis ) = $self->_rearrange(
+ $translation_end, $analysis ) = rearrange(
[qw(QUERY_IDENTITY TARGET_IDENTITY SCORE EVALUE CIGAR_LINE
QUERY_START QUERY_END TRANSLATION_START TRANSLATION_END
ANALYSIS)], @args);
@@ -90,6 +93,7 @@ sub new {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -112,6 +116,7 @@ sub query_identity{
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -135,6 +140,7 @@ sub target_identity{
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -153,6 +159,7 @@ sub cigar_line {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -171,6 +178,7 @@ sub translation_start {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -189,6 +197,7 @@ sub translation_end {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -207,6 +216,7 @@ sub query_start {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -225,6 +235,7 @@ sub query_end {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -243,6 +254,7 @@ sub score {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -261,6 +273,7 @@ sub evalue {
Returntype : Bio::EnsEMBL::Analysis
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -283,6 +296,7 @@ sub analysis {
Returntype : Bio::EnsEMBL::Mapper
Exceptions : none
Caller : general, ProteinDAS subsystem
+ Status : Stable
=cut
@@ -353,6 +367,7 @@ sub get_mapper {
Returntype : listref of whatever was put in
Exceptions : none
Caller : general, ProteinDAS subsystem
+ Status : Stable
=cut
@@ -395,6 +410,7 @@ sub transform_feature {
Returntype : list of Coordinates/Gaps which represents the mapping
Exceptions : none
Caller : another way of doing ProteinDAS
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/Intron.pm b/modules/Bio/EnsEMBL/Intron.pm
index 71424598ee..af2fb46a46 100644
--- a/modules/Bio/EnsEMBL/Intron.pm
+++ b/modules/Bio/EnsEMBL/Intron.pm
@@ -37,10 +37,11 @@ use Bio::EnsEMBL::Utils::Argument qw( rearrange );
Args : exon1, exon2. The two exons to build the Intron from.
Example : $intron = new Bio::EnsEMBL::Intron($exon1, $exon2)
- Description: create an Intron object
+ Description: create an Intron object from two exons.
Returntype : Bio::EnsEMBL::Intron
Exceptions : exons not on the same strand or slice.
Caller : general
+ Status : Stable
=cut
@@ -89,6 +90,7 @@ sub new {
Returntype : Bio::EnsEMBL::Exon
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -107,6 +109,7 @@ sub prev_Exon {
Returntype : Bio::EnsEMBL::Exon
Exceptions : none
Caller : general
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/KaryotypeBand.pm b/modules/Bio/EnsEMBL/KaryotypeBand.pm
index 3811182a95..be88d7ad4a 100644
--- a/modules/Bio/EnsEMBL/KaryotypeBand.pm
+++ b/modules/Bio/EnsEMBL/KaryotypeBand.pm
@@ -85,6 +85,7 @@ use Bio::EnsEMBL::Utils::Exception qw(deprecate warning);
Returntype : Bio::EnsEMBL::KarytotypeBand
Exceptions : none
Caller : Bio::EnsEMBL::KaryotypeBandAdaptor
+ Status : Stable
=cut
@@ -110,6 +111,7 @@ sub new {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -129,6 +131,7 @@ sub name{
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -149,6 +152,7 @@ sub stain{
Returntype : int (always 0)
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -169,6 +173,7 @@ sub strand {
Returntype : none
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -190,6 +195,7 @@ sub move {
Returntype : string
Exceptions : none
Caller : web drawing code
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/Mapper.pm b/modules/Bio/EnsEMBL/Mapper.pm
index 87aad593cd..77f7ed7b74 100644
--- a/modules/Bio/EnsEMBL/Mapper.pm
+++ b/modules/Bio/EnsEMBL/Mapper.pm
@@ -71,6 +71,7 @@ use Bio::EnsEMBL::Utils::Exception qw(throw);
Returntype : Bio::EnsEMBL::Mapper
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -112,6 +113,7 @@ sub new {
Returntype : none
Exceptions : none
Caller : AssemblyMapper, ChainedAssemblyMapper
+ Status : Stable
=cut
@@ -144,8 +146,10 @@ sub flush {
Function generic map method
Returntype array of Bio::EnsEMBL::Mapper::Coordinate
and/or Bio::EnsEMBL::Mapper::Gap
- Exceptions none
+ Exceptions throw if start,end,strand,id or type are missing
+ or type not one of the coord systems
Caller Bio::EnsEMBL::Mapper
+ Status : Stable
=cut
@@ -320,6 +324,7 @@ sub map_coordinates{
Returntype : list of Bio::EnsEMBL::Mapper::Coordinate and/or Gap objects
Exceptions : none
Caller : map_coordinates()
+ Status : Stable
=cut
@@ -402,8 +407,9 @@ sub map_insert {
Function inferior map method. Will only do ungapped unsplit mapping.
Will return id, start, end strand in a list.
Returntype list of results
- Exceptions none
+ Exceptions throws if type is neither to or from coordinate systems
Caller Bio::EnsEMBL::AssemblyMapper
+ Status : Stable
=cut
@@ -482,8 +488,9 @@ sub fastmap {
'source' and 'target'. Returns 1 if the pair was added, 0 if it
was already in.
Returntype int 0,1
- Exceptions none
+ Exceptions throws if one or more of the 7 arguments are missing
Caller Bio::EnsEMBL::Mapper
+ Status : Stable
=cut
@@ -534,6 +541,7 @@ sub add_map_coordinates{
Exceptions throw if 'to' and 'from' from both Bio::EnsEMBL::Mappers
are incompatible
Caller $mapper->methodname()
+ Status : Stable
=cut
@@ -584,8 +592,10 @@ sub add_Mapper{
coordinates to be transformed *from*
Function list all pairs of mappings in a region
Returntype list of Bio::EnsEMBL::Mapper::Pair
- Exceptions none
+ Exceptions throws if one or more of the 4 arguments are missing
+ throws if start > end
Caller Bio::EnsEMBL::Mapper
+ Status : Stable
=cut
@@ -656,6 +666,7 @@ sub list_pairs{
Returntype Bio::EnsEMBL::Mapper::Unit
Exceptions none
Caller Bio::EnsEMBL::Mapper
+ Status : Stable
=cut
@@ -678,15 +689,17 @@ sub from{
}
-# _dump
-#
-# Arg 1 *FileHandle $fh
-# Function convenience dump function
-# possibly useful for debugging
-# Returntype none
-# Exceptions none
-# Caller internal
-#
+=head2 _dump
+
+ Arg 1 : *FileHandle $fh
+ Description : convenience dump function
+ : possibly useful for debugging
+ Returntype : none
+ Exceptions : none
+ Caller : internal
+ Status : Medium Risk
+
+=cut
sub _dump{
my ($self,$fh) = @_;
@@ -705,15 +718,16 @@ sub _dump{
}
-# _sort
-#
-# Function sort function so that all
-# mappings are sorted by
-# chromosome start
-# Returntype none
-# Exceptions none
-# Caller internal
-#
+=head2 _sort
+
+ Description: sort function so that all mappings are sorted by
+ chromosome start
+ Returntype : none
+ Exceptions : none
+ Caller : internal
+ Status : Stable
+
+=cut
sub _sort{
my ($self) = @_;
@@ -804,15 +818,17 @@ sub _merge_pairs {
}
-# _is_sorted
-#
-# Arg 1 int $sorted
-# Function toggle for whether the (internal)
-# map data are sorted
-# Returntype int
-# Exceptions none
-# Caller internal
-#
+=head2 _is_sorted
+
+ Arg 1 : (optional) int $sorted
+ Description: getter.setter for togglewhether the (internal)
+ : map data are sorted
+ Returntype : int
+ Exceptions : none
+ Caller : internal
+ Status : Stable
+
+=cut
sub _is_sorted {
my ($self, $value) = @_;
diff --git a/modules/Bio/EnsEMBL/MiscFeature.pm b/modules/Bio/EnsEMBL/MiscFeature.pm
index ec41942076..e6e79e1713 100644
--- a/modules/Bio/EnsEMBL/MiscFeature.pm
+++ b/modules/Bio/EnsEMBL/MiscFeature.pm
@@ -100,6 +100,36 @@ use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Feature);
+=head2 new
+
+ Arg [-SLICE]: Bio::EnsEMBL::SLice - Represents the sequence that this
+ feature is on. The coordinates of the created feature are
+ relative to the start of the slice.
+ Arg [-START]: The start coordinate of this feature relative to the start
+ of the slice it is sitting on. Coordinates start at 1 and
+ are inclusive.
+ Arg [-END] : The end coordinate of this feature relative to the start of
+ the slice it is sitting on. Coordinates start at 1 and are
+ inclusive.
+ Arg [-STRAND]: The orientation of this feature. Valid values are 1,-1,0.
+ Arg [-SEQNAME] : A seqname to be used instead of the default name of the
+ of the slice. Useful for features that do not have an
+ attached slice such as protein features.
+ Arg [-dbID] : (optional) internal database id
+ Arg [-ADAPTOR]: (optional) Bio::EnsEMBL::DBSQL::BaseAdaptor
+ Example : $feature = Bio::EnsEMBL::MiscFeature->new(-start => 1,
+ -end => 100,
+ -strand => 1,
+ -slice => $slice,
+ -analysis => $analysis);
+ Description: Constructs a new Bio::EnsEMBL::Feature. Generally subclasses
+ of this method are instantiated, rather than this class itself.
+ Returntype : Bio::EnsEMBL::MiscFeature
+ Exceptions : Thrown on invalid -SLICE, -ANALYSIS, -STRAND ,-ADAPTOR arguments
+ Caller : general, subclass constructors
+ Status : Stable
+
+=cut
sub new {
@@ -113,6 +143,18 @@ sub new {
}
+=head2 new_fast
+
+ Arg [...] : hashref to bless as new MiscFeature
+ Example : $miscfeature = Bio::EnsEMBL::MiscFeature->new_fast();
+ Description: Creates a new Miscfeature.
+ Returntype : Bio::EnsEMBL::MiscFeature
+ Exceptions : none
+ Caller : general
+ Status : Stable
+
+=cut
+
sub new_fast {
my $class = shift;
@@ -133,6 +175,7 @@ sub new_fast {
Returntype : none
Exceptions : throw on wrong argument type
Caller : general
+ Status : Stable
=cut
@@ -159,6 +202,7 @@ sub add_Attribute {
Exceptions : throw if the set arg is not provided,
throw if the set to be added does not have a code
Caller : general
+ Status : Stable
=cut
@@ -188,6 +232,7 @@ sub add_MiscSet {
Returntype : listref of Bio::EnsEMBL::MiscSet
Exceptions : throw if the code arg is not provided
Caller : general
+ Status : Stable
=cut
@@ -216,6 +261,7 @@ sub get_all_MiscSets {
Returntype : listref of Bio::EnsEMBL::Attribute
Exceptions :
Caller : general
+ Status : Stable
=cut
@@ -234,12 +280,44 @@ sub get_all_Attributes {
}
}
+=head2 get_all_attribute_values
+
+ Arg [1] : string $code
+ The code of the Attribute object values to retrieve
+ Example : @attributes_vals = @{$misc_feature->get_all_attribute_values('name')};
+ Description: Retrieves a list of Attribute object values for given code or all
+ of the associated Attributes.
+ Returntype : listref of values
+ Exceptions :
+ Caller : general
+ Status : Stable
+
+=cut
+
sub get_all_attribute_values {
my $self = shift;
my $code = shift;
- my @results = map { uc( $_->code() ) eq uc( $code ) ? $_->value : () } @{$self->{'attributes'}};
+ my @results = map { uc( $_->code() ) eq uc( $code ) ? $_->value : () }
+ @{$self->{'attributes'}};
return \@results;
}
+
+=head2 get_scalar_attribute
+
+ Arg [1] : string $code
+ The code of the Attribute object values to retrieve
+ Example : $vals = $misc_feature->get_scalar_attribute('name');
+ Description: Retrieves a value for given code or all
+ of the associated Attributes.
+ Returntype : scalar value
+ Exceptions :
+ Caller : general
+ Status : Stable
+
+
+=cut
+
+
sub get_scalar_attribute {
my $self = shift;
my $code = shift;
@@ -257,6 +335,7 @@ sub get_scalar_attribute {
Returntype : string
Exceptions : none
Caller : web drawing code
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/MiscSet.pm b/modules/Bio/EnsEMBL/MiscSet.pm
index b92315033f..c1b04f88dd 100644
--- a/modules/Bio/EnsEMBL/MiscSet.pm
+++ b/modules/Bio/EnsEMBL/MiscSet.pm
@@ -77,6 +77,7 @@ use vars qw(@ISA);
Returntype : Bio::EnsEMBL::MiscSet
Exceptions : none
Caller : MiscFeatureAdaptor
+ Status : Stable
=cut
@@ -107,6 +108,7 @@ sub new {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -126,6 +128,7 @@ sub code{
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -145,6 +148,7 @@ sub name {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -164,6 +168,7 @@ sub description{
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/PepDnaAlignFeature.pm b/modules/Bio/EnsEMBL/PepDnaAlignFeature.pm
index d2787d441d..3a2dbd4d01 100644
--- a/modules/Bio/EnsEMBL/PepDnaAlignFeature.pm
+++ b/modules/Bio/EnsEMBL/PepDnaAlignFeature.pm
@@ -24,6 +24,16 @@ use strict;
@ISA = qw( Bio::EnsEMBL::BaseAlignFeature );
+=head2 transform
+
+ Arg [1] : none
+ Example : none
+ Description: Overwrites Bio:EnsEMBL:Feature->transform as
+ to give error message
+ Status : Stable
+
+=cut
+
sub transform {
my $self = shift;
@@ -31,10 +41,38 @@ sub transform {
" they are not on EnsEMBL coord system" );
}
+=head2 _hit_unit
+
+ Arg [1] : none
+ Example : none
+ Description: PRIVATE implementation of abstract superclass method. Returns
+ 3 as the 'unit' used for the hit sequence.
+ Returntype : int
+ Exceptions : none
+ Caller : Bio::EnsEMBL::BaseAlignFeature
+ Status : Stable
+
+
+=cut
+
sub _hit_unit {
return 3;
}
+=head2 _query_unit
+
+ Arg [1] : none
+ Example : none
+ Description: PRIVATE implementation of abstract superclass method. Returns
+ 1 as the 'unit' used for the query sequence.
+ Returntype : int
+ Exceptions : none
+ Caller : Bio::EnsEMBL::BaseAlignFeature
+ Status : Stable
+
+
+=cut
+
sub _query_unit {
return 1;
}
diff --git a/modules/Bio/EnsEMBL/PredictionExon.pm b/modules/Bio/EnsEMBL/PredictionExon.pm
index ae103db062..cfdd0083b0 100644
--- a/modules/Bio/EnsEMBL/PredictionExon.pm
+++ b/modules/Bio/EnsEMBL/PredictionExon.pm
@@ -15,7 +15,7 @@ ab initio prediction method
=head1 SYNOPSIS
- $ex = new Bio::EnsEMBL::Exon(-START => 100,
+ $exon = new Bio::EnsEMBL::PredictionExon(-START => 100,
-END => 200,
-STRAND => 1,
-SLICE => $slice,
@@ -69,9 +69,10 @@ use Bio::EnsEMBL::Utils::Argument qw( rearrange );
Args : see SUPERCLASS Bio::EnsEMBL::Exon
Example : none
Description: create an Exon object
- Returntype : Bio::EnsEMBL::Exon
+ Returntype : Bio::EnsEMBL::PredictionExon
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -101,6 +102,7 @@ sub new {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -121,6 +123,7 @@ sub score{
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -145,6 +148,7 @@ sub p_value{
Exceptions : warning if end_phase is called without an argument and the
value is not set.
Caller : general
+ Status : Stable
=cut
@@ -168,6 +172,7 @@ sub end_phase {
Returntype : Bio::EnsEMBL::Exon
Exceptions : wrong parameters
Caller : general
+ Status : Stable
=cut
@@ -201,6 +206,7 @@ sub transform {
Returntype : Bio::EnsEMBL::Gene
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -222,6 +228,7 @@ sub transfer {
Description: For compatibility with Bio::EnsEMBL::Exon
Does nothing.
Returntype : none
+ Status : Stable
=cut
@@ -233,6 +240,7 @@ sub add_supporting_features { }
Description: For compatibility with Bio::EnsEMBL::Exon
Does nothing and returns empty list
Returntype : empty list.
+ Status : Stable
=cut
@@ -244,6 +252,7 @@ sub get_all_supporting_features { return []; }
Description: For compatibility with Bio::EnsEMBL::Exon
Does nothing.
Returntype : empty list.
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/PredictionTranscript.pm b/modules/Bio/EnsEMBL/PredictionTranscript.pm
index 9a3ad61f69..5b451085f9 100644
--- a/modules/Bio/EnsEMBL/PredictionTranscript.pm
+++ b/modules/Bio/EnsEMBL/PredictionTranscript.pm
@@ -78,6 +78,7 @@ use Bio::EnsEMBL::Utils::Argument qw( rearrange );
Returntype : Bio::EnsEMBL::PredictionTranscript
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -109,6 +110,7 @@ sub new {
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -133,6 +135,7 @@ sub coding_region_start {
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -153,6 +156,7 @@ sub coding_region_end {
Returntype : listref of Bio::EnsEMBL::PredictionExons
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -172,6 +176,7 @@ sub get_all_translateable_Exons {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -195,12 +200,12 @@ sub display_label{
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
sub stable_id { return display_label(@_); }
-
sub get_all_DBEntries { return []; }
sub get_all_DBLinks { return []; }
@@ -228,6 +233,7 @@ sub is_known { return 0;}
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -279,6 +285,7 @@ sub translation {
Returntype: a Bio::Seq as in transcript->translate()
Exceptions: none
Caller : general
+ Status : Stable
=cut
@@ -313,6 +320,7 @@ sub translate {
Returntype : int
Exceptions : none
Caller : five_prime_utr, get_all_snps, general
+ Status : Stable
=cut
@@ -332,6 +340,7 @@ sub cdna_coding_start { return 1; }
Returntype : int
Exceptions : none
Caller : five_prime_utr, get_all_snps, general
+ Status : Stable
=cut
@@ -354,6 +363,7 @@ sub cdna_coding_end {
Returntype : Bio::EnsEMBL::PredictionTranscript
Exceptions : wrong parameters
Caller : general
+ Status : Stable
=cut
@@ -395,6 +405,7 @@ sub transform {
Returntype : Bio::EnsEMBL::PredictionTranscript
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -427,6 +438,7 @@ sub transfer {
Returntype : a list reference to Bio::EnsEMBL::Exon objects
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -450,6 +462,7 @@ sub get_all_Exons {
Returntype : string
Exceptions : none
Caller : web drawing code
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/ProjectionSegment.pm b/modules/Bio/EnsEMBL/ProjectionSegment.pm
index af780d1eea..03f64a321e 100644
--- a/modules/Bio/EnsEMBL/ProjectionSegment.pm
+++ b/modules/Bio/EnsEMBL/ProjectionSegment.pm
@@ -67,6 +67,7 @@ package Bio::EnsEMBL::ProjectionSegment;
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -85,6 +86,7 @@ sub from_start {
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -104,6 +106,7 @@ sub from_end {
Returntype : Bio::EnsEMBL::Slice
Exceptions : none
Caller : general
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/ProteinFeature.pm b/modules/Bio/EnsEMBL/ProteinFeature.pm
index f72aacdeed..9155e18edb 100755
--- a/modules/Bio/EnsEMBL/ProteinFeature.pm
+++ b/modules/Bio/EnsEMBL/ProteinFeature.pm
@@ -59,6 +59,7 @@ use vars qw(@ISA);
Returntype : Bio::EnsEMBL::FeaturePair
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -80,6 +81,15 @@ sub new {
}
+=head2 strand
+
+ Arg [1] : Ignored
+ Description: Overwrites Bio::EnsEMBL::Feature->strand to not allow
+ : the strand to be set.
+ Returntype : int
+ Status : Stable
+
+=cut
#do not allow the strand to be set
sub strand {
@@ -98,6 +108,7 @@ sub strand {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -118,6 +129,7 @@ sub idesc{
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/Registry.pm b/modules/Bio/EnsEMBL/Registry.pm
index 87f784ed07..b227d97c4d 100644
--- a/modules/Bio/EnsEMBL/Registry.pm
+++ b/modules/Bio/EnsEMBL/Registry.pm
@@ -50,9 +50,6 @@ So if before we had
my $sfa = $self->adaptor()->db()->get_db_adaptor('blast');
We now want to change this to
- my $sfa = Bio::EnsEMBL::Registry->get_db($self->adaptor->db,'blast');
-
-OR preferably if the blast adaptor was set up in configure
my $sfa = Bio::EnsEMBL::Registry->get_adaptor("Human","core","blast");
@@ -125,27 +122,27 @@ use vars qw(%registry_register);
Example : Bio::EnsEMBL::Registry->load_all();
Returntype : none
Exceptions : none
-
+ Status : Stable
=cut
sub load_all{
my $class = shift;
- my $web_reg = shift;
+ my $conf_file = shift;
if(defined($registry_register{'seen'})){
print STDERR "Clearing previuosly loaded configuration from Registry\n";
$class->clear();
}
$registry_register{'seen'}=1;
- if(defined($web_reg)){
- print STDERR "Loading conf from site defs file ".$web_reg."\n";
- if(-e $web_reg){
- unless (my $return = do $web_reg ){
+ if(defined($conf_file)){
+ print STDERR "Loading conf from site defs file ".$conf_file."\n";
+ if(-e $conf_file){
+ unless (my $return = do $conf_file ){
throw "Error in Configuration\n $!\n";
}
# other wise it gets done again by the web initialisation stuff
- delete $INC{$web_reg};
+ delete $INC{$conf_file};
}
}
elsif(defined($ENV{ENSEMBL_REGISTRY}) and -e $ENV{ENSEMBL_REGISTRY}){
@@ -181,7 +178,7 @@ sub load_all{
Example : Bio::EnsEMBL::Registry->clear();
Returntype : none
Exceptions : none
-
+ Status : Stable
=cut
@@ -197,7 +194,7 @@ sub clear{
}
#
-# add ons.
+# db adaptors. (for backwards compatibillity)
#
=head2 add_db
@@ -208,7 +205,11 @@ sub clear{
Example : Bio::EnsEMBL::Registry->add_db($db, "lite", $dba);
Returntype : none
Exceptions : none
-
+ Status : At Risk.
+ : This is here for backwards compatibillity only and may be removed
+ : eventually. Solution is to make sure the db and the adaptor have
+ : the same species and the call is then no longer needed.
+
=cut
sub add_db{
@@ -227,6 +228,10 @@ sub add_db{
Example : my $db = Bio::EnsEMBL::Registry->remove_db($db, "lite");
Returntype : adaptor
Exceptions : none
+ Status : At Risk.
+ : This is here for backwards compatibillity only and may be removed
+ : eventually. Solution is to make sure the db and the adaptor have
+ : the same species and the call is then no longer needed.
=cut
@@ -246,6 +251,10 @@ sub remove_db{
Example : my $db = Bio::EnsEMBL::Registry->get_db("Human", "core", "lite");
Returntype : adaptor
Exceptions : none
+ Status : At Risk.
+ : This is here for backwards compatibillity only and may be removed
+ : eventually. Solution is to make sure the db and the adaptor have
+ : the same species then call get_DBAdaptor instead.
=cut
@@ -266,6 +275,11 @@ sub get_db{
Example : my $db = Bio::EnsEMBL::Registry->get_all_db_adaptors($db);
Returntype : adaptor
Exceptions : none
+ Status : At Risk.
+ : This is here for backwards compatibillity only and may be removed
+ : eventually. Solution is to make sure the dbs all have
+ : the same species then call get_all_DBAdaptors(-species => "human");
+
=cut
@@ -302,6 +316,8 @@ sub get_all_db_adaptors{
Example : Bio::EnsEMBL::Registry->add_DBAdaptor("Human", "core", $dba);
Returntype : none
Exceptions : none
+ caller : internal
+ Status : Stable
=cut
@@ -337,6 +353,7 @@ sub add_DBAdaptor{
Example : $dba = Bio::EnsEMBL::Registry->get_DBAdaptor("Human", "core");
Returntype : DBAdaptor
Exceptions : none
+ Status : Stable
=cut
@@ -359,6 +376,7 @@ sub get_DBAdaptor{
: @human_dbas = @{Bio::EnsEMBL::Registry->get_all_DBAdaptors(-species => 'human')};
Returntype : list of DBAdaptors
Exceptions : none
+ Status : Stable
=cut
@@ -389,6 +407,7 @@ sub get_all_DBAdaptors{
Returntype : reference to list of DBAdaptors
Exceptions : none.
Example : @dba = @{Bio::EnsEMBL::Registry->get_all_DBAdaptors_by_connection($dbc);
+ Status : Stable
=cut
@@ -418,6 +437,7 @@ sub get_all_DBAdaptors_by_connection{
Example : Bio::EnsEMBL::Registry->add_DNAAdaptor("Human", "core", $dnaAdap);
Returntype : none
Exceptions : none
+ Status : Stable
=cut
@@ -442,6 +462,7 @@ sub add_DNAAdaptor{
Example : $dnaAdap = Bio::EnsEMBL::Registry->get_DNAAdaptor("Human", "core");
Returntype : adaptor
Exceptions : none
+ Status : Stable
=cut
@@ -472,6 +493,8 @@ sub get_DNAAdaptor{
Example : Bio::EnsEMBL::Registry->add_adaptor("Human", "core", "Gene", $adap);
Returntype : none
Exceptions : none
+ Caller : internal
+ Status : Stable
=cut
@@ -531,6 +554,7 @@ sub add_adaptor{
Example : $adap = Bio::EnsEMBL::Registry->get_adaptor("Human", "core", "Gene");
Returntype : adaptor
Exceptions : none
+ Status : Stable
=cut
@@ -577,8 +601,9 @@ sub get_adaptor{
Arg [TYPE] : (optional) string
type to get adaptors for
Example : @adaps = @{Bio::EnsEMBL::Registry->get_all_adaptors()};
- Returntype : list of adaptors
+ Returntype : ref to list of adaptors
Exceptions : none
+ Status : Stable
=cut
@@ -650,6 +675,7 @@ sub get_all_adaptors{
Description: add alternative name for the species.
Returntype : none
Exceptions : none
+ Status : Stable
=cut
@@ -666,6 +692,7 @@ sub add_alias{
Description: get proper species name.
Returntype : species name
Exceptions : none
+ Status : Stable
=cut
@@ -686,6 +713,7 @@ sub get_alias{
Description: does the species name exist.
Returntype : 1 if exists else 0
Exceptions : none
+ Status : Stable
=cut
@@ -705,6 +733,7 @@ sub alias_exists{
not being used on each database.
Returntype : none
Exceptions : none
+ Status : Stable
=cut
@@ -724,6 +753,7 @@ sub set_disconnect_when_inactive{
Description: disconnect from all the databases.
Returntype : none
Exceptions : none
+ Status : Stable
=cut
@@ -754,6 +784,7 @@ sub disconnect_all {
Description: change username and password on one or more databases
Returntype : none
Exceptions : none
+ Status : Stable
=cut
@@ -799,6 +830,7 @@ my $self = shift;
can find on a database instance into the registry.
Exceptions : None.
+ Status : Stable
=cut
@@ -1005,6 +1037,7 @@ sub load_registry_with_web_adaptors{
Example : $merged = Bio::EnsEMBL::Registry->set_default_track("Human","core");
Returntype : none
Exceptions : none
+ Status : At Risk.
=cut
@@ -1024,6 +1057,7 @@ sub set_default_track{
Example : $merged = Bio::EnsEMBL::Registry->set_default_track("Human","core");
Returntype : int
Exceptions : none
+ Status : At Risk.
=cut
@@ -1048,6 +1082,7 @@ sub default_track{
Returntype : none
Exceptions : none
Called by : UserConfig.pm
+ Status : At Risk.
=cut
diff --git a/modules/Bio/EnsEMBL/RegulatoryFactor.pm b/modules/Bio/EnsEMBL/RegulatoryFactor.pm
index 9227cfca25..f8edfee8f5 100644
--- a/modules/Bio/EnsEMBL/RegulatoryFactor.pm
+++ b/modules/Bio/EnsEMBL/RegulatoryFactor.pm
@@ -26,6 +26,8 @@ use vars qw(@ISA);
Returntype : Bio::EnsEMBL::RegulatoryFactor
Exceptions : none
Caller : RegulatoryFactor
+ Status : At Risk
+ : under development
=cut
@@ -61,6 +63,8 @@ sub new_fast {
Returntype : string
Exceptions : none
Caller : general
+ Status : At Risk
+ : under development
=cut
@@ -79,6 +83,8 @@ sub name {
Returntype : int
Exceptions : none
Caller : general
+ Status : At Risk
+ : under development
=cut
diff --git a/modules/Bio/EnsEMBL/RegulatoryFeature.pm b/modules/Bio/EnsEMBL/RegulatoryFeature.pm
index ec463c3a2e..f39814313f 100644
--- a/modules/Bio/EnsEMBL/RegulatoryFeature.pm
+++ b/modules/Bio/EnsEMBL/RegulatoryFeature.pm
@@ -67,6 +67,8 @@ use Bio::EnsEMBL::Utils::Argument qw(rearrange);
Description: Constructs a new Bio::EnsEMBL::RegulatoryFeature.
Exceptions : Thrown on invalid -SLICE, -ANALYSIS, -STRAND arguments
Caller : general, subclass constructors
+ Status : At Risk
+ : under development
=cut
@@ -101,6 +103,8 @@ sub new_fast {
Returntype : Bio::EnsEMBL::RegulatoryFactor
Exceptions : none
Caller : general
+ Status : At Risk
+ : under development
=cut
@@ -130,6 +134,8 @@ sub factor {
Returntype : string
Exceptions : none
Caller : web drawing code
+ Status : At Risk
+ : under development
=cut
@@ -148,6 +154,8 @@ sub name {
Returntype : listREF of Bio::EnsEMBL::RegulatoryFeatures
Exceptions : none
Caller : ?
+ Status : At Risk
+ : under development
=cut
@@ -188,6 +196,8 @@ sub regulated_transcripts {
Returntype : listREF of Bio::EnsEMBL::RegulatoryFeatures
Exceptions : none
Caller : ?
+ Status : At Risk
+ : under development
=cut
diff --git a/modules/Bio/EnsEMBL/RepeatConsensus.pm b/modules/Bio/EnsEMBL/RepeatConsensus.pm
index 7212ddd4a9..590bc02894 100644
--- a/modules/Bio/EnsEMBL/RepeatConsensus.pm
+++ b/modules/Bio/EnsEMBL/RepeatConsensus.pm
@@ -30,10 +30,11 @@ use vars qw(@ISA);
-LENGTH => '4',
-DBID => 1023,
-ADAPTOR => $rc_adaptor);
- Description: Creates a new Bio::EnsEMBL::RepeatFeature object
- Returntype : Bio::EnsEMBL::RepeatFeature
+ Description: Creates a new Bio::EnsEMBL::RepeatConsensus object
+ Returntype : Bio::EnsEMBL::RepeatConsensus
Exceptions : none
Caller : RepeatFeatureAdaptors
+ Status : Stable
=cut
@@ -57,6 +58,18 @@ sub new {
}
+=head2 new_fast
+
+ Arg [1] : hashref to bless as a new RepeatConsensus
+
+ Description: Creates a new Bio::EnsEMBL::RepeatConsensus object
+ Returntype : Bio::EnsEMBL::RepeatConsensus
+ Exceptions : none
+ Caller : internal
+ Status : Stable
+
+=cut
+
sub new_fast {
my $class = shift;
my $hashref = shift;
@@ -72,6 +85,7 @@ sub new_fast {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -90,6 +104,7 @@ sub name {
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -109,6 +124,7 @@ sub length {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -146,6 +162,7 @@ sub repeat_type {
Returntype : string
Exceptions : none
Caller : general
+ Status : Medium risk
=cut
@@ -186,6 +203,7 @@ sub repeat_consensus {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/RepeatFeature.pm b/modules/Bio/EnsEMBL/RepeatFeature.pm
index fe0f40fe17..3be6842dc3 100644
--- a/modules/Bio/EnsEMBL/RepeatFeature.pm
+++ b/modules/Bio/EnsEMBL/RepeatFeature.pm
@@ -110,6 +110,7 @@ sub new_fast {
Returntype : Bio::EnsEMBL::RepeatFeature
Exceptions : none
Caller : RepeatFeatureAdaptors
+ Status : Stable
=cut
@@ -140,6 +141,7 @@ sub new {
Returntype : Bio::EnsEMBL::RepeatConsensus
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -170,6 +172,7 @@ sub repeat_consensus {
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -188,6 +191,7 @@ sub hstart {
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -208,6 +212,7 @@ sub score {
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -227,7 +232,8 @@ sub hend {
features.
Returntype : int
Exceptions : none
- Caller :
+ Caller : general
+ Status : Stable
=cut
@@ -247,6 +253,7 @@ sub hstrand {
Returntype : string
Exceptions : none
Caller : web drawing code
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/RepeatMaskedSlice.pm b/modules/Bio/EnsEMBL/RepeatMaskedSlice.pm
index 8c32e05b2f..6995c1a72c 100644
--- a/modules/Bio/EnsEMBL/RepeatMaskedSlice.pm
+++ b/modules/Bio/EnsEMBL/RepeatMaskedSlice.pm
@@ -82,6 +82,7 @@ use vars qw(@ISA);
Returntype : Bio::EnsEMBL::RepeatMaskedSlice
Exceptions : none
Caller : RawComputes (PredictionTranscript creation code).
+ Status : Stable
=cut
@@ -119,6 +120,7 @@ sub new {
Returntype : reference to list of strings
Exceptions : none
Caller : seq() method
+ Status : Stable
=cut
@@ -145,6 +147,7 @@ sub repeat_mask_logic_names {
Returntype : boolean
Exceptions : none
Caller : seq() method
+ Status : Stable
=cut
@@ -176,6 +179,7 @@ sub soft_mask {
Returntype : hash reference
Exceptions : none
Caller : seq() and subseq() methods
+ Status : Stable
=cut
@@ -195,6 +199,7 @@ sub not_default_masking_cases {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -237,6 +242,7 @@ sub seq {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/SeqEdit.pm b/modules/Bio/EnsEMBL/SeqEdit.pm
index 726f1f7dfa..cdd3d7abc8 100644
--- a/modules/Bio/EnsEMBL/SeqEdit.pm
+++ b/modules/Bio/EnsEMBL/SeqEdit.pm
@@ -101,8 +101,10 @@ use Bio::EnsEMBL::Utils::Exception qw(throw);
Description: Constructs a SeqEdit representing a single edit to a
sequence, such as an rna modification or a selenocysteine.
Returntype : Bio::EnsEMBL::SeqEdit
- Exceptions : none
+ Exceptions : throws if attribute set and other args aswell
+ throws if start and end not set correctly of attribure not set
Caller : general
+ Status : Stable
=cut
@@ -177,6 +179,7 @@ sub new {
Returntype : int
Exceptions : none
Caller : Transcript, Translation
+ Status : Stable
=cut
@@ -209,8 +212,9 @@ sub start {
E.g. start = 1, end = 1 is a replacement of the first base but
start = 1, end = 0 is an insert BEFORE the first base.
Returntype : int
- Exceptions : none
+ Exceptions : throws if end <= 0
Caller : Transcript, Translation
+ Status : Stable
=cut
@@ -243,6 +247,7 @@ sub end {
Returntype : string
Exceptions : none
Caller : Transcript, Translation
+ Status : Stable
=cut
@@ -265,6 +270,7 @@ sub alt_seq {
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -286,6 +292,7 @@ sub length_diff {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -306,6 +313,7 @@ sub name {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -325,6 +333,7 @@ sub code {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -348,6 +357,7 @@ sub description {
Returntype : Bio::EnsEMBL::Attribute
Exceptions : warning if start/end or alt_seq properties are not defined
Caller : general
+ Status : Stable
=cut
@@ -390,6 +400,7 @@ sub get_Attribute {
Returntype : reference to the same sequence that was passed in
Exceptions : none
Caller : Transcript, Translation
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/SimpleFeature.pm b/modules/Bio/EnsEMBL/SimpleFeature.pm
index 29ce41214a..5d3debb60e 100644
--- a/modules/Bio/EnsEMBL/SimpleFeature.pm
+++ b/modules/Bio/EnsEMBL/SimpleFeature.pm
@@ -73,6 +73,7 @@ use Bio::EnsEMBL::Utils::Argument qw(rearrange);
Returntype : Bio::EnsEMBL::Feature
Exceptions : Thrown on invalid -SLICE, -ANALYSIS, -STRAND arguments
Caller : general, subclass constructors
+ Status : Stable
=cut
@@ -92,6 +93,18 @@ sub new {
}
+=head2 new_fast
+
+ Arg [1] : hashref to be blessed
+ Description: Construct a new Bio::EnsEMBL::Feature using the hashref.
+ Exceptions : none
+ Returntype : Bio::EnsEMBL::Feature
+ Caller : general, subclass constructors
+ Status : Stable
+
+=cut
+
+
sub new_fast {
my $class = shift;
my $hashref = shift;
@@ -108,6 +121,7 @@ sub new_fast {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -131,6 +145,7 @@ sub display_label{
Returntype : string
Exceptions : none
Caller : web drawing code
+ Status : Stable
=cut
@@ -150,6 +165,7 @@ sub display_id {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/Slice.pm b/modules/Bio/EnsEMBL/Slice.pm
index 6b2ebb168d..e509f926a3 100644
--- a/modules/Bio/EnsEMBL/Slice.pm
+++ b/modules/Bio/EnsEMBL/Slice.pm
@@ -58,24 +58,19 @@ package Bio::EnsEMBL::Slice;
use vars qw(@ISA);
use strict;
-use Bio::EnsEMBL::Root; # included for backwards compatibility
-
use Bio::PrimarySeqI;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Utils::Exception qw(throw deprecate warning stack_trace_dump);
-
use Bio::EnsEMBL::RepeatMaskedSlice;
use Bio::EnsEMBL::Utils::Sequence qw(reverse_comp);
-
use Bio::EnsEMBL::ProjectionSegment;
use Bio::EnsEMBL::Registry;
my $reg = "Bio::EnsEMBL::Registry";
-# inheritance to Bio::EnsEMBL::Root will eventually be removed
-@ISA = qw(Bio::EnsEMBL::Root Bio::PrimarySeqI);
+@ISA = qw(Bio::PrimarySeqI);
=head2 new
@@ -85,7 +80,8 @@ my $reg = "Bio::EnsEMBL::Registry";
string SEQ_REGION_NAME,
int START,
int END,
- string VERSION (optional, defaults to '')
+ int SEQ_REGION_LENGTH, (optional)
+ string SEQ (optional)
int STRAND, (optional, defaults to 1)
Bio::EnsEMBL::DBSQL::SliceAdaptor ADAPTOR (optional)
Example : $slice = Bio::EnsEMBL::Slice->new(-coord_system => $cs,
@@ -109,8 +105,9 @@ my $reg = "Bio::EnsEMBL::Registry";
(with the exception of the adaptor) may not be altered. To
change the attributes a new slice must be created.
Returntype : Bio::EnsEMBL::Slice
- Exceptions : none
+ Exceptions : throws if start, end, coordsystem or seq_region_name not specified or not of the correct type
Caller : general, Bio::EnsEMBL::SliceAdaptor
+ Status : Stable
=cut
@@ -188,8 +185,9 @@ sub new {
Description: Getter/Setter for the slice object adaptor used
by this slice for database interaction.
Returntype : Bio::EnsEMBL::DBSQL::SliceAdaptor
- Exceptions : none
+ Exceptions : thorws if argument passed is not a SliceAdaptor
Caller : general
+ Status : Stable
=cut
@@ -225,6 +223,7 @@ sub adaptor{
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -245,6 +244,7 @@ sub seq_region_name {
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -262,6 +262,7 @@ sub seq_region_length {
Returntype : Bio::EnsEMBL::CoordSystem
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -281,6 +282,7 @@ sub coord_system {
Returntype: string or undef
Exceptions: none
Caller : general
+ Status : Stable
=cut
@@ -301,6 +303,7 @@ sub coord_system_name {
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -322,6 +325,7 @@ sub centrepoint {
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -345,6 +349,7 @@ sub start {
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -364,6 +369,7 @@ sub end {
Returntype : int (either 1 or -1)
Exceptions : none
Caller : general, invert
+ Status : Stable
=cut
@@ -389,6 +395,7 @@ sub strand{
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -416,6 +423,7 @@ sub name {
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -436,6 +444,7 @@ sub length {
Returntype : Bio::EnsEMBL::Slice
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -464,6 +473,7 @@ sub invert {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -500,6 +510,7 @@ sub seq {
Exceptions : end should be at least as big as start
strand must be set
Caller : general
+ Status : Stable
=cut
@@ -565,6 +576,7 @@ sub subseq {
Returntype : hashref
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -638,6 +650,7 @@ sub get_base_count {
can also be used as [$start,$end,$slice] triplets
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -831,6 +844,7 @@ sub _constrain_to_region {
Returntype : Bio::EnsEMBL::Slice
Exceptions : warning if an attempt is made to contract the slice below 1bp
Caller : general
+ Status : Stable
=cut
@@ -907,6 +921,7 @@ sub expand {
Returntype : Bio::EnsEMBL::Slice or undef if arguments are wrong
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -969,6 +984,7 @@ sub sub_Slice {
Returntype : Bio::EnsEMBL::Slice
Exceptions : warning if called when sequence of Slice has been set manually.
Caller : general
+ Status : Stable
=cut
@@ -1008,6 +1024,7 @@ sub seq_region_Slice {
Returntype : int or undef if slices does not have attached adaptor
Exceptions : warning if slice is not associated with a SliceAdaptor
Caller : assembly loading scripts, general
+ Status : Stable
=cut
@@ -1034,6 +1051,7 @@ sub get_seq_region_id {
Returntype : listref Bio::EnsEMBL::Attribute
Exceptions : warning if slice does not have attached adaptor
Caller : general
+ Status : Stable
=cut
@@ -1080,6 +1098,7 @@ sub get_all_Attributes {
Returntype : listref of Bio::EnsEMBL::PredictionTranscript
Exceptions : warning if slice does not have attached adaptor
Caller : none
+ Status : Stable
=cut
@@ -1115,6 +1134,7 @@ sub get_all_PredictionTranscripts {
Returntype : listref of Bio::EnsEMBL::DnaDnaAlignFeatures
Exceptions : warning if slice does not have attached adaptor
Caller : general
+ Status : Stable
=cut
@@ -1153,7 +1173,7 @@ sub get_all_DnaAlignFeatures {
Arg [2] : (optional) float $score
The mimimum score of the features to retrieve
Arg [3] : (optional) string $dbtype
- The name of an attached datbase to retrieve features from
+ The name of an attached database to retrieve features from
instead.
Example : @dna_pep_align_feats = @{$slice->get_all_ProteinAlignFeatures};
Description: Retrieves the DnaPepAlignFeatures which overlap this slice with
@@ -1164,6 +1184,7 @@ sub get_all_DnaAlignFeatures {
Returntype : listref of Bio::EnsEMBL::DnaPepAlignFeatures
Exceptions : warning if slice does not have attached adaptor
Caller : general
+ Status : Stable
=cut
@@ -1210,6 +1231,7 @@ sub get_all_ProteinAlignFeatures {
Returntype : listref of Bio::EnsEMBL::BaseAlignFeatures
Exceptions : warning if slice does not have attached adaptor
Caller : general
+ Status : Stable
=cut
@@ -1242,6 +1264,7 @@ sub get_all_SimilarityFeatures {
Returntype : listref of Bio::EnsEMBL::SimpleFeatures
Exceptions : warning if slice does not have attached adaptor
Caller : general
+ Status : Stable
=cut
@@ -1275,6 +1298,7 @@ sub get_all_SimpleFeatures {
Returntype : listref of Bio::EnsEMBL::RepeatFeatures
Exceptions : warning if slice does not have attached adaptor
Caller : general
+ Status : Stable
=cut
@@ -1300,6 +1324,8 @@ sub get_all_RepeatFeatures {
ReturnType : Bio::EnsEMBL::Variation::LDFeatureContainer
Exceptions : none
Caller : contigview, snpview
+ Status : At Risk
+ : Variation database is under development.
=cut
@@ -1337,6 +1363,8 @@ sub get_all_LD_values{
ReturnType : listref of Bio::EnsEMBL::Variation::VariationFeature
Exceptions : none
Caller : contigview, snpview
+ Status : At Risk
+ : Variation database is under development.
=cut
@@ -1373,6 +1401,8 @@ sub get_all_VariationFeatures{
ReturnType : listref of Bio::EnsEMBL::Variation::VariationFeature
Exceptions : none
Caller : contigview, snpview, ldview
+ Status : At Risk
+ : Variation database is under development.
=cut
@@ -1479,6 +1509,7 @@ sub get_all_SNPs_transcripts {
Returntype : listref of Bio::EnsEMBL::Genes
Exceptions : none
Caller : none
+ Status : Stable
=cut
@@ -1531,6 +1562,7 @@ sub get_all_Genes{
Returntype : listref of Bio::EnsEMBL::Genes
Exceptions : none
Caller : genebuilder
+ Status : Stable
=cut
@@ -1563,6 +1595,7 @@ sub get_all_Genes_by_type{
Returntype : reference to a list of Bio::EnsEMBL::Transcripts
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -1590,6 +1623,7 @@ sub get_all_Transcripts {
Returntype : reference to a list of Bio::EnsEMBL::Exons
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -1614,6 +1648,7 @@ sub get_all_Exons {
Returntype : listref Bio::EnsEMBL::Map::QtlFeature
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -1646,6 +1681,7 @@ sub get_all_QtlFeatures {
Returntype : listref oif Bio::EnsEMBL::KaryotypeBands
Exceptions : none
Caller : general, contigview
+ Status : Stable
=cut
@@ -1695,6 +1731,7 @@ sub get_all_KaryotypeBands {
Returntype : Bio::EnsEMBL::RepeatMaskedSlice
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -1748,6 +1785,7 @@ sub get_repeatmasked_seq {
Returntype : none
Exceptions : none
Caller : seq
+ Status : Stable
=cut
@@ -1821,6 +1859,7 @@ sub _mask_features {
Returntype : listref of Bio::EnsEMBL::SeqFeatures
Exceptions : none
Caller : general (webby!)
+ Status : Stable
=cut
@@ -1860,6 +1899,7 @@ sub get_all_SearchFeatures {
Returntype : listref of Bio::EnsEMBL::AssemblyExceptionFeatures
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -1891,6 +1931,7 @@ sub get_all_AssemblyExceptionFeatures {
Returntype : listref of Bio::EnsEMBL::MiscFeatures
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -1916,6 +1957,17 @@ sub get_all_MiscFeatures {
+=head2 get_all_AffyFeatures
+
+ Arg [1] : (optional) array of names
+ Example : $slice->get_all_AffyFeatures();
+ Description: Retreives all affy features which overlap this slice.
+ Returntype : listref of Bio::EnsEMBL::AffyFeatures
+ Exceptions : none
+ Caller : general
+ Status : Stable
+
+=cut
sub get_all_AffyFeatures {
my $self = shift;
@@ -1953,6 +2005,7 @@ sub get_all_AffyFeatures {
Returntype : reference to a list of Bio::EnsEMBL::MarkerFeatures
Exceptions : none
Caller : contigview, general
+ Status : Stable
=cut
@@ -1995,6 +2048,7 @@ sub get_all_MarkerFeatures {
Returntype : reference to a list of Bio::EnsEMBL::DnaDnaAlignFeatures
Exceptions : warning if compara database is not available
Caller : contigview
+ Status : Stable
=cut
@@ -2023,6 +2077,15 @@ sub get_all_compara_DnaAlignFeatures {
return $dafa->fetch_all_by_Slice($self, $qy_species, $qy_assembly, $alignment_type);
}
+=head2 get_all_compara_Syntenies
+
+ Arg [1] : query species
+ Description: gets al the conpara syntenys fro a specfic species
+ Returns : arrayref of Bio::EnsEMBL::Compara::SyntenyRegion
+ Status : Stable
+
+=cut
+
sub get_all_compara_Syntenies {
my ($self, $qy_species ) = @_;
@@ -2060,6 +2123,7 @@ sub get_all_compara_Syntenies {
Returntype : listref of Bio::EnsEMBL::External::Haplotype::Haplotypes
Exceptions : warning is Haplotype database is not available
Caller : contigview, general
+ Status : Stable
=cut
@@ -2100,6 +2164,7 @@ sub get_all_Haplotypes {
Returntype : hashref of Bio::SeqFeatures
Exceptions : ?
Caller : webcode
+ Status : Stable
=cut
@@ -2132,6 +2197,7 @@ sub get_all_DASFeatures{
coordinates
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -2184,6 +2250,7 @@ sub get_all_ExternalFeatures {
Returntype : Hash of named features.
Exceptions : none
Caller : none
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/Storable.pm b/modules/Bio/EnsEMBL/Storable.pm
index 69d198a6a3..b46b600474 100644
--- a/modules/Bio/EnsEMBL/Storable.pm
+++ b/modules/Bio/EnsEMBL/Storable.pm
@@ -35,18 +35,23 @@ use warnings;
package Bio::EnsEMBL::Storable;
-use Bio::EnsEMBL::Root;
-use vars qw(@ISA);
-
-#
-# will eventually remove unneeded inheritance to Root
-#
-@ISA = qw(Bio::EnsEMBL::Root);
-
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
+=head2 new
+
+ Arg [-ADAPTOR] : Bio::EnsEMBL::DBSQL::BaseAdaptor
+ Arg [-dbID] : database internal id
+ Example : none
+ Caller : internal calls
+ Description : create a new Storable object
+ Returntype : Bio::EnsEMBL::Storable
+ Exceptions : Adaptor not a Bio::EnsEMBL::DBSQL::BaseAdaptor
+ Status : Stable
+
+=cut
+
sub new {
my $caller = shift;
my $class = ref($caller) || $caller;
@@ -71,6 +76,7 @@ sub new {
Returntype : int
Exceptions : none
Caller : general, set from adaptor on store
+ Status : Stable
=cut
@@ -87,9 +93,10 @@ sub dbID {
Arg [1] : Bio::EnsEMBL::DBSQL::BaseAdaptor $adaptor
Example : none
Description: get/set for this objects Adaptor
- Returntype : Bio::EnsEMBL::DBSQL::ChromsomeAdaptor
+ Returntype : Bio::EnsEMBL::DBSQL::BaseAdaptor
Exceptions : none
Caller : general, set from adaptor on store
+ Status : Stable
=cut
@@ -110,7 +117,8 @@ sub adaptor {
=head2 is_stored
- Arg [1] : Bio::EnsEMBL::DBSQL::DBConnection
+ Arg [1] : Bio::EnsEMBL::DBSQL::DBConnection
+ : or Bio::EnsEMBL::DBSQL::DBAdaptor
Example : do_something if($object->is_stored($db));
Description: Returns true if this object is stored in the provided database.
This works under the assumption that if the adaptor and dbID are
@@ -122,6 +130,7 @@ sub adaptor {
throw if adaptor is set but dbID is not
throw if incorrect argument is passed
Caller : store methods
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/TopLevelAssemblyMapper.pm b/modules/Bio/EnsEMBL/TopLevelAssemblyMapper.pm
index e7bc1354c4..ea24ab7b0a 100644
--- a/modules/Bio/EnsEMBL/TopLevelAssemblyMapper.pm
+++ b/modules/Bio/EnsEMBL/TopLevelAssemblyMapper.pm
@@ -56,6 +56,22 @@ use Bio::EnsEMBL::Utils::Exception qw(throw);
use Bio::EnsEMBL::Mapper;
use Bio::EnsEMBL::CoordSystem;
+=head2 new
+
+ Arg [1] : Bio::EnsEMBL::DBAdaptor $dbadaptor the adaptor for
+ the database this mapper is using.
+ Arg [2] : Toplevel CoordSystem
+ Arg [3] : Other CoordSystem
+ Description: Creates a new TopLevelAssemblyMapper object
+ Returntype : Bio::EnsEMBL::DBSQL::TopLevelAssemblyMapper
+ Exceptions : throws if any of the 3 arguments are missing/ not
+ : of the correct type.
+ Caller : Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor
+ Status : Stable
+
+=cut
+
+
sub new {
my ($caller, $adaptor, $toplevel_cs, $other_cs) = @_;
@@ -92,6 +108,32 @@ sub adaptor {
return $self->{'adaptor'};
}
+=head2 map
+
+ Arg [1] : string $frm_seq_region
+ The name of the sequence region to transform FROM
+ Arg [2] : int $frm_start
+ The start of the region to transform FROM
+ Arg [3] : int $frm_end
+ The end of the region to transform FROM
+ Arg [4] : int $strand
+ The strand of the region to transform FROM
+ Arg [5] : Bio::EnsEMBL::CoordSystem
+ The coordinate system to transform FROM
+ Arg [6] : if set will do a fastmap
+ Example : @coords = $mapper->map('X', 1_000_000, 2_000_000,
+ 1, $chr_cs);
+ Description: Transforms coordinates from one coordinate system
+ to another.
+ Returntype : List of Bio::EnsEMBL::Mapper::Coordinate and/or
+ Bio::EnsEMBL::Mapper:Gap objects
+ Exceptions : thrown if if the specified TO coordinate system is not one
+ of the coordinate systems associated with this mapper
+ Caller : general
+ Status : Stable
+
+=cut
+
sub map {
throw('Incorrect number of arguments.') if(@_ != 6 && @_ != 7);
@@ -160,18 +202,78 @@ sub map {
#
# for polymorphism with AssemblyMapper
#
+=head2 flush
+
+ Args : none
+ Example : none
+ Description: polymorphism with AssemblyMapper, does nothing
+ Returntype : none
+ Exceptions : none
+ Status : Stable
+
+=cut
+
sub flush {}
+=head2 fastmap
+
+ Arg [1] : string $frm_seq_region
+ The name of the sequence region to transform FROM
+ Arg [2] : int $frm_start
+ The start of the region to transform FROM
+ Arg [3] : int $frm_end
+ The end of the region to transform FROM
+ Arg [4] : int $strand
+ The strand of the region to transform FROM
+ Arg [5] : Bio::EnsEMBL::CoordSystem
+ The coordinate system to transform FROM
+ Example : @coords = $mapper->fastmap('X', 1_000_000, 2_000_000,
+ 1, $chr_cs);
+ Description: Transforms coordinates from one coordinate system
+ to another.
+ Returntype : List of Bio::EnsEMBL::Mapper::Coordinate and/or
+ Bio::EnsEMBL::Mapper:Gap objects
+ Exceptions : thrown if if the specified TO coordinate system is not one
+ of the coordinate systems associated with this mapper
+ Caller : general
+ Status : Stable
+
+=cut
+
sub fastmap {
my $self = shift;
return $self->map(@_,1);
}
+=head2 assembled_CoordSystem
+
+ Arg [1] : none
+ Example : $cs = $mapper->assembled_CoordSystem
+ Description: Retrieves the assembled CoordSystem from this mapper
+ Returntype : Bio::EnsEMBL::CoordSystem
+ Exceptions : none
+ Caller : internal, AssemblyMapperAdaptor
+ Status : Stable
+
+=cut
+
sub assembled_CoordSystem {
my $self = shift;
return $self->{'toplevel_cs'};
}
+=head2 component_CoordSystem
+
+ Arg [1] : none
+ Example : $cs = $mapper->component_CoordSystem
+ Description: Retrieves the component CoordSystem from this mapper
+ Returntype : Bio::EnsEMBL::CoordSystem
+ Exceptions : none
+ Caller : internal, AssemblyMapperAdaptor
+ Status : Stable
+
+=cut
+
sub component_CoordSystem {
my $self = shift;
return $self->{'other_cs'};
@@ -265,6 +367,7 @@ sub _list {
Returntype : List of strings
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -293,6 +396,7 @@ sub list_seq_regions {
Exceptions : thrown if the from CoordSystem is the toplevel coord system
thrown if the from CoordSystem is not the one used in the mapper
Caller : general
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/Transcript.pm b/modules/Bio/EnsEMBL/Transcript.pm
index eeb43a8116..946b69a97d 100755
--- a/modules/Bio/EnsEMBL/Transcript.pm
+++ b/modules/Bio/EnsEMBL/Transcript.pm
@@ -80,11 +80,22 @@ use Bio::EnsEMBL::Utils::Exception qw( deprecate warning throw );
Arg [-DISPLAY_XREF]:
Bio::EnsEMBL::DBEntry - The external database entry that is used
to label this transcript when it is displayed.
+ Arg [-CREATED_DATE]:
+ string - the date the transcript was created
+ Arg [-MODIFIED_DATE]:
+ string - the date the transcript was last modified
+ Arg [-DESCRIPTION]:
+ string - the transcipts description
+ Arg [-BIOTYPE]:
+ string - the biotype e.g. "protein_coding"
+ Arg [-CONFIDENCE]:
+ string - the transcripts confidence i.e. "KNOWN","NOVEL"
Example : $tran = new Bio::EnsEMBL::Transcript(-EXONS => \@exons);
Description: Constructor. Instantiates a Transcript object.
Returntype : Bio::EnsEMBL::Transcript
Exceptions : throw on bad arguments
Caller : general
+ Status : Stable
=cut
@@ -158,6 +169,7 @@ sub new {
priority (desc), external db name (asc), display_id (asc)
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -192,6 +204,7 @@ sub get_all_DBLinks {
Returntype : list reference to Bio::EnsEMBL::DBEntry objects
Exceptions : none
Caller : get_all_DBLinks, TranscriptAdaptor::store
+ Status : Stable
=cut
@@ -221,6 +234,7 @@ sub get_all_DBEntries {
Returntype : none
Exceptions : thrown on incorrect argument type
Caller : general
+ Status : Stable
=cut
@@ -247,6 +261,7 @@ sub add_DBEntry {
Returntype : listreference of Bio::EnsEMBL::FeaturePair
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -277,6 +292,7 @@ sub get_all_supporting_features {
throw if any of the features are not in the same coordinate
system as the Transcript
Caller : general
+ Status : Stable
=cut
@@ -327,6 +343,7 @@ sub add_supporting_features {
Function: external_name if available
Returns : the external db link for this transcript
Args : new external db (optional)
+ Status : Stable
=cut
@@ -359,6 +376,7 @@ sub external_db {
Function: external_name if available
Returns : the external db link for this transcript
Args : new external db (optional)
+ Status : Stable
=cut
@@ -392,6 +410,7 @@ sub external_status {
Example :
Returns : the external name of this transcript
Args : new external name (optional)
+ Status : Stable
=cut
@@ -425,6 +444,7 @@ sub external_name {
Returntype : 0,1
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -443,7 +463,8 @@ sub is_known {
Returntype : string
Exceptions : none
Caller : general
-
+ Status : At Risk
+ : will be replaced with biotype
=cut
sub type {
@@ -463,6 +484,7 @@ sub type {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -481,6 +503,7 @@ sub confidence {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -501,6 +524,7 @@ sub biotype {
Returntype : Bio::EnsEMBL::DBEntry
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -528,6 +552,7 @@ sub display_xref {
Returntype : Bio::EnsEMBL::Transcript
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -559,6 +584,7 @@ sub translation {
Returntype : txt
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -612,6 +638,7 @@ sub spliced_seq {
Returntype : txt
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -654,6 +681,7 @@ sub translateable_seq {
Returntype : int
Exceptions : none
Caller : five_prime_utr, get_all_snps, general
+ Status : Stable
=cut
@@ -717,6 +745,7 @@ sub cdna_coding_start {
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -781,6 +810,7 @@ sub cdna_coding_end {
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -826,6 +856,7 @@ sub coding_region_start {
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -865,6 +896,7 @@ sub coding_region_end {
Returntype : boolean - the current value of the edits
Exceptions : none
Caller : general, cdna_coding_start, cdna_coding_end, length
+ Status : Stable
=cut
@@ -892,6 +924,7 @@ sub edits_enabled {
Returntype : Bio::EnsEMBL::SeqEdit
Exceptions : none
Caller : spliced_seq()
+ Status : Stable
=cut
@@ -923,6 +956,7 @@ sub get_all_SeqEdits {
Exceptions : warning if transcript does not have attached adaptor and
attempts lazy load.
Caller : general
+ Status : Stable
=cut
@@ -961,6 +995,7 @@ sub get_all_Attributes {
Returntype : none
Exceptions : throw on incorrect arguments
Caller : general
+ Status : Stable
=cut
@@ -993,7 +1028,11 @@ sub add_Attributes {
Title : add_Exon
Usage : $trans->add_Exon($exon)
Returns : Nothing
- Args :
+ Args [1]: Bio::EnsEMBL::Exon object to add
+ Args [2]: rank
+ Exceptions: throws if not a valid Bio::EnsEMBL::Exon
+ : or exon clasjes with another one
+ Status : Stable
=cut
@@ -1082,6 +1121,7 @@ sub add_Exon{
Returntype : a list reference to Bio::EnsEMBL::Exon objects
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -1104,6 +1144,7 @@ sub get_all_Exons {
Returntype : a list reference to Bio::EnsEMBL::Intron objects
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -1127,11 +1168,13 @@ sub get_all_Introns {
=head2 length
-
- my $t_length = $transcript->length
-
-Returns the sum of the length of all the exons in
-the transcript.
+ Args : none
+ Example : my $t_length = $transcript->length
+ Description: Returns the sum of the length of all the exons in the transcript.
+ Returntype : int
+ Exceptions : none
+ Caller : general
+ Status : Stable
=cut
@@ -1166,6 +1209,7 @@ sub length {
Returntype : none
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -1197,6 +1241,7 @@ sub flush_Exons{
Returntype : Bio::Seq or undef
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -1231,6 +1276,7 @@ sub five_prime_utr {
Returntype : Bio::Seq or undef
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -1269,6 +1315,7 @@ sub three_prime_utr {
Returntype : listref Bio::EnsEMBL::Exon
Exceptions : throw if translation has invalid information
Caller : Genebuild
+ Status : Stable
=cut
@@ -1298,7 +1345,6 @@ sub get_all_translateable_Exons {
# Adjust to translation start if this is the start exon
if ($ex == $start_exon ) {
if ($t_start < 1 or $t_start > $length) {
-# throw("Translation start '$t_start' is outside exon $ex length=$length");
warn("WARN: Translation start '$t_start' is outside exon $ex length=$length");
return [];
}
@@ -1342,6 +1388,7 @@ sub get_all_translateable_Exons {
Returntype : Bio::Seq or undef
Exceptions : If no Translation is set in this Transcript
Caller : general
+ Status : Stable
=cut
@@ -1402,10 +1449,16 @@ sub translate {
=head2 seq
-Returns a Bio::Seq object which consists of just
-the sequence of the exons concatenated together,
-without messing about with padding with N\'s from
-Exon phases like B<dna_seq> does.
+ Description: Returns a Bio::Seq object which consists of just
+ : the sequence of the exons concatenated together,
+ : without messing about with padding with N\'s from
+ : Exon phases like B<dna_seq> does.
+ Args : none
+ Example : none
+ Returntype : Bio::Seq
+ Exceptions : none
+ Caller : general
+ Status : Stable
=cut
@@ -1475,6 +1528,7 @@ sub genomic2cdna {
Returntype : Bio::EnsEMBL::TranscriptMapper
Exceptions : none
Caller : cdna2genomic, pep2genomic, genomic2cdna, cdna2genomic
+ Status : Stable
=cut
@@ -1492,6 +1546,7 @@ sub get_TranscriptMapper {
Usage : $start_exon = $transcript->start_Exon;
Returns : The first exon in the transcript.
Args : NONE
+ Status : Stable
=cut
@@ -1506,6 +1561,7 @@ sub start_Exon{
Usage : $end_exon = $transcript->end_Exon;
Returns : The last exon in the transcript.
Args : NONE
+ Status : Stable
=cut
@@ -1523,7 +1579,7 @@ sub end_Exon{
Function:
Returns : value of description
Args : newvalue (optional)
-
+ Status : Stable
=cut
@@ -1541,6 +1597,7 @@ sub description{
Function:
Returns : value of version
Args :
+ Status : Stable
=cut
@@ -1558,7 +1615,7 @@ sub version{
Function:
Returns : value of stable_id
Args :
-
+ Status : Stable
=cut
@@ -1568,6 +1625,18 @@ sub stable_id{
return $self->{'stable_id'};
}
+=head2 created_date
+
+ Arg [1] : (optional) string to be used for the created date
+ Example : none
+ Description: get/set for attribute created date
+ Returntype : string
+ Exceptions : none
+ Caller : general
+ Status : Stable
+
+=cut
+
sub created_date {
my $self = shift;
$self->{'created_date'} = shift if ( @_ );
@@ -1575,6 +1644,18 @@ sub created_date {
}
+=head2 modified_date
+
+ Arg [1] : (optional) string to be used for the modified date
+ Example : none
+ Description: get/set for attribute modified date
+ Returntype : string
+ Exceptions : none
+ Caller : general
+ Status : Stable
+
+=cut
+
sub modified_date {
my $self = shift;
$self->{'modified_date'} = shift if ( @_ );
@@ -1596,6 +1677,7 @@ sub modified_date {
Returntype : none
Exceptions : none
Caller : GeneAdaptor->store()
+ Status : Stable
=cut
@@ -1634,6 +1716,8 @@ sub swap_exons {
Returntype : Bio::EnsEMBL::Transcript
Exceptions : wrong parameters
Caller : general
+ Status : Medium Risk
+ : deprecation needs to be removed at some time
=cut
@@ -1707,6 +1791,7 @@ sub transform {
Returntype : Bio::EnsEMBL::Transcript
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -1775,6 +1860,7 @@ sub transfer {
Returntype : none
Exceptions : none
Caller : internal
+ Status : Stable
=cut
@@ -1847,6 +1933,7 @@ sub recalculate_coordinates {
Returntype : string
Exceptions : none
Caller : web drawing code
+ Status : Stable
=cut
@@ -1858,7 +1945,10 @@ sub display_id {
=head2 get_all_peptide_variations
-Description: See Bio::EnsEMBL::Utils::TranscriptSNPs::get_all_peptide_variations
+ Description: See Bio::EnsEMBL::Utils::TranscriptSNPs::get_all_peptide_variations
+ Status : At Risk
+ : Will be replaced with modules from the ensembl-variation package
+
=cut
@@ -1876,7 +1966,10 @@ sub get_all_peptide_variations {
=head2 get_all_SNPs
-Description: See Bio::EnsEMBL::Utils::TranscriptSNPs::get_all_SNPs
+ Description: See Bio::EnsEMBL::Utils::TranscriptSNPs::get_all_SNPs
+
+ Status : At Risk
+ : Will be replaced with modules from the ensembl-variation package
=cut
@@ -1884,9 +1977,12 @@ sub get_all_SNPs {
return Bio::EnsEMBL::Utils::TranscriptSNPs::get_all_SNPs(@_);
}
-=head2 get_all_peptide_variations
+=head2 get_all_cdna_SNPs
-Description: See Bio::EnsEMBL::Utils::TranscriptSNPs::get_all_cdna_SNPs
+ Description: See Bio::EnsEMBL::Utils::TranscriptSNPs::get_all_cdna_SNPs
+
+ Status : At Risk
+ : Will be replaced with modules from the ensembl-variation package
=cut
@@ -1903,6 +1999,7 @@ sub get_all_cdna_SNPs {
Exceptions:
Caller :
Example : $dasref = $prot->get_all_DASFactories
+ Status : Stable
=cut
@@ -1923,6 +2020,7 @@ sub get_all_DASFactories {
Returntype : hashref of Bio::SeqFeatures
Exceptions : ?
Caller : webcode
+ Status : Stable
=cut
@@ -1963,6 +2061,7 @@ sub get_all_DAS_Features{
Returntype : Listref of Bio::EnsEMBL::RegulatoryFeature
Exceptions : If arg is not of correct type.
Caller : ?
+ Status : At Risk
=cut
diff --git a/modules/Bio/EnsEMBL/TranscriptMapper.pm b/modules/Bio/EnsEMBL/TranscriptMapper.pm
index 966bf1a105..d8b6d713b1 100644
--- a/modules/Bio/EnsEMBL/TranscriptMapper.pm
+++ b/modules/Bio/EnsEMBL/TranscriptMapper.pm
@@ -65,8 +65,9 @@ use Bio::EnsEMBL::Mapper::Coordinate;
'Genomic' coordinates are coordinates which are relative to the
slice that the Transcript is on.
Returntype : Bio::EnsEMBL::TranscriptMapper
- Exceptions : none
+ Exceptions : throws if a transcript is not an argument
Caller : Transcript::get_TranscriptMapper
+ Status : Stable
=cut
@@ -99,6 +100,18 @@ sub new {
}
+=head2 _load_mapper
+
+ Arg [1] : Bio::EnsEMBL::Transcript $transcript
+ The transcript for which a mapper should be created.
+ Example : my $mapper = _load_mapper($transcript);
+ Description: loads the mapper
+ Returntype : Bio::EnsEMBL::Mapper
+ Exceptions : none
+ Caller : Internal
+ Status : Stable
+
+=cut
sub _load_mapper {
my $transcript = shift;
@@ -209,8 +222,9 @@ sub _load_mapper {
return value is a list of coordinates and gaps.
Returntype : list of Bio::EnsEMBL::Mapper::Coordinate and
Bio::EnsEMBL::Mapper::Gap objects
- Exceptions : none
+ Exceptions : throws if no start or end
Caller : general
+ Status : Stable
=cut
@@ -234,7 +248,7 @@ sub cdna2genomic {
The start position in genomic coordinates
Arg [2] : $end
The end position in genomic coordinates
- Arg [3] : (optional) $strand
+ Arg [3] : $strand
The strand of the genomic coordinates (default value 1)
Example : @coords = $trans_mapper->genomic2cdna($start, $end, $strnd);
Description: Converts genomic coordinates to cdna coordinates. The
@@ -244,8 +258,9 @@ sub cdna2genomic {
represent genomic regions which map to exons (utrs included).
Returntype : list of Bio::EnsEMBL::Mapper::Coordinate and
Bio::EnsEMBL::Mapper::Gap objects
- Exceptions : none
+ Exceptions : throws if start, end or strand not defined
Caller : general
+ Status : Stable
=cut
@@ -277,8 +292,9 @@ sub genomic2cdna {
transcript used to construct this TranscriptMapper was on.
Returntype : list of Bio::EnsEMBL::Mapper::Gap and
Bio::EnsEMBL::Mapper::Coordinate objects
- Exceptions : none
+ Exceptions : throws if no end
Caller : general
+ Status : Stable
=cut
@@ -312,8 +328,9 @@ sub pep2genomic {
transcript that was used to create this transcript mapper.
Returntype : list of Bio::EnsEMBL::Mapper::Coordinate and
Bio::EnsEMBL::Mapper::Gap objects
- Exceptions : throw if incorrect arguments
+ Exceptions : throw if start, end or strand not defined
Caller : general
+ Status : Stable
=cut
@@ -405,8 +422,9 @@ sub genomic2cds {
return value is a list of coordinates and gaps.
Returntype : list of Bio::EnsEMBL::Mapper::Coordinate and
Bio::EnsEMBL::Mapper::Gap objects
- Exceptions : none
+ Exceptions : throw if start, end or strand not defined
Caller : general
+ Status : Stable
=cut
diff --git a/modules/Bio/EnsEMBL/Translation.pm b/modules/Bio/EnsEMBL/Translation.pm
index b852973482..5726d42e5c 100755
--- a/modules/Bio/EnsEMBL/Translation.pm
+++ b/modules/Bio/EnsEMBL/Translation.pm
@@ -56,6 +56,8 @@ use Bio::EnsEMBL::Storable;
Arg [-SEQ] : Manually sets the peptide sequence of this translation.
May be useful if this translation is not stored in
a database.
+ Arg [-CREATED_DATE]: the date the translation was created
+ Arg [-MODIFIED_DATE]: the date the translation was modified
Example : my $tl = Bio::EnsEMBL::Translation->new
(-START_EXON => $ex1,
-END_EXON => $ex2,
@@ -65,6 +67,7 @@ use Bio::EnsEMBL::Storable;
Returntype : Bio::EnsEMBL::Translation
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -106,7 +109,7 @@ sub new {
the exon given by start_exon_id.
Returns : value of start
Args : newvalue (optional)
-
+ Status : Stable
=cut
@@ -130,6 +133,7 @@ sub start{
the exon given by end_exon.
Returns : value of end
Args : newvalue (optional)
+ Status : Stable
=cut
@@ -155,6 +159,7 @@ sub end {
position indicated by start, see above).
Returns : value of start_exon (Exon object)
Args : newvalue (optional)
+ Status : Stable
=cut
@@ -184,7 +189,7 @@ sub start_Exon {
position indicated by end, see above).
Returns : value of end_exon (Exon object)
Args : newvalue (optional)
-
+ Status : Stable
=cut
@@ -211,6 +216,7 @@ sub end_Exon {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -229,6 +235,7 @@ sub version {
Returntype : string
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -238,6 +245,18 @@ sub stable_id {
return $self->{'stable_id'};
}
+=head2 created_date
+
+ Arg [1] : (optional) string to be used for the created date
+ Example : none
+ Description: get/set for attribute created date
+ Returntype : string
+ Exceptions : none
+ Caller : general
+ Status : Stable
+
+=cut
+
sub created_date {
my $self = shift;
$self->{'created_date'} = shift if ( @_ );
@@ -245,6 +264,18 @@ sub created_date {
}
+=head2 modified_date
+
+ Arg [1] : (optional) string to be used for the modified date
+ Example : none
+ Description: get/set for attribute modified date
+ Returntype : string
+ Exceptions : none
+ Caller : general
+ Status : Stable
+
+=cut
+
sub modified_date {
my $self = shift;
$self->{'modified_date'} = shift if ( @_ );
@@ -262,6 +293,7 @@ sub modified_date {
Returntype: none
Exceptions: none
Caller : Transcript->transform()
+ Status : Stable
=cut
@@ -299,6 +331,7 @@ sub transform {
Returntype : list reference to Bio::EnsEMBL::DBEntry objects
Exceptions : none
Caller : get_all_DBLinks, TranslationAdaptor::store
+ Status : Stable
=cut
@@ -333,6 +366,7 @@ sub get_all_DBEntries {
Returntype : none
Exceptions : thrown on incorrect argument type
Caller : general
+ Status : Stable
=cut
@@ -358,6 +392,7 @@ sub add_DBEntry {
Returntype : see get_all_DBEntries
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -382,6 +417,7 @@ sub get_all_DBLinks {
Returntype : Bio::EnsEMBL::ProteinFeature
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -446,6 +482,7 @@ sub get_all_ProteinFeatures {
Returntype : listref of Bio::EnsEMBL::ProteinFeatures
Exceptions : none
Caller : webcode (protview)
+ Status : Stable
=cut
@@ -479,6 +516,7 @@ sub get_all_DomainFeatures{
Returntype : string
Exceptions : none
Caller : web drawing code
+ Status : Stable
=cut
@@ -497,6 +535,7 @@ sub display_id {
Returntype : int
Exceptions : none
Caller : webcode (protview etc.)
+ Status : Stable
=cut
@@ -521,6 +560,7 @@ sub length {
Exceptions : warning if the sequence is not set and cannot be retrieved from
the database.
Caller : webcode (protview etc.)
+ Status : Stable
=cut
@@ -565,6 +605,7 @@ sub seq {
Exceptions : warning if translation does not have attached adaptor and
attempts lazy load.
Caller : general, modify_translation
+ Status : Stable
=cut
@@ -604,6 +645,7 @@ sub get_all_Attributes {
Returntype : none
Exceptions : throw on incorrect arguments
Caller : general
+ Status : Stable
=cut
@@ -632,6 +674,7 @@ sub add_Attributes {
Returntype : Bio::EnsEMBL::SeqEdit
Exceptions : none
Caller : spliced_seq()
+ Status : Stable
=cut
@@ -660,6 +703,7 @@ sub get_all_SeqEdits {
Returntype : Bio::Seq
Exceptions :
Caller : Bio::EnsEMBL::Transcript->translate
+ Status : Stable
=cut
@@ -704,8 +748,9 @@ sub temporary_id {
Function : Retrieves a listref of registered DAS objects
Returntype: [ DAS_objects ]
Exceptions:
- Caller :
+ Caller : webcode
Example : $dasref = $prot->get_all_DASFactories
+ Status : Stable
=cut
@@ -727,6 +772,7 @@ sub get_all_DASFactories {
Returntype : hashref of Bio::SeqFeatures
Exceptions : ?
Caller : webcode
+ Status : Stable
=cut
@@ -763,7 +809,7 @@ sub get_all_DASFeatures{
Returntype : hashref of Bio::SeqFeatures
Exceptions : ?
Caller : webcode
-
+ Status : Stable
=cut
@@ -807,6 +853,9 @@ sub get_all_DAS_Features{
Returntype : Listref of Bio::EnsEMBL::RegulatoryFeature
Exceptions : If arg is not of correct type.
Caller : ?
+ Status : At Risk
+ : Regulatory features are currently under development and are
+ : likely to change.
=cut
diff --git a/modules/Bio/EnsEMBL/Upstream.pm b/modules/Bio/EnsEMBL/Upstream.pm
index 06546eefd3..f467354267 100644
--- a/modules/Bio/EnsEMBL/Upstream.pm
+++ b/modules/Bio/EnsEMBL/Upstream.pm
@@ -70,6 +70,7 @@ use Bio::EnsEMBL::Utils::Argument qw(rearrange);
Returntype : Bio::EnsEMBL::Upstream
Exceptions : none
Caller : Bio::EnsEMBL::Transcript, general
+ Status : Stable
=cut
@@ -100,6 +101,7 @@ sub new {
or a Bio::EnsEMBL::Transcript
Caller : $self->new, $self->_derive_coords,
$self->_first_coding_Exon
+ Status : Stable
=cut
@@ -128,6 +130,7 @@ sub transcript {
Returntype : int
Exceptions : Throws if length is requested before it has been set.
Caller : $self->new, $self->_derive_coords
+ Status : Stable
=cut
@@ -154,6 +157,7 @@ sub length {
Returntype : none
Exceptions : none
Caller : $self->length, $self->transform
+ Status : Stable
=cut
@@ -178,6 +182,7 @@ sub _flush_cache {
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -209,6 +214,7 @@ sub upstart {
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -238,6 +244,7 @@ sub upend {
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -267,6 +274,7 @@ sub downstart {
Returntype : int
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -293,6 +301,7 @@ sub downend {
Returntype :
Exceptions :
Caller :
+ Status : At Risk
=cut
@@ -315,6 +324,7 @@ sub transform {
Returntype : arrayref
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -334,6 +344,7 @@ sub derive_upstream_coords {
Returntype : arrayref
Exceptions : none
Caller : general
+ Status : Stable
=cut
@@ -353,6 +364,7 @@ sub derive_downstream_coords {
Exceptions : Throws if argument is not either 'up' or 'down'
Caller : $self->upstart, $self->upend, $self->downstart,
$self->downend
+ Status : Stable
=cut
@@ -449,6 +461,7 @@ sub _derive_coords {
Exceptions : Throws if argument is not either 'right_end'
or 'left_end'
Caller : $self->_derive_coords
+ Status : Stable
=cut
@@ -531,6 +544,7 @@ sub _bases_to_trim {
Returntype : Bio::EnsEMBL::Exon
Exceptions : none
Caller : $self->_derive_coords, $self->_bases_to_trim
+ Status : Stable
=cut
--
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