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Commit d1b8f7f5 authored by Ian Longden's avatar Ian Longden
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status reports added plus some tiding up of docs

parent e8af8aa2
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Showing with 459 additions and 40 deletions
modules/Bio/EnsEMBL/AffyArray.pm
View file @ d1b8f7f5
......@@ -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
......
modules/Bio/EnsEMBL/AffyFeature.pm
View file @ d1b8f7f5
......@@ -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;
......
modules/Bio/EnsEMBL/AffyProbe.pm
View file @ d1b8f7f5
......@@ -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
......
modules/Bio/EnsEMBL/Analysis.pm
View file @ d1b8f7f5
......@@ -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
......
modules/Bio/EnsEMBL/ArchiveStableId.pm
View file @ d1b8f7f5
......@@ -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
......
modules/Bio/EnsEMBL/AssemblyExceptionFeature.pm
View file @ d1b8f7f5
......@@ -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
......
modules/Bio/EnsEMBL/AssemblyMapper.pm
View file @ d1b8f7f5
......@@ -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