Commit 0bd42aee authored by Kieron Taylor's avatar Kieron Taylor 😠
Browse files

POD corrections

parent f592a1fe
......@@ -169,7 +169,6 @@ sub new_fast {
=head2 db
Arg [1] : string $db
Example : none
Description: get/set for the attribute db
Returntype : string
Exceptions : none
......@@ -192,7 +191,6 @@ sub db {
=head2 db_version
Arg [1] : string $db_version
Example : none
Description: get/set for attribute db_version
Returntype : string
Exceptions : none
......@@ -215,7 +213,6 @@ sub db_version {
=head2 db_file
Arg [1] : string $db_file
Example : none
Description: get/set for attribute db_file
Returntype : string
Exceptions : none
......@@ -239,7 +236,6 @@ sub db_file {
=head2 program
Arg [1] : string $program
Example : none
Description: get/set for attribute program
Returntype : string
Exceptions : none
......@@ -262,7 +258,6 @@ sub program {
=head2 program_version
Arg [1] : string $program_version
Example : none
Description: get/set for attribute program_version
Returntype : string
Exceptions : none
......@@ -285,7 +280,6 @@ sub program_version {
=head2 program_file
Arg [1] : string $program_file
Example : none
Description: get/set for attribute program_file
Returntype : string
Exceptions : none
......@@ -308,7 +302,6 @@ sub program_file {
=head2 module
Arg [1] : string $module
Example : none
Description: get/set for attribute module. Usually a RunnableDB perl
module that executes this analysis job.
Returntype : string
......@@ -332,7 +325,6 @@ sub module {
=head2 module_version
Arg [1] : string $module_version
Example : none
Description: get/set for attribute module_version
Returntype : string
Exceptions : none
......@@ -355,7 +347,6 @@ sub module_version {
=head2 gff_source
Arg [1] : string $gff_source
Example : none
Description: get/set for attribute gff_source
Returntype : string
Exceptions : none
......@@ -378,7 +369,6 @@ sub gff_source {
=head2 gff_feature
Arg [1] : string $gff_feature
Example : none
Description: get/set for attribute gff_feature
Returntype : string
Exceptions : none
......@@ -401,7 +391,6 @@ sub gff_feature {
=head2 parameters
Arg [1] : string $parameters
Example : none
Description: get/set for attribute parameters. This should be evaluated
by the module if given or the program that is specified.
Returntype : string
......@@ -425,7 +414,6 @@ sub parameters {
=head2 created
Arg [1] : string $created
Example : none
Description: get/set for attribute created time.
Returntype : string
Exceptions : none
......@@ -448,7 +436,6 @@ sub created {
=head2 logic_name
Arg [1] : string $logic_name
Example : none
Description: Get/set method for the logic_name, the name under
which this typical analysis is known.
Returntype : string
......@@ -469,7 +456,6 @@ sub logic_name {
=head2 has_database
Args : none
Example : none
Description: tests if the db attribute is set, returns 1 if so,
0 if not.
Returntype : int 0,1
......@@ -513,7 +499,6 @@ sub description {
=head2 display_label
Arg [1] : string $display_label
Example : none
Description: get/set for attribute display_label
Returntype : string
Exceptions : none
......@@ -535,7 +520,6 @@ sub display_label {
=head2 displayable
Arg [1] : string $displayable
Example : none
Description: get/set for attribute displayable
Returntype : string
Exceptions : none
......@@ -558,7 +542,6 @@ sub displayable {
=head2 web_data
Arg [1] : string $web_data
Example : none
Description: get/set for attribute web_data
Returntype : string
Exceptions : none
......@@ -581,10 +564,9 @@ sub web_data {
Arg 1 : Bio::EnsEMBL::Analysis $ana
The analysis to compare to
Example : none
Description: returns 1 if this analysis is special case of given analysis
returns 0 if they are equal
returns -1 if they are completely different
returns -1 if they are completely different
Returntype : int -1,0,1
Exceptions : none
Caller : unknown
......
......@@ -18,15 +18,16 @@
=cut
# POD documentation - main docs before the code
=head1 NAME
PairAlign - Dna pairwise alignment module
=head1 SYNOPSIS
Give standard usage here
#To convert between coordinates:
my $cdna_coord = $pair->genomic2cDNA($gen_coord);
my $gen_coord = $pair->cDNA2genomic($cdna_coord);
=head1 DESCRIPTION
......@@ -48,16 +49,6 @@ Creation:
Any number of pair alignments can be added to the PairAlign object
Manipulation:
To convert between coordinates:
my $cdna_coord = $pair->genomic2cDNA($gen_coord);
my $gen_coord = $pair->cDNA2genomic($cdna_coord);
=head1 METHODS
=cut
package Bio::EnsEMBL::Analysis::PairAlign;
......@@ -90,14 +81,10 @@ sub addFeaturePair {
=head2 eachFeaturePair
Title : eachFeaturePait
Usage : my @pairs = $pair->eachFeaturePair
Function:
Example :
Title : eachFeaturePair
Example : my @pairs = $pair->eachFeaturePair
Returns : Array of Bio::SeqFeature::FeaturePair
Args : none
=cut
sub eachFeaturePair {
......@@ -121,11 +108,8 @@ sub get_hstrand {
Title : genomic2cDNA
Usage : my $cdna_coord = $pair->genomic2cDNA($gen_coord)
Function: Converts a genomic coordinate to a cdna coordinate
Example :
Returns : int
Args : int
=cut
sub genomic2cDNA {
......@@ -226,8 +210,7 @@ sub find_Pair {
Usage : my @newfeatures = $self->convert_cDNA_feature($f);
Function: Converts a feature on the cDNA into an array of
features on the genomic (for features that span across introns);
Example :
Returns : @Bio::EnsEMBL::FeaturePair
Returns : Array of Bio::EnsEMBL::FeaturePair
Args : Bio::EnsEMBL::FeaturePair
=cut
......
......@@ -22,8 +22,6 @@
Bio::EnsEMBL::ArchiveStableId
=head1 SYNOPSIS
=head1 DESCRIPTION
ArchiveStableId objects are the main workunit for retrieving stable id
......@@ -41,32 +39,7 @@ Attributes:
Status: At Risk. This module is in development.
=head1 METHODS
new
new_fast
get_history_tree
get_all_predecessors
get_all_successors
get_peptide
get_all_associated_archived
get_all_gene_archive_ids
get_all_transcript_archive_ids
get_all_translation_archive_ids
current_version
is_current
get_latest_incarnation
is_latest
stable_id
version
db_name
release
assembly
type
adaptor
successors
=head1 RELATED MODULES
=head1 SEE ALSO
Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor
Bio::EnsEMBL::StableIdEvent
......@@ -88,22 +61,21 @@ use Scalar::Util qw(weaken isweak);
=head2 new
Arg [STABLE_ID] : String $stable_id
Arg [VERSION] : Int $version
Arg [CURRENT_VERSION] : Int $current_version
Arg [DB_NAME] : String $db_name
Arg [RELEASE] : String $release
Arg [ASSEMBLY_NAME] : String $assembly
Arg [TYPE] : String $type - "Gene", "Transcript", "Translation", "Exon"
Arg [ADAPTOR] : Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor $adaptor
Example : none
Description : standard constructor with named arguments to create
ArchiveStableId
Returntype : Bio::EnsEMBL::ArchiveStableId
Exceptions : none
Caller : general, Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor
Status : At Risk
: under development
Arg [STABLE_ID] : String $stable_id
Arg [VERSION] : Int $version
Arg [CURRENT_VERSION]: Int $current_version
Arg [DB_NAME] : String $db_name
Arg [RELEASE] : String $release
Arg [ASSEMBLY_NAME] : String $assembly
Arg [TYPE] : String $type - "Gene", "Transcript", "Translation", "Exon"
Arg [ADAPTOR] : Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor $adaptor
Description : standard constructor with named arguments to create
ArchiveStableId
Returntype : Bio::EnsEMBL::ArchiveStableId
Exceptions : none
Caller : general, Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor
Status : At Risk
: under development
=cut
......@@ -140,7 +112,6 @@ sub new {
Arg [6] : String $type - "Gene", "Transcript", "Translation", "Exon"
Arg [7] : Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor $adaptor
Arg [8] : Int $current_version
Example : none
Description : faster version of above constructor
Returntype : Bio::EnsEMBL::ArchiveStableId
Exceptions : none
......@@ -204,7 +175,6 @@ sub get_history_tree {
=head2 get_all_predecessors
Args : none
Example : none
Description : Retrieve a list of ArchiveStableIds that were mapped to this
one.
Returntype : listref of Bio::EnsEMBL::ArchiveStableId
......@@ -231,7 +201,6 @@ sub get_all_predecessors {
=head2 get_all_successors
Args : none
Example : none
Description : Retrieve a list of ArchiveStableIds that this one was mapped to.
Returntype : listref Bio::EnsEMBL::ArchiveStableId
Exceptions : none
......@@ -255,7 +224,6 @@ sub get_all_successors {
=head2 get_peptide
Example : none
Description : Retrieves the peptide string for this ArchiveStableId.
Returntype : String, or undef if this is not a Translation or cant be found
in the database.
......@@ -326,7 +294,6 @@ sub get_all_gene_archive_ids {
=head2 get_all_transcript_archive_ids
Example : none
Example : my @archived_transcripts =
@{ $arch_id->get_all_transcript_archive_ids };
Description : Returns transcript ArchiveStableIds associated with this
......@@ -378,7 +345,7 @@ sub get_all_translation_archive_ids {
=head2 current_version
Example : if (my $v = $arch_id->current_version) {
print "Current version of this stable ID: ", $v, "\n";
print "Current version of this stable ID ", $v, "\n";
} else {
print "This stable ID is not in the current db.\n";
}
......
......@@ -765,7 +765,6 @@ sub component_CoordSystem {
=head2 adaptor
Arg [1] : Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor $adaptor
Example : None
Description: Getter/set terfor this object's database adaptor.
Returntype : Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor
Exceptions : None
......
......@@ -42,10 +42,11 @@ Bio::EnsEMBL::Attribute - A generic Attribute class.
This is a generic attribute class used to represent attributes
associated with seq_regions (and their Slices) and MiscFeatures.
Also see B<Bio::EnsEMBL::Slice>, B<Bio::EnsEMBL::MiscFeature> and
B<Bio::EnsEMBL::DBSQL::AttributeAdaptor>.
=head1 SEE ALSO
=head1 METHODS
Bio::EnsEMBL::Slice
Bio::EnsEMBL::MiscFeature
Bio::EnsEMBL::DBSQL::AttributeAdaptor
=cut
......@@ -59,20 +60,20 @@ use Scalar::Util qw(weaken isweak);
=head2 new
Arg [-CODE] : string - the code for this attribute
Arg [-NAME] : string - a human readable name for this attribute
Arg [-DESCRIPTION] : string - a description for this attribute
Arg [-VALUE] : value - the value of this attribute
Example : my $attribute = Bio::EnsEMBL::Attribute->new
(-CODE => 'myCode',
-NAME => 'My Attribute',
-DESCRIPTION => 'This is my attribute description.',
-VALUE => '10023');
Description: Constructor. Instantiates a Bio::EnsEMBL::Attribute object.
Returntype : Bio::EnsEMBL::Attribute
Exceptions : none
Caller : general
Status : Stable
Arg [-CODE] : string - the code for this attribute
Arg [-NAME] : string - a human readable name for this attribute
Arg [-DESCRIPTION] : string - a description for this attribute
Arg [-VALUE] : value - the value of this attribute
Example : my $attribute = Bio::EnsEMBL::Attribute->new
(-CODE => 'myCode',
-NAME => 'My Attribute',
-DESCRIPTION => 'This is my attribute description.',
-VALUE => '10023');
Description : Constructor. Instantiates a Bio::EnsEMBL::Attribute object.
Returntype : Bio::EnsEMBL::Attribute
Exceptions : none
Caller : general
Status : Stable
=cut
......@@ -115,7 +116,7 @@ sub new_fast {
=head2 code
Arg [1] : string $code (optional)x
Arg [1] : string $code (optional)
Example : $code = $attribute->code();
Description: Getter/Setter for code attribute
Returntype : string
......
......@@ -184,7 +184,7 @@ sub new_fast {
=head2 cigar_string
Arg [1] : string $cigar_string
Example : ( "12MI3M" )
Example : $feature->cigar_string( "12MI3M" );
Description: get/set for attribute cigar_string
cigar_string describes the alignment. "xM" stands for
x matches (mismatches), "xI" for inserts into query sequence
......@@ -207,7 +207,6 @@ sub cigar_string {
=head2 alignment_length
Arg [1] : None
Example :
Description: return the alignment length (including indels) based on the cigar_string
Returntype : int
Exceptions :
......@@ -264,7 +263,6 @@ sub ungapped_features {
=head2 strands_reversed
Arg [1] : int $strands_reversed
Example : none
Description: get/set for attribute strands_reversed
0 means that strand and hstrand are the original strands obtained
from the alignment program used
......@@ -294,7 +292,6 @@ sub strands_reversed {
=head2 reverse_complement
Args : none
Example : none
Description: reverse complement the FeaturePair,
modifing strand, hstrand and cigar_string in consequence
Returntype : none
......@@ -399,7 +396,6 @@ sub transform {
=head2 _parse_cigar
Args : none
Example : none
Description: PRIVATE (internal) method - creates ungapped features from
internally stored cigar line
Returntype : list of Bio::EnsEMBL::FeaturePair
......@@ -548,8 +544,7 @@ sub _parse_cigar {
=head2 _parse_features
Arg 1 : listref Bio::EnsEMBL::FeaturePair $ungapped_features
Example : none
Arg [1] : listref Bio::EnsEMBL::FeaturePair $ungapped_features
Description: creates internal cigarstring and start,end hstart,hend
entries.
Returntype : none, fills in values of self
......@@ -863,7 +858,6 @@ sub _parse_features {
=head2 _hit_unit
Args : none
Example : none
Description: abstract method, overwrite with something that returns
one or three
Returntype : int 1,3
......@@ -883,7 +877,6 @@ sub _hit_unit {
=head2 _query_unit
Args : none
Example : none
Description: abstract method, overwrite with something that returns
one or three
Returntype : int 1,3
......
......@@ -858,7 +858,6 @@ sub expand {
Arg 1 : int $start
Arg 2 : int $end
Arge [3] : int $strand
Example : none
Description: Makes another Slice that covers only part of this slice
If a slice is requested which lies outside of the boundaries
of this function will return undef. This means that
......@@ -1525,9 +1524,9 @@ sub get_all_LD_values {
=head2 get_all_VariationFeatures
Args : $filter [optional]
Description :returns all variation features on this slice. This function will only work
Description:returns all variation features on this slice. This function will only work
correctly if the variation database has been attached to the core database.
If $filter is "genotyped" return genotyped Snps only... (nice likkle hack);
If $filter is "genotyped" return genotyped Snps only... (nice likkle hack);
ReturnType : listref of Bio::EnsEMBL::Variation::VariationFeature
Exceptions : none
Caller : contigview, snpview
......@@ -1860,8 +1859,9 @@ sub calculate_pi {
=head2 get_all_genotyped_VariationFeatures
Args : none
Function : returns all variation features on this slice that have been genotyped. This function will only work
correctly if the variation database has been attached to the core database.
Description: returns all variation features on this slice that have been genotyped.
This function will only work correctly if the variation database has
been attached to the core database.
ReturnType : listref of Bio::EnsEMBL::Variation::VariationFeature
Exceptions : none
Caller : contigview, snpview, ldview
......@@ -1894,7 +1894,7 @@ sub get_all_genotyped_VariationFeatures {
=head2 get_all_SNPs
Description: DEPRECATED. Use get_all_VariationFeatures insted
Description: DEPRECATED. Use get_all_VariationFeatures instead
=cut
......@@ -1918,7 +1918,7 @@ sub get_all_SNPs {
=head2 get_all_genotyped_SNPs
Description : DEPRECATED. Use get_all_genotyped_VariationFeatures insted
Description : DEPRECATED. Use get_all_genotyped_VariationFeatures instead
=cut
......@@ -2247,7 +2247,6 @@ sub get_all_Exons {
=head2 get_all_QtlFeatures
Args : none
Example : none
Description: returns overlapping QtlFeatures
Returntype : listref Bio::EnsEMBL::Map::QtlFeature
Exceptions : none
......@@ -2433,7 +2432,6 @@ sub get_repeatmasked_seq {
but repeat_name AluSp (which are also from repeat_class SINE/MIR).
Your hash will be something like {"repeat_class_SINE/MIR" => 1,
"repeat_name_AluSp" => 0}
Example : none
Description: replaces string positions described in the RepeatFeatures
with Ns (default setting), or with the lower case equivalent
(soft masking). The reference to a dna string which is passed
......
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