Commit 1a236485 authored by Graham McVicker's avatar Graham McVicker
Browse files

updated PODs

parent 16745f6e
......@@ -40,7 +40,7 @@ Object to store details of an analysis run
=head1 CONTACT
Describe contact details here
Post questions to the EnsEMBL dev mailing list: <ensembl-dev@ebi.ac.uk>
=head1 APPENDIX
......
......@@ -96,13 +96,17 @@ use strict;
Arg [..] : List of named arguments. (-cigar_string , -features) defined
in this constructor, others defined in FeaturePair and
SeqFeature superclasses.
Example :
SeqFeature superclasses. Either cigar_string or a list
of ungapped features should be provided - not both.
Example : $baf = new BaseAlignFeatureSubclass(-cigar_string => '3M3I12M');
Description: Creates a new BaseAlignFeature using either a cigarstring or
a list of ungapped features.
Returntype :
Exceptions :
Caller :
a list of ungapped features. BaseAlignFeature is an abstract
baseclass and should not actually be instantiated - rather its
subclasses should be.
Returntype : Bio::EnsEMBL::BaseAlignFeature
Exceptions : thrown if both feature and cigar string args are provided
thrown if neither feature nor cigar string args are provided
Caller : general
=cut
......@@ -128,6 +132,7 @@ sub new {
}
=head2 cigar_string
Arg [1] : string $cigar_string
......@@ -135,16 +140,14 @@ sub new {
Description: get/set for attribute cigar_string
cigar_string describes the alignment. "xM" stands for
x matches (mismatches), "xI" for inserts into query sequence
(thats the ensembl sequence), "xD" for deletions (inserts in the
subject). an "x" that is 1 can be omitted.
(thats the ensembl sequence), "xD" for deletions
(inserts in the subject). an "x" that is 1 can be omitted.
Returntype : string
Exceptions : throws on a get without previous set
Caller : general
=cut
sub cigar_string {
my ($self,$arg) = @_;
......@@ -164,10 +167,11 @@ sub cigar_string {
}
=head2 ungapped_features
Args : none
Example : none
Example : @ungapped_features = $align_feature->get_feature
Description: converts the internal cigar_string into an array of
ungapped feature pairs
Returntype : list of Bio::EnsEMBL::FeaturePair
......@@ -176,8 +180,6 @@ sub cigar_string {
=cut
sub ungapped_features {
my ($self) = @_;
......@@ -199,11 +201,10 @@ sub ungapped_features {
Description: get/set for the database internal id
Returntype : int
Exceptions : none
Caller : general, set from adaptor on store
Caller : general, set from adaptor on store or retrieval
=cut
sub dbID{
my ($self, $arg) = @_;
......@@ -215,6 +216,8 @@ sub dbID{
}
=head2 adaptor
Arg [1] : Bio::EnsEMBL::DBSQL::BaseAlignFeatureAdaptor $adaptor
......@@ -236,6 +239,8 @@ sub adaptor {
}
=head2 reverse_complement
Args : none
......@@ -267,11 +272,14 @@ sub reverse_complement {
$self->cigar_string($cigar_string);
}
=head2 _parse_cigar
Args : none
Example : none
Description: creates ungapped features from internally stored cigar line
Description: PRIVATE (internal) method - creates ungapped features from
internally stored cigar line
Returntype : list of Bio::EnsEMBL::FeaturePair
Exceptions : none
Caller : ungapped_features
......@@ -413,7 +421,8 @@ sub _parse_cigar {
Description: creates internal cigarstring and start,end hstart,hend
entries.
Returntype : none, fills in values of self
Exceptions : argument list is sanity checked
Exceptions : argument list undergoes many sanity checks - throws under many
invalid conditions
Caller : new
=cut
......@@ -720,8 +729,17 @@ sub _parse_features {
=head2 _transform_to_RawContig
Arg [1] : none
Example : none
Description: PRIVATE method. Transforms this feature from slice coordinates
to rawcontig coodinates.
Returntype : list of BaseAlignFeatures
Exceptions : none
Caller : transform
=cut
sub _transform_to_RawContig{
my ($self) = @_;
......@@ -799,6 +817,8 @@ sub _hit_unit {
$self->throw( "Abstract method call!" );
}
=head2 _query_unit
Args : none
......@@ -817,6 +837,20 @@ sub _query_unit {
}
=head2 _transform_feature_to_RawContig
Arg [1] : Bio::EnsEMBL::FeaturePair
Example : none
Description: Transforms a component ungapped feature from slice coordinates
to RawContig coordinates.
Returntype : list of Bio::EnsEMBL::FeaturePairs
Exceptions : thrown if feature is not attached to a contig (slice)
thrown if attached slice does not have an adaptor
Caller : internal
=cut
sub _transform_feature_to_RawContig{
my($self, $feature) = @_;
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment