ensembl-pipeline
SimilarityInputIdConfig
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Synopsis
No synopsis!
Description
No description!
Methods
| BIOTYPES_TO_MASK | No description | Code |
| BLASTMINIGENEWISE_PARAMETERS | No description | Code |
| EXONERATE_PARAMETERS | No description | Code |
| EXON_BASED_MASKING | No description | Code |
| FEATURE_RANGE_PADDING | No description | Code |
| FILTER_OBJECT | No description | Code |
| FILTER_PARAMS | No description | Code |
| GENEWISE_PARAMETERS | No description | Code |
| GENE_BASED_MASKING | No description | Code |
| GENE_SOURCE_DB | No description | Code |
| LIMIT_TO_FEATURE_RANGE | No description | Code |
| MINIGENEWISE_PARAMETERS | No description | Code |
| MULTIMINIGENEWISE_PARAMETERS | No description | Code |
| OUTPUT_BIOTYPE | No description | Code |
| OUTPUT_DB | No description | Code |
| PAF_LOGICNAMES | No description | Code |
| PAF_MIN_SCORE_THRESHOLD | No description | Code |
| PAF_SOURCE_DB | No description | Code |
| PAF_UPPER_SCORE_THRESHOLD | No description | Code |
| POST_GENEWISE_MASK | No description | Code |
| PRE_GENEWISE_MASK | No description | Code |
| REJECTED_BIOTYPE | No description | Code |
| REPEATMASKING | No description | Code |
| SEQFETCHER_OBJECT | No description | Code |
| SEQFETCHER_PARAMS | No description | Code |
| SOFTMASKING | No description | Code |
| USE_KILL_LIST | No description | Code |
| WRITE_REJECTED | No description | Code |
| new | No description | Code |
Methods description
None available.
Methods code
| BIOTYPES_TO_MASK | description | prev | next | Top |
sub BIOTYPES_TO_MASK
{ my ($self, $arg) = @_;
if($arg){
$self->{BIOTYPES_TO_MASK} = $arg;
}
return $self->{BIOTYPES_TO_MASK}} | sub BLASTMINIGENEWISE_PARAMETERS
{ my ($self, $arg) = @_;
if($arg){
$self->{BLASTMINIGENEWISE_PARAMETERS} = $arg;
}
return $self->{BLASTMINIGENEWISE_PARAMETERS}} | sub EXONERATE_PARAMETERS
{ my ($self, $arg) = @_;
if($arg){
$self->{EXONERATE_PARAMETERS} = $arg;
}
return $self->{EXONERATE_PARAMETERS}} | sub EXON_BASED_MASKING
{ my ($self, $arg) = @_;
if($arg){
$self->{EXON_BASED_MASKING} = $arg;
}
return $self->{EXON_BASED_MASKING}} | sub FEATURE_RANGE_PADDING
{ my ($self, $arg) = @_;
if($arg){
$self->{FEATURE_RANGE_PADDING} = $arg;
}
return $self->{FEATURE_RANGE_PADDING}} | sub FILTER_OBJECT
{ my ($self, $arg) = @_;
if($arg){
$self->{FILTER_OBJECT} = $arg;
}
return $self->{FILTER_OBJECT}} | sub FILTER_PARAMS
{ my ($self, $arg) = @_;
if($arg){
$self->{FILTER_PARAMETERS} = $arg;
}
return $self->{FILTER_PARAMETERS}} | sub GENEWISE_PARAMETERS
{ my ($self, $arg) = @_;
if($arg){
$self->{GENEWISE_PARAMETERS} = $arg;
}
return $self->{GENEWISE_PARAMETERS}} | sub GENE_BASED_MASKING
{ my ($self, $arg) = @_;
if($arg){
$self->{GENE_BASED_MASKING} = $arg;
}
return $self->{GENE_BASED_MASKING}} | sub GENE_SOURCE_DB
{ my ($self, $arg) = @_;
if($arg){
$self->{GENE_SOURCE_DB} = $arg;
}
return $self->{GENE_SOURCE_DB}} | sub LIMIT_TO_FEATURE_RANGE
{ my ($self, $arg) = @_;
if($arg){
$self->{LIMIT_TO_FEATURE_RANGE} = $arg;
}
return $self->{LIMIT_TO_FEATURE_RANGE}} | sub MINIGENEWISE_PARAMETERS
{ my ($self, $arg) = @_;
if($arg){
$self->{MINIGENEWISE_PARAMETERS} = $arg;
}
return $self->{MINIGENEWISE_PARAMETERS}} | sub MULTIMINIGENEWISE_PARAMETERS
{ my ($self, $arg) = @_;
if($arg){
$self->{MULTIMINIGENEWISE_PARAMETERS} = $arg;
}
return $self->{MULTIMINIGENEWISE_PARAMETERS}} | sub OUTPUT_BIOTYPE
{ my ($self, $arg) = @_;
if($arg){
$self->{OUTPUT_BIOTYPE} = $arg;
}
return $self->{OUTPUT_BIOTYPE}} | sub OUTPUT_DB
{ my ($self, $arg) = @_;
if($arg){
$self->{OUTPUT_DB} = $arg;
}
return $self->{OUTPUT_DB}} | sub PAF_LOGICNAMES
{ my ($self, $arg) = @_;
if($arg){
$self->{PAF_LOGICNAMES} = $arg;
}
return $self->{PAF_LOGICNAMES}} | sub PAF_MIN_SCORE_THRESHOLD
{ my ($self, $arg) = @_;
if($arg){
$self->{PAF_MIN_SCORE_THRESHOLD} = $arg;
}
return $self->{PAF_MIN_SCORE_THRESHOLD}} | sub PAF_SOURCE_DB
{ my ($self, $arg) = @_;
if($arg){
$self->{PAF_SOURCE_DB} = $arg;
}
return $self->{PAF_SOURCE_DB}} | sub PAF_UPPER_SCORE_THRESHOLD
{ my ($self, $arg) = @_;
if($arg){
$self->{PAF_UPPER_SCORE_THRESHOLD} = $arg;
}
return $self->{PAF_UPPER_SCORE_THRESHOLD}} | sub POST_GENEWISE_MASK
{ my ($self, $arg) = @_;
if($arg){
$self->{POST_GENEWISE_MASK} = $arg;
}
return $self->{POST_GENEWISE_MASK}} | sub PRE_GENEWISE_MASK
{ my ($self, $arg) = @_;
if($arg){
$self->{PRE_GENEWISE_MASK} = $arg;
}
return $self->{PRE_GENEWISE_MASK}} | sub REJECTED_BIOTYPE
{ my ($self, $arg) = @_;
if($arg){
$self->{REJECTED_BIOTYPE} = $arg;
}
return $self->{REJECTED_BIOTYPE};} | sub REPEATMASKING
{ my ($self, $arg) = @_;
if($arg){
$self->{REPEATMASKING} = $arg;
}
return $self->{REPEATMASKING}} | sub SEQFETCHER_OBJECT
{ my ($self, $arg) = @_;
if($arg){
$self->{SEQFETCHER_OBJECT} = $arg;
}
return $self->{SEQFETCHER_OBJECT}} | sub SEQFETCHER_PARAMS
{ my ($self, $arg) = @_;
if($arg){
$self->{SEQFETCHER_PARAMS} = $arg;
}
return $self->{SEQFETCHER_PARAMS}} | sub SOFTMASKING
{ my ($self, $arg) = @_;
if($arg){
$self->{SOFTMASKING} = $arg;
}
return $self->{SOFTMASKING}
}
1;} | sub USE_KILL_LIST
{ my ($self, $arg) = @_;
if($arg){
$self->{USE_KILL_LIST} = $arg;
}
return $self->{USE_KILL_LIST}} | sub WRITE_REJECTED
{ my ($self, $arg) = @_;
if(defined($arg)){
$self->{WRITE_REJECTED} = $arg;
}
return $self->{WRITE_REJECTED};} | sub new
{ my ($class,@args) = @_;
my $self = bless {},$class;
return $self;} | General documentation
No general documentation available.