ensembl-pipeline SimilarityInputIdConfig
Package variablesGeneral documentationMethods
Toolbar
WebCvsRaw content
Package variables
No package variables defined.
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_MASKdescriptionprevnextTop
sub BIOTYPES_TO_MASK {
  my ($self, $arg) = @_;
  if($arg){
    $self->{BIOTYPES_TO_MASK} = $arg;
  }
  return $self->{BIOTYPES_TO_MASK}
}
BLASTMINIGENEWISE_PARAMETERSdescriptionprevnextTop
sub BLASTMINIGENEWISE_PARAMETERS {
  my ($self, $arg) = @_;
  if($arg){
    $self->{BLASTMINIGENEWISE_PARAMETERS} = $arg;
  }
  return $self->{BLASTMINIGENEWISE_PARAMETERS}
}
EXONERATE_PARAMETERSdescriptionprevnextTop
sub EXONERATE_PARAMETERS {
  my ($self, $arg) = @_;
  if($arg){
    $self->{EXONERATE_PARAMETERS} = $arg;
  }
  return $self->{EXONERATE_PARAMETERS}
}
EXON_BASED_MASKINGdescriptionprevnextTop
sub EXON_BASED_MASKING {
  my ($self, $arg) = @_;
  if($arg){
    $self->{EXON_BASED_MASKING} = $arg;
  }
  return $self->{EXON_BASED_MASKING}
}
FEATURE_RANGE_PADDINGdescriptionprevnextTop
sub FEATURE_RANGE_PADDING {
  my ($self, $arg) = @_;
  if($arg){
    $self->{FEATURE_RANGE_PADDING} = $arg;
  }
  return $self->{FEATURE_RANGE_PADDING}
}
FILTER_OBJECTdescriptionprevnextTop
sub FILTER_OBJECT {
  my ($self, $arg) = @_;
  if($arg){
    $self->{FILTER_OBJECT} = $arg;
  }
  return $self->{FILTER_OBJECT}
}
FILTER_PARAMSdescriptionprevnextTop
sub FILTER_PARAMS {
  my ($self, $arg) = @_;
  if($arg){
    $self->{FILTER_PARAMETERS} = $arg;
  }
  return $self->{FILTER_PARAMETERS}
}
GENEWISE_PARAMETERSdescriptionprevnextTop
sub GENEWISE_PARAMETERS {
  my ($self, $arg) = @_;
  if($arg){
    $self->{GENEWISE_PARAMETERS} = $arg;
  }
  return $self->{GENEWISE_PARAMETERS}
}
GENE_BASED_MASKINGdescriptionprevnextTop
sub GENE_BASED_MASKING {
  my ($self, $arg) = @_;
  if($arg){
    $self->{GENE_BASED_MASKING} = $arg;
  }
  return $self->{GENE_BASED_MASKING}
}
GENE_SOURCE_DBdescriptionprevnextTop
sub GENE_SOURCE_DB {
  my ($self, $arg) = @_;
  if($arg){
    $self->{GENE_SOURCE_DB} = $arg;
  }
  return $self->{GENE_SOURCE_DB}
}
LIMIT_TO_FEATURE_RANGEdescriptionprevnextTop
sub LIMIT_TO_FEATURE_RANGE {
  my ($self, $arg) = @_;
  if($arg){
    $self->{LIMIT_TO_FEATURE_RANGE} = $arg;
  }
  return $self->{LIMIT_TO_FEATURE_RANGE}
}
MINIGENEWISE_PARAMETERSdescriptionprevnextTop
sub MINIGENEWISE_PARAMETERS {
  my ($self, $arg) = @_;
  if($arg){
    $self->{MINIGENEWISE_PARAMETERS} = $arg;
  }
  return $self->{MINIGENEWISE_PARAMETERS}
}
MULTIMINIGENEWISE_PARAMETERSdescriptionprevnextTop
sub MULTIMINIGENEWISE_PARAMETERS {
  my ($self, $arg) = @_;
  if($arg){
    $self->{MULTIMINIGENEWISE_PARAMETERS} = $arg;
  }
  return $self->{MULTIMINIGENEWISE_PARAMETERS}
}
OUTPUT_BIOTYPEdescriptionprevnextTop
sub OUTPUT_BIOTYPE {
  my ($self, $arg) = @_;
  if($arg){
    $self->{OUTPUT_BIOTYPE} = $arg;
  }
  return $self->{OUTPUT_BIOTYPE}
}
OUTPUT_DBdescriptionprevnextTop
sub OUTPUT_DB {
  my ($self, $arg) = @_;
  if($arg){
    $self->{OUTPUT_DB} = $arg;
  }
  return $self->{OUTPUT_DB}
}
PAF_LOGICNAMESdescriptionprevnextTop
sub PAF_LOGICNAMES {
  my ($self, $arg) = @_;
  if($arg){
    $self->{PAF_LOGICNAMES} = $arg;
  }
  return $self->{PAF_LOGICNAMES}
}
PAF_MIN_SCORE_THRESHOLDdescriptionprevnextTop
sub PAF_MIN_SCORE_THRESHOLD {
  my ($self, $arg) = @_;
  if($arg){
    $self->{PAF_MIN_SCORE_THRESHOLD} = $arg;
  }
  return $self->{PAF_MIN_SCORE_THRESHOLD}
}
PAF_SOURCE_DBdescriptionprevnextTop
sub PAF_SOURCE_DB {
  my ($self, $arg) = @_;
  if($arg){
    $self->{PAF_SOURCE_DB} = $arg;
  }
  return $self->{PAF_SOURCE_DB}
}
PAF_UPPER_SCORE_THRESHOLDdescriptionprevnextTop
sub PAF_UPPER_SCORE_THRESHOLD {
  my ($self, $arg) = @_;
  if($arg){
    $self->{PAF_UPPER_SCORE_THRESHOLD} = $arg;
  }
  return $self->{PAF_UPPER_SCORE_THRESHOLD}
}
POST_GENEWISE_MASKdescriptionprevnextTop
sub POST_GENEWISE_MASK {
  my ($self, $arg) = @_;
  if($arg){
    $self->{POST_GENEWISE_MASK} = $arg;
  }
  return $self->{POST_GENEWISE_MASK}
}
PRE_GENEWISE_MASKdescriptionprevnextTop
sub PRE_GENEWISE_MASK {
  my ($self, $arg) = @_;
  if($arg){
    $self->{PRE_GENEWISE_MASK} = $arg;
  }
  return $self->{PRE_GENEWISE_MASK}
}
REJECTED_BIOTYPEdescriptionprevnextTop
sub REJECTED_BIOTYPE {
  my ($self, $arg) = @_;
  if($arg){
    $self->{REJECTED_BIOTYPE} = $arg;
  }
  return $self->{REJECTED_BIOTYPE};
}
REPEATMASKINGdescriptionprevnextTop
sub REPEATMASKING {
  my ($self, $arg) = @_;
  if($arg){
    $self->{REPEATMASKING} = $arg;
  }
  return $self->{REPEATMASKING}
}
SEQFETCHER_OBJECTdescriptionprevnextTop
sub SEQFETCHER_OBJECT {
  my ($self, $arg) = @_;
  if($arg){
    $self->{SEQFETCHER_OBJECT} = $arg;
  }
  return $self->{SEQFETCHER_OBJECT}
}
SEQFETCHER_PARAMSdescriptionprevnextTop
sub SEQFETCHER_PARAMS {
  my ($self, $arg) = @_;
  if($arg){
    $self->{SEQFETCHER_PARAMS} = $arg;
  }
  return $self->{SEQFETCHER_PARAMS}
}
SOFTMASKINGdescriptionprevnextTop
sub SOFTMASKING {
  my ($self, $arg) = @_;
  if($arg){
    $self->{SOFTMASKING} = $arg;
  }
  return $self->{SOFTMASKING}
}

1;
}
USE_KILL_LISTdescriptionprevnextTop
sub USE_KILL_LIST {
  my ($self, $arg) = @_;
  if($arg){
    $self->{USE_KILL_LIST} = $arg;
  }
  return $self->{USE_KILL_LIST}
}
WRITE_REJECTEDdescriptionprevnextTop
sub WRITE_REJECTED {
  my ($self, $arg) = @_;
  if(defined($arg)){
    $self->{WRITE_REJECTED} = $arg;
  }
  return $self->{WRITE_REJECTED};
}
newdescriptionprevnextTop
sub new {
  my ($class,@args) = @_;
  my $self = bless {},$class;
  return $self;
}
General documentation
No general documentation available.