Raw content of SimilarityInputIdConfig
<![CDATA[package SimilarityInputIdConfig;
use vars qw(@ISA);
use strict;
sub new{
my ($class,@args) = @_;
my $self = bless {},$class;
return $self;
}
sub PAF_LOGICNAMES{
my ($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 $self->{PAF_MIN_SCORE_THRESHOLD}
}
sub PAF_UPPER_SCORE_THRESHOLD{
my ($self, $arg) = @_;
if($arg){
$self->{PAF_UPPER_SCORE_THRESHOLD} = $arg;
}
return $self->{PAF_UPPER_SCORE_THRESHOLD}
}
sub PAF_SOURCE_DB{
my ($self, $arg) = @_;
if($arg){
$self->{PAF_SOURCE_DB} = $arg;
}
return $self->{PAF_SOURCE_DB}
}
sub GENE_SOURCE_DB{
my ($self, $arg) = @_;
if($arg){
$self->{GENE_SOURCE_DB} = $arg;
}
return $self->{GENE_SOURCE_DB}
}
sub OUTPUT_DB{
my ($self, $arg) = @_;
if($arg){
$self->{OUTPUT_DB} = $arg;
}
return $self->{OUTPUT_DB}
}
sub OUTPUT_BIOTYPE{
my ($self, $arg) = @_;
if($arg){
$self->{OUTPUT_BIOTYPE} = $arg;
}
return $self->{OUTPUT_BIOTYPE}
}
sub GENEWISE_PARAMETERS{
my ($self, $arg) = @_;
if($arg){
$self->{GENEWISE_PARAMETERS} = $arg;
}
return $self->{GENEWISE_PARAMETERS}
}
sub MINIGENEWISE_PARAMETERS{
my ($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 $self->{MULTIMINIGENEWISE_PARAMETERS}
}
sub BLASTMINIGENEWISE_PARAMETERS{
my ($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 $self->{EXONERATE_PARAMETERS}
}
sub FILTER_PARAMS{
my ($self, $arg) = @_;
if($arg){
$self->{FILTER_PARAMETERS} = $arg;
}
return $self->{FILTER_PARAMETERS}
}
sub FILTER_OBJECT{
my ($self, $arg) = @_;
if($arg){
$self->{FILTER_OBJECT} = $arg;
}
return $self->{FILTER_OBJECT}
}
sub BIOTYPES_TO_MASK{
my ($self, $arg) = @_;
if($arg){
$self->{BIOTYPES_TO_MASK} = $arg;
}
return $self->{BIOTYPES_TO_MASK}
}
sub EXON_BASED_MASKING{
my ($self, $arg) = @_;
if($arg){
$self->{EXON_BASED_MASKING} = $arg;
}
return $self->{EXON_BASED_MASKING}
}
sub GENE_BASED_MASKING{
my ($self, $arg) = @_;
if($arg){
$self->{GENE_BASED_MASKING} = $arg;
}
return $self->{GENE_BASED_MASKING}
}
sub POST_GENEWISE_MASK{
my ($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 $self->{PRE_GENEWISE_MASK}
}
sub REPEATMASKING{
my ($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 $self->{SEQFETCHER_PARAMS}
}
sub USE_KILL_LIST{
my ($self, $arg) = @_;
if($arg){
$self->{USE_KILL_LIST} = $arg;
}
return $self->{USE_KILL_LIST}
}
sub LIMIT_TO_FEATURE_RANGE{
my ($self, $arg) = @_;
if($arg){
$self->{LIMIT_TO_FEATURE_RANGE} = $arg;
}
return $self->{LIMIT_TO_FEATURE_RANGE}
}
sub FEATURE_RANGE_PADDING{
my ($self, $arg) = @_;
if($arg){
$self->{FEATURE_RANGE_PADDING} = $arg;
}
return $self->{FEATURE_RANGE_PADDING}
}
sub WRITE_REJECTED{
my ($self, $arg) = @_;
if(defined($arg)){
$self->{WRITE_REJECTED} = $arg;
}
return $self->{WRITE_REJECTED};
}
sub REJECTED_BIOTYPE{
my ($self, $arg) = @_;
if($arg){
$self->{REJECTED_BIOTYPE} = $arg;
}
return $self->{REJECTED_BIOTYPE};
}
sub SOFTMASKING{
my ($self, $arg) = @_;
if($arg){
$self->{SOFTMASKING} = $arg;
}
return $self->{SOFTMASKING}
}
1;
]]>