Commit 2d711c28 authored by Monika Komorowska's avatar Monika Komorowska
Browse files

removed user and pass methods, no longer required in DirectXrefs.pm

parent 4eda6b63
......@@ -49,26 +49,6 @@ sub xref{
return $self->{_xref};
}
# getter/setter for xref db user
sub user{
my ($self, $arg) = @_;
(defined $arg) &&
($self->{_user} = $arg );
return $self->{_user};
}
#getter/setter for xref db password
sub pass{
my ($self, $arg) = @_;
(defined $arg) &&
($self->{_pass} = $arg );
return $self->{_pass};
}
=head2 uniparc
Arg [1] : (optional)
......@@ -225,8 +205,6 @@ sub process_file {
my $self = shift;
my $file = shift;
my $verbose = shift;
my $no_xref = shift;
my $xref=undef;
......@@ -340,7 +318,7 @@ sub process_file {
}
if(defined($xref_hash{host}) and (!defined($no_xref))){
if(defined($xref_hash{host}) ){
my ($host, $user, $dbname, $pass, $port);
$host = $xref_hash{'host'};
$user = $xref_hash{'user'};
......@@ -381,12 +359,10 @@ sub process_file {
}
}
elsif(!defined($no_xref)){
else {
croak "No host name given for xref database\n";
}
else{
print "No xref database is too be used\n" if ($verbose)
}
#If we had UniParc information then create the settings
if($uniparc_hash{dbname}) {
......@@ -429,19 +405,19 @@ sub process_file {
-dbname => $dbname);
$mapper->core($core);
if(!defined($no_xref)){
$mapper->add_meta_pair("species", $host.":".$dbname);
$mapper->add_meta_pair("species", $host.":".$dbname);
if(defined($species_hash{'dir'})){
$core->dir($species_hash{'dir'});
if(!-d $species_hash{'dir'}){
if(defined($species_hash{'dir'})){
$core->dir($species_hash{'dir'});
if(!-d $species_hash{'dir'}){
croak "directory ".$species_hash{'dir'}." does not exist please create this\n";
}
}
else{
croak "No directory specified for the ensembl fasta files\n";
}
}
}
else{
croak "No directory specified for the ensembl fasta files\n";
}
$core->species($value);
#connect to previous release of core db if connection details specified in xref_input (pr_host, pr_port, pr_dbname, pr_user)
......
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