whitespace, remove old Glovar method!

modules/Bio/EnsEMBL/Utils/ConversionSupport.pm

@@ -342,16 +342,16 @@ sub list_all_params {
   $Text::Wrap::colums = 72;
   my @params = $self->allowed_params;
   foreach my $key (@params) {
-        my @vals = $self->param($key);
-        if (@vals) {
-            $txt .= Text::Wrap::wrap( sprintf('   %-21s', $key),
-                                      ' 'x24,
-                                      join(", ", @vals)
-                                    ) . "\n";
-        }
+    my @vals = $self->param($key);
+    if (@vals) {
+      $txt .= Text::Wrap::wrap( sprintf('   %-21s', $key),
+				' 'x24,
+				join(", ", @vals)
+			      ) . "\n";
     }
-    $txt .= "\n";
-    return $txt;
+  }
+  $txt .= "\n";
+  return $txt;
 }
 
 =head2 create_commandline_options
@@ -376,38 +376,37 @@ sub list_all_params {
 =cut
 
 sub create_commandline_options {
-    my ($self, $settings) = @_;
-    my %param_hash;
-
-    # get all allowed parameters
-    if ($settings->{'allowed_params'}) {
-        # exclude params explicitly stated
-        my %exclude = map { $_ => 1 } @{ $settings->{'exclude'} || [] };
-        foreach my $param ($self->allowed_params) {
-            unless ($exclude{$param}) {
-                my ($first, @rest) = $self->param($param);
-                next unless (defined($first));
-
-                if (@rest) {
-                    $first = join(",", $first, @rest);
-                }
-                $param_hash{$param} = $first;
-            }
-        }
-
+  my ($self, $settings) = @_;
+  my %param_hash;
+
+  # get all allowed parameters
+  if ($settings->{'allowed_params'}) {
+    # exclude params explicitly stated
+    my %exclude = map { $_ => 1 } @{ $settings->{'exclude'} || [] };
+    foreach my $param ($self->allowed_params) {
+      unless ($exclude{$param}) {
+	my ($first, @rest) = $self->param($param);
+	next unless (defined($first));
+	
+	if (@rest) {
+	  $first = join(",", $first, @rest);
+	}
+	$param_hash{$param} = $first;
+      }
     }
+  }
 
-    # replace values
-    foreach my $key (keys %{ $settings->{'replace'} || {} }) {
-        $param_hash{$key} = $settings->{'replace'}->{$key};
-    }
+  # replace values
+  foreach my $key (keys %{ $settings->{'replace'} || {} }) {
+    $param_hash{$key} = $settings->{'replace'}->{$key};
+  }
 
-    # create the commandline options string
-    my $options_string;
-    foreach my $param (keys %param_hash) {
-        $options_string .= sprintf("--%s %s ", $param, $param_hash{$param});
-    }
-    return $options_string;
+  # create the commandline options string
+  my $options_string;
+  foreach my $param (keys %param_hash) {
+    $options_string .= sprintf("--%s %s ", $param, $param_hash{$param});
+  }
+  return $options_string;
 }
 
 =head2 check_required_params
@@ -423,15 +422,15 @@ sub create_commandline_options {
 =cut
 
 sub check_required_params {
-    my ($self, @params) = @_;
-    my @missing = ();
-    foreach my $param (@params) {
-        push @missing, $param unless $self->param($param);
-    }
-    if (@missing) {
-        throw("Missing parameters: @missing.\nYou must specify them on the commandline or in your conffile.\n");
-    }
-    return(1);
+  my ($self, @params) = @_;
+  my @missing = ();
+  foreach my $param (@params) {
+    push @missing, $param unless $self->param($param);
+  }
+  if (@missing) {
+    throw("Missing parameters: @missing.\nYou must specify them on the commandline or in your conffile.\n");
+  }
+  return(1);
 }
 
 =head2 user_proceed
@@ -455,20 +454,20 @@ sub check_required_params {
 =cut
 
 sub user_proceed {
-    my ($self, $text) = @_;
-
-    if ($self->param('interactive')) {
-        print "$text\n" if $text;
-        print "[y/N] ";
-        my $input = lc(<>);
-        chomp $input;
-        unless ($input eq 'y') {
-            print "Skipping.\n";
-            return(0);
-        }
+  my ($self, $text) = @_;
+
+  if ($self->param('interactive')) {
+    print "$text\n" if $text;
+    print "[y/N] ";
+    my $input = lc(<>);
+    chomp $input;
+    unless ($input eq 'y') {
+      print "Skipping.\n";
+      return(0);
     }
+  }
 
-    return(1);
+  return(1);
 }
 
 =head2 user_confirm
@@ -478,8 +477,8 @@ sub user_proceed {
 =cut
 
 sub user_confirm {
-    my $self = shift;
-    exit unless $self->user_proceed("Continue?");
+  my $self = shift;
+  exit unless $self->user_proceed("Continue?");
 }
 
 =head2 read_user_input
@@ -499,14 +498,14 @@ sub user_confirm {
 =cut
 
 sub read_user_input {
-    my ($self, $text) = @_;
+  my ($self, $text) = @_;
 
-    if ($self->param('interactive')) {
-        print "$text\n" if $text;
-        my $input = <>;
-        chomp $input;
-        return $input;
-    }
+  if ($self->param('interactive')) {
+    print "$text\n" if $text;
+    my $input = <>;
+    chomp $input;
+    return $input;
+  }
 }
 
 =head2 comma_to_list
@@ -524,12 +523,12 @@ sub read_user_input {
 =cut
 
 sub comma_to_list {
-    my $self = shift;
-    foreach my $param (@_) {
-        $self->param($param,
-            split (/,/, join (',', $self->param($param))));
-    }
-    return(1);
+  my $self = shift;
+  foreach my $param (@_) {
+    $self->param($param,
+		 split (/,/, join (',', $self->param($param))));
+  }
+  return(1);
 }
 
 =head2 list_or_file
@@ -545,24 +544,24 @@ sub comma_to_list {
 =cut
 
 sub list_or_file {
-    my ($self, $param) = @_;
-    my @vals = $self->param($param);
-    return unless (@vals);
-
-    my $firstval = $vals[0];
-    if (scalar(@vals) == 1 && -e $firstval) {
-        # we didn't get a list of values, but a file to read values from
-        @vals = ();
-        open(IN, $firstval) or throw("Cannot open $firstval for reading: $!");
-        while(<IN>){
-            chomp;
-            push(@vals, $_);
-        }
-        close(IN);
-        $self->param($param, @vals);
+  my ($self, $param) = @_;
+  my @vals = $self->param($param);
+  return unless (@vals);
+
+  my $firstval = $vals[0];
+  if (scalar(@vals) == 1 && -e $firstval) {
+    # we didn't get a list of values, but a file to read values from
+    @vals = ();
+    open(IN, $firstval) or throw("Cannot open $firstval for reading: $!");
+    while(<IN>){
+      chomp;
+      push(@vals, $_);
     }
-    $self->comma_to_list($param);
-    return(1);
+    close(IN);
+    $self->param($param, @vals);
+  }
+  $self->comma_to_list($param);
+  return(1);
 }
 
 =head2 param
@@ -582,31 +581,31 @@ sub list_or_file {
 =cut
 
 sub param {
-    my $self = shift;
-    my $name = shift or throw("You must supply a parameter name");
-
-    # setter
-    if (@_) {
-        if (scalar(@_) == 1) {
-            # single value
-            $self->{'_param'}->{$name} = shift;
-        } else {
-            # list of values
-            undef $self->{'_param'}->{$name};
-            @{ $self->{'_param'}->{$name} } = @_;
-        }
-    }
+  my $self = shift;
+  my $name = shift or throw("You must supply a parameter name");
 
-    # getter
-    if (ref($self->{'_param'}->{$name}) eq 'ARRAY') {
-        # list parameter
-        return @{ $self->{'_param'}->{$name} };
-    } elsif (defined($self->{'_param'}->{$name})) {
-        # single-value parameter
-        return $self->{'_param'}->{$name};
+  # setter
+  if (@_) {
+    if (scalar(@_) == 1) {
+      # single value
+      $self->{'_param'}->{$name} = shift;
     } else {
-        return ();
+      # list of values
+      undef $self->{'_param'}->{$name};
+      @{ $self->{'_param'}->{$name} } = @_;
     }
+  }
+
+  # getter
+  if (ref($self->{'_param'}->{$name}) eq 'ARRAY') {
+    # list parameter
+    return @{ $self->{'_param'}->{$name} };
+  } elsif (defined($self->{'_param'}->{$name})) {
+    # single-value parameter
+    return $self->{'_param'}->{$name};
+  } else {
+    return ();
+  }
 }
 
 =head2 error
@@ -622,9 +621,9 @@ sub param {
 =cut
 
 sub error {
-    my $self = shift;
-    $self->{'_error'} = shift if (@_);
-    return $self->{'_error'};
+  my $self = shift;
+  $self->{'_error'} = shift if (@_);
+  return $self->{'_error'};
 }
 
 =head2 warnings
@@ -639,8 +638,8 @@ sub error {
 =cut
 
 sub warnings {
-    my $self = shift;
-    return $self->{'_warnings'};
+  my $self = shift;
+  return $self->{'_warnings'};
 }
 
 =head2 serverroot
@@ -657,9 +656,9 @@ sub warnings {
 =cut
 
 sub serverroot {
-    my $self = shift;
-    $self->{'_serverroot'} = shift if (@_);
-    return $self->{'_serverroot'};
+  my $self = shift;
+  $self->{'_serverroot'} = shift if (@_);
+  return $self->{'_serverroot'};
 }
 
 =head2 get_database
@@ -677,54 +676,52 @@ sub serverroot {
 =cut
 
 sub get_database {
-    my $self = shift;
-    my $database = shift or throw("You must provide a database");
-    my $prefix = shift || '';
-    $self->check_required_params(
-        "${prefix}host",
-        "${prefix}port",
-        "${prefix}user",
-        # "${prefix}pass", not required since might be empty
-        "${prefix}dbname",
-    );
-
-    my %adaptors = (
-        core    => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
-        ensembl => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
-        evega   => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
-        otter   => 'Bio::Otter::DBSQL::DBAdaptor',
-        vega    => 'Bio::Otter::DBSQL::DBAdaptor',
-		compara => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
-		loutre  => 'Bio::Vega::DBSQL::DBAdaptor',
-    );
-    throw("Unknown database: $database") unless $adaptors{$database};
-
-    $self->dynamic_use($adaptors{$database});
-    my $dba = $adaptors{$database}->new(
-            -host   => $self->param("${prefix}host"),
-            -port   => $self->param("${prefix}port"),
-            -user   => $self->param("${prefix}user"),
-            -pass   => $self->param("${prefix}pass") || '',
-            -dbname => $self->param("${prefix}dbname"),
-            -group  => $database,
-    );
-	#can use this approach to get dna from another db
-#	my $dna_db = $adaptors{$database}->new(
-#			-host => 'otterlive',
-#            -port => '3301',
-#			-user => $self->param("${prefix}user"),
-#			-pass => $self->param("${prefix}pass"),
-#            -dbname => 'loutre_human',
-#		);
-#	$dba->dnadb($dna_db);
-
-    # otherwise explicitely set the dnadb to itself - by default the Registry assumes
-    # a group 'core' for this now
-    $dba->dnadb($dba);
-
-    $self->{'_dba'}->{$database} = $dba;
-    $self->{'_dba'}->{'default'} = $dba unless $self->{'_dba'}->{'default'};
-    return $self->{'_dba'}->{$database};
+  my $self = shift;
+  my $database = shift or throw("You must provide a database");
+  my $prefix = shift || '';
+  $self->check_required_params(
+    "${prefix}host",
+    "${prefix}port",
+    "${prefix}user",
+    "${prefix}dbname",
+  );
+  my %adaptors = (
+    core    => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
+    ensembl => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
+    evega   => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
+    otter   => 'Bio::Otter::DBSQL::DBAdaptor',
+    vega    => 'Bio::Otter::DBSQL::DBAdaptor',
+    compara => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
+    loutre  => 'Bio::Vega::DBSQL::DBAdaptor',
+  );
+  throw("Unknown database: $database") unless $adaptors{$database};
+
+  $self->dynamic_use($adaptors{$database});
+  my $dba = $adaptors{$database}->new(
+    -host   => $self->param("${prefix}host"),
+    -port   => $self->param("${prefix}port"),
+    -user   => $self->param("${prefix}user"),
+    -pass   => $self->param("${prefix}pass") || '',
+    -dbname => $self->param("${prefix}dbname"),
+    -group  => $database,
+  );
+  #can use this approach to get dna from another db
+#  my $dna_db = $adaptors{$database}->new(
+#    -host => 'otterlive',
+#    -port => '3301',
+#    -user => $self->param("${prefix}user"),
+#    -pass => $self->param("${prefix}pass"),
+#    -dbname => 'loutre_human',
+#  );
+#  $dba->dnadb($dna_db);
+
+  # otherwise explicitely set the dnadb to itself - by default the Registry assumes
+  # a group 'core' for this now
+  $dba->dnadb($dba);
+
+  $self->{'_dba'}->{$database} = $dba;
+  $self->{'_dba'}->{'default'} = $dba unless $self->{'_dba'}->{'default'};
+  return $self->{'_dba'}->{$database};
 }
 
 
@@ -780,60 +777,6 @@ sub get_dbconnection {
 
 }
 
-=head2 get_glovar_database
-
-  Example     : my $dba = $support->get_glovar_database;
-  Description : Connects to the Glovar database.
-  Return type : Bio::EnsEMBL::ExternalData::Glovar::DBAdaptor
-  Exceptions  : thrown if no connection to a core db exists
-  Caller      : general
-
-=cut
-
-sub get_glovar_database {
-    my $self = shift;
-    $self->check_required_params(qw(
-        glovarhost
-        glovarport
-        glovaruser
-        glovarpass
-        glovardbname
-        oracle_home
-        ld_library_path
-        glovar_snp_consequence_exp
-    ));
-
-    # check for core dbadaptor
-    my $core_db = $self->dba;
-    unless ($core_db && (ref($core_db) =~ /Bio::.*::DBSQL::DBAdaptor/)) {
-        $self->log_error("You have to connect to a core db before you can get a glovar dbadaptor.\n");
-        exit;
-    }
-    
-    # setup Oracle environment
-    $ENV{'ORACLE_HOME'} = $self->param('oracle_home');
-    $ENV{'LD_LIBRARY_PATH'} = $self->param('ld_library_path');
-
-    # connect to Glovar db
-    $self->dynamic_use('Bio::EnsEMBL::ExternalData::Glovar::DBAdaptor');
-    my $dba = Bio::EnsEMBL::ExternalData::Glovar::DBAdaptor->new(
-            -host   => $self->param("glovarhost"),
-            -port   => $self->param("glovarport"),
-            -user   => $self->param("glovaruser"),
-            -pass   => $self->param("glovarpass"),
-            -dbname => $self->param("glovardbname"),
-            -group  => 'glovar',
-    );
-
-    # setup adaptor inter-relationships
-    $dba->dnadb($core_db);
-    $self->dynamic_use('Bio::EnsEMBL::ExternalData::Glovar::GlovarSNPAdaptor');
-    my $glovar_snp_adaptor = $dba->get_GlovarSNPAdaptor;
-    $glovar_snp_adaptor->consequence_exp($self->param('glovar_snp_consequence_exp'));
-    $core_db->add_ExternalFeatureAdaptor($glovar_snp_adaptor);
-
-    return $dba;
-}
 
 =head2 dba
 
@@ -848,8 +791,8 @@ sub get_glovar_database {
 =cut
 
 sub dba {
-    my ($self, $database) = shift;
-    return $self->{'_dba'}->{$database} || $self->{'_dba'}->{'default'};
+  my ($self, $database) = shift;
+  return $self->{'_dba'}->{$database} || $self->{'_dba'}->{'default'};
 }
 
 =head2 dynamic_use
@@ -866,19 +809,18 @@ sub dba {
 =cut
 
 sub dynamic_use {
-    my ($self, $classname) = @_;
-    my ($parent_namespace, $module) = $classname =~/^(.*::)(.*)$/ ?
-                                        ($1,$2) : ('::', $classname);
-
-    no strict 'refs';
-    # return if module has already been imported
-    return 1 if $parent_namespace->{$module.'::'} && %{ $parent_namespace->{$module.'::'}||{} };
-    
-    eval "require $classname";
-    throw("Failed to require $classname: $@") if ($@);
-    $classname->import();
-
-    return 1;
+  my ($self, $classname) = @_;
+  my ($parent_namespace, $module) = $classname =~/^(.*::)(.*)$/ ? ($1,$2) : ('::', $classname);
+
+  no strict 'refs';
+  # return if module has already been imported
+  return 1 if $parent_namespace->{$module.'::'} && %{ $parent_namespace->{$module.'::'}||{} };
+
+  eval "require $classname";
+  throw("Failed to require $classname: $@") if ($@);
+  $classname->import();
+
+  return 1;
 }
 
 =head2 get_chrlength
@@ -898,48 +840,48 @@ sub dynamic_use {
 =cut
 
 sub get_chrlength {
-    my ($self, $dba, $version,$type,$include_non_reference) = @_;
-    $dba ||= $self->dba;
-	$type ||= 'toplevel';
-    throw("get_chrlength should be passed a Bio::EnsEMBL::DBSQL::DBAdaptor\n")
-        unless ($dba->isa('Bio::EnsEMBL::DBSQL::DBAdaptor'));
-
-    my $sa = $dba->get_SliceAdaptor;
-
-    my @chromosomes = map { $_->seq_region_name } 
-                            @{ $sa->fetch_all($type, $version,$include_non_reference) };
-    my %chr = map { $_ => $sa->fetch_by_region($type, $_, undef, undef, undef, $version)->length } @chromosomes;
-
-    my @wanted = $self->param('chromosomes');
-    if (@wanted) {
-        # check if user supplied invalid chromosome names
-        foreach my $chr (@wanted) {
-            my $found = 0;
-            foreach my $chr_from_db (keys %chr) {
-                if ($chr_from_db eq $chr) {
-                    $found = 1;
-                    last;
-                }
-            }
-            unless ($found) {
-                warning("Didn't find chromosome $chr in database " .
-                         $self->param('dbname'));
-            }
-        }
-        
-        # filter to requested chromosomes only
-        HASH: 
-        foreach my $chr_from_db (keys %chr) {
-            foreach my $chr (@wanted) {
-                if ($chr_from_db eq $chr) {
-                    next HASH;
-                }
-            }
-            delete($chr{$chr_from_db});
-        }
+  my ($self, $dba, $version,$type,$include_non_reference) = @_;
+  $dba ||= $self->dba;
+  $type ||= 'toplevel';
+  throw("get_chrlength should be passed a Bio::EnsEMBL::DBSQL::DBAdaptor\n")
+    unless ($dba->isa('Bio::EnsEMBL::DBSQL::DBAdaptor'));
+
+  my $sa = $dba->get_SliceAdaptor;
+
+  my @chromosomes = map { $_->seq_region_name } 
+    @{ $sa->fetch_all($type, $version,$include_non_reference) };
+  my %chr = map { $_ => $sa->fetch_by_region($type, $_, undef, undef, undef, $version)->length } @chromosomes;
+
+  my @wanted = $self->param('chromosomes');
+  if (@wanted) {
+    # check if user supplied invalid chromosome names
+    foreach my $chr (@wanted) {
+      my $found = 0;
+      foreach my $chr_from_db (keys %chr) {
+	if ($chr_from_db eq $chr) {
+	  $found = 1;
+	  last;
+	}
+      }
+      unless ($found) {