diff --git a/modules/Bio/EnsEMBL/Utils/Converter.pm b/modules/Bio/EnsEMBL/Utils/Converter.pm
new file mode 100644
index 0000000000000000000000000000000000000000..dcbcc4eb1d2bb66714ee2e55378410a8913848fa
--- /dev/null
+++ b/modules/Bio/EnsEMBL/Utils/Converter.pm
@@ -0,0 +1,279 @@
+# EnsEMBL module for conversion of objects between EnsEMBL and other project, such as BioPerl
+#
+# Created and Cared for by Juguang Xiao <juguang@fugu-sg.org>
+#
+# Copyright Juguang Xiao
+#
+# You may distribute this module under the same terms as perl itself
+#
+# POD documentation
+#
+
+=head1 NAME
+
+Bio::EnsEMBL::Utils::Converter, a converter factory
+
+=head1 SYNOPSIS
+
+ my $converter = Bio::EnsEMBL::Utils::Converter->new(
+ -in => 'Bio::SeqFeature::Generic',
+ -out => 'Bio::EnsEMBL::SimpleFeature'
+ );
+
+ my ($fearture1, $feature2);
+ my $ens_simple_features = $converter->convert([$feature1, $feature2]);
+ my @ens_simple_features = @{$ens_simple_features};
+
+=head1 DESCRIPTION
+
+ Module to converter the business objects between EnsEMBL and any other projects, currently BioPerl.
+
+=head1 FEEDBACK
+
+
+=head1 AUTHOR - Juguang Xiao
+
+Juguang Xiao <juguang@fugu-sg.org>
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods.
+Internal methods are usually preceded with a _
+
+=cut
+
+# Let the code begin ...
+
+
+package Bio::EnsEMBL::Utils::Converter;
+
+use strict;
+use vars qw(@ISA);
+
+use Bio::EnsEMBL::Root;
+
+@ISA =qw(Bio::EnsEMBL::Root);
+
+=head2 new
+ Title : new
+ Usage :
+ my $converter = Bio::EnsEMBL::Utils::Converter->new(
+ -in => 'Bio::SeqFeature::Generic',
+ -out => 'Bio::EnsEMBL::SimpleFeature'
+ );
+
+ Function: constructor for converter object
+ Returns : L<Bio::EnsEMBL::Utils::Converter>
+ Args :
+ in - the module name of the input.
+ out - the module name of the output.
+ analysis - a Bio::EnsEMBL::Analysis object, if converting other objects to EnsEMBL features.
+ contig - a Bio::EnsEMBL::RawContig object, if converting other objects to EnsEMBL features.
+
+=cut
+
+sub new {
+ my ($caller, @args) = @_;
+ my $class = ref($caller) || $caller;
+
+ if($class =~ /Bio::EnsEMBL::Utils::Converter::(\S+)/){
+ my $self = $class->SUPER::new(@args);
+ $self->_initialize(@args);
+ return $self;
+ }else{
+ my %params = @args;
+ @params{map {lc $_} keys %params} = values %params;
+ my $module = $class->_guess_module($params{-in}, $params{-out});
+
+ return undef unless($class->_load_module($module));
+ return "$module"->new(@args);
+ }
+}
+
+# This would be invoked by sub-module's _initialize.
+
+sub _initialize {
+ my ($self, @args) = @_;
+
+ my ($in, $out) = $self->_rearrange([qw(IN OUT)], @args);
+
+ $self->in($in);
+ $self->out($out);
+}
+
+=head2 _guess_module
+ Usage : $module = $class->_guess_module(
+ 'Bio::EnsEMBL::SimpleFeature',
+ 'Bio::EnsEMBL::Generic'
+ );
+=cut
+
+sub _guess_module {
+ my ($self, $in, $out) = @_;
+ if($in =~ /^Bio::EnsEMBL::(\S+)/ and $out =~ /^Bio::EnsEMBL::(\S+)/){
+ $self->throw("Cannot convert between EnsEMBL objects.\n[$in] to [$out]");
+ }elsif($in =~ /^Bio::EnsEMBL::(\S+)/){
+ return 'Bio::EnsEMBL::Utils::Converter::ens_bio';
+ }elsif($out =~ /^Bio::EnsEMBL::(\S+)/){
+ return 'Bio::EnsEMBL::Utils::Converter::bio_ens';
+ }else{
+ $self->throw("Cannot convert between non-EnsEMBL objects.\n[$in] to [$out]");
+ }
+}
+
+=head2 convert
+ Title : convert
+ Usage : my $array_ref = $converter->convert(\@input);
+ Function: does the actual conversion
+ Returns : an array ref of converted objects
+ Args : an array ref of converting objects
+
+=cut
+
+sub convert{
+ my ($self, $input) = @_;
+
+ $input || $self->throw("Need a ref of array of input objects to convert");
+
+ my $output_module = $self->out;
+ $self->throw("Cannot load [$output_module] perl module")
+ unless $self->_load_module($output_module);
+
+ unless(ref($input) eq 'ARRAY'){
+ $self->warn("The input is supposed to be an array ref");
+ return $self->_convert_single($input);
+ }
+
+ my @output = ();
+ foreach(@{$input}){
+ push(@output, $self->_convert_single($_));
+ }
+
+ return \@output;
+}
+
+sub _converter_single{
+ my ($self, $input) = @_;
+ $self->throw("Not implemented. Please check the instance subclass");
+}
+
+=head2 in
+
+ Title : in
+ Useage : $self->in
+ Function : get and set for in
+ Return :
+ Args :
+
+=cut
+
+sub in {
+ my($self, $arg) = @_;
+ if(defined($arg)){
+ $self->{_in} = $arg;
+ }
+ return $self->{_in};
+}
+
+=head2 out
+
+ Title : out
+ Useage : $self->out
+ Function : get and set for out
+ Return :
+ Args :
+
+=cut
+
+sub out {
+ my($self, $arg) = @_;
+ if(defined($arg)){
+ $self->{_out} = $arg;
+ }
+ return $self->{_out};
+}
+
+=head2 analysis
+
+ Title : analysis
+ Useage : $self->analysis
+ Function : get and set for analysis
+ Return : L<Bio::EnsEMBL::Analysis>
+ Args : L<Bio::EnsEMBL::Analysis>
+
+=cut
+
+sub analysis {
+ my($self, $arg) = @_;
+ if(defined($arg)){
+ $self->throws("A Bio::EnsEMBL::Analysis object expected.") unless(defined $arg);
+ $self->{_analysis} = $arg;
+ }
+ return $self->{_analysis};
+}
+
+=head2 contig
+
+ Title : contig
+ Useage : $self->contig
+ Function : get and set for contig
+ Return : L<Bio::EnsEMBL::RawContig>
+ Args : L<Bio::EnsEMBL::RawContig>
+
+=cut
+
+sub contig {
+ my($self, $arg) = @_;
+ if(defined($arg)){
+ $self->throws("A Bio::EnsEMBL::RawContig object expected.") unless(defined $arg);
+ $self->{_contig} = $arg;
+ }
+ return $self->{_contig};
+}
+
+sub _getset {
+ my ($self, $tag, $value, $type) = @_;
+
+ $tag || $self->throw("a tag needed");
+
+ if(defined($value)){
+ $self->{_$tag} = $value;
+ }
+ return $self->{_$tag};
+}
+
+sub getset{
+ my ($self, $arg) = @_;
+ return $self->_getset('getset', $arg);
+}
+
+=head2 _load_module
+ This method is copied from Bio::Root::Root
+=cut
+
+sub _load_module {
+ my ($self, $name) = @_;
+ my ($module, $load, $m);
+ $module = "_<$name.pm";
+ return 1 if $main::{$module};
+
+ # untaint operation for safe web-based running (modified after a fix
+ # a fix by Lincoln) HL
+ if ($name !~ /^([\w:]+)$/) {
+ $self->throw("$name is an illegal perl package name");
+ }
+
+ $load = "$name.pm";
+ my $io = Bio::Root::IO->new();
+ # catfile comes from IO
+ $load = $io->catfile((split(/::/,$load)));
+ eval {
+ require $load;
+ };
+ if ( $@ ) {
+ $self->throw("Failed to load module $name. ".$@);
+ }
+ return 1;
+}
+
+1;
diff --git a/modules/Bio/EnsEMBL/Utils/Converter/bio_ens.pm b/modules/Bio/EnsEMBL/Utils/Converter/bio_ens.pm
new file mode 100644
index 0000000000000000000000000000000000000000..9677ac17ded5b93ab3828352254918c984c9ac33
--- /dev/null
+++ b/modules/Bio/EnsEMBL/Utils/Converter/bio_ens.pm
@@ -0,0 +1,141 @@
+# Bio::EnsEMBL::Utils::Converter::bio_ens
+#
+# Created and cared for by Juguang Xiao <juguang@fugu-sg.org>
+# Created date: 4/3/2003
+#
+# Copyright Juguang Xiao
+#
+# You may distribute this module under the same terms as perl itself
+#
+# POD documentation
+#
+
+=head1 NAME
+
+Bio::EnsEMBL::Utils::Converter::bio_ens
+
+=head1 SYNOPISIS
+
+You should not use this module directly. Please check out the
+Bio::EnsEMBL::Utils::Converter module.
+
+=head1 DESCRIPTION
+
+
+=head1 FEEDBACK
+
+=head2 Mailing Lists
+
+=head2 Reporting Bugs
+
+
+=head1 AUTHOR Juguang Xiao
+
+Juguang Xiao <juguang@fugu-sg.org>
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods.
+Internal methods are usually preceded with a _
+
+=cut
+
+# Let the code begin ...
+
+package Bio::EnsEMBL::Utils::Converter::bio_ens;
+
+use strict;
+use vars qw(@ISA);
+use Bio::EnsEMBL::Analysis;
+use Bio::EnsEMBL::Utils::Converter;
+@ISA = qw(Bio::EnsEMBL::Utils::Converter);
+
+=head2 new
+
+Please see Bio::EnsEMBL::Utils::Converter::new
+
+=cut
+
+sub new {
+ my ($caller, @args) = @_;
+ my $class = ref($caller) || $caller;
+
+ if($class eq 'Bio::EnsEMBL::Utils::Converter::bio_ens'){
+ my %params = @args;
+ @params{map{lc $_} keys %params} = values %params;
+ my $module = $class->_guess_module($params{-in}, $params{-out});
+ return undef unless ($class->_load_module($module));
+ return "$module"->new(@args);
+ }else{
+ my $self = $class->SUPER::new(@args);
+# $self->_initialize(@args);
+ return $self;
+ }
+}
+
+sub _initialize {
+ my ($self, @args) = @_;
+ $self->SUPER::_initialize(@args);
+
+ my ($analysis, $contig) =
+ $self->_rearrange([qw(analysis contig)], @args);
+
+ $self->analysis($analysis);
+ $self->contig($contig);
+}
+
+
+sub _guess_module {
+ my ($self, $in, $out) = @_;
+ my $tail;
+ if($in eq 'Bio::Search::HSP::GenericHSP'){
+ $tail = 'bio_ens_hit';
+ }elsif($in eq 'Bio::SeqFeature::Generic'){
+ $tail = 'bio_ens_seqFeature';
+ }elsif($in eq 'Bio::SeqFeature::FeaturePair'){
+ $tail = 'bio_ens_featurePair';
+ }else{
+ $self->throw("[$in] to [$out], not supported");
+ }
+ return "Bio::EnsEMBL::Utils::Converter::$tail";
+}
+
+
+=head2 analysis
+ Title : analysis
+ Usage : $self->analysis
+ Function: get and set for analysis
+ Return : L<Bio::EnsEMBL::Analysis>
+ Args : L<Bio::EnsEMBL::Analysis>
+=cut
+
+sub analysis {
+ my ($self, $arg) = @_;
+ if(defined($arg)){
+ $self->throws("A Bio::EnsEMBL::Analysis object expected.") unless(defined $arg);
+ $self->{_analysis} = $arg;
+ }
+ return $self->{_analysis};
+}
+
+
+
+=head2 contig
+ Title : contig
+ Usage : $self->contig
+ Function: get and set for contig
+ Return :
+ Args :
+=cut
+
+sub contig {
+ my ($self, $arg) = @_;
+ if(defined($arg)){
+ $self->{_contig} = $arg;
+ }
+ return $self->{_contig};
+}
+
+
+
+1;
diff --git a/modules/Bio/EnsEMBL/Utils/Converter/bio_ens_featurePair.pm b/modules/Bio/EnsEMBL/Utils/Converter/bio_ens_featurePair.pm
new file mode 100644
index 0000000000000000000000000000000000000000..99744ceca5d5175e6d28a1f5fcd47192cd9c9e59
--- /dev/null
+++ b/modules/Bio/EnsEMBL/Utils/Converter/bio_ens_featurePair.pm
@@ -0,0 +1,111 @@
+# Bio::EnsEMBL::Utils::Converter::bio_ens_featurePair
+#
+# Created and cared for by Juguang Xiao <juguang@fugu-sg.org>
+# Created date: 5/3/2003
+#
+# Copyright Juguang Xiao
+#
+# You may distribute this module under the same terms as perl itself
+#
+# POD documentation
+#
+
+=head1 NAME
+
+Bio::EnsEMBL::Utils::Converter::bio_ens_featurePair
+
+=head1 SYNOPISIS
+
+
+
+=head1 DESCRIPTION
+
+
+=head1 FEEDBACK
+
+=head2 Mailing Lists
+
+=head2 Reporting Bugs
+
+
+=head1 AUTHOR Juguang Xiao
+
+Juguang Xiao <juguang@fugu-sg.org>
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods.
+Internal methods are usually preceded with a _
+
+=cut
+
+# Let the code begin ...
+
+package Bio::EnsEMBL::Utils::Converter::bio_ens_featurePair;
+
+use strict;
+use vars qw(@ISA);
+
+use Bio::EnsEMBL::RepeatConsensus;
+
+use Bio::EnsEMBL::Utils::Converter::bio_ens;
+@ISA = qw(Bio::EnsEMBL::Utils::Converter::bio_ens);
+
+sub _convert_single {
+ my ($self, $pair) = @_;
+ if($self->out eq 'Bio::EnsEMBL::RepeatFeature'){
+ return $self->_convert_single_to_repeatFeature($pair);
+ }else{
+ my $output_module = $self->out;
+ $self->throw("Cannot covert to [$output_module]");
+ }
+}
+
+sub _convert_single_to_repeatFeature {
+ my ($self, $pair) = @_;
+ my $feature1 = $pair->feature1;
+ my $feature2 = $pair->feature2;
+ my $ens_repeatfeature = new Bio::EnsEMBL::RepeatFeature(
+ -seqname => $feature1->seq_id,
+ -start => $feature1->start,
+ -end => $feature1->end,
+ -strand => $feature1->strand,
+ -source_tag => $feature1->source_tag,
+ );
+
+ my ($h_start, $h_end);
+ if($feature1->strand == 1){
+ $h_start = $feature2->start;
+ $h_end = $feature2->end;
+ }elsif($feature1->strand == -1){
+ $h_start = $feature2->end;
+ $h_end = $feature2->start;
+ }else{
+ $self->throw("strand cannot be outside of (1, -1)");
+ }
+
+ $ens_repeatfeature->hstart($h_start);
+ $ens_repeatfeature->hend($h_end);
+ my $repeat_name = $feature2->seq_id;
+ my $repeat_class = $feature1->primary_tag;
+ $repeat_class ||= $feature2->primary_tag;
+ $repeat_class ||= "not sure";
+ my $ens_repeat_consensus =
+ $self->_create_consensus($repeat_name, $repeat_class);
+ $ens_repeatfeature->repeat_consensus($ens_repeat_consensus);
+
+ $ens_repeatfeature->attach_seq($self->contig);
+ $ens_repeatfeature->analysis($self->analysis);
+ return $ens_repeatfeature;
+}
+
+sub _create_consensus{
+ my ($self, $repeat_name, $repeat_class) = @_;
+ my $consensus = new Bio::EnsEMBL::RepeatConsensus;
+ $consensus->name($repeat_name);
+ $consensus->repeat_class($repeat_class);
+ return $consensus;
+}
+
+
+1;
diff --git a/modules/Bio/EnsEMBL/Utils/Converter/bio_ens_seqFeature.pm b/modules/Bio/EnsEMBL/Utils/Converter/bio_ens_seqFeature.pm
new file mode 100644
index 0000000000000000000000000000000000000000..9812b461d1cd927d6e14c94eb5dcb9b0fa1cfa28
--- /dev/null
+++ b/modules/Bio/EnsEMBL/Utils/Converter/bio_ens_seqFeature.pm
@@ -0,0 +1,87 @@
+# Bio::EnsEMBL::Utils::Converter::bio_ens_seqFeature
+#
+# Created and cared for by Juguang Xiao <juguang@fugu-sg.org>
+# Created date: 5/3/2003
+#
+# Copyright Juguang Xiao
+#
+# You may distribute this module under the same terms as perl itself
+#
+# POD documentation
+#
+
+=head1 NAME
+
+Bio::EnsEMBL::Utils::Converter::bio_ens_seqFeature
+
+=head1 SYNOPISIS
+
+Please read Bio::EnsEMBL::Utils::Converter
+
+=head1 DESCRIPTION
+
+
+=head1 FEEDBACK
+
+=head2 Mailing Lists
+
+=head2 Reporting Bugs
+
+
+=head1 AUTHOR Juguang Xiao
+
+Juguang Xiao <juguang@fugu-sg.org>
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods.
+Internal methods are usually preceded with a _
+
+=cut
+
+# Let the code begin ...
+
+package Bio::EnsEMBL::Utils::Converter::bio_ens_seqFeature;
+
+use strict;
+use vars qw(@ISA);
+use Bio::EnsEMBL::Utils::Converter::bio_ens;
+@ISA = qw(Bio::EnsEMBL::Utils::Converter::bio_ens);
+
+sub _convert_single {
+ my ($self, $in) = @_;
+
+ unless($in && defined($in) && ref($in) && $in->isa('Bio::SeqFeature::Generic')){
+ $self->throw("a Bio::SeqFeature::Generic object needed");
+ }
+
+ my $ens_seqFeature;
+ my @args = (
+ -start => $in->start,
+ -end => $in->end,
+ -strand => $in->strand,
+ -score => $in->score
+ -analysis => $self->analysis,
+ -source_tag => $in->source_tag
+ -seqname => $in->seq_id
+ );
+
+ my $output_module = $self->out;
+
+ if($output_module eq 'Bio::EnsEMBL::SeqFeature'){
+
+ $ens_seqFeature = new Bio::EnsEMBL::SeqFeature(@args);
+ }elsif($self->out eq 'Bio::EnsEMBL::SimpleFeature'){
+ $ens_seqFeature = new Bio::EnsEMBL::SimpleFeature(@args);
+ # The field that there is in SimpleFeature, but not in SeqFeature.
+ $ens_seqFeature->display_label('__NONE__');
+ }else{
+ $self->throw("[$output_module] as -out, not supported");
+ }
+
+ $ens_seqFeature->attach_seq($self->contig);
+
+ return $ens_seqFeature;
+}
+
+1;
diff --git a/modules/Bio/EnsEMBL/Utils/Converter/ens_bio.pm b/modules/Bio/EnsEMBL/Utils/Converter/ens_bio.pm
new file mode 100644
index 0000000000000000000000000000000000000000..37575aff63a5f48c174bd0a22e1126b0af7293d7
--- /dev/null
+++ b/modules/Bio/EnsEMBL/Utils/Converter/ens_bio.pm
@@ -0,0 +1,93 @@
+# Bio::EnsEMBL::Utils::Converter::ens_bio
+#
+# Created and cared for by Juguang Xiao <juguang@fugu-sg.org>
+# Created date: 5/3/2003
+#
+# Copyright Juguang Xiao
+#
+# You may distribute this module under the same terms as perl itself
+#
+# POD documentation
+#
+
+=head1 NAME
+
+Bio::EnsEMBL::Utils::Converter::ens_bio
+
+=head1 SYNOPISIS
+
+You are not supposed to use this module directly. Please read
+Bio::EnsEMBL::Utils::Converter
+
+=head1 DESCRIPTION
+
+This is a helper module to assist Bio::EnsEMBL::Utils::Converter find which
+converter instance should be used, based on the -in and -out parameters.
+
+=head1 FEEDBACK
+
+=head2 Mailing Lists
+
+=head2 Reporting Bugs
+
+
+=head1 AUTHOR Juguang Xiao
+
+Juguang Xiao <juguang@fugu-sg.org>
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods.
+Internal methods are usually preceded with a _
+
+=cut
+
+# Let the code begin ...
+
+package Bio::EnsEMBL::Utils::Converter::ens_bio;
+
+use strict;
+use vars qw(@ISA);
+use Bio::EnsEMBL::Utils::Converter;
+@ISA = qw(Bio::EnsEMBL::Utils::Converter);
+
+=head2 new
+ Please see Bio::EnsEMBL::Utils::Converter::new
+=cut
+
+sub new {
+ my ($caller, @args) = @_;
+ my $class = ref($caller) || $caller;
+
+ if($class eq 'Bio::EnsEMBL::Utils::Converter::ens_bio'){
+ my %params = @args;
+ @params{map{lc $_} keys %params} = values %params;
+ my $module = $class->_guess_module($params{-in}, $params{-out});
+ return undef unless ($class->_load_module($module));
+ return "$module"->new(@args);
+ }else{
+ my $self = $class->SUPER::new(@args);
+# $self->_initialize(@args);
+ return $self;
+ }
+
+}
+
+# Unlike bio_ens, ens_bio does not need _initialize method for analysis and
+# contig information.
+#
+
+sub _guess_module {
+ my ($self, $in, $out) = @_;
+ my $tail;
+ if($in eq 'Bio::EnsEMBL::SeqFeature'){
+ $tail = 'ens_bio_seqFeature';
+ }elsif($in eq 'Bio::Ens::EMBL::FeaturePair'){
+ $tail = 'ens_bio_featurePair';
+ }else{
+ $self->throw("[$in] to [$out], not supported");
+ }
+ return "Bio::EnsEMBL::Utils::Converter::$tail";
+}
+
+1;
diff --git a/modules/Bio/EnsEMBL/Utils/Converter/ens_bio_featurePair.pm b/modules/Bio/EnsEMBL/Utils/Converter/ens_bio_featurePair.pm
new file mode 100644
index 0000000000000000000000000000000000000000..b46760d0a5439a2ea3e40c38af98020d2e552cb8
--- /dev/null
+++ b/modules/Bio/EnsEMBL/Utils/Converter/ens_bio_featurePair.pm
@@ -0,0 +1,100 @@
+# Bio::EnsEMBL::Utils::Converter::ens_bio_featurePair
+#
+# Created and cared for by Juguang Xiao <juguang@fugu-sg.org>
+# Created date: 5/3/2003
+#
+# Copyright Juguang Xiao
+#
+# You may distribute this module under the same terms as perl itself
+#
+# POD documentation
+#
+
+=head1 NAME
+
+Bio::EnsEMBL::Utils::Converter::ens_bio_featurePair
+
+=head1 SYNOPISIS
+
+
+
+=head1 DESCRIPTION
+
+
+=head1 FEEDBACK
+
+=head2 Mailing Lists
+
+=head2 Reporting Bugs
+
+
+=head1 AUTHOR Juguang Xiao
+
+Juguang Xiao <juguang@fugu-sg.org>
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods.
+Internal methods are usually preceded with a _
+
+=cut
+
+# Let the code begin ...
+
+package Bio::EnsEMBL::Utils::Converter::ens_bio_featurePair;
+
+use strict;
+use vars qw(@ISA);
+use Bio::SeqFeature::Generic;
+use Bio::SeqFeature::FeaturePair;
+use Bio::EnsEMBL::Utils::Converter::ens_bio;
+@ISA = qw(Bio::EnsEMBL::Utils::Converter::ens_bio);
+
+sub _convert_single {
+ my ($self, @args) = @_;
+
+}
+
+# convert object from Bio::EnsEMBL::RepeatFeature
+# to Bio::SeqFeature::FeaturePair
+
+sub _convert_single_repeatFeature {
+ my ($self, $ens_repeat) = @_;
+
+ my $feature1 = new Bio::SeqFeature::Generic(
+ -start => $ens_repeat->start,
+ -end => $ens_repeat->end,
+ -strand => $ens_repeat->strand,
+ -source_tag => $ens_repeat->source_tag
+ -primary_tag => $ens_repeat->repeat_class,
+ -seq_id => $ens_repeat->seqname
+ );
+
+ my ($start2, $end2);
+ if($ens_repeat->strand == 1){
+ $start2 = $ens_repeat->hstart;
+ $end2 = $ens_repeat->hend;
+ }elsif($ens_repeat->strand == -1){
+ $start2 = $ens_repeat->hend;
+ $end2 = $ens_repeat->hstart;
+ }else{
+ $self->throw("strand cannot be out of range (1, -1)");
+ }
+
+ my $feature2 = new Bio::SeqFeature::Generic(
+ -start => $start2,
+ -end => $end2,
+ -source_tag => $ens_repeat->source_tag,
+ -primary_tag => $ens_repeat->repeat_class,
+ -seq_id => $ens_repeat->repeat_name
+ );
+
+ my $output_module = $self->out;
+ require "$output_module";
+ return new Bio::SeqFeature::FeaturePair(
+ -feature1 => $feature1,
+ -feature2 => $feature2
+ );
+}
+
+1;
diff --git a/modules/Bio/EnsEMBL/Utils/Converter/ens_bio_seqFeature.pm b/modules/Bio/EnsEMBL/Utils/Converter/ens_bio_seqFeature.pm
new file mode 100644
index 0000000000000000000000000000000000000000..fbbdde585a4befc591db3b493e3795b643f3011b
--- /dev/null
+++ b/modules/Bio/EnsEMBL/Utils/Converter/ens_bio_seqFeature.pm
@@ -0,0 +1,73 @@
+# Bio::EnsEMBL::Utils::Converter::ens_bio_seqFeature
+#
+# Created and cared for by Juguang Xiao <juguang@fugu-sg.org>
+# Created date: 5/3/2003
+#
+# Copyright Juguang Xiao
+#
+# You may distribute this module under the same terms as perl itself
+#
+# POD documentation
+#
+
+=head1 NAME
+
+Bio::EnsEMBL::Utils::Converter::ens_bio_seqFeature
+
+=head1 SYNOPISIS
+
+
+
+=head1 DESCRIPTION
+
+
+=head1 FEEDBACK
+
+=head2 Mailing Lists
+
+=head2 Reporting Bugs
+
+
+=head1 AUTHOR Juguang Xiao
+
+Juguang Xiao <juguang@fugu-sg.org>
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods.
+Internal methods are usually preceded with a _
+
+=cut
+
+# Let the code begin ...
+
+package Bio::EnsEMBL::Utils::Converter::ens_bio_seqFeature;
+
+use strict;
+use vars qw(@ISA);
+use Bio::EnsEMBL::Utils::Converter::ens_bio;
+@ISA = qw(Bio::EnsEMBL::Utils::Converter::ens_bio);
+
+sub _convert_single {
+ my ($self, $in) = @_;
+
+ $self->throw("Input not defined") unless($in && defined($in));
+ unless(ref($in) && $in->isa('Bio::EnsEMBL::SeqFeature')){
+ $self->throw('A Bio::EnsEMBL::SeqFeature object needed');
+ }
+
+ my @args = (
+ -start => $in->start,
+ -end => $in->end,
+ -strand => $in->strand,
+ -score => $in->score,
+ -source_tag => $in->source_tag,
+ -seq_id => $in->seqname
+ );
+
+ my $seqFeature = new Bio::SeqFeature::Generic(@args);
+
+ return $seqFeature;
+}
+
+1;
diff --git a/modules/t/converter.t b/modules/t/converter.t
new file mode 100644
index 0000000000000000000000000000000000000000..85fecca2c8babf3a2959455832b623a24693310c
--- /dev/null
+++ b/modules/t/converter.t
@@ -0,0 +1,133 @@
+use lib 't';
+use strict;
+
+BEGIN {
+ $| = 1;
+ use Test;
+ plan tests => 22;
+}
+
+use Bio::EnsEMBL::Utils::Converter;
+
+END {
+
+}
+
+
+use Bio::EnsEMBL::Utils::Converter;
+
+use Bio::EnsEMBL::Analysis;
+use Bio::EnsEMBL::RawContig;
+use Bio::SeqFeature::Generic;
+use Bio::SeqFeature::FeaturePair;
+
+# Global constants
+
+my $ens_analysis = new Bio::EnsEMBL::Analysis(
+ -dbID => 1,
+ -logic_name => 'test_fake_analysis'
+);
+
+my $ens_contig = new Bio::EnsEMBL::RawContig();
+
+my $seqFeature1 = new Bio::SeqFeature::Generic(
+ -start => 100,
+ -end => 200,
+ -strand => 1,
+ -score => 10
+);
+
+my $seqFeature2 = new Bio::SeqFeature::Generic(
+ -start => 1234,
+ -end => 5678,
+ -strand => -1,
+ -score => 14
+);
+
+my $featurePair1 = new Bio::SeqFeature::FeaturePair(
+ -feature1 => $seqFeature1,
+ -feature2 => $seqFeature2
+);
+
+&test_SeqFeature;
+&test_FeaturePair;
+&test_hit;
+
+# Test for SeqFeature, 10 OKs
+sub test_SeqFeature{
+ # bio to ens
+ my $converter = new Bio::EnsEMBL::Utils::Converter(
+ -in => 'Bio::SeqFeature::Generic',
+ -out => 'Bio::EnsEMBL::SeqFeature',
+ -analysis => $ens_analysis,
+ -contig => $ens_contig
+ );
+
+ my ($ens_seqFeature1, $ens_seqFeature2) =
+ @{$converter->convert([$seqFeature1, $seqFeature2])};
+
+ ok ref($ens_seqFeature1), 'Bio::EnsEMBL::SeqFeature';
+ ok ref($ens_seqFeature2), 'Bio::EnsEMBL::SeqFeature';
+
+ ok $seqFeature1->start, $ens_seqFeature1->start;
+ ok $seqFeature1->end, $ens_seqFeature1->end;
+ ok $seqFeature1->strand, $ens_seqFeature1->strand;
+ ok $seqFeature1->score, $ens_seqFeature1->score;
+ ok $seqFeature1->source_tag, $ens_seqFeature1->source_tag;
+
+ # from ens to bio
+ $converter = new Bio::EnsEMBL::Utils::Converter(
+ -in => 'Bio::EnsEMBL::SeqFeature',
+ -out => 'Bio::SeqFeature::Generic',
+ );
+
+ my ($bio_seqFeature1, $bio_seqFeature2) =
+ @{$converter->convert([$ens_seqFeature1, $ens_seqFeature2])};
+
+ ok ref($bio_seqFeature1), 'Bio::SeqFeature::Generic';
+ ok ref($bio_seqFeature2), 'Bio::SeqFeature::Generic';
+
+ ok $seqFeature1->start, $bio_seqFeature1->start;
+ ok $seqFeature1->end, $bio_seqFeature1->end;
+ ok $seqFeature1->strand, $bio_seqFeature1->strand;
+ ok $seqFeature1->score, $bio_seqFeature1->score;
+ ok $seqFeature1->source_tag, $bio_seqFeature1->source_tag;
+
+}
+
+
+sub test_FeaturePair{
+
+ my $converter = new Bio::EnsEMBL::Utils::Converter(
+ -in => 'Bio::SeqFeature::FeaturePair',
+ -out => 'Bio::EnsEMBL::RepeatFeature',
+ -analysis => $ens_analysis,
+ -contig => $ens_contig
+ );
+
+ my ($ens_repeatFeature1) = @{$converter->convert([$featurePair1])};
+
+ ok ref($ens_repeatFeature1), 'Bio::EnsEMBL::RepeatFeature';
+
+ ok $ens_repeatFeature1->start, $featurePair1->feature1->start;
+ ok $ens_repeatFeature1->end, $featurePair1->feature1->end;
+ ok $ens_repeatFeature1->strand, $featurePair1->feature1->strand;
+ ok $ens_repeatFeature1->seqname, $featurePair1->feature1->seq_id;
+ ok $ens_repeatFeature1->repeat_consensus->name, $featurePair1->feature2->seq_id;
+
+ if($featurePair1->feature1->strand == 1){
+ ok $ens_repeatFeature1->hstart, $featurePair1->feature2->start;
+ ok $ens_repeatFeature1->hend, $featurePair1->feature2->end;
+ }else{
+ ok $ens_repeatFeature1->hstart, $featurePair1->feature2->end;
+ ok $ens_repeatFeature1->hend, $featurePair1->feature2->start;
+ }
+
+}
+
+
+sub test_hit {
+
+
+}
+