From f098d487a231a0d9f2ad31ac61d6c1102147045b Mon Sep 17 00:00:00 2001
From: Patrick Meidl <pm2@sanger.ac.uk>
Date: Thu, 31 Aug 2006 11:47:22 +0000
Subject: [PATCH] first (draft) version of new modules for ID mapping
---
modules/Bio/EnsEMBL/IdMapping/Entry.pm | 78 +++++
.../Bio/EnsEMBL/IdMapping/ExonScoreBuilder.pm | 147 +++++++++
modules/Bio/EnsEMBL/IdMapping/ScoreBuilder.pm | 102 ++++++
.../EnsEMBL/IdMapping/ScoredMappingMatrix.pm | 305 ++++++++++++++++++
modules/Bio/EnsEMBL/IdMapping/TinyExon.pm | 205 ++++++++++++
modules/Bio/EnsEMBL/IdMapping/TinyGene.pm | 60 ++++
.../Bio/EnsEMBL/IdMapping/TinyTranscript.pm | 72 +++++
.../Bio/EnsEMBL/IdMapping/TinyTranslation.pm | 43 +++
8 files changed, 1012 insertions(+)
create mode 100644 modules/Bio/EnsEMBL/IdMapping/Entry.pm
create mode 100644 modules/Bio/EnsEMBL/IdMapping/ExonScoreBuilder.pm
create mode 100644 modules/Bio/EnsEMBL/IdMapping/ScoreBuilder.pm
create mode 100644 modules/Bio/EnsEMBL/IdMapping/ScoredMappingMatrix.pm
create mode 100644 modules/Bio/EnsEMBL/IdMapping/TinyExon.pm
create mode 100644 modules/Bio/EnsEMBL/IdMapping/TinyGene.pm
create mode 100644 modules/Bio/EnsEMBL/IdMapping/TinyTranscript.pm
create mode 100644 modules/Bio/EnsEMBL/IdMapping/TinyTranslation.pm
diff --git a/modules/Bio/EnsEMBL/IdMapping/Entry.pm b/modules/Bio/EnsEMBL/IdMapping/Entry.pm
new file mode 100644
index 0000000000..41765bfff9
--- /dev/null
+++ b/modules/Bio/EnsEMBL/IdMapping/Entry.pm
@@ -0,0 +1,78 @@
+package Bio::EnsEMBL::IdMapping::Entry;
+
+=head1 NAME
+
+
+=head1 SYNOPSIS
+
+
+=head1 DESCRIPTION
+
+
+=head1 METHODS
+
+
+=head1 LICENCE
+
+This code is distributed under an Apache style licence. Please see
+http://www.ensembl.org/info/about/code_licence.html for details.
+
+=head1 AUTHOR
+
+Patrick Meidl <meidl@ebi.ac.uk>, Ensembl core API team
+
+=head1 CONTACT
+
+Please post comments/questions to the Ensembl development list
+<ensembl-dev@ebi.ac.uk>
+
+=cut
+
+use strict;
+use warnings;
+no warnings 'uninitialized';
+
+use Bio::EnsEMBL::Utils::Exception qw(throw warning);
+
+
+sub new {
+ my $caller = shift;
+ my $class = ref($caller) || $caller;
+
+ my $self = [];
+ bless ($self, $class);
+
+ return $self;
+}
+
+
+sub new_fast {
+ my $class = shift;
+ my $array_ref = shift;
+ return bless $array_ref, $class;
+}
+
+
+sub source {
+ my $self = shift;
+ $self->[0] = shift if (@_);
+ return $self->[0];
+}
+
+
+sub target {
+ my $self = shift;
+ $self->[1] = shift if (@_);
+ return $self->[1];
+}
+
+
+sub score {
+ my $self = shift;
+ $self->[2] = shift if (@_);
+ return $self->[2];
+}
+
+
+1;
+
diff --git a/modules/Bio/EnsEMBL/IdMapping/ExonScoreBuilder.pm b/modules/Bio/EnsEMBL/IdMapping/ExonScoreBuilder.pm
new file mode 100644
index 0000000000..0041bc6de8
--- /dev/null
+++ b/modules/Bio/EnsEMBL/IdMapping/ExonScoreBuilder.pm
@@ -0,0 +1,147 @@
+package Bio::EnsEMBL::IdMapping::ExonScoreBuilder;
+
+=head1 NAME
+
+
+=head1 SYNOPSIS
+
+
+=head1 DESCRIPTION
+
+
+=head1 METHODS
+
+
+=head1 LICENCE
+
+This code is distributed under an Apache style licence. Please see
+http://www.ensembl.org/info/about/code_licence.html for details.
+
+=head1 AUTHOR
+
+Patrick Meidl <meidl@ebi.ac.uk>, Ensembl core API team
+
+=head1 CONTACT
+
+Please post comments/questions to the Ensembl development list
+<ensembl-dev@ebi.ac.uk>
+
+=cut
+
+
+use strict;
+use warnings;
+no warnings 'uninitialized';
+
+use Bio::EnsEMBL::IdMapping::ScoreBuilder;
+our @ISA = qw(Bio::EnsEMBL::IdMapping::ScoreBuilder);
+
+use Bio::EnsEMBL::Utils::Argument qw(rearrange);
+use Bio::EnsEMBL::Utils::Exception qw(throw warning);
+use Bio::EnsEMBL::Utils::ScriptUtils qw(parse_bytes);
+use Bio::EnsEMBL::IdMapping::ScoredMappingMatrix;
+
+
+sub score_exons {
+ my $self = shift;
+
+ my $matrix = Bio::EnsEMBL::IdMapping::ScoredMappingMatrix->new(
+ -DUMP_PATH => $self->conf('dumppath')
+ );
+
+ my $cache_file = $matrix->cache_file;
+
+ if (-s $cache_file) {
+ # read from file
+ $self->logger->log_stamped("Reading exon scoring matrix from file...\n");
+ $self->logger->log("Cache file $cache_file.\n", 1);
+ $matrix->read_from_file;
+ $self->logger->log_stamped("Done.\n");
+ } else {
+ #
+ # build scoring matrix
+ #
+
+ # direct mapping (by overlap, if common coord_system exists)
+ if ($self->cache->highest_common_cs) {
+ $matrix = $self->build_overlap_scores($matrix);
+ }
+
+
+ # map the remaining exons using exonerate
+
+ # dump exons to fasta files
+ my $dump_size = $self->cache->dump_filtered_exons;
+
+ if ($dump_size) {
+ # run exonerate
+ my $exonerate_matrix;
+
+ # merge matrices
+ $matrix->merge($exonerate_matrix);
+ }
+
+
+ #
+ # write scoring matrix to file
+ #
+ $matrix->write_to_file;
+
+ return $matrix;
+ }
+
+ return $matrix;
+}
+
+
+sub build_overlap_scores {
+ my $self = shift;
+ my $matrix = shift;
+
+ unless ($matrix and
+ $matrix->isa('Bio::EnsEMBL::IdMapping::ScoredMappingMatrix')) {
+ throw('Need a Bio::EnsEMBL::IdMapping::ScoredMappingMatrix.');
+ }
+
+ my @s_exons = $self->sort_exons(
+ [values %{ $self->cache->get_by_name('exons_by_id', 'source') }
+ );
+ my @t_exons = $self->sort_exons(
+ [values %{ $self->cache->get_by_name('exons_by_id', 'target') }
+ );
+
+
+}
+
+
+#
+# Return a list of exons, sorted by seq_region_name, then location (where
+# location is either start-1 or end, so each exon is in the list twice)
+#
+# TODO: this implementation isn't good enough, since you'll need location later
+# to compare source and target exons again. best add this as an instance
+# variable to the TinyExon returned
+#
+sub sort_exons {
+ my $self = shift;
+ my $exons = shift;
+
+ return
+ map { $_->[2] }
+ sort { $a->[0] cmp $b->[0] || $a->[1] <=> $b->[1] }
+ (
+ map { [$_->common_name, $_->common_start - 1, $_] } @$exons,
+ map { [$_->common_name, $_->common_end, $_] } @$exons
+ );
+
+}
+
+
+sub compare_exons {
+ my $self = shift;
+ my $e1 = shift;
+ my $e2 = shift;
+
+ return ( $e1->
+}
+
diff --git a/modules/Bio/EnsEMBL/IdMapping/ScoreBuilder.pm b/modules/Bio/EnsEMBL/IdMapping/ScoreBuilder.pm
new file mode 100644
index 0000000000..3a249d46ed
--- /dev/null
+++ b/modules/Bio/EnsEMBL/IdMapping/ScoreBuilder.pm
@@ -0,0 +1,102 @@
+package Bio::EnsEMBL::IdMapping::ScoreBuilder;
+
+=head1 NAME
+
+
+=head1 SYNOPSIS
+
+
+=head1 DESCRIPTION
+
+
+=head1 METHODS
+
+
+=head1 LICENCE
+
+This code is distributed under an Apache style licence. Please see
+http://www.ensembl.org/info/about/code_licence.html for details.
+
+=head1 AUTHOR
+
+Patrick Meidl <meidl@ebi.ac.uk>, Ensembl core API team
+
+=head1 CONTACT
+
+Please post comments/questions to the Ensembl development list
+<ensembl-dev@ebi.ac.uk>
+
+=cut
+
+
+use strict;
+use warnings;
+no warnings 'uninitialized';
+
+use Bio::EnsEMBL::Utils::Exception qw(throw warning);
+
+
+=head2 new
+
+ Arg[1] :
+ Example :
+ Description : constructor
+ Return type :
+ Exceptions :
+ Caller : general
+
+=cut
+
+sub new {
+ my $caller = shift;
+ my $class = ref($caller) || $caller;
+
+ my ($logger, $conf, $cache) = rearrange(['LOGGER', 'CONF', 'CACHE'], @_);
+
+ unless ($logger->isa('Bio::EnsEMBL::Utils::Logger')) {
+ throw("You must provide a Bio::EnsEMBL::Utils::Logger for logging.");
+ }
+
+ unless ($conf->isa('Bio::EnsEMBL::Utils::ConfParser')) {
+ throw("You must provide configuration as a Bio::EnsEMBL::Utils::ConfParser object.");
+ }
+
+ unless ($cache->isa('Bio::EnsEMBL::IdMapping::Cache')) {
+ throw("You must provide configuration as a Bio::EnsEMBL::IdMapping::Cache object.");
+ }
+
+ my $self = {};
+ bless ($self, $class);
+
+ # initialise
+ $self->logger($logger);
+ $self->conf($conf);
+ $self->cache($cache);
+
+ return $self;
+}
+
+
+sub logger {
+ my $self = shift;
+ $self->{'_logger'} = shift if (@_);
+ return $self->{'_logger'};
+}
+
+
+sub conf {
+ my $self = shift;
+ $self->{'_conf'} = shift if (@_);
+ return $self->{'_conf'};
+}
+
+
+sub cache {
+ my $self = shift;
+ $self->{'_cache'} = shift if (@_);
+ return $self->{'_cache'};
+}
+
+
+1;
+
diff --git a/modules/Bio/EnsEMBL/IdMapping/ScoredMappingMatrix.pm b/modules/Bio/EnsEMBL/IdMapping/ScoredMappingMatrix.pm
new file mode 100644
index 0000000000..4e2d1a7a4c
--- /dev/null
+++ b/modules/Bio/EnsEMBL/IdMapping/ScoredMappingMatrix.pm
@@ -0,0 +1,305 @@
+package Bio::EnsEMBL::IdMapping::ScoredMappingMatrix;
+
+=head1 NAME
+
+
+=head1 SYNOPSIS
+
+
+=head1 DESCRIPTION
+
+
+=head1 METHODS
+
+
+=head1 LICENCE
+
+This code is distributed under an Apache style licence. Please see
+http://www.ensembl.org/info/about/code_licence.html for details.
+
+=head1 AUTHOR
+
+Patrick Meidl <meidl@ebi.ac.uk>, Ensembl core API team
+
+=head1 CONTACT
+
+Please post comments/questions to the Ensembl development list
+<ensembl-dev@ebi.ac.uk>
+
+=cut
+
+
+use strict;
+use warnings;
+no warnings 'uninitialized';
+
+use Bio::EnsEMBL::Utils::Argument qw(rearrange);
+use Bio::EnsEMBL::Utils::Exception qw(throw warning);
+use Bio::EnsEMBL::Utils::ScriptUtils qw(parse_bytes);
+use Bio::EnsEMBL::IdMapping::Entry;
+
+
+sub new {
+ my $caller = shift;
+ my $class = ref($caller) || $caller;
+
+ my ($dump_path) = rearrange(['DUMP_PATH'], @_);
+
+ throw("You must provide a dump path") unless ($dump_path);
+
+ my $self = {};
+ bless ($self, $class);
+
+ # initialise internal datastructure
+ $self->{'matrix'} = {};
+ $self->{'source_list'} = {};
+ $self->{'target_list'} = {};
+ $self->{'dump_path'} = $dump_path;
+
+ return $self;
+}
+
+
+sub add_Entry {
+ my $self = shift;
+ my $entry = shift;
+
+ unless ($entry and $entry->isa('Bio::EnsEMBL::IdMapping::Entry')) {
+ throw("Need a Bio::EnsEMBL::IdMapping::Entry");
+ }
+
+ return $self->add_score($entry->source, $entry->target, $entry->score);
+}
+
+
+sub remove_Entry {
+}
+
+
+sub add_score {
+ my $self = shift;
+ my $source = shift;
+ my $target = shift;
+ my $score = shift;
+
+ # make sure you don't put duplicates on the source and target lists
+ unless (exists($self->{'matrix'}->{"$source:$target"})) {
+ push @{ $self->{'source_list'}->{$source} }, $target;
+ push @{ $self->{'target_list'}->{$target} }, $source;
+ }
+
+ $self->{'matrix'}->{"$source:$target"} = $score;
+}
+
+
+sub get_Entry {
+ my $self = shift;
+ my $source = shift;
+ my $target = shift;
+
+ if (exists($self->{'matrix'}->{"$source:$target"}) {
+ return Bio::EnsEMBL::IdMapping::Entry->new_fast(
+ [$source, $target, $self->{'matrix'}->{"$source:$target"}]
+ );
+ } else {
+ return undef;
+ }
+}
+
+
+sub get_score {
+ my $self = shift;
+ my $source = shift;
+ my $target = shift;
+
+
+ if (exists($self->{'matrix'}->{"$source:$target"}) {
+ return $self->{'matrix'}->{"$source:$target"};
+ } else {
+ return undef;
+ }
+}
+
+
+sub get_targets_for_source {
+ my $self = shift;
+ my $source = shift;
+
+ return($self->{'source_list'}->{$source} || []);
+}
+
+
+sub get_sources_for_target {
+ my $self = shift;
+ my $target = shift;
+
+ return($self->{'target_list'}->{$target} || []);
+}
+
+
+sub get_all_Entries {
+ my $self = shift;
+
+ my @result = ();
+
+ foreach my $key (keys %{ $self->{'matrix'} }) {
+ my ($source, $target) = split(/:/, $key);
+ push @result, Bio::EnsEMBL::IdMapping::Entry->new_fast(
+ [$source, $target, $self->{'matrix'}->{$key}]
+ );
+ }
+
+ return \@result;
+}
+
+
+sub get_all_sources {
+ return [keys %{ $_->{'source_list'} }];
+}
+
+
+sub get_all_targets {
+ return [keys %{ $_->{'target_list'} }];
+}
+
+
+sub get_entry_count {
+ return scalar(keys %{ $_->{'matrix'} });
+}
+
+
+sub get_source_count {
+ return scalar(keys %{ $_->{'source_list'} });
+}
+
+
+sub get_target_count {
+ return scalar(keys %{ $_->{'target_list'} });
+}
+
+
+sub get_min_scores {
+ my $self = shift;
+
+ my @keys = keys %{ $self->{'matrix'} };
+
+ return [undef, undef] unless (@keys);
+
+ # initialise; this should make loop quicker
+ my $min = $self->{'matrix'}->{$keys[0]};
+ my $max = $self->{'matrix'}->{$keys[0]};
+
+ foreach my $key (@keys) {
+ $min = $self->{'matrix'}->{$key} if ($min > $self->{'matrix'}->{$key});
+ $max = $self->{'matrix'}->{$key} if ($max < $self->{'matrix'}->{$key});
+ }
+
+ return [$min, $max];
+}
+
+
+sub get_average_score {
+ my $self = shift;
+
+ my @keys = keys %{ $self->{'matrix'} };
+
+ return undef unless (@keys);
+
+ my $total = 0;
+
+ foreach my $key (@keys) {
+ $total += $self->{'matrix'}->{$key};
+ }
+
+ return $total/scalar(@keys);
+}
+
+
+sub write_to_file {
+}
+
+
+sub merge {
+ my $self = shift;
+ my $matrix = shift;
+
+ unless ($matrix and
+ $matrix->isa('Bio::EnsEMBL::IdMapping::ScoredMappingMatrix')) {
+ throw('You must provide a Bio::EnsEMBL::IdMapping::ScoredMappingMatrix');
+ }
+
+ my $c = 0;
+
+ foreach my $key (keys %{ $matrix->{'matrix'} }) {
+ if (!defined($self->{'matrix'}->{$key}) or
+ $self->{'matrix'}->{$key} < $matrix->{'matrix'}->{$key}) {
+ $self->{'matrix'}->{$key} = $matrix->{'matrix'}->{$key};
+ $c++;
+ }
+ }
+
+ return $c;
+}
+
+
+sub write_to_file {
+ my $self = shift;
+
+ # create dump directory if it doesn't exist
+ if (my $dump_path = $self->dump_path) {
+ unless (-d $dump_path) {
+ system("mkdir -p $dump_path") == 0 or
+ throw("Unable to create directory $dump_path.\n");
+ }
+ }
+
+ my $cache_file = $self->cache_file;
+
+ eval { nstore($self, $cache_file) };
+ if ($@) {
+ throw("Unable to store $cache_file: $@\n");
+ }
+
+ my $size = -s $cache_file;
+ return parse_bytes($size);
+}
+
+
+sub read_from_file {
+ my $self = shift;
+
+ my $cache_file = $self->cache_file;
+
+ unless (-s $cache_file) {
+ throw("No valid cache file found at $cache_file.");
+ }
+
+ eval { $self = retrieve($cache_file); };
+ if ($@) {
+ throw("Unable to retrieve cache: $@");
+ }
+
+ return $self;
+}
+
+
+sub cache_file {
+ my $self = shift;
+ my $cache_file = ($self->dump_path || '.').'/exon_scoring_matrix.ser';
+ return $cache_file;
+}
+
+
+#
+# getter/setters
+#
+
+sub dump_path {
+ my $self = shift;
+ $self->{'dump_path'} = shift if (@_);
+ return $self->{'dump_path'};
+}
+
+
+1;
+
diff --git a/modules/Bio/EnsEMBL/IdMapping/TinyExon.pm b/modules/Bio/EnsEMBL/IdMapping/TinyExon.pm
new file mode 100644
index 0000000000..ec7080b084
--- /dev/null
+++ b/modules/Bio/EnsEMBL/IdMapping/TinyExon.pm
@@ -0,0 +1,205 @@
+package Bio::EnsEMBL::IdMapping::TinyGene;
+
+=head1 NAME
+
+
+=head1 SYNOPSIS
+
+
+=head1 DESCRIPTION
+
+
+=head1 METHODS
+
+
+=head1 LICENCE
+
+This code is distributed under an Apache style licence. Please see
+http://www.ensembl.org/info/about/code_licence.html for details.
+
+=head1 AUTHOR
+
+Patrick Meidl <meidl@ebi.ac.uk>, Ensembl core API team
+
+=head1 CONTACT
+
+Please post comments/questions to the Ensembl development list
+<ensembl-dev@ebi.ac.uk>
+
+=cut
+
+
+# internal data structure (array indices):
+#
+# 0 dbID
+# 1 stable_id
+# 2 start
+# 3 end
+# 4 strand
+# 5 seq_region_name
+# 6 coord_system_name
+# 7 coord_system_version
+# 8 seq
+# 9 need_project
+# 10 common_start
+# 11 common_end
+# 12 common_strand
+# 13 common_sr_name
+
+
+use strict;
+use warnings;
+no warnings 'uninitialized';
+
+use Bio::EnsEMBL::IDMapping::TinyFeature;
+our @ISA = qw(Bio::EnsEMBL::IDMapping::TinyFeature);
+
+use Bio::EnsEMBL::Utils::Exception qw(throw warning);
+
+
+sub start {
+ my $self = shift;
+ $self->[2] = shift if (@_);
+ return $self->[2];
+}
+
+
+sub end {
+ my $self = shift;
+ $self->[3] = shift if (@_);
+ return $self->[3];
+}
+
+
+sub strand {
+ my $self = shift;
+ $self->[4] = shift if (@_);
+ return $self->[4];
+}
+
+
+sub seq_region_name {
+ my $self = shift;
+ $self->[5] = shift if (@_);
+ return $self->[5];
+}
+
+
+sub coord_system_name {
+ my $self = shift;
+ $self->[6] = shift if (@_);
+ return $self->[6];
+}
+
+
+sub coord_system_version {
+ my $self = shift;
+ $self->[7] = shift if (@_);
+ return $self->[7];
+}
+
+
+sub seq {
+ my $self = shift;
+ $self->[8] = shift if (@_);
+ return $self->[8];
+}
+
+
+sub need_project {
+ my $self = shift;
+ $self->[9] = shift if (@_);
+ return $self->[9];
+}
+
+
+sub common_start {
+ my $self = shift;
+
+ # when used as a setter, always set a value
+ $self->[10] = shift if (@_);
+
+ # when used as a getter
+ if (scalar(@$self > 9) {
+ # return value for common coord_system if available (but avoid
+ # autovivification gotcha!)
+ return $self->[10];
+ } elsif ($self->need_project) {
+ # return undef if common value expected but not there (e.g. no projection
+ # found
+ return undef;
+ } else {
+ # return native value
+ return $self->start;
+ }
+}
+
+
+sub common_end {
+ my $self = shift;
+
+ # when used as a setter, always set a value
+ $self->[11] = shift if (@_);
+
+ # when used as a getter
+ if (scalar(@$self > 9) {
+ # return value for common coord_system if available (but avoid
+ # autovivification gotcha!)
+ return $self->[11];
+ } elsif ($self->need_project) {
+ # return undef if common value expected but not there (e.g. no projection
+ # found
+ return undef;
+ } else {
+ # return native value
+ return $self->end;
+ }
+}
+
+
+sub common_strand {
+ my $self = shift;
+
+ # when used as a setter, always set a value
+ $self->[12] = shift if (@_);
+
+ # when used as a getter
+ if (scalar(@$self > 9) {
+ # return value for common coord_system if available (but avoid
+ # autovivification gotcha!)
+ return $self->[12];
+ } elsif ($self->need_project) {
+ # return undef if common value expected but not there (e.g. no projection
+ # found
+ return undef;
+ } else {
+ # return native value
+ return $self->strand;
+ }
+}
+
+
+sub common_sr_name {
+ my $self = shift;
+
+ # when used as a setter, always set a value
+ $self->[13] = shift if (@_);
+
+ # when used as a getter
+ if (scalar(@$self > 9) {
+ # return value for common coord_system if available (but avoid
+ # autovivification gotcha!)
+ return $self->[13];
+ } elsif ($self->need_project) {
+ # return undef if common value expected but not there (e.g. no projection
+ # found
+ return undef;
+ } else {
+ # return native value
+ return $self->seq_region_name;
+ }
+}
+
+
+1;
+
diff --git a/modules/Bio/EnsEMBL/IdMapping/TinyGene.pm b/modules/Bio/EnsEMBL/IdMapping/TinyGene.pm
new file mode 100644
index 0000000000..0cd2d7ce72
--- /dev/null
+++ b/modules/Bio/EnsEMBL/IdMapping/TinyGene.pm
@@ -0,0 +1,60 @@
+package Bio::EnsEMBL::IdMapping::TinyGene;
+
+=head1 NAME
+
+
+=head1 SYNOPSIS
+
+
+=head1 DESCRIPTION
+
+
+=head1 METHODS
+
+
+=head1 LICENCE
+
+This code is distributed under an Apache style licence. Please see
+http://www.ensembl.org/info/about/code_licence.html for details.
+
+=head1 AUTHOR
+
+Patrick Meidl <meidl@ebi.ac.uk>, Ensembl core API team
+
+=head1 CONTACT
+
+Please post comments/questions to the Ensembl development list
+<ensembl-dev@ebi.ac.uk>
+
+=cut
+
+
+use strict;
+use warnings;
+no warnings 'uninitialized';
+
+use Bio::EnsEMBL::IDMapping::TinyFeature;
+our @ISA = qw(Bio::EnsEMBL::IDMapping::TinyFeature);
+
+use Bio::EnsEMBL::Utils::Exception qw(throw warning);
+
+
+sub add_Transcript {
+ my $self = shift;
+ my $tr = shift;
+
+ unless ($tr && $tr->isa('Bio::EnsEMBL::IdMapping::TinyTranscript')) {
+ throw('Need a Bio::EnsEMBL::IdMapping::TinyTranscript.');
+ }
+
+ push @{ $self->[9] }, $tr;
+}
+
+
+sub get_all_Transcripts {
+ return $_->[9] || [];
+}
+
+
+1;
+
diff --git a/modules/Bio/EnsEMBL/IdMapping/TinyTranscript.pm b/modules/Bio/EnsEMBL/IdMapping/TinyTranscript.pm
new file mode 100644
index 0000000000..a0fe549041
--- /dev/null
+++ b/modules/Bio/EnsEMBL/IdMapping/TinyTranscript.pm
@@ -0,0 +1,72 @@
+package Bio::EnsEMBL::IdMapping::TinyTranscript;
+
+=head1 NAME
+
+
+=head1 SYNOPSIS
+
+
+=head1 DESCRIPTION
+
+
+=head1 METHODS
+
+
+=head1 LICENCE
+
+This code is distributed under an Apache style licence. Please see
+http://www.ensembl.org/info/about/code_licence.html for details.
+
+=head1 AUTHOR
+
+Patrick Meidl <meidl@ebi.ac.uk>, Ensembl core API team
+
+=head1 CONTACT
+
+Please post comments/questions to the Ensembl development list
+<ensembl-dev@ebi.ac.uk>
+
+=cut
+
+
+use strict;
+use warnings;
+no warnings 'uninitialized';
+
+use Bio::EnsEMBL::IDMapping::TinyFeature;
+our @ISA = qw(Bio::EnsEMBL::IDMapping::TinyFeature);
+
+use Bio::EnsEMBL::Utils::Exception qw(throw warning);
+
+
+sub add_Translation {
+ my $self = shift;
+ my $tl = shift;
+
+ unless ($self->[0] eq 'tr' and $tl->[0] eq 'tl') {
+ throw('You can only add a translation to a transcript.');
+ }
+
+ $self->[10] = $tl;
+}
+
+
+sub add_Exon {
+ my $self = shift;
+ my $exon = shift;
+
+ unless ($exon && $exon->isa('Bio::EnsEMBL::IdMapping::TinyExon')) {
+ throw('Need a Bio::EnsEMBL::IdMapping::TinyExon.');
+ }
+
+ push @{ $self->[11] }, $exon;
+}
+
+
+sub get_all_Exons {
+ return $_->[11] || [];
+}
+
+
+1;
+
diff --git a/modules/Bio/EnsEMBL/IdMapping/TinyTranslation.pm b/modules/Bio/EnsEMBL/IdMapping/TinyTranslation.pm
new file mode 100644
index 0000000000..9fdc7c64ac
--- /dev/null
+++ b/modules/Bio/EnsEMBL/IdMapping/TinyTranslation.pm
@@ -0,0 +1,43 @@
+package Bio::EnsEMBL::IdMapping::TinyGene;
+
+=head1 NAME
+
+
+=head1 SYNOPSIS
+
+
+=head1 DESCRIPTION
+
+
+=head1 METHODS
+
+
+=head1 LICENCE
+
+This code is distributed under an Apache style licence. Please see
+http://www.ensembl.org/info/about/code_licence.html for details.
+
+=head1 AUTHOR
+
+Patrick Meidl <meidl@ebi.ac.uk>, Ensembl core API team
+
+=head1 CONTACT
+
+Please post comments/questions to the Ensembl development list
+<ensembl-dev@ebi.ac.uk>
+
+=cut
+
+
+use strict;
+use warnings;
+no warnings 'uninitialized';
+
+use Bio::EnsEMBL::IDMapping::TinyFeature;
+our @ISA = qw(Bio::EnsEMBL::IDMapping::TinyFeature);
+
+use Bio::EnsEMBL::Utils::Exception qw(throw warning);
+
+
+1;
+
--
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