aditional attributes and functions for mapping coordinates by alignment

modules/Bio/EnsEMBL/IdentityXref.pm

@@ -46,10 +46,24 @@ use strict;
 sub new {
     my ($class, @args) = @_;
     my $self = $class->SUPER::new(@args);
-    my ($query_identity, $target_identity) = $self->_rearrange(
-        [qw(QUERY_IDENTITY TARGET_IDENTITY)], @args);
-    if(defined $query_identity) { $self->query_identity($query_identity); }
-    if(defined $target_identity) { $self->target_identity($target_identity); }
+    my ($query_identity, $target_identity, $score, $evalue, 
+        $cigar_line, $hit_start, $hit_end, $translation_start,
+        $translation_end, $analysis ) = $self->_rearrange(
+        [qw(QUERY_IDENTITY TARGET_IDENTITY SCORE EVALUE CIGAR_LINE 
+            HIT_START HIT_END TRANSLATION_START TRANSLATION_END
+            ANALYSIS)], @args);
+    
+    $self->{'query_identity'} = $query_identity;
+    $self->{'traget_identity'} = $target_identity;
+    $self->{'score'} = $score;
+    $self->{'evalue'} = $evalue;
+    $self->{'cigar_line'} = $cigar_line;
+    $self->{'hit_start'} = $hit_start;
+    $self->{'hit_end'} = $hit_end;
+    $self->{'translation_start'} = $translation_start;
+    $self->{'translation_end'} = $translation_end;
+    $self->{'analysis'} = $analysis;
+
     return $self;
 }
 
@@ -96,4 +110,289 @@ sub target_identity{
 
 }
 
+
+
+=head2 cigar_line
+
+  Arg [1]    : string $cigar_line
+  Example    : none
+  Description: get/set for attribute cigar_line
+  Returntype : string
+  Exceptions : none
+  Caller     : general
+
+=cut
+
+sub cigar_line {
+  my $self = shift;
+  $self->{'cigar_line'} = shift if( @_ );
+  return $self->{'cigar_line'};
+}
+
+
+=head2 translation_start
+
+  Arg [1]    : string $translation_start
+  Example    : none
+  Description: get/set for attribute translation_start
+  Returntype : string
+  Exceptions : none
+  Caller     : general
+
+=cut
+
+sub translation_start {
+   my $self = shift;
+  $self->{'translation_start'} = shift if( @_ );
+  return $self->{'translation_start'};
+}
+
+
+=head2 translation_end
+
+  Arg [1]    : string $translation_end
+  Example    : none
+  Description: get/set for attribute translation_end
+  Returntype : string
+  Exceptions : none
+  Caller     : general
+
+=cut
+
+sub translation_end {
+   my $self = shift;
+  $self->{'translation_end'} = shift if( @_ );
+  return $self->{'translation_end'};
+}
+
+
+=head2 hit_start
+
+  Arg [1]    : string $hit_start
+  Example    : none
+  Description: get/set for attribute hit_start
+  Returntype : string
+  Exceptions : none
+  Caller     : general
+
+=cut
+
+sub hit_start {
+   my $self = shift;
+  $self->{'hit_start'} = shift if( @_ );
+  return $self->{'hit_start'};
+}
+
+
+=head2 hit_end
+
+  Arg [1]    : string $hit_end
+  Example    : none
+  Description: get/set for attribute hit_end
+  Returntype : string
+  Exceptions : none
+  Caller     : general
+
+=cut
+
+sub hit_end {
+   my $self = shift;
+  $self->{'hit_end'} = shift if( @_ );
+  return $self->{'hit_end'};
+}
+
+
+=head2 score
+
+  Arg [1]    : string $score
+  Example    : none
+  Description: get/set for attribute score
+  Returntype : string
+  Exceptions : none
+  Caller     : general
+
+=cut
+
+sub score {
+   my $self = shift;
+  $self->{'score'} = shift if( @_ );
+  return $self->{'score'};
+}
+
+
+=head2 evalue
+
+  Arg [1]    : string $evalue
+  Example    : none
+  Description: get/set for attribute evalue
+  Returntype : string
+  Exceptions : none
+  Caller     : general
+
+=cut
+
+sub evalue {
+   my $self = shift;
+  $self->{'evalue'} = shift if( @_ );
+  return $self->{'evalue'};
+}
+
+
+=head2 analysis
+
+  Arg [1]    : Bio::EnsEMBL::Analysis $analysis
+  Example    : none
+  Description: get/set for attribute analysis
+  Returntype : Bio::EnsEMBL::Analysis
+  Exceptions : none
+  Caller     : general
+
+=cut
+
+sub analysis {
+   my $self = shift;
+  $self->{'analysis'} = shift if( @_ );
+  return $self->{'analysis'};
+}
+
+
+
+
+=head2 get_mapper
+
+  Args       : none
+  Example    : none
+  Description: produces a mapper object that takes coordinates from one side of 
+               the alignment to the other side. "ensembl" and "external" are the 
+               two coordinate systems contained. 
+  Returntype : Bio::EnsEMBL::Mapper
+  Exceptions : none
+  Caller     : general, ProteinDAS subsystem
+
+=cut
+
+
+sub get_mapper {
+  my ( $self ) = @_;
+  # parse the cigar_line and create a mapper ...
+  if( exists $self->{'_cached_mapper'} ) {
+    return $self->{'_cached_mapper'};
+  }
+
+  my @pre_lens = split( '[DMI]', $self->cigar_line() );
+  my @lens = map { if( ! $_ ) { 1 } else { $_ }} @pre_lens;
+  my @chars = grep { /[DMI]/ } split( //, $self->cigar_line() );
+
+  my $translation_start = $self->translation_start();
+  my $translation_end = $self->translation_end();
+  my $hit_start = $self->hit_start();
+  my $hit_end = $self->hit_end();
+
+#  my $hit_id = $self->display_id();
+  my $hit_id = "external_id";
+  my $translation_id = "translation_id";
+
+  # now build the mapper
+  my $mapper = Bio::EnsEMBL::Mapper->new( "ensembl", "external" );
+  for( my $i=0; $i<=$#lens; $i++ ) {
+    my $length = $lens[$i];
+    my $char = $chars[$i];
+    if( $char eq "M" ) {
+      $mapper->add_map_coordinates( $translation_id, $translation_start,
+				    $translation_start + $length - 1,
+				    1, $hit_id, $hit_start, $hit_start + $length - 1 );
+      $hit_start += $length;
+      $translation_start += $length;
+
+    } elsif( $char eq "D" ) {
+      $hit_start += $length;
+    } elsif( $char eq "I" ) {
+      $translation_start += $length;
+    }
+  }
+
+  $self->{'_cached_mapper'} = $mapper;
+
+  return $mapper;
+}
+
+
+
+=head2 transform_feature
+
+  Arg [1]    : a feature type with start and end $feature
+               This doesnt need to be a Bio::EnsEMBL::Feature as it doesnt 
+               need an attached slice. We may have to introduce an appropriate
+               object type.
+  Example    : my $ens_prot_feature_list = $ident_xref->
+                         transform_feature( $swiss_prot_feature ); 
+  Description: a list of potential partial features which represent all mappable places
+               of the original feature in ensembl translation coordinates.
+  Returntype : listref of whatever was put in
+  Exceptions : none
+  Caller     : general, ProteinDAS subsystem
+
+=cut
+
+
+sub transform_feature {
+  my $self= shift;
+  my $feature = shift;
+
+  my $fstart = $feature->start();
+  my $fend = $feature->end();
+  
+  my $mapper = $self->get_mapper();
+  my @result;
+
+  my @coords = $mapper->map_coordinates( "external_id", $fstart, $fend, 1, "external" );
+  
+  for my $coord ( @coords ) {
+    if( $coord->isa( "Bio::EnsEMBL::Mapper::Coordinate" )) {
+      my $new_feature;
+      %{$new_feature} = %$feature;
+      bless $new_feature, ref( $feature );
+      $new_feature->start( $coord->start() );
+      $new_feature->end( $coord->end() );
+      
+      push( @result, $new_feature );
+    }
+  }
+
+  return \@result;
+}
+
+
+
+=head2 map_feature
+
+  Arg [1]    : a start,end capable feature object
+  Example    : none
+  Description: 
+  Returntype : list of Coordinates/Gaps which represents the mapping
+  Exceptions : none
+  Caller     : another way of doing ProteinDAS
+
+=cut
+
+sub map_feature {
+  my $self = shift;
+  my $feature = shift;
+
+
+  my $fstart = $feature->start();
+  my $fend = $feature->end();
+  
+  my $mapper = $self->get_mapper();
+  my @coords = $mapper->map_coordinates( "external_id", $fstart, $fend, 1, "external" );
+  
+  return @coords;
+}
+
+
+
+
+
+
+
 1;