Commit 440b54e9 authored by Bronwen Aken's avatar Bronwen Aken
Browse files

Added external_db_id and hcoverage, for the 2 new columns in dna_align_feature...

Added external_db_id and hcoverage, for the 2 new columns in dna_align_feature and protein_align_feature.
parent 1298052d
......@@ -114,6 +114,7 @@ use strict;
=cut
sub new {
my $caller = shift;
my $class = ref($caller) || $caller;
......@@ -474,6 +475,7 @@ sub _parse_cigar {
$start2 = $hstart - 1;
}
push @features, Bio::EnsEMBL::FeaturePair->new
(-SLICE => $self->{'slice'},
-SEQNAME => $self->{'seqname'},
......@@ -489,6 +491,8 @@ sub _parse_cigar {
-PERCENT_ID => $self->{'percent_id'},
-ANALYSIS => $self->{'analysis'},
-P_VALUE => $self->{'p_value'},
-EXTERNAL_DB_ID => $self->{'external_db_id'},
-HCOVERAGE => $self->{'hcoverage'},
-GROUP_ID => $self->{'group_id'},
-LEVEL_ID => $self->{'level_id'});
......@@ -574,7 +578,8 @@ sub _parse_features {
my $percent = $f[0]->percent_id;
my $analysis = $f[0]->analysis;
my $pvalue = $f[0]->p_value();
my $external_db_id = $f[0]->external_db_id;
my $hcoverage = $f[0]->hcoverage;
my $group_id = $f[0]->group_id;
my $level_id = $f[0]->level_id;
......@@ -825,6 +830,8 @@ sub _parse_features {
$self->{'hseqname'} = $hname;
$self->{'cigar_string'} = $string;
$self->{'p_value'} = $pvalue;
$self->{'external_db_id'} = $external_db_id;
$self->{'hcoverage'} = $hcoverage;
$self->{'group_id'} = $group_id;
$self->{'level_id'} = $level_id;
}
......
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