Commit 054348b2 authored by Philip Lijnzaad's avatar Philip Lijnzaad
Browse files

fixed error message, docu.

parent b3c75e98
......@@ -1617,7 +1617,7 @@ sub _reverse_map_Exon {
# print STDERR "Straight forward mapping\n";
my $rmexon = Bio::EnsEMBL::Exon->new();
my $rmexon = Bio::EnsEMBL::Exon->new(); # the re-mapped exon
$rmexon->id($exon->id);
$rmexon->created($exon->created);
$rmexon->modified($exon->modified);
......@@ -1776,7 +1776,6 @@ sub _check_exon_start_end {
my $to_test;
# depending on the 'which_one' arg, check beginning or end of it.
# (PL: might be too slow)
if ($which_one eq 'start' ) {
$to_test = $transl->start;
} elsif ($which_one eq 'end' ) {
......@@ -1786,18 +1785,20 @@ sub _check_exon_start_end {
}
if ( $to_test < 1 ) {
$message .= "Translation's $which_one < 1: " . $transl->start
. "(translation:". $transl->id() . ")";
$message .= "Translation's $which_one < 1: "
. (($which_one eq 'start')?$transl->start :$transl->end)
. " (translation:". $transl->id() . ")";
}
if ( $to_test > $exon->length) {
$message .= "Translation's $which_one (".$transl->start
.") > exon length (".$exon->length.") "
. "(translation:". $transl->id() . ",exon:".$exon->id().")";
$message .= "Translation's $which_one ("
. (($which_one eq 'start')?$transl->start :$transl->end)
.") > exon length (".$exon->length.")"
. " (translation:". $transl->id() . ",exon:".$exon->id().")";
}
return $message;
}
} # _check_exon_start_end
=head2 _sanity_check
......@@ -1912,7 +1913,7 @@ sub _sanity_check{
if( $error ) {
$self->throw("Cannot write gene due to: $message");
}
}
} # _sanity_check
=head1 Get/Set for Virtual::Contig orientated datastructures.
......
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