diff --git a/modules/Bio/EnsEMBL/Exon.pm b/modules/Bio/EnsEMBL/Exon.pm
index fb9cbad7b96d6e7fb4088ae2020643aa895875f1..b24ecbad79f6f19a12c4388d6ad3c9dbfcbacd9d 100755
--- a/modules/Bio/EnsEMBL/Exon.pm
+++ b/modules/Bio/EnsEMBL/Exon.pm
@@ -1550,12 +1550,13 @@ sub adjust_start_end {
my $new_exon = Bio::EnsEMBL::Exon->new();
%{$new_exon} = %{$self};
+
if( $self->strand() == 1 ) {
$new_exon->start( $self->start() + $start_adjust );
$new_exon->end( $self->end() + $end_adjust )
} else {
- $new_exon->start( $self->end() - $start_adjust );
- $new_exon->end( $self->start() - $end_adjust )
+ $new_exon->start( $self->start() - $end_adjust );
+ $new_exon->end( $self->end() - $start_adjust )
}
return $new_exon;
diff --git a/modules/Bio/EnsEMBL/Protein.pm b/modules/Bio/EnsEMBL/Protein.pm
index 3c4ab8d9a5e462cd4e9f628666eeec5fd5c40c66..07e2d64ed127f14caecbaeb2252b67d0b642ad2e 100644
--- a/modules/Bio/EnsEMBL/Protein.pm
+++ b/modules/Bio/EnsEMBL/Protein.pm
@@ -51,7 +51,9 @@ package Bio::EnsEMBL::Protein;
use vars qw(@ISA);
use strict;
-use Bio::Root::Object;
+
+use Bio::EnsEMBL::Root;
+
use Bio::SeqI;
use Bio::EnsEMBL::Transcript;
use Bio::DBLinkContainerI;
@@ -60,34 +62,13 @@ use Bio::Tools::SeqStats;
# Object preamble - inheriets from Bio::Root::Object
-@ISA = qw(Bio::PrimarySeq Bio::SeqI);
+@ISA = qw( Bio::PrimarySeq Bio::SeqI);
=head2 SeqI interface features
=cut
-
-#=head2 add_date
-
-# Title : add_date
-# Usage : $self->add_date($ref)
-# Function: adds a date
-# Example :
-# Returns :
-# Args :
-
-#=cut
-
-#sub add_date {
-# my ($self) = shift;
-# foreach my $dt ( @_ ) {
-# push(@{$self->{'date'}},$dt);
-# }
-#}
-
-
-
=head2 adaptor
Title : adaptor
@@ -109,31 +90,6 @@ sub adaptor {
}
-#=head2 get_dates
-
-# Title : get_dates
-# Usage : foreach $dt ( $self->get_dates() )
-# Function: gets an array of dates
-# Example :
-# Returns :
-# Args :
-
-#=cut
-
-#sub get_dates {
-# my ($self) = @_;
-
-# $self->warn("In giving back dates, have not sorted out how stable id system works with proteins");
-
-# return ();
-# return @{$self->{'date'}};
-#}
-
-
-#sub each_date {
-# my ($self) = @_;
-# return $self->get_dates;
-#}
=head2 species
@@ -441,7 +397,7 @@ sub get_all_ProfileFeatures{
}
}
- return $self->{'_profile'};
+ return ( $self->{'_profile'} || [] );
}
=head2 add_Profile
@@ -494,7 +450,7 @@ sub get_all_blastpFeatures{
}
}
- return $self->{'_blastp'};
+ return ( $self->{'_blastp'} || [] );
}
=head2 add_blastp
@@ -543,7 +499,7 @@ sub get_all_PrintsFeatures{
$self->add_Prints($in);
}
}
- return $self->{'_prints'};
+ return ( $self->{'_prints'} || [] );
}
=head2 add_Prints
@@ -594,7 +550,7 @@ sub get_all_PfamFeatures{
$self->add_Pfam($in);
}
}
- return $self->{'_pfam'};
+ return ( $self->{'_pfam'} || [] );
}
=head2 add_Pfam
@@ -643,7 +599,7 @@ sub get_all_PrositeFeatures{
$self->add_Prosite($in);
}
}
- return $self->{'_prosite'};
+ return ( $self->{'_prosite'} || [] );
}
=head2 add_Prosite
@@ -692,7 +648,7 @@ sub get_all_SigpFeatures{
$self->add_Sigp($in);
}
}
- return $self->{'_sigp'};
+ return ( $self->{'_sigp'} || [] );
}
=head2 add_Sigp
@@ -743,7 +699,7 @@ sub get_all_TransmembraneFeatures{
}
}
- return $self->{'_transmembrane'};
+ return ( $self->{'_transmembrane'} || [] );
}
@@ -794,7 +750,7 @@ sub get_all_CoilsFeatures{
$self->add_Coils($in);
}
}
- return $self->{'_coils'};
+ return ( $self->{'_coils'} || [] );
}
=head2 add_Coils
@@ -841,7 +797,7 @@ sub get_all_LowcomplFeatures{
$self->add_Lowcompl($in);
}
}
- return $self->{'_lowcompl'};
+ return ( $self->{'_lowcompl'} || [] );
}
=head2 add_LowCompl
@@ -891,7 +847,7 @@ sub get_all_SuperfamilyFeatures{
$self->add_Superfamily($in);
}
}
- return $self->{'_superfamily'};
+ return ( $self->{'_superfamily'} || [] );
}
=head2 add_Superfamily
@@ -917,129 +873,6 @@ sub add_Superfamily{
}
-#=head2 add_intron
-
-# Title : add_intron
-# Usage :
-# Function:
-# Example :
-# Returns :
-# Args :
-
-
-#=cut
-
-#sub add_intron{
-# my ($self,$value) = @_;
-# if ((!defined $value) || (!$value->isa('Bio::EnsEMBL::ProteinFeature'))) {
-# $self->throw("The Protein Feature added is not defined or is not a protein feature object");
-# }
-# push(@{$self->{'_intron'}},$value);
-
-#}
-
-
-#=head2 get_all_IntronFeatures
-
-# Title : get_all_IntronFeatures
-# Usage :my @introns_feature = $protein->get_all_IntronFeatures($proteinid)
-# Function:Get all of the introns as ProteinFeatures for a given peptide and add them to protein features
-# Example :
-# Returns : Nothing
-# Args :Peptide ID
-
-
-#=cut
-
-#sub get_all_IntronFeatures{
-# my ($self) = @_;
-# if (defined ($self->{'_intron'})) {
-# return @{$self->{'_intron'}};
-# }
-# else {
-# my $proteinid = $self->id();
-# my $pa = $self->adaptor()->db()->get_ProteinAdaptor();
-# my @array_introns = $pa->get_Introns($proteinid);
-# foreach my $in (@array_introns) {
-# $self->add_intron($in);
-# }
-# return @array_introns;
-# }
-#}
-
-#=head2 add_snps
-
-# Title : add_snps
-# Usage :
-# Function:
-# Example :
-# Returns :
-# Args :
-
-
-#=cut
-
-#sub add_snps{
-# my ($self,$value) = @_;
-
-# if ((!defined $value)) {
-# $self->throw("Value is not defined");
-# }
-
-# push(@{$self->{'_snp'}},$value);
-#}
-
-
-#=head2 get_all_SnpsFeatures
-
-# Title : get_all_SnpsFeatures
-# Usage :
-# Function:
-# Example :
-# Returns :
-# Args :
-
-
-#=cut
-
-#sub get_all_SnpsFeatures{
-# my ($self) = @_;
-# if (defined ($self->{'_snp'})) {
-# return @{$self->{'_snp'}};
-# }
-# else {
-# my $gbdb = $self->gbrowser_adaptor();
-# my $snpdb = $self->snp_adaptor();
-# my @snps_array = $self->adaptor->get_snps($self,$snpdb,$gbdb);
-# foreach my $sn (@snps_array) {
-# $self->add_snps($sn);
-# }
-# return @snps_array;
-# }
-
-#}
-
-
-
-#Title : add_ProteinFeature (formerly add_Protein_feature)
-# Usage :
-# Function:
-# Example :
-# Returns :
-# Args :
-
-
-#=cut
-
-#sub add_ProteinFeature{
-# my ($self,$value) = @_;
-
-# if ((!defined $value) || (!$value->isa('Bio::EnsEMBL::ProteinFeature'))) {
-# $self->throw("[$value] is not a protein feature object");
-# }
-
-# push(@{$self->{'_prot_feat'}},$value);
-# }
=head2 length
@@ -1093,81 +926,6 @@ sub get_all_DBLinks{
return $self->{'_dblinks'};
}
-#=head2 molecular_weight
-
-# Title : molecular_weight
-# Usage :
-# Function: This method has been placed here for convenience function. This gets and return the molecular weight of the protein
-# Example : my $mw = $protein->molecular_weight
-# Returns : Moleculat weight of the peptide
-# Args :
-
-#=cut
-
-#sub molecular_weight{
-# my ($self) = @_;
-# my $mw = ${Bio::Tools::SeqStats->get_mol_wt($self)}[0];
-# return $mw;
-#}
-
-#=head2 checksum
-
-# Title : checksum
-# Usage : my $checksum = $protein->checksum()
-# Function: Get the crc64 for the sequence of the protein (this method has been copied from _crc64 method which is in swiss.pm in Bioperl and have been placed here for convenience function
-# Example :
-# Returns : CRC64
-# Args : Nothing
-
-
-#=cut
-
-#sub checksum{
-# my ($self) = @_;
-
-# my $sequence = \$self->seq();
-
-# my $POLY64REVh = 0xd8000000;
-# my @CRCTableh = 256;
-# my @CRCTablel = 256;
-# my $initialized;
-
-
-# my $seq = $$sequence;
-
-# my $crcl = 0;
-# my $crch = 0;
-# if (!$initialized) {
-# $initialized = 1;
-# for (my $i=0; $i<256; $i++) {
-# my $partl = $i;
-# my $parth = 0;
-# for (my $j=0; $j<8; $j++) {
-# my $rflag = $partl & 1;
-# $partl >>= 1;
-# $partl |= (1 << 31) if $parth & 1;
-# $parth >>= 1;
-# $parth ^= $POLY64REVh if $rflag;
-# }
-# $CRCTableh[$i] = $parth;
-# $CRCTablel[$i] = $partl;
-# }
-# }
-
-# foreach (split '', $seq) {
-# my $shr = ($crch & 0xFF) << 24;
-# my $temp1h = $crch >> 8;
-# my $temp1l = ($crcl >> 8) | $shr;
-# my $tableindex = ($crcl ^ (unpack "C", $_)) & 0xFF;
-# $crch = $temp1h ^ $CRCTableh[$tableindex];
-# $crcl = $temp1l ^ $CRCTablel[$tableindex];
-# }
-# my $crc64 = sprintf("%08X%08X", $crch, $crcl);
-
-# return $crc64;
-
-#}
-
diff --git a/modules/Bio/EnsEMBL/Transcript.pm b/modules/Bio/EnsEMBL/Transcript.pm
index 2389cecc6bcb352f5cd09ec668033f7946940530..89bcdb4761efbc5a25b17366b5afbd3c9fd721d0 100755
--- a/modules/Bio/EnsEMBL/Transcript.pm
+++ b/modules/Bio/EnsEMBL/Transcript.pm
@@ -722,30 +722,21 @@ sub get_all_translateable_Exons {
my( @translateable );
foreach my $ex (@{$self->get_all_Exons}) {
- my $ex_id = $ex->dbID;
if ($ex ne $start_exon and ! @translateable) {
next; # Not yet in translated region
}
- my $start = $ex->start;
- my $end = $ex->end;
+
my $length = $ex->length;
- my $strand = $ex->strand;
-
- my $trunc_start = $start;
- my $trunc_end = $end;
+ my $adjust_start = 0;
+ my $adjust_end = 0;
# Adjust to translation start if this is the start exon
if ($ex == $start_exon ) {
if ($t_start < 1 or $t_start > $length) {
$self->throw("Translation start '$t_start' is outside exon $ex length=$length");
}
- if ($strand == 1) {
- $trunc_start = $start + $t_start - 1;
- }
- else {
- $trunc_end = $end - $t_start + 1;
- }
+ $adjust_start = $t_start - 1;
}
# Adjust to translation end if this is the end exon
@@ -753,22 +744,15 @@ sub get_all_translateable_Exons {
if ($t_end < 1 or $t_end > $length) {
$self->throw("Translation end '$t_end' is outside exon $ex length=$length");
}
- if ($strand == 1) {
- $trunc_end = $end - $length + $t_end;
- }
- else {
- $trunc_start = $start + $length - $t_end;
- }
+ $adjust_end = $t_end - $length;
}
-
+
# Make a truncated exon if the translation start or
# end causes the coordinates to be altered.
- if ($trunc_start != $start or $trunc_end != $end) {
- my ( $adjust_start, $adjust_end );
- $adjust_start = $trunc_start - $start;
- $adjust_end = $trunc_end - $end;
+ if ($adjust_end || $adjust_start) {
+ my $newex = $ex->adjust_start_end( $adjust_start, $adjust_end );
- push( @translateable, $ex->adjust_start_end( $adjust_start, $adjust_end ));
+ push( @translateable, $newex );
} else {
push(@translateable, $ex);
}
diff --git a/modules/runtests.pl b/modules/runtests.pl
index 25da55a6190295c1c687ab76c5f74f3826bb871e..10726266926b7ab2e0a98c1495fe46d95633b125 100755
--- a/modules/runtests.pl
+++ b/modules/runtests.pl
@@ -26,6 +26,8 @@ if($opt_l) {
}
#run all of the specified tests
+$ENV{'RUNTEST_ACTIVE'} = 1;
+
runtests(@{&get_all_tests('.', \@ARGV)});
diff --git a/modules/t/MultiTestDB.conf b/modules/t/MultiTestDB.conf
index 14bc2b5043013302ffd9488ffdf4c562e4c36755..6db4f8f8b71d966607b895c99d444bef1bdf82ff 100644
--- a/modules/t/MultiTestDB.conf
+++ b/modules/t/MultiTestDB.conf
@@ -4,7 +4,7 @@
'user' => 'ensadmin',
'pass' => 'ensembl',
'host' => 'ecs1c',
- 'zip' => 'multidb.zip',
+ 'zip' => 'test_genome.zip',
#add a line with the dbname and module
'databases' => { 'core' => 'Bio::EnsEMBL::DBSQL::DBAdaptor',