From c3803bcf6bc7f1e5e39db4f669624d40bb0b97aa Mon Sep 17 00:00:00 2001
From: Daniel Rios <dr2@sanger.ac.uk>
Date: Wed, 29 Oct 2008 11:10:20 +0000
Subject: [PATCH] modified to include new_fast method to allow fast creation of
objects within the adaptors
---
modules/Bio/EnsEMBL/Exon.pm | 58 +++++++++++++++---------------
modules/Bio/EnsEMBL/Feature.pm | 25 ++++++++++---
modules/Bio/EnsEMBL/Gene.pm | 25 +++++++------
modules/Bio/EnsEMBL/Transcript.pm | 22 ++++++------
modules/Bio/EnsEMBL/Translation.pm | 26 +++++++++++---
5 files changed, 94 insertions(+), 62 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Exon.pm b/modules/Bio/EnsEMBL/Exon.pm
index 607c711422..8034877cb9 100755
--- a/modules/Bio/EnsEMBL/Exon.pm
+++ b/modules/Bio/EnsEMBL/Exon.pm
@@ -103,11 +103,11 @@ sub new {
my $self = $class->SUPER::new( @_ );
+
my ( $phase, $end_phase, $stable_id, $version, $created_date, $modified_date,
- $is_current ) =
- rearrange( [ "PHASE", "END_PHASE", "STABLE_ID", "VERSION",
+ $is_current ) =
+ rearrange( [ "PHASE", "END_PHASE", "STABLE_ID", "VERSION",
"CREATED_DATE", "MODIFIED_DATE", "IS_CURRENT" ], @_ );
-
$self->phase($phase) if (defined $phase); # make sure phase is valid.
$self->{'end_phase'} = $end_phase;
$self->{'stable_id'} = $stable_id;
@@ -123,40 +123,40 @@ sub new {
}
-=head2 new_fast
+# =head2 new_fast
- Arg [1] : Bio::EnsEMBL::Slice $slice
- Arg [2] : int $start
- Arg [3] : int $end
- Arg [4] : int $strand (1 or -1)
- Example : none
- Description: create an Exon object
- Returntype : Bio::EnsEMBL::Exon
- Exceptions : throws if end < start
- Caller : general, creation in Bio::EnsEMBL::Lite::GeneAdaptor
- Status : Stable
+# Arg [1] : Bio::EnsEMBL::Slice $slice
+# Arg [2] : int $start
+# Arg [3] : int $end
+# Arg [4] : int $strand (1 or -1)
+# Example : none
+# Description: create an Exon object
+# Returntype : Bio::EnsEMBL::Exon
+# Exceptions : throws if end < start
+# Caller : general, creation in Bio::EnsEMBL::Lite::GeneAdaptor
+# Status : Stable
-=cut
+# =cut
-sub new_fast {
- my ($class, $slice, $start, $end, $strand) = @_;
+# sub new_fast {
+# my ($class, $slice, $start, $end, $strand) = @_;
- my $self = bless {}, $class;
+# my $self = bless {}, $class;
- # Swap start and end if they're in the wrong order
- # We assume that the strand is correct and keep the input value.
+# # Swap start and end if they're in the wrong order
+# # We assume that the strand is correct and keep the input value.
- if ($start > $end) {
- throw( "End smaller than start not allowed" );
- }
+# if ($start > $end) {
+# throw( "End smaller than start not allowed" );
+# }
- $self->start ($start);
- $self->end ($end);
- $self->strand($strand);
- $self->slice($slice);
+# $self->start ($start);
+# $self->end ($end);
+# $self->strand($strand);
+# $self->slice($slice);
- return $self;
-}
+# return $self;
+# }
=head2 end_phase
diff --git a/modules/Bio/EnsEMBL/Feature.pm b/modules/Bio/EnsEMBL/Feature.pm
index a571499391..700ee05582 100644
--- a/modules/Bio/EnsEMBL/Feature.pm
+++ b/modules/Bio/EnsEMBL/Feature.pm
@@ -99,11 +99,9 @@ sub new {
my $caller = shift;
my $class = ref($caller) || $caller;
-
- my($start, $end, $strand, $slice, $analysis,$seqname, $dbID, $adaptor) =
- rearrange(['START','END','STRAND','SLICE','ANALYSIS', 'SEQNAME',
- 'DBID', 'ADAPTOR'], @_);
-
+ my ( $start, $end, $strand, $slice, $analysis,$seqname, $dbID, $adaptor ) =
+ rearrange(['START','END','STRAND','SLICE','ANALYSIS', 'SEQNAME',
+ 'DBID', 'ADAPTOR'], @_);
if($slice) {
if(!ref($slice) || !$slice->isa('Bio::EnsEMBL::Slice')) {
throw('-SLICE argument must be a Bio::EnsEMBL::Slice not '.$slice);
@@ -140,6 +138,23 @@ sub new {
}
+=head2 new_fast
+
+ Arg [1] : hashref to be blessed
+ Description: Construct a new Bio::EnsEMBL::Feature using the hashref.
+ Exceptions : none
+ Returntype : Bio::EnsEMBL::Feature
+ Caller : general, subclass constructors
+ Status : Stable
+
+=cut
+
+
+sub new_fast {
+ my $class = shift;
+ my $hashref = shift;
+ return bless $hashref, $class;
+}
=head2 start
diff --git a/modules/Bio/EnsEMBL/Gene.pm b/modules/Bio/EnsEMBL/Gene.pm
index 23297ba7f8..3cada903db 100755
--- a/modules/Bio/EnsEMBL/Gene.pm
+++ b/modules/Bio/EnsEMBL/Gene.pm
@@ -106,19 +106,18 @@ sub new {
my $class = ref($caller) || $caller;
my $self = $class->SUPER::new(@_);
-
my ( $stable_id, $version, $external_name, $type, $external_db,
- $external_status, $display_xref, $description, $transcripts,
- $created_date, $modified_date, $confidence, $biotype, $source,
- $status, $is_current, $canonical_transcript, $canonical_annotation ) =
- rearrange( [ 'STABLE_ID', 'VERSION', 'EXTERNAL_NAME', 'TYPE',
- 'EXTERNAL_DB', 'EXTERNAL_STATUS', 'DISPLAY_XREF',
- 'DESCRIPTION',
- 'TRANSCRIPTS', 'CREATED_DATE', 'MODIFIED_DATE',
- 'CONFIDENCE', 'BIOTYPE', 'SOURCE', 'STATUS', 'IS_CURRENT',
- 'CANONICAL_TRANSCRIPT', 'CANONICAL_ANNOTATION'
- ],
- @_ );
+ $external_status, $display_xref, $description, $transcripts,
+ $created_date, $modified_date, $confidence, $biotype, $source,
+ $status, $is_current, $canonical_transcript, $canonical_annotation ) =
+ rearrange( [ 'STABLE_ID', 'VERSION', 'EXTERNAL_NAME', 'TYPE',
+ 'EXTERNAL_DB', 'EXTERNAL_STATUS', 'DISPLAY_XREF',
+ 'DESCRIPTION',
+ 'TRANSCRIPTS', 'CREATED_DATE', 'MODIFIED_DATE',
+ 'CONFIDENCE', 'BIOTYPE', 'SOURCE', 'STATUS', 'IS_CURRENT',
+ 'CANONICAL_TRANSCRIPT', 'CANONICAL_ANNOTATION'
+ ],
+ @_ );
if ($transcripts) {
$self->{'_transcript_array'} = $transcripts;
@@ -187,7 +186,7 @@ sub external_name {
$self->{'external_name'} = shift if (@_);
- if (exists $self->{'external_name'}) {
+ if (defined $self->{'external_name'}) {
return $self->{'external_name'};
}
diff --git a/modules/Bio/EnsEMBL/Transcript.pm b/modules/Bio/EnsEMBL/Transcript.pm
index e65faf69e0..838da3fb17 100755
--- a/modules/Bio/EnsEMBL/Transcript.pm
+++ b/modules/Bio/EnsEMBL/Transcript.pm
@@ -119,19 +119,19 @@ sub new {
deprecate("Transcript constructor should use named arguments.\n" .
'Use Bio::EnsEMBL::Transcript->new(-EXONS => \@exons);' .
"\ninstead of Bio::EnsEMBL::Transcript->new(\@exons);");
- }
+}
else {
- ( $exons, $stable_id, $version, $external_name, $external_db,
- $external_status, $display_xref, $created_date, $modified_date,
- $description, $biotype, $confidence, $external_db_name, $status,
- $is_current ) =
- rearrange( [ "EXONS", 'STABLE_ID', 'VERSION', 'EXTERNAL_NAME',
- 'EXTERNAL_DB', 'EXTERNAL_STATUS', 'DISPLAY_XREF',
- 'CREATED_DATE', 'MODIFIED_DATE', 'DESCRIPTION',
- 'BIOTYPE', 'CONFIDENCE', 'EXTERNAL_DB_NAME', 'STATUS',
- 'IS_CURRENT' ], @_ );
+ ( $exons, $stable_id, $version, $external_name, $external_db,
+ $external_status, $display_xref, $created_date, $modified_date,
+ $description, $biotype, $confidence, $external_db_name, $status,
+ $is_current ) =
+ rearrange( [ "EXONS", 'STABLE_ID', 'VERSION', 'EXTERNAL_NAME',
+ 'EXTERNAL_DB', 'EXTERNAL_STATUS', 'DISPLAY_XREF',
+ 'CREATED_DATE', 'MODIFIED_DATE', 'DESCRIPTION',
+ 'BIOTYPE', 'CONFIDENCE', 'EXTERNAL_DB_NAME', 'STATUS',
+ 'IS_CURRENT' ], @_ );
}
-
+
if( $exons ) {
$self->{'_trans_exon_array'} = $exons;
$self->recalculate_coordinates();
diff --git a/modules/Bio/EnsEMBL/Translation.pm b/modules/Bio/EnsEMBL/Translation.pm
index 08a9ba375e..ee3a43cef1 100755
--- a/modules/Bio/EnsEMBL/Translation.pm
+++ b/modules/Bio/EnsEMBL/Translation.pm
@@ -91,10 +91,10 @@ sub new {
my ( $start_exon, $end_exon, $seq_start, $seq_end,
$stable_id, $version, $dbID, $adaptor, $seq,
- $created_date, $modified_date ) =
- rearrange( [ "START_EXON", "END_EXON", "SEQ_START", "SEQ_END",
- "STABLE_ID", "VERSION", "DBID", "ADAPTOR",
- "SEQ", "CREATED_DATE", "MODIFIED_DATE" ], @_ );
+ $created_date, $modified_date ) =
+ rearrange( [ "START_EXON", "END_EXON", "SEQ_START", "SEQ_END",
+ "STABLE_ID", "VERSION", "DBID", "ADAPTOR",
+ "SEQ", "CREATED_DATE", "MODIFIED_DATE" ], @_ );
my $self = bless {
'start_exon' => $start_exon,
@@ -113,6 +113,24 @@ sub new {
return $self;
}
+=head2 new_fast
+
+ Arg [1] : hashref to be blessed
+ Description: Construct a new Bio::EnsEMBL::Translation using the hashref.
+ Exceptions : none
+ Returntype : Bio::EnsEMBL::Translation
+ Caller : general, subclass constructors
+ Status : Stable
+
+=cut
+
+
+sub new_fast {
+ my $class = shift;
+ my $hashref = shift;
+ return bless $hashref, $class;
+}
+
=head2 start
--
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