make the flexible way to accept database information as well as analysis and...

make the flexible way to accept database information as well as analysis and contig, during the conversion of seqfeature a sort from bioperl to ensembl.

modules/Bio/EnsEMBL/Utils/Converter/bio_ens.pm

@@ -47,6 +47,7 @@ package Bio::EnsEMBL::Utils::Converter::bio_ens;
 use strict;
 use vars qw(@ISA);
 use Bio::EnsEMBL::Analysis;
+use Bio::EnsEMBL::DBSQL::DBAdaptor;
 use Bio::EnsEMBL::Utils::Converter;
 @ISA = qw(Bio::EnsEMBL::Utils::Converter);
 
@@ -77,20 +78,46 @@ sub _initialize {
     my ($self, @args) = @_;
     $self->SUPER::_initialize(@args);
     
-    my ($analysis, $contig) =
-        $self->_rearrange([qw(ANALYSIS CONTIG)], @args);
-
-    if(defined($analysis) && $analysis->isa('Bio::Pipeline::Analysis')){
-        my $converter_for_analysis = new Bio::EnsEMBL::Utils::Converter(
-            -in => 'Bio::Pipeline::Analysis',
-            -out => 'Bio::EnsEMBL::Analysis'
-        );
-        ($analysis) = @{$converter_for_analysis->convert([$analysis])};
-    }
+    my ($dbadaptor, 
+        $dbdriver, $dbhost, $dbport, $dbuser, $dbpass, $dbname,
+        $analysis, $analysis_dbid, $analysis_logic_name, 
+        $contig, $contig_dbid, $contig_name) =
+        
+        $self->_rearrange([qw(DBADAPTOR 
+            DBDRIVER DBHOST DBPORT DBUSER DBPASS DBNAME
+            ANALYSIS ANALYSIS_DBID ANALYSIS_LOGIC_NAME 
+            CONTIG CONTIG_DBID CONTIG_NAME)], @args);
 
-    $self->analysis($analysis);
-    ($contig) = ref($contig) eq 'ARRAY' ? @{$contig} : $contig;
-    $self->contig($contig);
+    
+    if(defined $dbadaptor){
+        $self->dbadaptor($dbadaptor);
+    }elsif(defined $dbname){
+        $self->ensembl_db(@args);
+    }else{
+        # No db information.
+    }
+    
+    if(defined $analysis){
+        $self->analysis($analysis);
+        # then ignore the analysis_dbid and analysis_logic_name
+    }elsif(defined $analysis_dbid){
+        $self->analysis_dbID($analysis_dbid);
+    }elsif(defined $analysis_logic_name){
+        $self->analysis_logic_name($analysis_logic_name);
+    }else{
+        # No analysis information offered
+    }
+    
+    if(defined $contig){
+        ($contig) = ref($contig) eq 'ARRAY' ? @{$contig} : $contig;
+        $self->contig($contig);
+    }elsif(defined $contig_dbid){
+        $self->contig_dbID($contig_dbid);
+    }elsif(defined $contig_name){
+        $self->contig_name($contig_name);
+    }else{
+        # No contig information
+    }
 }
 
 
@@ -127,12 +154,23 @@ sub _guess_module {
 sub analysis {
     my ($self, $arg) = @_;
     if(defined($arg)){
-        $self->throws("A Bio::EnsEMBL::Analysis object expected.") unless(defined $arg);
+        # convert the analysis, if it's not Bio::Pipeline::Analysis
+        if($arg->isa('Bio::Pipeline::Analysis')){
+            my $converter_for_analysis = new Bio::EnsEMBL::Utils::Converter(
+                -in => 'Bio::Pipeline::Analysis',
+                -out => 'Bio::EnsEMBL::Analysis'
+            );
+            ($arg) = @{ $converter_for_analysis->convert([$arg]) };
+        }
+
+        $self->throws("A Bio::EnsEMBL::Analysis object expected.") 
+            unless($arg->isa('Bio::EnsEMBL::Analysis'));
         $self->{_analysis} = $arg;
+        $self->{_analysis_dbid} = $arg->dbID;
+        $self->{_analysis_logic_name} = $arg->logic_name;
     }
     return $self->{_analysis};
 }
-    
 
 
 =head2 contig
@@ -146,11 +184,143 @@ sub analysis {
 sub contig {
     my ($self, $arg) = @_;
     if(defined($arg)){
+        $self->throw("a Bio::EnsEMBL::RawContig needed")
+            unless($arg->isa('Bio::EnsEMBL::RawContig'));
         $self->{_contig} = $arg;
+        $self->{_contig_dbid} = $arg->dbID;
+        $self->{_contig_name} = $arg->name;
     }
     return $self->{_contig};
 }
     
+=head2 dbadaptor
+  Title   : dbadaptor
+  Usage   : $self->dbadaptor
+  Function: get and set for dbadaptor
+  Return  : L<Bio::EnsEMBL::DBSQL::DBAdaptor>
+  Args    : L<Bio::EnsEMBL::DBSQL::DBAdaptor>   
+=cut
+
+sub dbadaptor {
+    my ($self, $arg) = @_;
+    if(defined($arg)){
+        $self->throws("A Bio::EnsEMBL::DBSQL::DBAdaptor object expected.") unless(defined $arg);
+        $self->{_dbadaptor} = $arg;
+    }
+    return $self->{_dbadaptor};
+}
+
+=head2 ensembl_db
+  Title   : ensembl_db
+  Usage   : 
+  Function: 
+  Return  :
+  Args    :
+=cut
+
+sub ensembl_db {
+    my ($self, @args) = @_;
+    
+    my ($dbdriver, $dbhost, $dbport, $dbuser, $dbpass, $dbname) = $self->_rearrange(
+        [qw(DBDRIVER DBHOST DBPORT DBUSER DBPASS DBNAME)], @args);
+
+    my $dbadaptor = new Bio::EnsEMBL::DBSQL::DBAdaptor(
+        -driver => $dbdriver,
+        -host => $dbhost,
+        -port => $dbport,
+        -user => $dbuser,
+        -pass => $dbpass,
+        -dbname => $dbname
+    );
+    $self->dbadaptor($dbadaptor);
+}
+
+=head2 analysis_dbID
+  Title   : analysis_dbID
+  Usage   : 
+  Function: 
+  Return  :
+  Args    :
+=cut
 
+sub analysis_dbID {
+    my ($self, $arg) = @_;
+
+    if(defined $arg){
+        my $analysis;
+        eval{
+            $analysis = $self->dbadaptor->get_AnalysisAdaptor->fetch_by_dbID($arg);
+        };
+        $self->throw("Failed during fetching analysis by dbID\n$@") if($@);
+        $self->analysis($analysis);
+    }
+    $self->{_analysis_dbid};    
+}
+
+
+=head2 analysis_logic_name
+  Title   : analysis_logic_name
+  Usage   : 
+  Function: 
+  Return  :
+  Args    :
+=cut
+
+sub analysis_logic_name {
+    my ($self, $arg) = @_;
+    
+    if(defined $arg){
+        my $analysis;
+        eval{
+            $analysis = $self->dbadaptor->get_AnalysisAdaptor->fetch_by_logic_name($arg);
+        };
+        $self->throw("Problem happens when fetching analysis by logic name\n$@") if($@);
+
+        $self->analysis($analysis);
+    }
+    return $self->{_analysis_logic_name};
+}
+
+=head2 contig_dbID
+  Title   : contig_dbID
+  Usage   : $self->contig_dbID
+  Function: get and set for contig_dbID
+  Return  : 
+  Args    :    
+=cut
+
+sub contig_dbID {
+    my ($self, $arg) = @_;
+    if(defined($arg)){
+        my $contig;
+        eval{
+            $contig = $self->dbadaptor->get_RawContigAdaptor->fetch_by_dbID($arg);
+        };
+        $self->throw("Failed during fetching contig by dbID\n$@") if($@);
+        $self->contig($contig);
+    }
+    return $self->{_contig_dbid};
+}
+
+=head2 contig_name
+  Title   : contig_name
+  Usage   : $self->contig_name
+  Function: get and set for contig_name
+  Return  : 
+  Args    :    
+=cut
+
+sub contig_name {
+    my ($self, $arg) = @_;
+    if(defined($arg)){
+        my $contig;
+        eval{
+            $contig = $self->dbadaptor->get_RawContigAdaptor->fetch_by_name($arg);
+        };
+        $self->throw("Failed during fetching contig by dbID\n$@") if($@);
+        $self->contig($contig);
+    }
+    return $self->{_contig_name};
+}
 
 1;

modules/t/converter.t

@@ -115,9 +115,8 @@ sub test_FeaturePair{
         -in => 'Bio::SeqFeature::FeaturePair',
         -out => 'Bio::EnsEMBL::RepeatFeature',
         -analysis => $ens_analysis,
-        -contig => $ens_contig
     );
-
+    $converter->contig($ens_contig);
     my ($ens_repeatFeature1) = @{$converter->convert([$featurePair1])};
 
     ok ref($ens_repeatFeature1), 'Bio::EnsEMBL::RepeatFeature';