[MOBY-guts] biomoby commit

[Mark Wilkinson]

mwilkinson
Wed Jul  9 23:37:13 EDT 2003
Update of /home/repository/moby/moby-live/Perl/scripts/Services
In directory pub.open-bio.org:/tmp/cvs-serv1839/Perl/scripts/Services

Modified Files:
	LocalServices.pm 
Log Message:
yeah yeah, I register services with more than one bug.  Sue me :-) 

moby-live/Perl/scripts/Services LocalServices.pm,1.7,1.8
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm	2003/07/10 03:13:43	1.7
+++ /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm	2003/07/10 03:37:13	1.8
@@ -72,19 +72,19 @@
 
 	my @input_nodes = $self->_getSimpleChildNodes($data);
 	@accessions = $self->_getIDs("NCBI_Acc", \@input_nodes);
-	foreach (@accessions){
-		unless (defined $_){
+	foreach my $acc (@accessions){
+		unless (defined $acc){
 			$response .= simpleResponse("");
 			next;
 		}
 		use Bio::DB::GenBank;
 		my $gb = new Bio::DB::GenBank;
-		my $seq = $gb->get_Seq_by_acc($_);
+		my $seq = $gb->get_Seq_by_acc($acc);
 		my $length;
 		if ($seq){$length = $seq->length;}
 		if ($length){
 			$response .= simpleResponse("
-		<moby:VirtualSequence namespace='NCBI_Acc' id='$_'>
+		<moby:VirtualSequence namespace='NCBI_Acc' id='$acc'>
 			<moby:Int namespace='' id='' articleName='Length'>$length</moby:Int>
 		</moby:VirtualSequence>");
 		} else {
@@ -103,19 +103,19 @@
 
 	my @input_nodes = $self->_getSimpleChildNodes($data);
 	@accessions = $self->_getIDs("NCBI_Acc", \@input_nodes);
-	foreach (@accessions){
-		unless (defined $_){
+	foreach my $acc(@accessions){
+		unless (defined $acc){
 			$response .= simpleResponse("");
 			next;
 		}
 		use Bio::DB::GenBank;
 		my $gb = new Bio::DB::GenBank;
-		my $seq = $gb->get_Seq_by_acc($_);
+		my $seq = $gb->get_Seq_by_acc($acc);
 		my $length;my $sequence;
 		if ($seq){$length = $seq->length;$sequence = $seq->seq}
 		if ($length){
 			$response .= simpleResponse("
-		<moby:GenericSequence namespace='NCBI_Acc' id='$_'>
+		<moby:GenericSequence namespace='NCBI_Acc' id='$acc'>
 			<moby:Int namespace='' id='' articleName='Length'>$length</moby:Int>
 			<moby:String namespace='' id='' articleName='SequenceString'>$sequence</moby:Int>
 		</moby:GenericSequence>");
@@ -135,19 +135,19 @@
 
 	my @input_nodes = $self->_getSimpleChildNodes($data);
 	@accessions = $self->_getIDs("NCBI_gi", \@input_nodes);
-	foreach (@accessions){
-		unless (defined $_){
+	foreach my $acc(@accessions){
+		unless (defined $acc){
 			$response .= simpleResponse("");
 			next;
 		}
 		use Bio::DB::GenBank;
 		my $gb = new Bio::DB::GenBank;
-		my $seq = $gb->get_Seq_by_gi($_);
+		my $seq = $gb->get_Seq_by_gi($acc);
 		my $length;
 		if ($seq){$length = $seq->length;}
 		if ($length){
 			$response .= simpleResponse("
-		<moby:VirtualSequence namespace='NCBI_gi' id='$_'>
+		<moby:VirtualSequence namespace='NCBI_gi' id='$acc'>
 			<moby:Int namespace='' id='' articleName='Length'>$length</moby:Int>
 		</moby:VirtualSequence>");
 		} else {
@@ -166,19 +166,19 @@
 
 	my @input_nodes = $self->_getSimpleChildNodes($data);
 	@accessions = $self->_getIDs("NCBI_gi", \@input_nodes);
-	foreach (@accessions){
-		unless (defined $_){
+	foreach my $acc(@accessions){
+		unless (defined $acc){
 			$response .= simpleResponse("");
 			next;
 		}
 		use Bio::DB::GenBank;
 		my $gb = new Bio::DB::GenBank;
-		my $seq = $gb->get_Seq_by_gi($_);  # get the sequence object for each gi
+		my $seq = $gb->get_Seq_by_gi($acc);  # get the sequence object for each gi
 		my $length;my $sequence;
 		if ($seq){$length = $seq->length;$sequence = $seq->seq}  # if it exists, get the length and sequence
 		if ($length){  # and construct the response
 			$response .= simpleResponse("
-		<moby:GenericSequence namespace='NCBI_gi' id='$_'>
+		<moby:GenericSequence namespace='NCBI_gi' id='$acc'>
 			<moby:Int namespace='' id='' articleName='Length'>$length</moby:Int>
 			<moby:String namespace='' id='' articleName='SequenceString'>$sequence</moby:Int>
 		</moby:GenericSequence>");