[Bioperl-guts-l] bioperl commit

Lincoln Stein lstein at pub.open-bio.org
Tue Jul 20 13:54:08 EDT 2004


lstein
Tue Jul 20 13:54:07 EDT 2004
Update of /home/repository/bioperl/bioperl-live/Bio/DB/GFF/Adaptor/dbi
In directory pub.open-bio.org:/tmp/cvs-serv8160/Bio/DB/GFF/Adaptor/dbi

Modified Files:
	mysql.pm 
Log Message:
added warnings regarding the maxbin value

bioperl-live/Bio/DB/GFF/Adaptor/dbi mysql.pm,1.55,1.56
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/DB/GFF/Adaptor/dbi/mysql.pm,v
retrieving revision 1.55
retrieving revision 1.56
diff -u -r1.55 -r1.56
--- /home/repository/bioperl/bioperl-live/Bio/DB/GFF/Adaptor/dbi/mysql.pm	2004/07/17 18:32:49	1.55
+++ /home/repository/bioperl/bioperl-live/Bio/DB/GFF/Adaptor/dbi/mysql.pm	2004/07/20 17:54:07	1.56
@@ -683,6 +683,12 @@
   defined(my $typeid  = $self->get_table_id('ftype', $gff->{method} => $gff->{source})) or return;
   defined(my $groupid = $self->get_table_id('fgroup',$gff->{gname}  => $gff->{gclass})) or return;
 
+  if ($gff->{stop}-$gff->{start}+1 > $self->max_bin) {
+    warn "$gff->{gclass}:$gff->{gname} is longer than ",$self->_maxbin,".\n";
+    warn "Please set the maxbin value to a larger length than the largest feature you wish to store.\n";
+    warn "With the command-line tools you do with this with --maxfeature option.\n";
+  }
+
   my $bin =  bin($gff->{start},$gff->{stop},$self->min_bin);
   my $result = $s->{sth}{insert_fdata}->execute($gff->{ref},
 					       $gff->{start},$gff->{stop},$bin,



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