[Gmod-gbrowse-cmts] Generic-Genome-Browser/lib/Bio/DB/Das Chado.pm,1.68.4.5,1.68.4.6

[Scott C. <sco...@us...>]

Update of /cvsroot/gmod/Generic-Genome-Browser/lib/Bio/DB/Das
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv3971/lib/Bio/DB/Das

Modified Files:
      Tag: release_1_62-bugfixes
	Chado.pm 
Log Message:
simplfying the get_feature_by_name method to make it faster; some functionality is lost, but it behaves as expected in gbrowse


Index: Chado.pm
===================================================================
RCS file: /cvsroot/gmod/Generic-Genome-Browser/lib/Bio/DB/Das/Chado.pm,v
retrieving revision 1.68.4.5
retrieving revision 1.68.4.6
diff -C2 -d -r1.68.4.5 -r1.68.4.6
*** Chado.pm	5 Jul 2005 20:48:41 -0000	1.68.4.5
--- Chado.pm	28 Jul 2005 19:04:48 -0000	1.68.4.6
***************
*** 444,500 ****
         = $self->_rearrange([qw(NAME CLASS REF START END)],@_);
  
!    warn "name:$name in get_feature_by_name" if DEBUG;
  
!   $name =~ s/_/\\_/g;  # escape underscores in name
!   $name =~ s/\%/\\%/g; # ditto for percent signs
  
!    warn "name after protecting _ and % in the string:$name\n" if DEBUG;
  
    my (@features,$sth);
    
!   if ($name =~ /^\s*\S+\s*$/) {
!     # get feature_id
!     # foreach feature_id, get the feature info
!     # then get src_feature stuff (chromosome info) and create a parent feature,
! 
!     $name =~ s/[?*]\s*$/%/;
  
!     my $select_part = "select distinct fs.feature_id \n";
!     my $from_part   = "from feature_synonym fs, synonym s ";
!     my $where_part  = "where fs.synonym_id = s.synonym_id and\n"
!                     . "s.synonym_sgml ilike ?";
!                     #this ilike should probably be replace with a 'lower' index
!     if ($class) {
!         my $type = $self->name2term($class);
!         return unless $type;
!         $from_part .= ", feature f \n";
!         $where_part.= "\nand fs.feature_id = f.feature_id and\n"
!                     . "f.type_id = $type";
!     }
  
!     my $query = $select_part . $from_part . $where_part;
  
-     warn "first get_feature_by_name query:$query" if DEBUG;
  
!     $sth = $self->dbh->prepare($query);
!     $sth->execute($name) or $self->throw("getting the feature_ids failed");
  
!     if ($sth->rows == 0) {
!         warn "trying a complex search for $name\n" if DEBUG;
!         ($name,$query) = $self->_complex_search($name,$class);
  
!         $sth = $self->dbh->prepare($query);
!         $sth->execute($name) or $self->throw("getting the feature_ids failed");
!     }
  
!   } else { # not a simple wild card search
!     
!     my $query;
!     ($name,$query) = $self->_complex_search($name,$class);
  
!     $sth = $self->dbh->prepare($query);
!     $sth->execute($name) or $self->throw("getting the feature_ids failed");
  
-   }
  
       # prepare sql queries for use in while loops
--- 444,511 ----
         = $self->_rearrange([qw(NAME CLASS REF START END)],@_);
  
!   my $wildcard = 0;
!   if ($name =~ /\*/) {
!     $wildcard = 1;
!   }
  
!   warn "name:$name in get_feature_by_name" if DEBUG;
  
!   $name = $self->_search_name_prep($name);
! 
!   warn "name after protecting _ and % in the string:$name\n" if DEBUG;
  
    my (@features,$sth);
    
!   # get feature_id
!   # foreach feature_id, get the feature info
!   # then get src_feature stuff (chromosome info) and create a parent feature,
  
!   my $select_part = "select distinct fs.feature_id \n";
!   my $from_part   = "from feature_synonym fs, synonym s ";
  
!   my $where_part;
!   if ($wildcard) {
!     $where_part  = "where fs.synonym_id = s.synonym_id and\n"
!                     . "lower(s.synonym_sgml) like ?";
!   } else {
!     $where_part  = "where fs.synonym_id = s.synonym_id and\n"
!                     . "lower(s.synonym_sgml) = ?";
!   }
  
  
!   if ($class) {
!       my $type = $self->name2term($class);
!       return unless $type;
!       $from_part .= ", feature f \n";
!       $where_part.= "\nand fs.feature_id = f.feature_id and\n"
!                     . "f.type_id = $type";
!   }
  
!   my $query = $select_part . $from_part . $where_part;
  
!   warn "first get_feature_by_name query:$query" if DEBUG;
  
!   $sth = $self->dbh->prepare($query);
!   $sth->execute($name) or $self->throw("getting the feature_ids failed");
  
! # this makes performance awful!  It does a wildcard search on a view
! # that has several selects in it.  For any reasonably sized database,
! # this won't work.
! #
! #  if ($sth->rows < 1 and 
! #      $class ne 'chromosome' and
! #      $class ne 'region' and
! #      $class ne 'contig') {  
! #
! #    my $query;
! #    ($name,$query) = $self->_complex_search($name,$class,$wildcard);
! #
! #    warn "complex_search query:$query\n";
! #
! #    $sth = $self->dbh->prepare($query);
! #    $sth->execute($name) or $self->throw("getting the feature_ids failed");
! #
! #  }
  
  
       # prepare sql queries for use in while loops
***************
*** 641,647 ****
      warn "name before wildcard subs:$name\n" if DEBUG;
  
-     
- 
-     $name =~ s/\*/%/g;
      $name = "\%$name" unless (0 == index($name, "%"));
      $name = "$name%"  unless (0 == index(reverse($name), "%"));
--- 652,655 ----
***************
*** 651,655 ****
      my $select_part = "select ga.feature_id ";
      my $from_part   = "from gffatts ga ";
!     my $where_part  = "where ga.attribute ilike ? ";
                                                                                                                            
      if ($class) {
--- 659,663 ----
      my $select_part = "select ga.feature_id ";
      my $from_part   = "from gffatts ga ";
!     my $where_part  = "where lower(ga.attribute) like ? ";
                                                                                                                            
      if ($class) {
***************
*** 664,667 ****
--- 672,687 ----
  }
  
+ sub _search_name_prep {
+   my $self = shift;
+   my $name = shift;
+ 
+   $name =~ s/_/\\_/g;  # escape underscores in name
+   $name =~ s/\%/\\%/g; # ditto for percent signs
+ 
+   $name =~ s/\*/%/g;
+ 
+   return lc($name);
+ }
+ 
  
  =head2 srcfeature2name