[Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature/Store/DBI mysql.pm, 1.30, 1.31

[Lincoln Stein]

Update of /home/repository/bioperl/bioperl-live/Bio/DB/SeqFeature/Store/DBI
In directory dev.open-bio.org:/tmp/cvs-serv32245/Bio/DB/SeqFeature/Store/DBI

Modified Files:
	mysql.pm 
Log Message:
linewidth setting was being ignored when drawing filled arrows

Index: mysql.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/DB/SeqFeature/Store/DBI/mysql.pm,v
retrieving revision 1.30
retrieving revision 1.31
diff -C2 -d -r1.30 -r1.31
*** mysql.pm	18 Apr 2007 15:21:53 -0000	1.30
--- mysql.pm	24 Aug 2007 21:15:40 -0000	1.31
***************
*** 278,282 ****
    attribute_value  text,
    index(id),
!   index(attribute_id,attribute_value(10))
  )
  END
--- 278,283 ----
    attribute_value  text,
    index(id),
!   index(attribute_id,attribute_value(10)),
!   FULLTEXT(attribute_value)
  )
  END
***************
*** 836,840 ****
    my $sql_regexp = join ' AND ',("a.attribute_value REGEXP ?")  x @words;
    my $sql = <<END;
! SELECT name,attribute_value
    FROM $name_table as n,$attribute_table as a,$attributelist_table as al
    WHERE n.id=a.id
--- 837,841 ----
    my $sql_regexp = join ' AND ',("a.attribute_value REGEXP ?")  x @words;
    my $sql = <<END;
! SELECT name,attribute_value,n.id
    FROM $name_table as n,$attribute_table as a,$attributelist_table as al
    WHERE n.id=a.id
***************
*** 850,858 ****
  
    my @results;
!   while (my($name,$value) = $sth->fetchrow_array) {
      my (@hits) = $value =~ /$perl_regexp/ig;
      my @words_in_row = split /\b/,$value;
      my $score  = int(@hits*100/@words/@words_in_row);
!     push @results,[$name,$value,$score];
    }
    $sth->finish;
--- 851,859 ----
  
    my @results;
!   while (my($name,$value,$id) = $sth->fetchrow_array) {
      my (@hits) = $value =~ /$perl_regexp/ig;
      my @words_in_row = split /\b/,$value;
      my $score  = int(@hits*100/@words/@words_in_row);
!     push @results,[$name,$value,$score,$id];
    }
    $sth->finish;
***************
*** 897,901 ****
    my $attributelist_table   = $self->_attributelist_table;
  
!   my $from = "$attribute_table as a, $attributelist_table as al";
  
    my $where = <<END;
--- 898,902 ----
    my $attributelist_table   = $self->_attributelist_table;
  
!   my $from = "$attribute_table as a use index(attribute_id), $attributelist_table as al";
  
    my $where = <<END;