[Gmod-gbrowse-cmts] Generic-Genome-Browser/libnew/Bio/Graphics Karyotype.pm, 1.4, 1.5

[Lincoln S. <ls...@us...>]

Update of /cvsroot/gmod/Generic-Genome-Browser/libnew/Bio/Graphics
In directory sc8-pr-cvs2.sourceforge.net:/tmp/cvs-serv9223/libnew/Bio/Graphics

Modified Files:
	Karyotype.pm 
Log Message:
made the 'mysql lost connection during query' error 'go away' by caching the region and whole segments between calls. Possibly too many simultaneous queries kills the server?

Index: Karyotype.pm
===================================================================
RCS file: /cvsroot/gmod/Generic-Genome-Browser/libnew/Bio/Graphics/Karyotype.pm,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** Karyotype.pm	22 Aug 2008 14:57:01 -0000	1.4
--- Karyotype.pm	25 Aug 2008 23:10:42 -0000	1.5
***************
*** 59,62 ****
--- 59,63 ----
    my $features = shift;
    $self->{hits} ||= {};
+ 
    for my $f (@$features) {
      my $ref = $f->seq_id;
***************
*** 99,102 ****
--- 100,105 ----
  sub to_html {
    my $self     = shift;
+   my $terms2hilite = shift;
+ 
    my $sort_order = $self->seqid_order;  # returns a hash of {seqid=>index}
  
***************
*** 126,130 ****
    }
  
!   my $table = $self->hits_table();
  
    return $html.br({-clear=>'all'}).$table;
--- 129,133 ----
    }
  
!   my $table = $self->hits_table($terms2hilite);
  
    return $html.br({-clear=>'all'}).$table;
***************
*** 230,234 ****
  			-height  => 6,
  			-bgcolor => 'red',
! 			-fgcolor => 'red');
      }
  
--- 233,239 ----
  			-height  => 6,
  			-bgcolor => 'red',
! 			-fgcolor => 'red',
! 			-bump    => -1,
! 	  );
      }
  
***************
*** 252,258 ****
      my $self              = shift;
      my $feature           = shift;
!     my $id = $feature->can('id')        ? $feature->id
!             :$feature->can('primary_id')? $feature->primary_id
! 	    : overload::StrVal($feature);
      my $seqid = $feature->seq_id;
      return "${seqid}.${id}";
--- 257,261 ----
      my $self              = shift;
      my $feature           = shift;
!     my $id = overload::StrVal($feature);
      my $seqid = $feature->seq_id;
      return "${seqid}.${id}";
***************
*** 262,265 ****
--- 265,269 ----
      my $self                  = shift;
      my $term2hilite           = shift;
+     warn "term2hilite = $term2hilite";
  
      my @hits = $self->hits;
***************
*** 270,277 ****
  	if defined $term2hilite;
  
      my $na   = $self->trans('NOT_APPLICABLE') || '-';
  
      my $sort_order = $self->seqid_order;
- 
      
      # a big long map call here
--- 274,282 ----
  	if defined $term2hilite;
  
+     warn "regexp = $regexp";
+ 
      my $na   = $self->trans('NOT_APPLICABLE') || '-';
  
      my $sort_order = $self->seqid_order;
      
      # a big long map call here
***************
*** 279,284 ****
  	my $name  = $_->display_name;
  	my $class = eval {$_->class};
! 	my $fid   =  $_->can('id')         ? "id:".$_->id 
! 	           : $_->can('primary_id') ? "id:".$_->primary_id     # for inserting into the gbrowse search field
                     : $class                ? "$class:$name" 
                     : $name;
--- 284,289 ----
  	my $name  = $_->display_name;
  	my $class = eval {$_->class};
! 	my $fid   =  $_->can('primary_id') ? "id:".$_->primary_id      # for inserting into the gbrowse search field
! 	           : $_->can('id')         ? "id:".$_->id
                     : $class                ? "$class:$name" 
                     : $name;
***************
*** 295,298 ****
--- 300,304 ----
  	   },
  	    th({-align=>'left'},a({-href=>"$url$fid"},$name)),
+ 	    td($_->method),
  	    td($desc),
  	    td(a({-href=>"$url$pos"},$pos)),
***************
*** 300,304 ****
  	    )
      } sort {
! 	$sort_order->{$a->seq_id} <=> $sort_order->{$b->seq_id}
          || $a->start <=> $b->start
  	|| $a->end   <=> $b->end
--- 306,311 ----
  	    )
      } sort {
! 	$b->score    <=> $a->score
! 	|| $sort_order->{$a->seq_id} <=> $sort_order->{$b->seq_id}
          || $a->start <=> $b->start
  	|| $a->end   <=> $b->end
***************
*** 314,317 ****
--- 321,325 ----
  		      th({-align=>'left'},
  			 [$self->trans('NAME'),
+ 			  $self->trans('Type'),
  			  $self->trans('Description'),
  			  $self->trans('Position'),