[Gmod-gbrowse-cmts] Generic-Genome-Browser/cgi-bin gbrowse.PLS,1.137,1.138

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Update of /cvsroot/gmod/Generic-Genome-Browser/cgi-bin
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv14272/cgi-bin

Modified Files:
	gbrowse.PLS 
Log Message:
Fixed the multiple segment screen


Index: gbrowse.PLS
===================================================================
RCS file: /cvsroot/gmod/Generic-Genome-Browser/cgi-bin/gbrowse.PLS,v
retrieving revision 1.137
retrieving revision 1.138
diff -C2 -d -r1.137 -r1.138
*** gbrowse.PLS	21 Dec 2005 19:49:05 -0000	1.137
--- gbrowse.PLS	22 Dec 2005 01:47:30 -0000	1.138
***************
*** 426,430 ****
    my %seen; #used to keep track of available ranges for display
  
!   my $detailpanel = detail_panel_with_timeout( $segment, $page_settings, $feature_files );
  
    my %div_visibility = map {$_ => scalar(param($_))} grep /_vis$/, param();
--- 426,435 ----
    my %seen; #used to keep track of available ranges for display
  
!   my $multiple_segments = ( scalar @{ $segments || [] } > 1 ) ? 1 : 0;
! 
!   my $detailpanel;
!   if (!$multiple_segments){
!     $detailpanel = detail_panel_with_timeout( $segment, $page_settings, $feature_files );
!   }
  
    my %div_visibility = map {$_ => scalar(param($_))} grep /_vis$/, param();
***************
*** 504,508 ****
          },
  
!         #FIXME    multiple_segments => multiple_choices($features),
          detailpanel           => $detailpanel,
          toggle_cookie_name    => 'GBROWSE_TOGGLE',
--- 509,514 ----
          },
  
!         multiple_segment_data => $multiple_segments?multiple_segment_data($page_settings,$features):{},
!         multiple_segments => $multiple_segments,
          detailpanel           => $detailpanel,
          toggle_cookie_name    => 'GBROWSE_TOGGLE',
***************
*** 1307,1382 ****
  
  ################ format keyword search ###################
! sub multiple_choices {
!   my ($settings,$results) = @_;
  
!   my $db   = open_database();
!   my $name = $settings->{name};
!   my $regexp = join '|',($name =~ /(\w+)/g);
  
!   # sort into bins by reference and version
!   my %refs;
!   foreach (@$results) {
!     my $version = eval {$_->isa('Bio::SeqFeatureI') ? undef : $_->version};
!     my $ref = $_->seq_id;
!     $ref .= " version $version" if defined $version;    
!     push @{$refs{$ref}},$_;
!   }
  
!   $CONFIG->width($settings->{width}*OVERVIEW_RATIO);
!   my $overviews = $CONFIG->hits_on_overview($db,$results,$settings->{features});
!   my $count = @$results;
  
!   print start_table();
!   print TR({-class=>'datatitle'},
! 	   th({-colspan=>4},
! 	      $CONFIG->tr('Hit_count',$count)));
!   print TR({-class=>'datatitle'},
! 	   th({-colspan=>4},
! 	      $CONFIG->tr('Possible_truncation',MAX_KEYWORD_RESULTS)))
!     if $count >= MAX_KEYWORD_RESULTS;
  
!   local $^W = 0;  # get rid of non-numeric warnings coming out of by_score_and_position
!   for my $ref(sort keys %refs) {
!     my ($id) = split /\s/, $ref; 
!     my @results = @{$refs{$ref}};
!     print TR(th({-class=>'databody',-colspan=>4,-align=>'center'},$CONFIG->tr('Matches_on_ref',$ref),br,
! 		$overviews->{$ref}));
  
!     my $padding = $CONFIG->setting(general=>'landmark_padding') || 0;
!     my $units    = $CONFIG->setting(general=>'units') || $CONFIG->tr('bp');
!     my $divisor  = $CONFIG->setting(general=>'unit_divider') || 1;
  
!     for my $r (sort by_score_and_position @results) {
!       my $version = eval {$r->isa('Bio::SeqFeatureI') ? undef : $r->version};
!       my $name        = eval {$r->name}  || $r->primary_tag;
  
!       my $class       = eval {$r->class} || $CONFIG->tr('Sequence');
!       my $score       = eval {$r->score} || $CONFIG->tr('NOT_APPLICABLE');
!       my ($start,$stop) = ($r->start,$r->end);
!       my $padstart = $start - $padding;
!       my $padstop  = $stop  + $padding;
!       my $description = escapeHTML(eval{join ' ',$r->attributes('Note')}
! 				   ||eval{$r->method}||eval{$r->source_tag}||$r->{ref});
!       if (my @aliases = eval{$r->attributes('Alias')}) {
! 	$description .= escapeHTML " [@aliases]";
!       }
!       my $n           = escape("$name");
!       my $c           = escape($class);
!       $description =~ s/($regexp)/<b class="keyword">$1<\/b>/ig;
!       $description =~ s/(\S{60})/$1 /g;  # wrap way long lines
  
!       my $objref     = $class ? "?name=$c:$n" : "?name=$n";
!       my $posref     = "?ref=$id;start=$padstart;stop=$padstop;version=$version";
!       my $position = format_segment($r);
!       my $length   = unit_label($stop-$start+1);
!       print TR({-class=>'databody',-valign=>'TOP'},
! 	       th({-align=>'right'},ref($name) ? a({-href=>$objref},$name):tt($name)),
! 	       td($description),
! 	       td(a({-href=>$posref},$position . " ($length)")),
! 	       td($CONFIG->tr('SCORE',$score)));
      }
!   }
!   print end_table;
  
  }
  
--- 1313,1396 ----
  
  ################ format keyword search ###################
! sub multiple_segment_data {
!     my ( $settings, $results ) = @_;
  
!     my %multiple_segment_data;
!     my %ref_data;
  
!     my $db     = open_database();
!     my $name   = $settings->{name};
!     my $regexp = join '|', ( $name =~ /(\w+)/g );
  
!     # sort into bins by reference and version
!     my %refs;
!     foreach my $result (@$results) {
!         my $version = eval {
!             $result->isa('Bio::SeqFeatureI') ? undef: $result->version;
!         };
!         my $ref = $result->seq_id;
!         $ref .= " version $version" if defined $version;
!         push @{ $refs{$ref} }, $result;
!     }
  
!     $CONFIG->width( $settings->{width} * OVERVIEW_RATIO );
!     $multiple_segment_data{'overviews'}
!         = $CONFIG->hits_on_overview( $db, $results, $settings->{features} );
!     $multiple_segment_data{'count'}               = scalar @$results;
!     $multiple_segment_data{'max_keyword_results'} = MAX_KEYWORD_RESULTS;
  
!     local $^W = 0; # get rid of non-numeric warnings coming out of by_score_and_position
!     for my $ref ( sort keys %refs ) {
!         my ($id) = split /\s/, $ref;
!         my @results = @{ $refs{$ref} };
  
!         my $padding = $CONFIG->setting( general => 'landmark_padding' ) || 0;
!         my $units = $CONFIG->setting( general => 'units' )
!             || $CONFIG->tr('bp');
!         my $divisor = $CONFIG->setting( general => 'unit_divider' ) || 1;
  
!         for my $r ( sort by_score_and_position @results ) {
!             my $version
!                 = eval { $r->isa('Bio::SeqFeatureI') ? undef: $r->version };
!             my $name = eval { $r->name } || $r->primary_tag;
  
!             my $class = eval { $r->class } || $CONFIG->tr('Sequence');
!             my $score = eval { $r->score } || $CONFIG->tr('NOT_APPLICABLE');
!             my ( $start, $stop ) = ( $r->start, $r->end );
!             my $padstart = $start - $padding;
!             my $padstop  = $stop + $padding;
!             my $description
!                 = escapeHTML( eval { join ' ', $r->attributes('Note') }
!                     || eval { $r->method }
!                     || eval { $r->source_tag }
!                     || $r->{ref} );
  
!             if ( my @aliases = eval { $r->attributes('Alias') } ) {
!                 $description .= escapeHTML " [@aliases]";
!             }
!             my $n = escape("$name");
!             my $c = escape($class);
!             $description =~ s/($regexp)/<b class="keyword">$1<\/b>/ig;
!             $description =~ s/(\S{60})/$1 /g;    # wrap way long lines
! 
!             my $objref = $class ? "?name=$c:$n" : "?name=$n";
!             my $posref
!                 = "?ref=$id;start=$padstart;stop=$padstop;version=$version";
!             my $position = format_segment($r);
!             my $length   = unit_label( $stop - $start + 1 );
!             push @{ $ref_data{$ref} },
!                 {
!                 name                 => $name,
!                 objref               => $objref,
!                 description          => $description,
!                 posref               => $posref,
!                 position_description => "$position ($length)",
!                 score                => $score,
!                 };
!         }
      }
!     $multiple_segment_data{'ref_data'} = \%ref_data;
  
+     return \%multiple_segment_data;
  }