improve dynamic range of wiggle tracks

GMOD · Dec 8, 2011 · eefe6e3 · eefe6e3
1 parent f97cec5
commit eefe6e3
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Showing 4 changed files with 11 additions and 4 deletions.
diff --git a/Changes b/Changes
@@ -1,4 +1,5 @@
 2.44
+  * Modest performance improvements when rendering multiple tracks.
   * Set absolute cap of 5000 features per track to avoid performance issues on NGS data.
     This cap can be changed by setting "maximum features" in the [GENERAL] section. Set
     to 0 to return to unlimited behavior.
@@ -15,6 +16,7 @@
   * Fix bad database pathnames in yeast configuration file examples.
   * Fix track finder plugin to avoid annoying extra refresh after leaving text entry field.
   * Fix broken sorting of subtracks.
+  * Improve dynamic range of wiggle tracks.
   * mod_perl is no longer supported due to unfixable issues with zombie processes.
 
 2.43

diff --git a/conf/languages/POSIX.pm b/conf/languages/POSIX.pm
@@ -30,6 +30,8 @@ END
 
    SHOWING_FROM_TO => '%s from %s:%s..%s',
 
+   CURRENTLY_SHOWING => '(Currently showing %s)',
+
    INSTRUCTIONS      => 'Instructions',
 
    HIDE              => 'Hide',

diff --git a/lib/Bio/Graphics/Browser2/Render.pm b/lib/Bio/Graphics/Browser2/Render.pm
@@ -2182,7 +2182,7 @@ sub reconfigure_track {
 	    }
 	}
     }
-    if (defined $o->{autoscale} && $o->{autoscale} eq 'local') { 
+    if (defined $o->{autoscale} && $o->{autoscale}=~/local|global|chromosome/) { 
 	undef $o->{min_score}; 
 	undef $o->{max_score} 
     }

diff --git a/lib/Bio/Graphics/Browser2/Render/TrackConfig.pm b/lib/Bio/Graphics/Browser2/Render/TrackConfig.pm
@@ -66,7 +66,7 @@ sub config_dialog {
     my $return_html = start_html();
 
     my $showing = $render->data_source->unit_label($scaled_length);
-    my $title   = div({-class=>'config-title'},$key,br(),div({-style=>'font-size:9pt'},"(Currently showing $showing)"));
+    my $title   = div({-class=>'config-title'},$key,br(),div({-style=>'font-size:9pt'},$render->translate('Currently_Showing',$showing)));
     my $dynamic = $render->translate('DYNAMIC_VALUE');
 
     my $height        = $self->setting( $label => 'height' ,        $length, $summary_mode)    || 10;
@@ -86,7 +86,7 @@ sub config_dialog {
     $autoscale  ||= 'local';
 
     my $sd_fold   = $self->setting( $label => 'z_score_bound' ,     $length, $summary_mode);
-    $sd_fold    ||= 4;
+    $sd_fold    ||= 8;
 
     my $bicolor_pivot = $self->setting( $label => 'bicolor_pivot' ,  $length, $summary_mode);
     my $graph_type    = $self->setting( $label => 'graph_type' ,     $length, $summary_mode);
@@ -395,13 +395,16 @@ END
 		    th( { -align => 'right' },$render->translate('SD_MULTIPLES')),
 		    td( $picker->popup_menu(
 			    -name    => "conf_z_score_bound",
-			    -values  => [qw(1 2 3 4 5 6)],
+			    -values  => [qw(1 2 3 4 5 6 8 10 20)],
 			    -labels  => {1   =>'1 SD',
 					 2   =>'2 SD',
 					 3   =>'3 SD',
 					 4   =>'4 SD',
 					 5   =>'5 SD',
 					 6   =>'6 SD',
+					 8   =>'8 SD',
+					 10   =>'10 SD',
+					 20   =>'20 SD',
 					 },
 			    -default => $sd_fold,
 			    -current => $override->{z_score_bound}