fixed cm issue

GMOD · Sep 28, 2010 · 1fab29d · 1fab29d
1 parent bc58741
commit 1fab29d
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Showing 8 changed files with 81 additions and 27 deletions.
diff --git a/Changes b/Changes
@@ -11,6 +11,7 @@
        another, this will not be reflected in the summary density plots, which will show all features
        of the matching type regardless of the filter.
      * Basic support for Google federated login via openid.
+     * "unit label" and "unit divider" should now work as advertised.
 
 2.15 Mon Sep 13 11:22:40 EDT 2010
      * Set the "DNA accessor" for databases to the default database. Assuming that the backend supports
@@ -31,6 +32,7 @@
        Bio::DB::GFF database backend.
      * Fixed problems with losing all default tracks when first loading the browser (this was a bug
        introduced in SVN and never released.)
+     * You can now override the "buttons" images path in individual datasource files.
 
 2.14 Fri Aug 27 11:05:08 EDT 2010
      * Prevent a blank-screen crash when searching for chromosomes not in the database.

diff --git a/htdocs/js/controller.js b/htdocs/js/controller.js
@@ -1067,6 +1067,24 @@ function set_dragcolors(color) {
      detailsObject.background  = color;
 }
 
+// set the colors for the rubberband regions
+function set_dragunits(unit,divider) {
+    if (unit == null)    unit    = 'bp';
+    if (divider == null) divider = 1;
+    if (overviewObject != null) {
+	overviewObject.unit    = unit;
+        overviewObject.divider = divider;
+    }
+    if (regionObject != null) {
+	regionObject.unit      = unit;
+	regionObject.divider   = divider;
+    }
+    if (detailsObject != null) {
+	detailsObject.unit    = unit;
+	detailsObject.divider = divider;
+    }
+}
+
 function create_time_key () {
     time_obj = new Date();
     return time_obj.getTime();

diff --git a/htdocs/js/rubber.js b/htdocs/js/rubber.js
@@ -12,6 +12,9 @@ var selectAreaIsActive;
 
 // Constructor
 var SelectArea = function () {
+    this.background = 'yellow';
+    this.unit      = 'bp';
+    this.divider   = 1;
   return this;
 }
 
@@ -295,14 +298,16 @@ SelectArea.prototype.moveRubber = function(event) {
     self.overrideAutoSubmit = false;
   }
 
-  var unit = 'bp';
+  var unit     = self.unit;
+  var divider  = self.divider;
+  selectSequenceWidth /= divider;
   if (selectSequenceWidth > 1000 && selectSequenceWidth < 1000000) {
     selectSequenceWidth = selectSequenceWidth/1000;
-    unit = 'kbp';
+    unit = 'k'+unit;
   }
   else if (selectSequenceWidth > 1000000) {
     selectSequenceWidth = selectSequenceWidth/1000000;
-    unit = 'Mbp';
+    unit = 'M'+unit;
   }
 
   if (Math.floor(selectSequenceWidth) != selectSequenceWidth) {

diff --git a/lib/Bio/Graphics/Browser2/DataSource.pm b/lib/Bio/Graphics/Browser2/DataSource.pm
@@ -253,7 +253,8 @@ sub unit_label {
   my $abs = abs($value);
 
   my $label;
-  $label = $abs >= 1e9  ? sprintf("%.4g G%s",$value/1e9,$unit)
+  $label = $unit =~ /^[kcM]/ ? sprintf("%.4g %s",$value,$unit)
+         : $abs >= 1e9  ? sprintf("%.4g G%s",$value/1e9,$unit)
          : $abs >= 1e6  ? sprintf("%.4g M%s",$value/1e6,$unit)
          : $abs >= 1e3  ? sprintf("%.4g k%s",$value/1e3,$unit)
 	 : $abs >= 1    ? sprintf("%.4g %s", $value,    $unit)
@@ -572,9 +573,14 @@ sub show_section {  # one of instructions, upload_tracks, search, overview, regi
     return $setting eq 'hide' || $setting eq 'off' ? 0 : 1;
 }
 
+sub unit_divider {
+    my $self = shift;
+    return $self->global_setting('unit_divider') || 1;    
+}
+
 sub get_ranges {
   my $self      = shift;
-  my $divisor   = $self->global_setting('unit_divider') || 1;
+  my $divisor   = $self->unit_divider;
   my $rangestr  = $self->global_setting('zoom levels')  || '100 1000 10000 100000 1000000 10000000';
   if ($divisor == 1 ) {
     return split /\s+/,$rangestr;

diff --git a/lib/Bio/Graphics/Browser2/Region.pm b/lib/Bio/Graphics/Browser2/Region.pm
@@ -122,7 +122,8 @@ sub whole_seg {
 sub set_features_by_region {
     my $self = shift;
     my ($ref,$start,$stop) = @_;
-    my $features = $self->lookup_features($ref,$start,$stop);
+    my $divider  = $self->source->unit_divider;
+    my $features = $self->lookup_features($ref,$start/$divider,$stop/$divider);
     $self->features($features);
     return $features;
 }
@@ -221,7 +222,7 @@ sub lookup_features {
 
   my $db      = $self->db;
 
-  my $divisor = $source->global_setting('unit_divider') || 1;
+  my $divisor = $source->unit_divider;
   $start *= $divisor if defined $start;
   $stop  *= $divisor if defined $stop;
 

diff --git a/lib/Bio/Graphics/Browser2/Render.pm b/lib/Bio/Graphics/Browser2/Render.pm
@@ -204,7 +204,7 @@ sub run {
   warn "[$$] add_user_tracks()" if $debug;
   $self->add_user_tracks($self->data_source);
 
-  warn "user = ",$self->session->username;
+#  warn "user = ",$self->session->username;
 
   warn "[$$] testing for asynchronous event()" if $debug;
   if ($self->run_asynchronous_event) {
@@ -798,6 +798,7 @@ sub generate_title {
     my $dsn         = $self->data_source;
     my $state       = $self->state;
     my $description = $dsn->description;
+    my $divider     = $self->data_source->unit_divider;
 
     return $description unless $features;
     return !$features || !$state->{name}     ? $description
@@ -806,8 +807,8 @@ sub generate_title {
 				   $self->tr('SHOWING_FROM_TO',
 					     scalar $dsn->unit_label($features->[0]->length),
 					     $features->[0]->seq_id,
-					     $dsn->commas($features->[0]->start),
-					     $dsn->commas($features->[0]->end))
+					     $dsn->commas($features->[0]->start/$divider),
+					     $dsn->commas($features->[0]->end/$divider))
 	 : $description;
 }
 
@@ -1540,8 +1541,7 @@ sub cleanup {
   my $self = shift;
   warn "cleanup()" if DEBUG;
   my $state = $self->state;
-  $state->{name} = "$state->{ref}:$state->{start}..$state->{stop}"
-      if $state->{ref};  # to remember us by :-)
+  $state->{name} = $self->region_string if $state->{ref};  # to remember us by :-)
 }
 
 sub fatal_error {
@@ -2309,7 +2309,7 @@ sub update_coordinates {
       }
 
       # update our "name" state and the CGI parameter
-      $state->{name} = "$state->{ref}:$state->{start}..$state->{stop}";
+      $state->{name} = $self->region_string;
       param(name => $state->{name});
 
       warn "name = $state->{name}" if DEBUG;
@@ -2491,7 +2491,7 @@ sub asynchronous_update_sections {
     return $return_object;
 }
 
-# asynchronous_update_element has been DEPRICATED
+# asynchronous_update_element has been DEPRECATED
 # in favor of asynchronous_update_sections
 sub asynchronous_update_element {
     my $self    = shift;
@@ -2503,13 +2503,14 @@ sub asynchronous_update_element {
         my $segment     = $self->segment;
         my $dsn         = $self->data_source;
         my $description = $dsn->description;
+	my $divider     = $dsn->unit_divider;
         return $description . '<br>'
             . $self->tr(
             'SHOWING_FROM_TO',
             scalar $source->unit_label( $segment->length ),
             $segment->seq_id,
-            $source->commas( $segment->start ),
-            $source->commas( $segment->end )
+            $source->commas( $segment->start/$divider ),
+            $source->commas( $segment->end/$divider )
             );
     }
     elsif ( $element eq 'span' ) {  # this is the popup menu that shows ranges
@@ -2637,13 +2638,24 @@ sub asynchronous_update_coordinates {
 	}
 
 	# update our "name" state and the CGI parameter
-	$state->{name} = "$state->{ref}:$state->{start}..$state->{stop}";
+	$state->{name} = $self->region_string;
     }
 
     $self->session->flush();
     $position_updated;
 }
 
+sub region_string {
+    my $self    = shift;
+    my $state   = $self->state;
+    my $source  = $self->data_source;
+    my $divider = $source->unit_divider;
+    $state->{name} = "$state->{ref}:".
+	              $source->commas($state->{start}/$divider).
+		      '..'.
+		      $source->commas($state->{stop}/$divider);
+}
+
 sub zoom_to_span {
   my $self = shift;
   my ($state,$new_span) = @_;
@@ -3194,6 +3206,7 @@ sub get_panel_renderer {
   my $seg    = shift || $self->segment;
   my $whole  = shift || $self->whole_segment;
   my $region = shift || $self->region_segment;
+
   return Bio::Graphics::Browser2::RenderPanels->new(-segment        => $seg,
 						   -whole_segment  => $whole,
 						   -region_segment => $region,

diff --git a/lib/Bio/Graphics/Browser2/Render/HTML.pm b/lib/Bio/Graphics/Browser2/Render/HTML.pm
@@ -391,6 +391,10 @@ sub render_html_head {
       $fill =~ s/^(\w+):[\d.]+$/$1/;
       $set_dragcolors = "set_dragcolors('$fill')";
   }
+  my $units   = $self->data_source->setting('units') || 'bp';
+  my $divider = $self->data_source->unit_divider;
+  my $set_units = "set_dragunits('$units',$divider)";
+
   my @extra_headers;
   push @extra_headers, $self->render_user_head;
 
@@ -405,17 +409,19 @@ sub render_html_head {
 
   # add body's onload arguments, including ones used by plugins
   my $autocomplete = '';
-  my $body_onLoads = "initialize_page();$set_dragcolors;$autocomplete";
-  while(my($keys, $values) = each(%plugin_onLoads)) {
-    if ($keys eq "body") {
-      $body_onLoads .= $values;
-    }
-  }
-  push @args,(-onLoad => "$body_onLoads");
+
+  # this looks wrong
+#  my $body_onLoads = "initialize_page();$set_dragcolors;$set_units;$autocomplete";
+#  while(my($keys, $values) = each(%plugin_onLoads)) {
+#    if ($keys eq "body") {
+#      $body_onLoads .= $values;
+#    }
+#  }
+#  push @args,(-onLoad => $body_onLoads);
 
   my $plugin_onloads  = join ';',map {eval{$_->body_onloads}} @plugin_list;
   my $other_actions   = join ';',@other_initialization;
-  push @args,(-onLoad => "initialize_page(); $set_dragcolors; $plugin_onloads; $other_actions");
+  push @args,(-onLoad => "initialize_page(); $set_dragcolors; $set_units; $plugin_onloads; $other_actions");
 
   return start_html(@args);
 }
@@ -1877,12 +1883,14 @@ sub zoomBar {
 
   my ($length,$max) = @_;
 
+
   my $show   = $self->tr('Show');
 
   my %seen;
   my @r         = sort {$a<=>$b} $self->data_source->get_ranges();
-  my @ranges	= grep {!$seen{$_}++ && $_<=$max} sort {$b<=>$a} @r,$length;
+  $max         *= $self->data_source->unit_divider;
 
+  my @ranges	= grep {!$seen{$self->data_source->unit_label($_)}++ && $_<=$max} sort {$b<=>$a} @r,$length;
   my %labels    = map {$_=>$show.' '.$self->data_source->unit_label($_)} @ranges;
   return popup_menu(-class   => 'searchtitle',
 		    -name    => 'span',

diff --git a/lib/Bio/Graphics/Browser2/RenderPanels.pm b/lib/Bio/Graphics/Browser2/RenderPanels.pm
@@ -956,14 +956,15 @@ sub render_scale_bar {
 		-label_position => 'left'
 		);
 	}
+
         $panel->add_track(
              $wide_segment,
             -glyph          => 'arrow',
             -double         => 1,
             -tick           => 2,
             -units_in_label => $no_tick_units,
             -units          => $units,
-            -unit_divider   => $source->global_setting('unit_divider') || 1,
+            -unit_divider   => $source->unit_divider,
             %add_track_extra_args,
         );