@@ -159,6 +159,10 @@ module Bio::Graphics end @format = fmt end + + def pixel_position(pos) + (pos - self.lend) / self.rescale_factor + end # Adds a Bio::Graphics::Track container to this panel. A panel contains a # logical grouping of features, e.g. (for sequence annotation:) genes, lib/bio/graphics/panel.rb @@ -42,36 +42,38 @@ class Bio::Graphics::SubFeature @hidden_subfeatures_at_start = false @hidden_subfeatures_at_stop = false + panel = @feature.track.panel + # Get all pixel ranges for the subfeatures @locations.each do |l| # xxxxxx [ ] - if l.to < @feature.track.panel.lend + if l.to < panel.lend @hidden_subfeatures_at_start = true next # [ ] xxxxx - elsif l.from > @feature.track.panel.rend + elsif l.from > panel.rend @hidden_subfeatures_at_stop = true next # xxxx[xxx ] - elsif l.from < @feature.track.panel.lend and l.to > @feature.track.panel.lend + elsif l.from < panel.lend and l.to > panel.lend start_pixel = 1 - stop_pixel = ( l.to - @feature.track.panel.lend ).to_f / @feature.track.panel.rescale_factor + stop_pixel = panel.pixel_position(l.to) @chopped_at_start = true # [ xxxx]xxxx - elsif l.from < @feature.track.panel.rend and l.to > @feature.track.panel.rend - start_pixel = ( l.from - @feature.track.panel.lend ).to_f / @feature.track.panel.rescale_factor - stop_pixel = @feature.track.panel.width + elsif l.from < panel.rend and l.to > panel.rend + start_pixel = panel.pixel_position(l.from) + stop_pixel = panel.width @chopped_at_stop = true # xxxx[xxxxxxxxxx]xxxx - elsif l.from < @feature.track.panel.lend and l.to > @feature.track.panel.rend + elsif l.from < panel.lend and l.to > panel.rend start_pixel = 1 - stop_pixel = @feature.track.panel.width + stop_pixel = panel.width @chopped_at_start = true @chopped_at_stop = true # [ xxxxx ] else - start_pixel = ( l.from - @feature.track.panel.lend ).to_f / @feature.track.panel.rescale_factor - stop_pixel = ( l.to - @feature.track.panel.lend ).to_f / @feature.track.panel.rescale_factor + start_pixel = panel.pixel_position(l.from) + stop_pixel = panel.pixel_position(l.to) end @pixel_range_collection.push(Range.new(start_pixel, stop_pixel)) lib/bio/graphics/subfeature.rb b08f5639be09a25b7eae9ca322ce654c7fe87c29 Charles Comstock dgtized@gmail.com http://github.com/jandot/bio-graphics/commit/9c67fa2ddb58dd9fc298b2ca9185752149a2e6dd 9c67fa2ddb58dd9fc298b2ca9185752149a2e6dd 2008-08-21T05:46:55-07:00 2008-07-22T14:55:44-07:00 added Panel.pixel_position for determining pixel offsets from a panel db4f5bbc06b5d6f3e15a79ab21cc99a34ad68575 Jan Aerts jan.aerts@gmail.com