When viewing any given graph or set of graph tracks, there are three primary organization questions addressed by BQGB: does this track contain scored data or annotations only, what feature is represented in this track and what sequence is associated with the current stack of tracks?
BQGB divides representations into two general categories: score displays and annotation dispalys. In both cases, data may be bound to a single position or shown over a range. Score data may also have annotations, meta-data, etc... associated with a record, but data whose only numeric attribute is position, ie. lacking range information will be shown as an annotation display. The screenshot below shows two annotation tracks and a score track.
Generally when a file is read into memory, it will be partitioned into features, ie. data bound to some similar morphology, ontology or other classificaiton such as "genes" and "exons". How this is done depends on the file type. In most cases, each feature will be displayed in its own track. In the screenshot above, the annotations, though coming from the same file, have been broken into two tracks: one showing gene and showing coding regions. BQGB considers a "track" to be an group of data sharing an ordinate (ie. on the same y-axis whether there's score data or not or if the score is shown along a z-axis or as heat map). It is, of course, possible to write graph types that display multiple features within a single track such as the oft seen block and line annotations. BQGB also offers block and line annotations, for instance using thicker and thinner lines to denote coding and non-coding regions of a gene. To display such a graph, however, the software must have additional knowledge of the relationships within the data. Currently, in BQGB, relationship definitions are provided by the user via the annotation preferences dialog (choose from menu File->Preferences).
Only a single given sequence definition may be viewed among a stack of tracks, ie. if there are three tracks open and the currently selected sequence is 2L, all three tracks should be showing 2L data. BQGB offers a synonym tool, please see tools page for more information on the synonym setter. Its existence arose from the comparing of two data sets that chose different naming conventions, such as "2L" and "chr2L". Once the synonym for "2L" has been set to "chr2L", sequences bearing either "2L" or "chr2L" may be viewed in the same track stack. This can be helpful in a pinch, but dangerous! Be careful!
In order to improve navigation fluidity, ie. smoothness of scrolling and zooming, each display type generally considers data density and pixel availability when rendering. Two separate strategies are used when when data density exceeds pixel availability. First, data will be subsampled, ie. when data becomes so dense that many data points would be drawn on the same pixel, some data is dropped. This may be done with or without regard to what data is dropped and generally, when these thresholds are exceeded, BQGB just subsamples at some fixed interval, for instance every third record. Second, displays may choose to draw more or less information depending on zoom level. For instance, when there's no space to draw a gene's name, it may not be drawn. As with many maps, particularly digital maps, as zoom increases, so does detail.