The browser is likely having trouble finding the dlls that ship along with it. The libraries are in the same directory as the browser application. In times past, MS Windows would check this directory for the libraries, but apparently not anymore. The quickest fix I know of is to add the path to the directory containing the dlls (and browser executable) to your PATH environment envariable. From the command prompt, this can be done with something like "PATH = C:\path\to\directory\containing\browser\exectutable\and\dlls;%PATH%". If a Win32 user can give me a better way to get this to work (and doesn't involve writing platform specific code), I'd love to know.
When opening a file via the "File" menu, a file open dialog window gives options for opening *sgr, *gff, and *fasta files along with an option to view all other file types. The best supported file types are *sgr and *gff (versions 2 and 3). While BQGB currently reads fasta files, none of the visualizations make use of this information (yet!) BQGB will also open any text delimited file such as tab delimited, comma separated values or, for example, *.bed files. The only rule is that one column in a file should give a sequence name such as the chromosome and one column should provide a numeric base pair position. The catch is, of course, that the user must supply the column definitions to BQGB for the novel file type to be parsed. A dialog will pop-up requesting this information when an unknown file type is opened. While any file, including *.sgr and *.gff can be opened this way, there is a memory penalty, ie. one will find memory performance better if they, for instance, converted their tab delimited file to gff then to open the tab delimited file directly into BQGB.
As an aside, *.bed files will probably be supported in the near future along with improved memory performance for this file type. There's also a plan to introduce a binary format to improve performance.
My preference is to have as little clutter on a screen as possible. Depending on the build you have, the screen may open with some of the tools shown in a tabben frame or may not show any tools at all. To view additional tools that may exist or, possibly, any tools at all, use your mouse's right button over the menu bar. This will pop-up a menu providing the options to show or hide various tools.
A right mouse click over the menu bar will pop-up the tools menu
The sequence selector is the device used for toggling between sequences. For instance, if one opens a file containing data for sequence "2L" and seqeunce "2R", only one sequence will be displayed at a time. Use this tool to move to another sequence name. Additionally, this tool provides a tree outlining the currently opened data tracks. The tree's hierarchy is FILE NAME -> FEATURE NAME -> SEQUENCE NAME. A right mouse click over items in this tree brings up a menu controlling visibility as well as the option to close (and remove from memory) a file. At this time, it's not possible to close only a sequence or feature.
The sequence selector controls which sequences are currently visible; the tree under "Sequences by File" provides track level control of visibility (right mouse click) as well as showing the relationship of FILE NAME -> FEATURE NAME -> SEQUENCE NAME, for instance here: exon_intron_gene_dmel.gff -> gene -> 2L; finally, in this example the sequence names "2L" and "chr2L" have been set as synonyms
The synonym setter is meant to address the inconvenience from having a given sequence with two different names, for instance, because they were originally generated by two different software, labs, etc... For instance, if "2R" and "Chr2R" are synonyms, the synonym setter may be used to establish the realationship and thus allow the two to be viewed or transformed in parallel. BEWARE: there's nothing stopping a use from setting something erroneous like "2R" is synonymous with "3R".
First, if the Search/Filter tools window is not open, use your right mouse button over the menu bar. Select "Search/Filter" from the pop-up menu. A search or filter operation will only be run against tracks that have been selected. To select a track, double click over the track causing the track to be redrawn with a black border. Multiple tracks may be selected... the default behavior is to run the search or filter across all tracks in parallel. In other words, if two tracks are selected and a search run, the screen will move to the first occurrence of the search item in either track.
At the moment, the graphical transforms are fairly small in number. However, color is certainly among them. Color is mostly controlled via the appearance menu. To affect a change on a track, that track must be selected (double click on the track).
Yes. First, select the track(s) by double clicking over the track(s). To move the tracks up/down, use the shift + up-arrow and shift + down-arrow keys respectively. A track cannot move beyond the top or bottom of the screen. To make a track or tracks smaller or larger, select the track(s) and use the "-" or "+" keys. Again, the sum total of the track's heights will not exceed the screen height, ie. to make one track larger, you may have to make another track smaller first!
This slider is the "cursor". It's used for the following:
Double clicking on the cursor will toggle a dotted line to be drawn over all tracks.