This is the new server for GMOD.org. Please let us know if you notice anything weird while it's getting broken in.
This article describes popup balloons and how to configure them in GBrowse.
For the main GBrowse configuration article, see:
Configuring Balloon Tooltips
GBrowse can display popup balloons when the user hovers over or clicks on a feature. The balloons can display arbitrary HTML, either provided in the config file, or fetched remotely via a URL. You can use this feature to create multiple choice menus when the user clicks on the feature, to pop up images on mouse hovers, or even to create little embedded query forms. See http://mckay.cshl.edu/balloons.html for examples.
In the config file for the database you wish to modify, set "balloon tips" to a true value:
[GENERAL] ... balloon tips = 1
Then add "balloon hover" and/or "balloon click" options to the track stanzas that you wish to add buttons to. You can also place these options in [TRACK DEFAULTS] to create a default balloon.
"balloon hover" specifies HTML or a URL that will be displayed when the user hovers over a feature. "balloon click" specifies HTML or a URL that will appear when the user clicks on a feature. The HTML can contain images, formatted text, and even controls. Examples:
balloon hover = <h2>Gene $name</h2> balloon click = <h2>Gene $name</h2> <a href='http://www.google.com/search?q=$name'>Search Google</a><br> <a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&term=$name'>Search NCBI</a><br>
Alternatively, you can populate the balloon using data from an HTML page or dynamic CGI script running on the same server as GBrowse. This uses AJAX; it can often speed up page loading by reducing the amount of text that must be downloaded by the client. To dynamically load the balloon contents from the server, use a balloon hover or balloon click option like this:
balloon click = /cgi-bin/get_gene_data?gene=$name
In this case, when the user clicks on the feature, it creates a balloon whose content contains the HTML returned by the CGI script "get_gene_data". GBrowse knows that this is a URL rather than the contents of the balloon by looking for the leading slash. However, to reduce ambiguity, we recommend that you prefix the URL with "url:" as so:
balloon click = url:/cgi-bin/get_gene_data?gene=$name
This also allows you to refer to relative URLs:
balloon click = url:../../get_gene_data?gene=$name
It is also possible to fill the balloon with content from a remote source. Simply specify a full URL beginning with "http:" "https:" or "ftp:"
balloon hover = http://www.wormbase.org/db/get?name=$name;class=gene
Note that the balloon library uses an internal <iframe> to populate the balloon with the content of external URLs. This means that vertical and horizontal scrollbars will appear if the content is too large to be contained within the balloon. If the formatting does not look right, you can design a custom balloon of the proper size as described in the next section.
The usual option value substitution rules ($name, $start, etc) work with balloons, as do callbacks. GBrowse will automatically escapes single (') and double (") quotes in the values returned by the "balloon hover" and "balloon click" options so that you don't have to worry about them messing up the HTML.
You might also wish to specify "titles are balloons" in the [GENERAL] section:
[GENERAL] titles are balloons = 1
This will generate balloons on all mouse hover events, using the content that would otherwise have been placed in the built-in browser tooltip.
There is a limited amount of balloon customization that you can perform within the [track] section. If you wish the balloon to be sticky (require the user to press the close button) even if it is a hover balloon, then place this option in the [track section]:
balloon sticky = 1
Setting "balloon sticky" to 0 will have the effect of making balloons disappear as soon as the mouse leaves them, even if it was created by a mouse click event.
If you are displaying content from a remote web or FTP server and you do not like the height of the balloon, you can adjust the height with the "balloon height" option:
balloon height = 400
GBrowse supports multiple balloons with different shapes, sizes, background images and timing properties. There is one built-in balloon, named "balloon", which should meet most peoples' needs. However, you can configure any number of custom balloons.
To declare two new balloons, create a "custom balloons" option in the [GENERAL] section:
custom balloons = [blue_balloon] images = /gbrowse/images/blue_balloons maxWidth = 300 shadow = 0
[wide_balloon] maxWidth = 800
This creates two new balloons. The first, named "blue_balloon" will look for its images and icons at the local URL /gbrowse/images/blue_balloons. It will have a maximum width of 300 pixels, and will cast no shadow. The second, named "wide_balloon" takes all the defaults for the default balloon, including the location of its images in the directory /gbrowse/images/balloons, except that it has a maximum width of 800 pixels. The various balloon options are described well on the Popup Balloons page.
To use the blue balloon rather than the standard one, format the "balloon hover" and/or "balloon click" options like this:
balloon click = [blue_balloon] /cgi-bin/get_gene_data?gene=$name
The [blue_balloon] keyword tells gbrowse to use the blue balloon for clicks on these features. The standard balloon is called "balloon", and so the following two options are equivalent:
balloon click = /cgi-bin/get_gene_data?gene=$name balloon click = [balloon] /cgi-bin/get_gene_data?gene=$name
The images for custom balloons reside in the default location of /gbrowse/images/balloons, unless indicated otherwise using the "images" config option. To use custom balloon images, point "images" to a a web-accessible directory in your document tree which contains the seven PNG images described on the Popup Balloons page. These images must be named as follows:
balloon.png down_right.png up_right.png balloon_ie.png down_left.png up_left.png close.png
Tips for creating these images can be found on Popup Balloons.
It looks like displayTime is the variable you're after, and you should be able to set it from the GBrowse config and not muck around with js files.
So simply adding the line displayTime = 10000 as a line in the config should help!