Caryoscope allows you to specify a piece of text that is dynamically generated based on the annotations on the data element to which you are pointing with your mouse. When you enter such text, simply enter the name of the annotation you want to substitute with a dollar sign and curly braces. So, for example, if you know your data includes two annotations, RAT2N and GBACC, and you specify:
The ratio is ${RAT2N} for Genbank ${GBACC}
If your mouse pointer is over a data element for which, say, RAT2N is 1.097 and GBACC is "N000701", the above text will be converted to:
The ratio is 1.097 for Genbank N000701
Caryoscope uses expressions using annotations in the Feature tooltip expression and Feature URL expression settings.
Some of the Caryoscope command line options (see Section 3.1.2.2, “Running from the command line”) require you to specify a color. Caryoscope uses the same conventions as HTML as described in many books and HTML tutorial sites, including Anabella's HTML Help - Colors.
Essentially, a color is specified via the "hexadecimal" numbers describing its red, green and blue components. For example, a pure red color is #ff0000; pure green is #00ff00; pure blue is #0000ff; black is #000000 and white is #ffffff.