In the circular molecule mode of the user interface, when an annotation is selected, the selected annotation is made bold in color black.

I believe the user's attention will be drawn to the selected annotation if instead it is made in another color.  As a default, a bright red (hex FF0000) might do.  But I recommend that the color be user-customizable, and that even the font family and style (and perhaps size within a limited range) also be customizable.

In the linear molecule mode, there might be a way to improve the highlighting scheme using color contrasting or something to draw the attention of the user to the selected region.  Dim gray coloring doesn't immediately grab the user's attention, particularly the novice.

Konstantin Okonechnikov wrote on May 31^st, 2012 at 4:58am:


Oh, I leave it to you to see what you think is the best default color.  I am quite sure you have excellent judgment, given the product you have developed.  

Certainly the coding required to make user-customizable interfaces will be more challenging.

Quote:


I have attached an image showing what I am talking about.  It is in the sequence overview panel or subwindow at the top.  The current interface shows light gray or silver-colored solid lines that delimit the selected annotation, along with the bp length and the delimiting nucleotide positions in light blue.  The interface also has the movable sequence detail position indicator, with dashed very light gray lines showing which part of the overall sequence is detailed.

I modified both of these.  I played around with a few styles of presentation and came up with what is imaged below.  For the movable sequence detail indicator, I thought a solid light gray rectangle with the width spanning the presented sequence detail.  For the elements (annotations, scale numbers, horizontal lines) with the sequence overiew, these elements should always be placed in front of the shaded rectangle.

As for the solid vertical lines highlighting the selected annotation, I went with a different color other than a silver-colored solid line.

It's just my opinion, but I think that light gray- and silver-colored thin lines against a white background doesn't provide eye-catching contrast for the user.