To reproduce the problem:

1) Open ProtAnnot preferences and choose a new color for something, for example, the exon summary.
2) Select Apply to change to your selected color.
3) Now select "Cancel"

*Observe: Your selected color goes back to the last color used when "Cancel" is selected.

4) Now repeat steps 1 and 2 above but instead of hitting "Cancel", hit the red "X" to close the window.

*Observe: Your selected color remains in ProtAnnot.

The steps and observations above illustrate a usability problem in the preferences window of ProtAnnot. Many users may think that the "Cancel" button has the same function as the red "X". If you attempt to use the color preferences you will find that it can be a little confusing and this could be cleaned up a bit.

It may be best to just remove the "Save" and "Cancel" buttons from the ProtAnnot color preferences window. Instead, "Apply" would function as the "Save" button does. We would lose the ability to preview the selected color before applying it but this may be unnecessary anyways. If a user does not like their color they can simply select a new color.

Think of the way the control panel in Windows works. When you click the "Apply" button the settings are saved. To have a "Save" and an "Apply" button would be confusing.