Nice game, good program, but is all about incremental improvements.
Not being able to find a suggestion box for the program, here goes.
I would like to suggest some additions that can be toggled.
In target mode I would like a togglable marker for the sections that are either correct, white in the minimap, or incorrect, red in the minimap, marked with a black or white ring like a ctrl click or in a similar manner.
A geometric figure such as when you have more like bases in a row than allowed could be used as well to indicate an area.
I would also like to see a togglable marker for effected bases, a warbling or wavy flashing between black and white, scrolling horizontal or vertical lines of alternating colors would be as good, of the rings like a control click, when the cursor hovers over a particular base for a second, or longer.
Perhaps give it an adjustable delay before it starts in.
I would also like ot be able to keep the minimap expanded please.
Perhaps as a glass effect so it can be seen through.
In native mode, I would like to be able to have a line between two bases previously marked in target mode, to indicate such things as they are supposed to be side by side, or other relative positioning.
I really like this idea. The shift between target and natural mode happens very fast, so one does not necessarily see the cause of the changes. Also this would spare us from copying the puzzle sequence into the puzzlemaker and cut out a portion of the puzzle to work on a hard section.
I was thinking it would be nice to have something similar to what Doors is describing above with the change between native and target mode. A way to radioactively or fluorescently label a pair of bases to see where they go when you toggle the two modes.
To a certain extent that can already be done with a control click.
The difficulty with that in its current form is that depending where the movement is it can move the whole molecule.
That obscures the location by either moving it off screen, or forcing you to be far enough out you can’t see any detail.
Now what would be nice is when in target mode, hovering over a base would highlight whatever it would match up to in native mode.
As an extension of the swap function might be nice, you click to swap pairs and if they are adjacent in native mode, it simply highlights both while still target mode.
Even a togglable wire frame overlay in target and native mode both that can either singly or in mass draw lines from one side of a pair to the other.
In target mode it would show where something really pairs.
In native mode it would show where something is supposed to go.
Perhaps base it on an alt click for individual base pairs.