rationalise/simplify setting of parse/display gaps/hsp lines. Fix bug in displaying gaps, shown when they shouldn't be, now shown only on bumping.

Fix for some of the coord space issues and fix for an update issue

i.e the group is positioned at zero and the text positioned at feature start.

remove some unused code

Affected items are DNA, Translation in 3 Frames, and Show Translation in zmap

Get item bound  coordinates of the character at an index

make bumping so it respects the column display mode, e.g. if SHOW then matches outside Mark are _not_ hidden.

Fix user data passed to parser