Bug in Highlight by Trimming or Flagging Methods

[Wayne Maddison]

There's a potentially dangerous bug, as follows:

• In the character matrix editor Display>Color Matrix Cells>Highlight by Trimming or Flagging Methods. 
• When you have that active, it darkens the parts of the sequences that would be trimmed by a trimming method such as trimAl or PhyIN. 
• After you show that, there is an option to "Delete Parts Highlighted Dark". That should work OK if that's what you do. 
• HOWEVER, if you first ask to "Invert Highlights" and then ask to Delete Parts, it won't delete the inverted parts, but instead delete the uninverted parts. This is dangerous because it could mean you think you've deleted something, but you've actually you've deleted something else. In most cases you'd notice right away that something looks wrong -- we hope!

We have this fixed, and plan to release 4.01 in the next few days.

Wayne