[Biojava-l] SimpleGappedSymbolList from a String

[Don Naki]

Hi all,
I have a couple of 'novice' questions...

I can't seem to figure out how to create a SimpleGappedSymbolList from a String. I want to parse "-AQSD--VP-" and create a SimpleGappedSymbolList from it.
ProteinTools has methods to return a SymbolList, Sequence, and GappedSequence from a String, but not a GappedSymbolList. I understand GappedSequence extends GappedSymbolList, but I want just the GappedSymbolList. Alternatively, is there a way to get a GappedSymbolList from a GappedSequence?

A second question is that ProteinTools.createGappedProteinSequence("-AQSD--VP-").seqString() results in the String "XAQSD--VPX". The first and last '-' characters are now represented by 'X'. Is this a special kind of gap symbol? If so, how can I distinguish between '-' and 'X' Symbols?

Thanks in advance,
Don