[Biojava-l] query in suffixtree

[Hemant Katta]

Sir,

//Genrating  a suffixtree.

FiniteAlphabet alpha = DNATools.getDNA();
SymbolList sml = DNATools.createDNA("atggtggtcct");

SuffixTree suf = new SuffixTree(alpha);
suf.addSymbols(sml,sml.length);


now I have listed queries.
1. what is role of window size in addSymbols(SymbolList sml, int Window)
function.

2. why getFrequency(int i) always return the same value, whatever int i
value have been passed but the result is always same.
It should return the No. of motifs of int i length.

3. How can i print Suffix whatever are made in my SuffixTree.

4. How can i search  a  suffix of  given length.

I know these are quite basic Queries for U, but your Suggestion is really
very Helpful to me.Because whatever i came to know about SuffuxTree  on net
they  all created Suffix without any window size, this thing puzzled me a
lot.

With Regards
Hemant