Hi there!
I have some runtime problems creating a SymbolList using an IntegerAlphabet
to create the Symbols. That's what my code looks like:
public static SymbolList integerArray2IntegerSymbolList(int[] intAln)
throws IllegalAlphabetException {
int len = intAln.length;
Symbol[] syms = new Symbol[len];
IntegerAlphabet ialph = IntegerAlphabet.getInstance();
for(int i=0; i<len; i++) {
syms[i] = ialph.getSymbol(intAln[i]);
}
end = System.nanoTime();
SymbolList symList = new SimpleSymbolList(syms,len,ialph);
return symList;
}
The command IntegerAlphabet ialph = IntegerAlphabet.getInstance() take 0.4
seconds on my machine and makes up most of runtime of my program. Is there
a more efficient way to create IntegerSymbols? Thank you, Tilman
Dr. rer. nat. Dipl.-Chem. Tilman Sauer
Department of Bioinformatics
UKG, Georg-August-University of Goettingen
Goldschmidtstr. 1
37077 Goettingen
Germany
phone: +49 551 39 14915
fax: +49 551 39 14914
email: [EMAIL PROTECTED]
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