Hello,
I'am a new biojava user.
Someone could help me to use readFastaProtein
because when i use it in the following code i have an error :
org.biojava.bio.BioException: Could not read sequence!
When i looked for the alphabet ProteinTools SymbolList, i saw that a
symbol is an 3c code (ex Alanine : Ala and not A).
Is the error due to the use of the 3c code ?
Best Regards
public int[][] protCompo(String typeseq, BufferedReader path) throws
Exception
{
/*FiniteAlphabet fa = ProteinTools.getAlphabet();
int nb = fa.size();
System.out.println("fa = " + fa);
System.out.println("fa.size() = " + nb);
SymbolList sl = fa.symbols();
Iterator it = sl.iterator();
while (it.hasNext())
{
Object c = it.next();
System.out.println("-> c : " + c);
}*/
if (typeseq.compareTo("protein") == 0)
{
SequenceIterator stream = SeqIOTools.readFastaProtein(path);
while(stream.hasNext())
{
Sequence seq = stream.nextSequence(); <- the problem
seems to come from here
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