Hi Josselin,
Could you send in an example protein file and example java program that
this fails on and the complete stack-trace you get? Also, the version of
BioJava and Java that you are running would help. Then we can probably
track down the problem quite quickly.
Matthew
Josselin Madec wrote:
> 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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> .
>
>
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