[Biojava-l] What is the maximum length for a Sequence

[Sylvain Foisy]

Hi,

I wrote a program that would read and load huge genomic sequence files 
(in my case, the H. sapiens genomic contigs from GenBank) into Sequences 
(one per contig) to select sections of it for further analysis. It seems 
to load the Sequence OK but when I am creating SubSequence objects from 
this Sequence with SubSequence(Sequence, int start,int finish), I am 
getting an error message.

If my start and/or my finish is above 230000, I get an 
IndexArrayOutOfBoundException. Since I am quite new at programming, I 
must either do something totally hideous or I do not have the right 
approach of dealing with such a huge sequence.

Any input would be greatly appreciated

++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Sylvain Foisy, Ph. D.
Directeur-Operations / Project Manager
BioNEQ - Le Reseau quebecois de bioinformatique
Genome-Quebec
Tel.: (514) 878-9911
E-mail: sylvain.foisy@bioneq.qc.ca
++++++++++++++++++++++++++++++++++++++++++++++++++++++++