I'm trying to create a das service for a complete genome using the dazzle servlet. The underlying sequences are stored in plain flatfiles of about 200M each. Now unfortunately dazzle requires a Sequence object of every contig that corresponds to an entry point. If I try to read in one of the files into a String or directly with DNATools.readFastaDNA, I get an OutOfMemoryError, or if I push the max. heap size I get a java.nio.BufferOverflowException in String. How could I represent such large Sequences without the necessity to store them in memory?
Any comment is greatly appreciated, best regards,
Benjamin Schuster-B�ckler
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